From dc6e622f1a365d37278c1adca17b7131196f5eba Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 24 Mar 2025 14:22:25 +0100 Subject: [PATCH 001/872] merge dev --- CHANGELOG.md | 1 + README.md | 5 +- assets/schema_input.json | 75 +++++- conf/modules/raredisease.config | 13 ++ conf/test.config | 2 +- docs/usage.md | 8 +- modules.json | 5 + .../nf-core/spring/decompress/environment.yml | 5 + modules/nf-core/spring/decompress/main.nf | 54 +++++ modules/nf-core/spring/decompress/meta.yml | 51 ++++ .../spring/decompress/test/main.nf.test | 155 +++++++++++++ .../spring/decompress/test/main.nf.test.snap | 218 ++++++++++++++++++ .../spring/decompress/test/nextflow.config | 5 + .../nf-core/spring/decompress/test/tags.yml | 3 + samplesheet_test.csv | 5 - .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- .../utils_nfcore_raredisease_pipeline/main.nf | 41 ++-- workflows/raredisease.nf | 36 ++- 18 files changed, 642 insertions(+), 42 deletions(-) create mode 100644 modules/nf-core/spring/decompress/environment.yml create mode 100644 modules/nf-core/spring/decompress/main.nf create mode 100644 modules/nf-core/spring/decompress/meta.yml create mode 100644 modules/nf-core/spring/decompress/test/main.nf.test create mode 100644 modules/nf-core/spring/decompress/test/main.nf.test.snap create mode 100644 modules/nf-core/spring/decompress/test/nextflow.config create mode 100644 modules/nf-core/spring/decompress/test/tags.yml delete mode 100644 samplesheet_test.csv diff --git a/CHANGELOG.md b/CHANGELOG.md index 419de8f4b..4410bcd06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - A feature to start the workflow from duplicate-marked bam files [#682](https://github.com/nf-core/raredisease/pull/682) +- A functionality to take spring files as input [#678](https://github.com/nf-core/raredisease/pull/678) ### `Changed` diff --git a/README.md b/README.md index 1b0e10841..05edf157f 100644 --- a/README.md +++ b/README.md @@ -33,6 +33,9 @@ **nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP). +> [!NOTE] +> We do not support single-end data from Illumina, as some tools in the pipeline are not compatible with this type of data. + The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results). @@ -132,7 +135,7 @@ sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id hugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky ``` -Each row represents a fastq file (single-end) or a pair of fastq files (paired end). +Each row represents a pair of fastq files (paired end). Second, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md). diff --git a/assets/schema_input.json b/assets/schema_input.json index 93d7eda30..b486dc23f 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -26,25 +26,64 @@ "meta": ["lane"] }, "fastq_1": { - "type": "string", + "errorMessage": "Gzipped FastQ file for reads 1 must be provided. Cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$" + }, + { + "type": "string", + "maxLength": 0 + } + ], "format": "file-path", - "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "exists": true }, "fastq_2": { - "type": "string", - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "errorMessage": "Gzipped FastQ file for reads 2. Cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", "anyOf": [ { - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "format": "file-path", - "exists": true + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$" }, { + "type": "string", "maxLength": 0 } - ] + ], + "format": "file-path", + "exists": true + }, + "spring_1": { + "errorMessage": "Gzipped and spring-compressed FastQ file for reads 1 cannot contain spaces and must have extension '.spring'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+.spring$" + }, + { + "type": "string", + "maxLength": 0 + } + ], + "format": "file-path", + "exists": true + }, + "spring_2": { + "errorMessage": "Gzipped and spring-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.spring'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+.spring$" + }, + { + "type": "string", + "maxLength": 0 + } + ], + "format": "file-path", + "exists": true }, "bam": { "errorMessage": "BAM file cannot contain spaces and must have extension '.bam'", @@ -115,8 +154,22 @@ "errorMessage": "Case name must be provided and cannot contain spaces" } }, + "uniqueEntries": ["case_id"], + "anyOf": [ + { + "dependentRequired": { + "lane": ["fastq_1"] + } + }, + { + "dependentRequired": { + "lane": ["spring_1"] + } + } + ], "dependentRequired": { - "lane": ["fastq_1"], + "fastq_2": ["fastq_1"], + "spring_2": ["spring_1"], "bam": ["bai"] }, "required": ["sample", "sex", "phenotype", "case_id"] diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index f41634562..aba94c337 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -11,6 +11,19 @@ ---------------------------------------------------------------------------------------- */ +// +// Spring decompress options +// + +process { + withName: '.*RAREDISEASE:SPRING_DECOMPRESS_.*' { + ext.prefix = { "${spring.simpleName}" } + publishDir = [ + enabled: false + ] + } +} + // // Read QC options // diff --git a/conf/test.config b/conf/test.config index 9703eba88..3a9dd6077 100644 --- a/conf/test.config +++ b/conf/test.config @@ -32,7 +32,7 @@ params { skip_tools = 'haplogrep3,peddy,germlinecnvcaller' // Input data - input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_trio.csv' + input = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_fq_spring.csv' // Genome references fasta = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta' diff --git a/docs/usage.md b/docs/usage.md index 3b30ccae3..65257ca28 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -98,9 +98,9 @@ Running the pipeline involves three steps: #### Samplesheet -A samplesheet is used to pass the information about the sample(s), such as the path to the FASTQ files and other meta data (sex, phenotype, etc.,) to the pipeline in csv format. +A samplesheet is used to provide information about the sample(s) to the pipeline in CSV format, including the path to the FASTQ files and other metadata such as sex and phenotype. -nf-core/raredisease will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The pedigree information in the samplesheet (sex and phenotype) should be provided as they would be for a [ped file](https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format) (i.e. 1 for male, 2 for female, other for unknown). +The nf-core/raredisease pipeline accepts FASTQ files, SPRING files, or BAM files as input. Currently, the pipeline does not support single-end data from Illumina. The pedigree information in the samplesheet (sex and phenotype) should be provided in the same format as a [PED file](https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format), with sex indicated as 1 for male, 2 for female, and other for unknown. | Fields | Description | | ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | @@ -108,6 +108,8 @@ nf-core/raredisease will auto-detect whether a sample is single- or paired-end u | `lane` | Used to generate separate channels during the alignment step. It is of string type, and we recommend using a combination of flowcell and lane to distinguish between different runs of the same sample. | | `fastq_1` | Absolute path to FASTQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | Absolute path to FASTQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `spring_1` | Full path to spring-compressed file for read 1 or for reads 1 and 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.spring`. | +| `spring_2` | Full path to spring-compressed file for read 2. The Fastq file has to be first gzipped, then spring-compressed, and it must have the extension `.spring`. | | `sex` | Sex (1=male; 2=female; for unknown sex use 0 or 'other'). | | `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | | `paternal_id` | Sample ID of the father, can be blank if the father isn't part of the analysis or for samples other than the proband. | @@ -140,7 +142,7 @@ The nf-core/raredisease pipeline can handle duplicate-marked BAM files as input. | `maternal_id` | Sample ID of the mother, can be blank if the mother isn't part of the analysis or for samples other than the proband. | | `case_id` | Case ID, for the analysis used when generating a family VCF. | -If you would like to see an example of what a typical samplesheet looks like in this case, follow this link, [singleton](https://github.com/nf-core/test-datasets/blob/raredisease/testdata/samplesheet_bam.csv) +If you would like to see an example of what a typical samplesheet looks like in this case, follow this [link.](https://github.com/nf-core/test-datasets/blob/raredisease/testdata/samplesheet_bam.csv) #### Reference files and parameters diff --git a/modules.json b/modules.json index 08b8ef795..68be77b7f 100644 --- a/modules.json +++ b/modules.json @@ -453,6 +453,11 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "spring/decompress": { + "branch": "master", + "git_sha": "d7462e71f9129083ce10c3fe953ed401781e0ebd", + "installed_by": ["modules"] + }, "stranger": { "branch": "master", "git_sha": "26cdbf29e76695c7fd85e42e0015c7e96f979fe9", diff --git a/modules/nf-core/spring/decompress/environment.yml b/modules/nf-core/spring/decompress/environment.yml new file mode 100644 index 000000000..abeb16b09 --- /dev/null +++ b/modules/nf-core/spring/decompress/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::spring=1.1.1 diff --git a/modules/nf-core/spring/decompress/main.nf b/modules/nf-core/spring/decompress/main.nf new file mode 100644 index 000000000..86ced2690 --- /dev/null +++ b/modules/nf-core/spring/decompress/main.nf @@ -0,0 +1,54 @@ +process SPRING_DECOMPRESS { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/spring:1.1.1--h4ac6f70_2' : + 'biocontainers/spring:1.1.1--h4ac6f70_2' }" + + input: + tuple val(meta), path(spring) + val(write_one_fastq_gz) + + output: + tuple val(meta), path("*.fastq.gz"), emit: fastq + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def output = write_one_fastq_gz ? "-o ${prefix}.fastq.gz" : "-o ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz" + + """ + spring \\ + -d \\ + -g \\ + -t ${task.cpus} \\ + $args \\ + -i ${spring} \\ + ${output} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + spring: ${VERSION} + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def output = write_one_fastq_gz ? "echo '' | gzip > ${prefix}.fastq.gz" : "echo '' | gzip > ${prefix}_R1.fastq.gz; echo '' | gzip > ${prefix}_R2.fastq.gz" + """ + ${output} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + spring: ${VERSION} + END_VERSIONS + """ +} diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml new file mode 100644 index 000000000..72b72b75d --- /dev/null +++ b/modules/nf-core/spring/decompress/meta.yml @@ -0,0 +1,51 @@ +name: "spring_decompress" +description: Fast, efficient, lossless decompression of FASTQ files. +keywords: + - FASTQ + - decompression + - lossless +tools: + - "spring": + description: "SPRING is a compression tool for Fastq files (containing up to 4.29 + Billion reads)" + homepage: "https://github.com/shubhamchandak94/Spring" + documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" + tool_dev_url: "https://github.com/shubhamchandak94/Spring" + doi: "10.1093/bioinformatics/bty1015" + licence: ["Free for non-commercial use"] + identifier: biotools:spring +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - spring: + type: file + description: Spring file to decompress. + pattern: "*.{spring}" + - - write_one_fastq_gz: + type: boolean + description: | + Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions + pattern: "true or false" +output: + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Decompressed FASTQ file(s). + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@xec-cm" +maintainers: + - "@xec-cm" diff --git a/modules/nf-core/spring/decompress/test/main.nf.test b/modules/nf-core/spring/decompress/test/main.nf.test new file mode 100644 index 000000000..9428a86bc --- /dev/null +++ b/modules/nf-core/spring/decompress/test/main.nf.test @@ -0,0 +1,155 @@ +nextflow_process { + + name "Test Process SPRING_DECOMPRESS" + tag "modules_nfcore" + tag "modules" + tag "spring" + tag "spring/decompress" + script "../main.nf" + process "SPRING_DECOMPRESS" + + + + test("Write-One-File") { + + setup { + run("SPRING_COMPRESS") { + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = true // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Write-Two-Files") { + + setup { + run("SPRING_COMPRESS") { + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = false // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Write-One-File-stub") { + + options "-stub" + + setup { + run("SPRING_COMPRESS") { + options "-stub" + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = true // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Write-Two-Files-stub") { + + options "-stub" + + setup { + run("SPRING_COMPRESS") { + options "-stub" + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = false // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/test/main.nf.test.snap 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+ { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec", + "test2_R2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" + ] + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec", + "test2_R2.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" + ] + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T13:41:46.090761471" + }, + "Write-One-File": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T13:02:07.466039653" + }, + "Write-One-File-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T13:55:53.594615215" + }, + "Write-Two-Files-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test2_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test2_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T13:56:01.212228909" + } +} \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/test/nextflow.config b/modules/nf-core/spring/decompress/test/nextflow.config new file mode 100644 index 000000000..50f50a7a3 --- /dev/null +++ b/modules/nf-core/spring/decompress/test/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/test/tags.yml b/modules/nf-core/spring/decompress/test/tags.yml new file mode 100644 index 000000000..1fe70aec9 --- /dev/null +++ b/modules/nf-core/spring/decompress/test/tags.yml @@ -0,0 +1,3 @@ +spring/decompress: + - modules/nf-core/spring/compress/** + - modules/nf-core/spring/decompress/** diff --git a/samplesheet_test.csv b/samplesheet_test.csv deleted file mode 100644 index d6045119b..000000000 --- a/samplesheet_test.csv +++ /dev/null @@ -1,5 +0,0 @@ -sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id -earlycasualcaiman_1,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz,1,1,,,justhusky -slowlycivilbuck_1,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz,2,1,,,justhusky -hugelymodel_1,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz,1,2,earlycasualcaiman_1,slowlycivilbuck_1,justhusky -hugelymodel_2,1,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz,1,2,earlycasualcaiman_1,slowlycivilbuck_1,justhusky diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 934948edd..0fe5d66b4 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -70,7 +70,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { ch_align .map{ meta, bam -> def new_id = meta.sample - def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') + def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane','data_type') [groupKey(new_meta, new_meta.num_lanes), bam] } .groupTuple() diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index 5d9f0e4f3..c62714b3e 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -75,21 +75,29 @@ workflow PIPELINE_INITIALISATION { Channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .tap { ch_original_input } - .map { meta, fastq1, fastq2, bam, bai -> meta.id } + .map { meta, fastq1, fastq2, spring1, spring2, bam, bai -> meta.id } .reduce([:]) { counts, sample -> //get counts of each sample in the samplesheet - for groupTuple counts[sample] = (counts[sample] ?: 0) + 1 counts } .combine( ch_original_input ) - .map { counts, meta, fastq1, fastq2, bam, bai -> - def new_meta = meta + [num_lanes:counts[meta.id], - read_group:"\'@RG\\tID:"+ fastq1.simpleName + "_" + meta.lane + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'"] - if (fastq1 && !fastq2) { - return [ new_meta + [ single_end:true ], [ fastq1 ] ] - } else if (fastq1 && fastq2) { - return [ new_meta + [ single_end:false ], [ fastq1, fastq2 ] ] - } else { - return [ new_meta, [bam, bai] ] + .map { counts, meta, fastq1, fastq2, spring1, spring2, bam, bai -> + def new_meta = meta + [num_lanes:counts[meta.id]] + if (fastq1 && fastq2) { + new_meta += [read_group: generateReadGroupLine(fastq1, meta, params)] + return [new_meta + [single_end: false, data_type: "fastq_gz"], [fastq1, fastq2]] + } else if (fastq1 && !fastq2) { + new_meta += [read_group: generateReadGroupLine(fastq1, meta, params)] + return [new_meta + [single_end: true, data_type: "fastq_gz"], [fastq1]] + } else if (spring1 && spring2) { + new_meta += [read_group: generateReadGroupLine(spring1, meta, params)] + return [new_meta + [single_end: false, data_type: "separate_spring"], [spring1, spring2]] + } else if (spring1 && !spring2) { + new_meta += [read_group: generateReadGroupLine(spring1, meta, params)] + return [new_meta + [single_end: false, data_type: "interleaved_spring"], [spring1]] + } else if (bam && bai) { + new_meta += [read_group: generateReadGroupLine(bam, meta, params)] + return [new_meta, [bam, bai]] } } .tap{ ch_input_counts } @@ -181,6 +189,9 @@ workflow PIPELINE_COMPLETION { FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +def generateReadGroupLine(file, meta, params) { + return "\'@RG\\tID:" + file.simpleName + "_" + meta.lane + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'" +} def boolean isNonZeroNonEmpty(value) { return (value instanceof String && value != "" && value != "0") || @@ -258,7 +269,7 @@ def checkRequiredParameters(params) { def conditionalParamsTools = [ gens : ["gens_gnomad_pos", "gens_interval_list", "gens_pon_female", "gens_pon_male"], - germlinecnvcaller : ["ploidy_mmodel", "gcnvcaller_model", "readcount_intervals"], + germlinecnvcaller : ["ploidy_model", "gcnvcaller_model", "readcount_intervals"], smncopynumbercaller : ["genome"] ] @@ -446,14 +457,14 @@ def toolCitationText() { ] preprocessing_text = [ "FastQC (Andrews 2010),", - params.skip_tools && params.skip_tools.split(',').contains('fastp') ? "" : "Fastp (Chen, 2023)," + (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "Fastp (Chen, 2023)," ] other_citation_text = [ "BCFtools (Danecek et al., 2021),", "BEDTools (Quinlan & Hall, 2010),", "GATK (McKenna et al., 2010),", "MultiQC (Ewels et al. 2016),", - params.skip_tools && params.skip_tools.split(',').contains('peddy') ? "" : "Peddy (Pedersen & Quinlan, 2017),", + (params.skip_tools && params.skip_tools.split(',').contains('peddy')) ? "" : "Peddy (Pedersen & Quinlan, 2017),", params.run_rtgvcfeval ? "RTG Tools (Cleary et al., 2015)," : "", "SAMtools (Li et al., 2009),", (!(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) && params.analysis_type.equals("wgs")) ? "SMNCopyNumberCaller (Chen et al., 2020)," : "", @@ -575,14 +586,14 @@ def toolBibliographyText() { ] preprocessing_text = [ "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    • ", - params.skip_tools && params.skip_tools.split(',').contains('fastp') ? "" : "
  • Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107
    • " + (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "
  • Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107
    • " ] other_citation_text = [ "
  • Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008
    • ", "
  • McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110
    • ", "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. https://doi.org/10.1093/bioinformatics/btw354
    • ", - params.skip_tools && params.skip_tools.split(',').contains('peddy') ? "" : "
  • Pedersen, B. S., & Quinlan, A. R. (2017). Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. The American Journal of Human Genetics, 100(3), 406–413. https://doi.org/10.1016/j.ajhg.2017.01.017
    • ", + (params.skip_tools && params.skip_tools.split(',').contains('peddy')) ? "" : "
  • Pedersen, B. S., & Quinlan, A. R. (2017). Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. The American Journal of Human Genetics, 100(3), 406–413. https://doi.org/10.1016/j.ajhg.2017.01.017
    • ", params.run_rtgvcfeval ? "
  • Cleary, J. G., Braithwaite, R., Gaastra, K., Hilbush, B. S., Inglis, S., Irvine, S. A., Jackson, A., Littin, R., Rathod, M., Ware, D., Zook, J. M., Trigg, L., & Vega, F. M. D. L. (2015). Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines (p. 023754). bioRxiv. https://doi.org/10.1101/023754
    • " : "", "
  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
    • ", (!(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) && params.analysis_type.equals("wgs")) ? "
  • Chen, X., Sanchis-Juan, A., French, C. E., Connell, A. J., Delon, I., Kingsbury, Z., Chawla, A., Halpern, A. L., Taft, R. J., Bentley, D. R., Butchbach, M. E. R., Raymond, F. L., & Eberle, M. A. (2020). Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine, 22(5), 945–953. https://doi.org/10.1038/s41436-020-0754-0
    • " : "", diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 815a02fc4..3ef93eb99 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -19,10 +19,13 @@ include { methodsDescriptionText } from '../subworkflows/local/utils // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { PEDDY } from '../modules/nf-core/peddy/main' -include { SMNCOPYNUMBERCALLER } from '../modules/nf-core/smncopynumbercaller/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { PEDDY } from '../modules/nf-core/peddy/main' +include { SMNCOPYNUMBERCALLER } from '../modules/nf-core/smncopynumbercaller/main' +include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R1_FQ } from '../modules/nf-core/spring/decompress/main' +include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R2_FQ } from '../modules/nf-core/spring/decompress/main' +include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../modules/nf-core/spring/decompress/main' // // MODULE: Local modules @@ -287,6 +290,29 @@ workflow RAREDISEASE { .txt .set {ch_hgnc_ids} + // + // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) + // + + ch_input_by_sample_type = ch_reads.branch{ + fastq_gz: it[0].data_type == "fastq_gz" + interleaved_spring: it[0].data_type == "interleaved_spring" + separate_spring: it[0].data_type == "separate_spring" + } + + // Just one fastq.gz.spring-file with both R1 and R2 + ch_one_fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(ch_input_by_sample_type.interleaved_spring, false).fastq + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_FQ_PAIR.out.versions.first()) + + // Two fastq.gz.spring-files - one for R1 and one for R2 + ch_r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[0] ]}, true).fastq + ch_r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[1] ]}, true).fastq + ch_two_fastq_gz_from_spring = ch_r1_fastq_gz_from_spring.join(ch_r2_fastq_gz_from_spring).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]} + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R1_FQ.out.versions.first()) + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R2_FQ.out.versions.first()) + + ch_input_fastqs = ch_input_by_sample_type.fastq_gz.mix(ch_one_fastq_gz_pair_from_spring).mix(ch_two_fastq_gz_from_spring) + // // Create chromosome bed and intervals for splitting and gathering operations // @@ -316,7 +342,7 @@ workflow RAREDISEASE { */ ALIGN ( - ch_reads, + ch_input_fastqs, ch_alignments, ch_genome_fasta, ch_genome_fai, From 0a51411fcd99a8d0531fe37bb6cde99b9ce01a6b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 26 Mar 2025 22:47:40 +0100 Subject: [PATCH 002/872] first test yaay! --- .gitignore | 1 + .nf-test.log | 22 ++++ nf-test.config | 12 ++ .../tests/main.nf.test | 124 ++++++++++++++++++ .../tests/main.nf.test.snap | 94 +++++++++++++ .../tests/nextflow.config | 39 ++++++ tests/nextflow.config | 0 7 files changed, 292 insertions(+) create mode 100644 .nf-test.log create mode 100644 nf-test.config create mode 100644 subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test create mode 100644 subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap create mode 100644 subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config create mode 100644 tests/nextflow.config diff --git a/.gitignore b/.gitignore index 574075bad..fc41b698f 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc null/ .prettierignore +.nf-test/ diff --git a/.nf-test.log b/.nf-test.log new file mode 100644 index 000000000..a89688b54 --- /dev/null +++ b/.nf-test.log @@ -0,0 +1,22 @@ +Mar-26 17:07:14.105 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2 +Mar-26 17:07:14.138 [main] INFO com.askimed.nf.test.App - Arguments: [test, --only-changed, --profile, singularity, subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test, --update-snapshot] +Mar-26 17:07:15.883 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.5 +Mar-26 17:07:15.887 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/ramprasad.neethiraj/nextflow/raredisease/nf-test.config... +Mar-26 17:10:10.849 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 338 files from directory /home/ramprasad.neethiraj/nextflow/raredisease in 172.857 sec +Mar-26 17:10:10.850 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests for file [/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap, /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test.log, /home/ramprasad.neethiraj/nextflow/raredisease/nf-test.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/.gitignore, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap] in 0.0 sec +Mar-26 17:10:11.232 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 2 tests to execute. +Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan +Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME' from file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test'. +Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'dfe67d65: align bwamem2'. type: com.askimed.nf.test.lang.workflow.WorkflowTest +Mar-26 17:10:44.776 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' +Mar-26 17:10:44.806 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'align bwamem2' do not match. Update snapshots flag set. +Mar-26 17:10:44.806 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'align bwamem2' +Mar-26 17:10:44.820 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' +Mar-26 17:10:44.821 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'dfe67d65: align bwamem2' finished. status: PASSED +Mar-26 17:10:44.823 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '6b77a48f: align bwameme'. type: com.askimed.nf.test.lang.workflow.WorkflowTest +Mar-26 17:11:36.424 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'align bwameme' do not match. Update snapshots flag set. +Mar-26 17:11:36.425 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'align bwameme' +Mar-26 17:11:36.457 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' +Mar-26 17:11:36.457 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '6b77a48f: align bwameme' finished. status: PASSED +Mar-26 17:11:36.458 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME' finished. snapshot file: true, skipped tests: false, failed tests: false +Mar-26 17:11:36.462 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 2 tests. 0 tests failed. Done! diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 000000000..d768f4d77 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,12 @@ +config { + // location for all nf-tests + testsDir "." + + // nf-test directory including temporary files for each test + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + + // Include plugins + plugins { + load "nft-bam@0.4.0" + } +} diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test new file mode 100644 index 000000000..d2084c431 --- /dev/null +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -0,0 +1,124 @@ +nextflow_workflow { + + name "Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME" + script "subworkflows/local/align_bwa_bwamem2_bwameme/main.nf" + workflow "ALIGN_BWA_BWAMEM2_BWAMEME" + tag "subworkflows" + tag "align_bwa_bwamem2_bwameme" + config "./nextflow.config" + + test("align bwamem2") { + + setup { + run("BWAMEM2_INDEX") { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = "bwamem2" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + save_mapped_as_cram = true + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = [[:],[]] + input[2] = BWAMEM2_INDEX.out.index + input[3] = [[:],[]] + input[4] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[6] = 3072 + input[7] = "illumina" + input[8] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.versions + ).match() + } + ) + } + } + + test("align bwameme") { + + setup { + run("BWAMEME_INDEX") { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = "bwameme" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + save_mapped_as_cram = false + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map + [ + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = [[:],[]] + input[2] = [[:],[]] + input[3] = BWAMEME_INDEX.out.index + input[4] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[6] = 3072 + input[7] = "illumina" + input[8] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.versions + ).match() + } + ) + } + } + +} diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap new file mode 100644 index 000000000..eaa46753e --- /dev/null +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -0,0 +1,94 @@ +{ + "align bwamem2": { + "content": [ + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "25560381cc0aa918291edbe063985a30" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "af8628d9df18b2d3d4f6fd47ef2bb872" + ] + ], + [ + "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", + "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", + "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", + "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", + "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-26T17:10:44.806666276" + }, + "align bwameme": { + "content": [ + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "dc8900ed9754ed2dd3160462d0f8a5fa" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "af8628d9df18b2d3d4f6fd47ef2bb872" + ] + ], + [ + "versions.yml:md5,390a09ae83280da84de93856149cc3a1", + "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", + "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", + "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", + "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-26T17:11:36.42521993" + } +} \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config new file mode 100644 index 000000000..b1fadfb59 --- /dev/null +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config @@ -0,0 +1,39 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: 'BWAMEME_INDEX' { + ext.args = '-a meme' + } + + withName: 'BWAMEME_MEM' { + ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'BWAMEM2_MEM' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'SAMTOOLS_STATS' { + ext.args = '-s --remove-overlaps' + } + + withName: 'SAMTOOLS_MERGE' { + ext.prefix = { "${meta.id}_sorted_merged" } + } + + withName: 'EXTRACT_ALIGNMENTS' { + ext.prefix = { "${meta.id}_sorted_merged_extracted" } + ext.args2 = { params.restrict_to_contigs } + } + + withName: 'MARKDUPLICATES' { + ext.args = "--TMP_DIR ." + ext.prefix = { "${meta.id}_sorted_md" } + } + +} diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 000000000..e69de29bb From c852f4dc8b331b5f76f0fd01e023f939319ae08c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Mar 2025 08:48:21 +0100 Subject: [PATCH 003/872] test_one_sample to singleton --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/ci.yml | 2 +- conf/modules/annotate_cadd.config | 2 +- conf/modules/annotate_genome_snvs.config | 6 +++--- conf/modules/annotate_rhocallviz.config | 2 +- conf/modules/qc_bam.config | 2 +- conf/{test_one_sample.config => test_singleton.config} | 0 docs/usage.md | 2 +- nextflow.config | 2 +- 9 files changed, 10 insertions(+), 10 deletions(-) rename conf/{test_one_sample.config => test_singleton.config} (100%) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index bc89d691d..266a933f7 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rare - [ ] If necessary, also make a PR on the nf-core/raredisease _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). -- [ ] Ensure the test suite passes (`nextflow run . -profile test_one_sample,docker --outdir `). +- [ ] Ensure the test suite passes (`nextflow run . -profile test_singleton,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d4998c68b..fb8e74351 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: - "singularity" test_name: - "test" - - "test_one_sample" + - "test_singleton" - "test_bam" isMaster: - ${{ github.base_ref == 'master' }} diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index b71de347d..9034887fc 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -17,7 +17,7 @@ process { withName: '.*:ANNOTATE_CADD.*' { - ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun) } + ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun) } } withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' { diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index b8ada200d..de3b4210b 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -42,13 +42,13 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:UPD_SITES' { ext.prefix = { "${meta.upd_child}_upd_sites" } ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} sites"} - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } } withName: '.*ANNOTATE_GENOME_SNVS:UPD_REGIONS' { ext.prefix = { "${meta.upd_child}_upd_regions" } ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} regions --min-size 5 --min-sites 1"} - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } } withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES' { @@ -65,7 +65,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS' { ext.prefix = { "${meta6.upd_child}_chromograph_regions" } ext.args = { '--euploid' } - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } tag = {"${meta6.upd_child}"} publishDir = [ path: { "${params.outdir}/annotate_snv/genome" }, diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config index 5311bfd26..82cc1f7bb 100644 --- a/conf/modules/annotate_rhocallviz.config +++ b/conf/modules/annotate_rhocallviz.config @@ -45,7 +45,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG' { ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" } ext.args = { "--euploid" } - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } publishDir = [ path: { "${params.outdir}/annotate_snv/genome/" }, mode: params.publish_dir_mode, diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index afa9f2408..ef8603419 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -60,7 +60,7 @@ process { withName: '.*QC_BAM:NGSBITS_SAMPLEGENDER' { // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } ext.prefix = { "${meta.id}_ngsbits_sex" } publishDir = [ path: { "${params.outdir}/ngsbits_samplegender" }, diff --git a/conf/test_one_sample.config b/conf/test_singleton.config similarity index 100% rename from conf/test_one_sample.config rename to conf/test_singleton.config diff --git a/docs/usage.md b/docs/usage.md index 65257ca28..e68072f80 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -78,7 +78,7 @@ work # Directory containing the Nextflow working files # Other Nextflow hidden files, like history of pipeline logs. ``` -Test profile runs the pipeline with a case containing three samples, but if you would like to test the pipeline with one sample, use `-profile test_one_sample,`. +Test profile runs the pipeline with a case containing three samples, but if you would like to test the pipeline with one sample, use `-profile test_singleton,`. :::note The default cpu and memory configurations used in raredisease are written keeping the test profile (&dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform. diff --git a/nextflow.config b/nextflow.config index c858057f3..f33364a12 100644 --- a/nextflow.config +++ b/nextflow.config @@ -266,7 +266,7 @@ profiles { } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } - test_one_sample { includeConfig 'conf/test_one_sample.config' } + test_singleton { includeConfig 'conf/test_singleton.config' } test_sentieon { includeConfig 'conf/test_sentieon.config' } test_bam { includeConfig 'conf/test_bam.config' } } From caacc6620172b30670a9124b1ef97eed6fe043dc Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Mar 2025 06:31:19 +0100 Subject: [PATCH 004/872] second test --- .../main.nf} | 60 +- .../prepare_references/tests/main.nf.test | 45 + .../tests/main.nf.test.snap | 887 ++++++++++++++++++ .../prepare_references/tests/nextflow.config | 128 +++ tests/nextflow.config | 7 + 5 files changed, 1097 insertions(+), 30 deletions(-) rename subworkflows/local/{prepare_references.nf => prepare_references/main.nf} (89%) create mode 100644 subworkflows/local/prepare_references/tests/main.nf.test create mode 100644 subworkflows/local/prepare_references/tests/main.nf.test.snap create mode 100644 subworkflows/local/prepare_references/tests/nextflow.config diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references/main.nf similarity index 89% rename from subworkflows/local/prepare_references.nf rename to subworkflows/local/prepare_references/main.nf index e651a5218..61557e7a1 100644 --- a/subworkflows/local/prepare_references.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -2,36 +2,36 @@ // Prepare reference files // -include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED } from '../../modules/nf-core/bedtools/slop/main' -include { BWA_INDEX as BWA_INDEX_GENOME } from '../../modules/nf-core/bwa/index/main' -include { BWA_INDEX as BWA_INDEX_MT } from '../../modules/nf-core/bwa/index/main' -include { BWA_INDEX as BWA_INDEX_MT_SHIFT } from '../../modules/nf-core/bwa/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../modules/nf-core/bwamem2/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../modules/nf-core/bwamem2/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../modules/nf-core/bwamem2/index/main' -include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME } from '../../modules/nf-core/bwameme/index/main' -include { CAT_CAT as CAT_CAT_BAIT } from '../../modules/nf-core/cat/cat/main' -include { GATK4_BEDTOINTERVALLIST as GATK_BILT } from '../../modules/nf-core/gatk4/bedtointervallist/main' -include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD } from '../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../modules/nf-core/gatk4/intervallisttools/main' -include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../modules/nf-core/gatk4/shiftfasta/main' -include { GET_CHROM_SIZES } from '../../modules/local/get_chrom_sizes' -include { RTGTOOLS_FORMAT } from '../../modules/nf-core/rtgtools/format/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../modules/nf-core/samtools/faidx/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../modules/nf-core/samtools/faidx/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../modules/nf-core/samtools/faidx/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../modules/nf-core/sentieon/bwaindex/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../modules/nf-core/sentieon/bwaindex/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../modules/nf-core/sentieon/bwaindex/main' -include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_PT } from '../../modules/nf-core/tabix/tabix/main' -include { UNTAR as UNTAR_VEP_CACHE } from '../../modules/nf-core/untar/main' +include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED } from '../../../modules/nf-core/bedtools/slop/main' +include { BWA_INDEX as BWA_INDEX_GENOME } from '../../../modules/nf-core/bwa/index/main' +include { BWA_INDEX as BWA_INDEX_MT } from '../../../modules/nf-core/bwa/index/main' +include { BWA_INDEX as BWA_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwa/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME } from '../../../modules/nf-core/bwameme/index/main' +include { CAT_CAT as CAT_CAT_BAIT } from '../../../modules/nf-core/cat/cat/main' +include { GATK4_BEDTOINTERVALLIST as GATK_BILT } from '../../../modules/nf-core/gatk4/bedtointervallist/main' +include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../../modules/nf-core/gatk4/intervallisttools/main' +include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../../modules/nf-core/gatk4/shiftfasta/main' +include { GET_CHROM_SIZES } from '../../../modules/local/get_chrom_sizes' +include { RTGTOOLS_FORMAT } from '../../../modules/nf-core/rtgtools/format/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../../modules/nf-core/samtools/faidx/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../../modules/nf-core/samtools/faidx/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../../modules/nf-core/samtools/faidx/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_PT } from '../../../modules/nf-core/tabix/tabix/main' +include { UNTAR as UNTAR_VEP_CACHE } from '../../../modules/nf-core/untar/main' workflow PREPARE_REFERENCES { take: diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test new file mode 100644 index 000000000..4e1451fa0 --- /dev/null +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -0,0 +1,45 @@ +nextflow_workflow { + + name "Test Workflow PREPARE_REFERENCES" + script "subworkflows/local/prepare_references/main.nf" + workflow "PREPARE_REFERENCES" + config "./nextflow.config" + + test("Should run without failures") { + + when { + params { + aligner = "bwamem2" + mt_aligner = "bwa" + variant_caller = "deepvariant" + mito_name = "MT" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/' + fasta = params.testdata_base_path + 'reference.fasta' + fai = params.testdata_base_path + 'reference.fasta.fai' + target_bed = params.testdata_base_path + 'target.bed' + vep_cache = params.testdata_base_path + 'vep_cache_and_plugins.tar.gz' + + } + workflow { + """ + input[0] = Channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() + input[1] = Channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() + input[2] = Channel.empty() + input[3] = Channel.empty() + input[4] = Channel.value([[:],[]]) + input[5] = Channel.value([[:],[]]) + input[6] = Channel.of(params.target_bed).map {it -> [[id:'genome'], it]}.collect() + input[7] = Channel.empty() + input[8] = Channel.of(params.vep_cache).map {it -> [[id:'genome'], it]}.collect() + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + +} diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap new file mode 100644 index 000000000..686a1ba92 --- /dev/null +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -0,0 +1,887 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + [ + "reference.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", + "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", + "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" + ] + ] + ], + "1": [ + [ + { + "id": "genome" + }, + [ + "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b", + "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0", + "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2" + ] + ] + ], + "10": [ + [ + { + "id": "genome" + }, + "genome_mt.dict:md5,249ad4680360e4a9fc1e3b44ed54f568" + ] + ], + "11": [ + [ + { + "id": "genome" + }, + "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + ] + ], + "12": [ + [ + { + "id": "genome" + }, + "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + ] + ], + "13": [ + [ + "genome_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + ] + ], + "14": [ + [ + { + "id": "genome" + }, + "genome_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + ] + ], + "15": [ + [ + { + "id": "genome" + }, + "genome_shift.dict:md5,a714408661d0f6403f417304342574fc" + ] + ], + "16": [ + [ + { + "id": "genome" + }, + "genome_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + ] + ], + "17": [ + [ + { + "id": "genome" + }, + "genome_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + ] + ], + "18": [ + [ + { + "id": "genome" + }, + [ + "genome_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "genome_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "genome_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "genome_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "genome_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + ] + ] + ], + "19": [ + + ], + "2": [ + + ], + "20": [ + + ], + "21": [ + + ], + "22": [ + [ + { + "id": "genome" + }, + 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b/subworkflows/local/prepare_references/tests/nextflow.config new file mode 100644 index 000000000..451952698 --- /dev/null +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -0,0 +1,128 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +// +// Genome and reference preparation options +// + +process { + + withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME' { + ext.when = {!params.bwamem2 && (params.aligner == "bwamem2" || params.mt_aligner == "bwamem2")} + } + + withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { + ext.args = '-a meme' + ext.when = {!params.bwameme && params.aligner == "bwameme"} + } + + withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' { + ext.when = {!params.bwa && (!(params.aligner == "sentieon") || params.mt_aligner == "bwa")} + } + + withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' { + ext.when = {!params.bwa && (params.aligner == "sentieon" || params.mt_aligner == "sentieon")} + } + + withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT.*' { + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} + } + + withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT.*' { + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} + } + + withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT.*' { + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} + } + + withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' { + ext.when = {!params.fai} + } + + withName: '.*PREPARE_REFERENCES:RTGTOOLS_FORMAT' { + ext.when = { !params.sdf && params.run_rtgvcfeval } + } + + withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' { + ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" } + ext.when = {!params.mt_fasta} + } + + withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT' { + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) } + } + + withName: '.*PREPARE_REFERENCES:GATK_SD' { + ext.when = {!params.sequence_dictionary} + } + + withName: '.*PREPARE_REFERENCES:GATK_SHIFTFASTA' { + ext.args = { "--interval-file-name ${meta.id}_mt" } + } + + withName: '.*PREPARE_REFERENCES:GATK_SD_MT' { + ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes)} + } + + withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { + ext.when = {params.known_dbsnp && !params.known_dbsnp_tbi} + } + + withName: '.*PREPARE_REFERENCES:TABIX_GNOMAD_AF' { + ext.when = {params.gnomad_af && !params.gnomad_af_idx} + ext.args = '-s 1 -b 2 -e 2' + } + + withName: '.*PREPARE_REFERENCES:TABIX_PT' { + ext.when = { !params.target_bed.equals(null) && params.target_bed.endsWith(".gz") } + } + + withName: '.*PREPARE_REFERENCES:TABIX_PBT' { + ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") } + } + + withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_VCFANNOEXTRA' { + ext.args2 = '--csi' + } + + withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' { + ext.when = { params.target_bed && params.bait_padding > 0 } + ext.prefix = { "${meta.id}_pad${params.bait_padding}" } + ext.args = { "-b ${params.bait_padding}" } + } + + withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED' { + ext.prefix = { "${meta.id}_pad${params.bait_padding}" } + } + + withName: '.*PREPARE_REFERENCES:GATK_BILT' { + ext.when = { !params.target_bed.equals(null) } + ext.prefix = { "${meta.id}_target" } + } + + withName: '.*PREPARE_REFERENCES:GATK_ILT' { + ext.when = { !params.target_bed.equals(null) } + ext.args = { "--PADDING ${params.bait_padding} -SUBDIVISION_MODE INTERVAL_SUBDIVISION --SCATTER_COUNT 2" } + } + + withName: '.*PREPARE_REFERENCES:CAT_CAT_BAIT' { + ext.when = { !params.target_bed.equals(null) } + ext.prefix = { "${meta.id}" } + } + + withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' { + ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) } + } + +} diff --git a/tests/nextflow.config b/tests/nextflow.config index e69de29bb..39d3f8ead 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} From 648c6038cc73626d074c7f7f08e49c5b54c4866a Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 31 Mar 2025 11:52:22 +0200 Subject: [PATCH 005/872] add scatter genome test --- .../main.nf} | 4 +- .../local/scatter_genome/tests/main.nf.test | 33 ++++ .../scatter_genome/tests/main.nf.test.snap | 161 ++++++++++++++++++ .../scatter_genome/tests/nextflow.config | 7 + 4 files changed, 203 insertions(+), 2 deletions(-) rename subworkflows/local/{scatter_genome.nf => scatter_genome/main.nf} (85%) create mode 100644 subworkflows/local/scatter_genome/tests/main.nf.test create mode 100644 subworkflows/local/scatter_genome/tests/main.nf.test.snap create mode 100644 subworkflows/local/scatter_genome/tests/nextflow.config diff --git a/subworkflows/local/scatter_genome.nf b/subworkflows/local/scatter_genome/main.nf similarity index 85% rename from subworkflows/local/scatter_genome.nf rename to subworkflows/local/scatter_genome/main.nf index db95dfb23..2859f1bff 100644 --- a/subworkflows/local/scatter_genome.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -2,8 +2,8 @@ // A subworkflow to create genome interval files necessary for bam/vcf scatter operations. // -include { BUILD_BED } from '../../modules/local/create_bed_from_fai' -include { GATK4_SPLITINTERVALS } from '../../modules/nf-core/gatk4/splitintervals/main' +include { BUILD_BED } from '../../../modules/local/create_bed_from_fai' +include { GATK4_SPLITINTERVALS } from '../../../modules/nf-core/gatk4/splitintervals/main' workflow SCATTER_GENOME { diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test new file mode 100644 index 000000000..6125792f9 --- /dev/null +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test Workflow SCATTER_GENOME" + script "subworkflows/local/scatter_genome/main.nf" + workflow "SCATTER_GENOME" + config "./nextflow.config" + + test("Should run without failures") { + + when { + params { + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/' + fasta = params.testdata_base_path + 'reference.fasta' + fai = params.testdata_base_path + 'reference.fasta.fai' + dict = params.testdata_base_path + 'reference.dict' + } + workflow { + """ + input[0] = Channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() + input[1] = Channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() + input[2] = Channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + +} diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap new file mode 100644 index 000000000..93e51e4d5 --- /dev/null +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -0,0 +1,161 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + "reference.fasta.bed:md5,77b5bd8a06d9f25356c233413bf0318d" + ] + ], + "1": [ + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" + ], + [ + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73" + ], + [ + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646" + ], + [ + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2" + ], + [ + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319" + ], + [ + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4" + ], + [ + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91" + ], + [ + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0" + ], + [ + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac" + ], + [ + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e" + ], + [ + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88" + ], + [ + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe" + ], + [ + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0" + ], + [ + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4" + ], + [ + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003" + ], + [ + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760" + ], + [ + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e" + ], + [ + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411" + ], + [ + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03" + ], + [ + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ], + "2": [ + "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", + "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" + ], + "bed": [ + [ + { + "id": "genome" + }, + "reference.fasta.bed:md5,77b5bd8a06d9f25356c233413bf0318d" + ] + ], + "split_intervals": [ + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" + ], + [ + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73" + ], + [ + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646" + ], + [ + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2" + ], + [ + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319" + ], + [ + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4" + ], + [ + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91" + ], + [ + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0" + ], + [ + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac" + ], + [ + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e" + ], + [ + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88" + ], + [ + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe" + ], + [ + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0" + ], + [ + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4" + ], + [ + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003" + ], + [ + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760" + ], + [ + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e" + ], + [ + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411" + ], + [ + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03" + ], + [ + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ], + "versions": [ + "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", + "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-31T11:51:27.737317" + } +} \ No newline at end of file diff --git a/subworkflows/local/scatter_genome/tests/nextflow.config b/subworkflows/local/scatter_genome/tests/nextflow.config new file mode 100644 index 000000000..5d85dbbfb --- /dev/null +++ b/subworkflows/local/scatter_genome/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: '.*SCATTER_GENOME:GATK4_SPLITINTERVALS' { + ext.args = { "--scatter-count ${params.scatter_count}" } + ext.prefix = { "${meta.id}_intervals" } + } +} From 87a96eb3ac29afc5442a66ec38193459cfe6fd77 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 31 Mar 2025 11:53:34 +0200 Subject: [PATCH 006/872] add ignore to nf-test config --- nf-test.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf-test.config b/nf-test.config index d768f4d77..4e9dd8f4f 100644 --- a/nf-test.config +++ b/nf-test.config @@ -5,6 +5,9 @@ config { // nf-test directory including temporary files for each test workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + // ignore tests coming from the nf-core/modules repo + ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*' + // Include plugins plugins { load "nft-bam@0.4.0" From 3ce92921b167f4cd4f186440f23885869c91c124 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 8 Apr 2025 16:28:32 +0200 Subject: [PATCH 007/872] add test for align --- .../local/{align.nf => align/main.nf} | 14 +- subworkflows/local/align/tests/main.nf.test | 207 ++++++++++++++++++ .../local/align/tests/main.nf.test.snap | 198 +++++++++++++++++ .../local/align/tests/nextflow.config | 125 +++++++++++ 4 files changed, 537 insertions(+), 7 deletions(-) rename subworkflows/local/{align.nf => align/main.nf} (94%) create mode 100644 subworkflows/local/align/tests/main.nf.test create mode 100644 subworkflows/local/align/tests/main.nf.test.snap create mode 100644 subworkflows/local/align/tests/nextflow.config diff --git a/subworkflows/local/align.nf b/subworkflows/local/align/main.nf similarity index 94% rename from subworkflows/local/align.nf rename to subworkflows/local/align/main.nf index b88dd8627..cba43665f 100644 --- a/subworkflows/local/align.nf +++ b/subworkflows/local/align/main.nf @@ -2,13 +2,13 @@ // Map to reference // -include { FASTP } from '../../modules/nf-core/fastp/main' -include { ALIGN_BWA_BWAMEM2_BWAMEME } from './align_bwa_bwamem2_bwameme' -include { ALIGN_SENTIEON } from './align_sentieon' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' -include { ALIGN_MT } from './align_MT' -include { ALIGN_MT as ALIGN_MT_SHIFT } from './align_MT' -include { CONVERT_MT_BAM_TO_FASTQ } from './convert_mt_bam_to_fastq' +include { FASTP } from '../../../modules/nf-core/fastp/main' +include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' +include { ALIGN_SENTIEON } from '../align_sentieon' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { ALIGN_MT } from '../align_MT' +include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' +include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' workflow ALIGN { take: diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test new file mode 100644 index 000000000..adb028291 --- /dev/null +++ b/subworkflows/local/align/tests/main.nf.test @@ -0,0 +1,207 @@ +nextflow_workflow { + + name "Test Workflow ALIGN" + script "subworkflows/local/align/main.nf" + workflow "ALIGN" + tag "subworkflows" + tag "align" + config "./nextflow.config" + + setup { + run("BWAMEM2_INDEX", alias: 'MT_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + run("BWAMEM2_INDEX", alias: 'SHIFTMT_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'shiftmt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_shift.fasta', checkIfExists: true) + ]) + """ + } + } + } + + test("align bwamem2") { + + setup { + run("BWAMEM2_INDEX", alias: 'GENOME_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = 'bwamem2' + mt_aligner = 'bwamem2' + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + save_mapped_as_cram = true + analysis_type = "wgs" + skip_tools = null + platform = "illumina" + min_trimmed_length = 50 + mito_name = "MT" + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.fromList([ + [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ]] + ]) + input[1] = Channel.empty() + input[2] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[4] = [[:],[]] + input[5] = GENOME_MEM2.out.index + input[6] = [[:],[]] + input[7] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) + input[8] = [[:],[]] + input[9] = MT_MEM2.out.index + input[10] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[13] = [[:],[]] + input[14] = SHIFTMT_MEM2.out.index + input[15] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[18] = 3072 + input[19] = "illumina" + input[20] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }, + workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.versions + ).match() + } + ) + } + } + + test("align bwameme") { + + setup { + run("BWAMEME_INDEX", alias: 'GENOME_MEME') { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = 'bwameme' + mt_aligner = 'bwamem2' + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + save_mapped_as_cram = true + analysis_type = "wgs" + skip_tools = null + platform = "illumina" + min_trimmed_length = 50 + mito_name = "MT" + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.fromList([ + [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ]] + ]) + input[1] = Channel.empty() + input[2] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = GENOME_MEME.out.index + input[7] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) + input[8] = [[:],[]] + input[9] = MT_MEM2.out.index + input[10] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[13] = [[:],[]] + input[14] = SHIFTMT_MEM2.out.index + input[15] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[18] = 3072 + input[19] = "illumina" + input[20] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }, + workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.versions + ).match() + } + ) + } + } + +} diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap new file mode 100644 index 000000000..728de7e2c --- /dev/null +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -0,0 +1,198 @@ +{ + "align bwamem2": { + "content": [ + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "8aa7930105c6aa55f96e3719de968144", + "slowlycivilbuck_sorted_md.bam.bai:md5,b6c5d2736032f5e1cb190853ca366afe" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "a5d6892191a2c8c1f29966448623ca1b", + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", 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b/subworkflows/local/align/tests/nextflow.config new file mode 100644 index 000000000..d93f81889 --- /dev/null +++ b/subworkflows/local/align/tests/nextflow.config @@ -0,0 +1,125 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: 'BWAMEME_INDEX' { + ext.args = '-a meme' + } + + withName: 'FASTP' { + ext.args = { [ + params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '', + '--correction', + '--overrepresentation_analysis' + ].join(' ').trim() } + } + + withName: 'SAMTOOLS_VIEW' { + ext.args = { '--output-fmt cram --write-index' } + ext.prefix = { "${meta.id}_sorted_md" } + } + + withName: 'BWAMEM2_MEM' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'BWAMEM_FALLBACK' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'BWAMEME_MEM' { + ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + ext.when = { params.aligner.equals("bwameme") } + } + + withName: 'BWA' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'SAMTOOLS_STATS' { + ext.args = '-s --remove-overlaps' + } + + withName: 'SAMTOOLS_MERGE' { + ext.prefix = { "${meta.id}_sorted_merged" } + } + + withName: 'EXTRACT_ALIGNMENTS' { + ext.prefix = { "${meta.id}_sorted_merged_extracted" } + ext.args2 = { params.restrict_to_contigs } + } + + withName: 'MARKDUPLICATES' { + ext.args = "--TMP_DIR ." + ext.prefix = { "${meta.id}_sorted_md" } + } + + withName: 'GATK4_PRINTREADS_MT' { + ext.args = { [ + "-L ${params.mito_name}", + "--read-filter MateOnSameContigOrNoMappedMateReadFilter", + "--read-filter MateUnmappedAndUnmappedReadFilter", + "--tmp-dir ." + ].join(" ").trim() } + } + + withName: 'GATK4_REVERTSAM_MT' { + ext.args = '--TMP_DIR . --OUTPUT_BY_READGROUP false --VALIDATION_STRINGENCY LENIENT --ATTRIBUTE_TO_CLEAR FT --ATTRIBUTE_TO_CLEAR CO --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES false' + } + + withName: 'GATK4_SAMTOFASTQ_MT' { + ext.args = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR .' + } + + withName: 'BWAMEM2_MEM_MT' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'BWA_MEM_MT' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'SENTIEON_BWAMEM_MT' { + ext.args = { "-M -K 10000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'GATK4_MERGEBAMALIGNMENT_MT' { + ext.args = '--TMP_DIR . --CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT' + ext.prefix = { "${meta.id}_sorted_merged" } + } + + withName: 'PICARD_ADDORREPLACEREADGROUPS_MT' { + ext.args = { [ + "--VALIDATION_STRINGENCY LENIENT", + "--RGLB lib", + "--RGPL ${params.platform}", + "--RGPU barcode", + "--RGSM ${meta.id}", + "--TMP_DIR ./temp_folder" + ].join(' ').trim() } + } + + withName: 'PICARD_MARKDUPLICATES_MT' { + ext.args = '--TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true' + ext.prefix = { "${meta.id}_sorted_merged_md" } + } + + withName: 'SAMTOOLS_SORT_MT' { + ext.prefix = { "${meta.id}_sorted_merged_md_sorted" } + } + +} From 9213c9cba914afa8f181a28bb541f804f8b62438 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Apr 2025 00:23:35 +0200 Subject: [PATCH 008/872] align MT test --- .../local/align_MT/tests/main.nf.test | 143 ++++++ .../local/align_MT/tests/main.nf.test.snap | 456 ++++++++++++++++++ .../local/align_MT/tests/nextflow.config | 46 ++ 3 files changed, 645 insertions(+) create mode 100644 subworkflows/local/align_MT/tests/main.nf.test create mode 100644 subworkflows/local/align_MT/tests/main.nf.test.snap create mode 100644 subworkflows/local/align_MT/tests/nextflow.config diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test new file mode 100644 index 000000000..4b977279c --- /dev/null +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -0,0 +1,143 @@ +nextflow_workflow { + + name "Test Workflow ALIGN_MT" + script "subworkflows/local/align_MT/main.nf" + workflow "ALIGN_MT" + tag "subworkflows" + tag "align_mt" + config "./nextflow.config" + + test("align mt - bwamem2") { + + setup { + run("BWAMEM2_INDEX", alias: 'MT_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + when { + params { + mt_aligner = 'bwamem2' + outdir = "$outputDir" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = Channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[1] = Channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[2] = [[:],[]] + input[3] = MT_MEM2.out.index.collect() + input[4] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + + test("align mt - bwa") { + + setup { + run("BWA_INDEX", alias: 'MT_BWA') { + script "modules/nf-core/bwa/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + when { + params { + mt_aligner = 'bwa' + outdir = "$outputDir" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = Channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[1] = Channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[2] = MT_BWA.out.index.collect() + input[3] = [[:],[]] + input[4] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } +} diff --git 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"slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,99bda57b9440fc0815b4646655fdf527" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,19f330a6d9a9289eb73ade4daca3d6e2" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,70263f625d6fdf2a396404948d821b63" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,10e8c7915c92dde1f78139cee8559140" + ] + ], + "versions": [ + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7beb4095e697b250b91b3219646aeaea", + "versions.yml:md5,9a55207ee07d44c3c1e5dd2ca507d010", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-09T00:22:56.160477" + } +} \ No newline at end of file diff --git a/subworkflows/local/align_MT/tests/nextflow.config b/subworkflows/local/align_MT/tests/nextflow.config new file mode 100644 index 000000000..d894a94c4 --- /dev/null +++ b/subworkflows/local/align_MT/tests/nextflow.config @@ -0,0 +1,46 @@ +process { + + withName: 'BWAMEM2_MEM_MT' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'BWA_MEM_MT' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'SENTIEON_BWAMEM_MT' { + ext.args = { "-M -K 10000000 -R ${meta.read_group}" } + ext.args2 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + + withName: 'GATK4_MERGEBAMALIGNMENT_MT' { + ext.args = '--TMP_DIR . --CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT' + ext.prefix = { "${meta.id}_sorted_merged" } + } + + withName: 'PICARD_ADDORREPLACEREADGROUPS_MT' { + ext.args = { [ + "--VALIDATION_STRINGENCY LENIENT", + "--RGLB lib", + "--RGPL ${params.platform}", + "--RGPU barcode", + "--RGSM ${meta.id}", + "--TMP_DIR ./temp_folder" + ].join(' ').trim() } + } + + withName: 'PICARD_MARKDUPLICATES_MT' { + ext.args = '--TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true' + ext.prefix = { "${meta.id}_sorted_merged_md" } + } + + withName: 'SAMTOOLS_SORT_MT' { + ext.prefix = { "${meta.id}_sorted_merged_md_sorted" } + } + +} From 93645a30c81f0c61e8f0a0025bc51f0641a8f58a Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Apr 2025 08:58:07 +0200 Subject: [PATCH 009/872] add sentieon test --- .../local/align_sentieon/tests/main.nf.test | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 subworkflows/local/align_sentieon/tests/main.nf.test diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test new file mode 100644 index 000000000..afb866822 --- /dev/null +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_workflow { + + name "Test Workflow ALIGN_SENTIEON" + script "subworkflows/local/align_sentieon/main.nf" + workflow "ALIGN_SENTIEON" + tag "subworkflows" + tag "align_sentieon" + config "./nextflow.config" + + test("align sentieon") { + + setup { + run("SENTIEON_BWAINDEX") { + script "modules/nf-core/sentieon/bwaindex/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = "sentieon" + testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + save_mapped_as_cram = true + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[2] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[3] = SENTIEON_BWAINDEX.out.index + input[4] = "illumina" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + +} From 6a3add3b0aa3c6cf78f3b8ab1671a41ff8c96197 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Apr 2025 14:39:40 +0200 Subject: [PATCH 010/872] sentieon align test --- .../align_sentieon/tests/main.nf.test.snap | 263 ++++++++++++++++++ .../align_sentieon/tests/nextflow.config | 37 +++ 2 files changed, 300 insertions(+) create mode 100644 subworkflows/local/align_sentieon/tests/main.nf.test.snap create mode 100644 subworkflows/local/align_sentieon/tests/nextflow.config diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap new file mode 100644 index 000000000..fbaaf1ac7 --- /dev/null +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -0,0 +1,263 @@ +{ + "align sentieon": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,0dda7e8e144c07591f06330b07b36071" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,0458a0ef98b3a86ba28a2bcac628f7d4" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,1ba9b952749ad4e5310598fe23c02085" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,5294d174c6ffaaf47ceb02befbbffc40" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,96c951444c7f5af19c60d5262e74fb1c" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,77045bf67dbc251523af0d5bf9b57dbf" + ] + ], + "6": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,f4681d1f08b687f424af70772cfb597a" + ] + ], + "7": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,90bfb2b94b01074d93e6da1b69c4e494" + ] + ], + "8": [ + "versions.yml:md5,01896e6794bd10730ddfe6872631bdde", + "versions.yml:md5,2b8ad96b3aa67e6563e8a05744db6174", + "versions.yml:md5,c0917d5569d12b01718342f7aac5cbbd" + ], + "aln_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,f4681d1f08b687f424af70772cfb597a" + ] + ], + "gc_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,96c951444c7f5af19c60d5262e74fb1c" + ] + ], + "gc_summary": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,77045bf67dbc251523af0d5bf9b57dbf" + ] + ], + "is_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,90bfb2b94b01074d93e6da1b69c4e494" + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,0458a0ef98b3a86ba28a2bcac628f7d4" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,0dda7e8e144c07591f06330b07b36071" + ] + ], + "mq_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,1ba9b952749ad4e5310598fe23c02085" + ] + ], + "qd_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,5294d174c6ffaaf47ceb02befbbffc40" + ] + ], + "versions": [ + "versions.yml:md5,01896e6794bd10730ddfe6872631bdde", + "versions.yml:md5,2b8ad96b3aa67e6563e8a05744db6174", + "versions.yml:md5,c0917d5569d12b01718342f7aac5cbbd" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-09T14:36:45.125659653" + } +} \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/nextflow.config b/subworkflows/local/align_sentieon/tests/nextflow.config new file mode 100644 index 000000000..12943e0ac --- /dev/null +++ b/subworkflows/local/align_sentieon/tests/nextflow.config @@ -0,0 +1,37 @@ +env { + // NOTE This is how nf-core/raredisease users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + + // NOTE This is how nf-core/raredisease users will test out Sentieon in raredisease with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) + + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA +} + +process { + + withName: 'SENTIEON_BWAMEM' { + ext.args = { "-M -K 10000000 -R ${meta.read_group} " } + ext.prefix = { "${meta.id}_sorted.bam" } + } + + withName: 'SENTIEON_DATAMETRICS' { + ext.prefix = { "${meta.id}_datametrics" } + } + + withName: 'SENTIEON_READWRITER' { + ext.prefix = { "${meta.id}_merged.bam" } + } + + withName: 'EXTRACT_ALIGNMENTS' { + ext.prefix = { "${meta.id}_merged_extracted" } + ext.args2 = { params.restrict_to_contigs } + } + + withName: 'SENTIEON_DEDUP' { + ext.args4 = { params.rmdup ? "--rmdup" : '' } + ext.prefix = { "${meta.id}_dedup.bam" } + } +} From c1583f2d31433fc0dd9e5aa68f065c517f5cde07 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Apr 2025 16:17:42 +0200 Subject: [PATCH 011/872] add nftest log to gitignore --- .gitignore | 2 ++ .nf-test.log | 22 ---------------------- 2 files changed, 2 insertions(+), 22 deletions(-) delete mode 100644 .nf-test.log diff --git a/.gitignore b/.gitignore index fc41b698f..c8e6bd9d3 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,5 @@ testing* null/ .prettierignore .nf-test/ +.nf-test.log + diff --git a/.nf-test.log b/.nf-test.log deleted file mode 100644 index a89688b54..000000000 --- a/.nf-test.log +++ /dev/null @@ -1,22 +0,0 @@ -Mar-26 17:07:14.105 [main] INFO com.askimed.nf.test.App - nf-test 0.9.2 -Mar-26 17:07:14.138 [main] INFO com.askimed.nf.test.App - Arguments: [test, --only-changed, --profile, singularity, subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test, --update-snapshot] -Mar-26 17:07:15.883 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.5 -Mar-26 17:07:15.887 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/ramprasad.neethiraj/nextflow/raredisease/nf-test.config... -Mar-26 17:10:10.849 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 338 files from directory /home/ramprasad.neethiraj/nextflow/raredisease in 172.857 sec -Mar-26 17:10:10.850 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests for file [/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap, /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test.log, /home/ramprasad.neethiraj/nextflow/raredisease/nf-test.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/.gitignore, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap] in 0.0 sec -Mar-26 17:10:11.232 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Found 2 tests to execute. -Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan -Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME' from file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test'. -Mar-26 17:10:11.234 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'dfe67d65: align bwamem2'. type: com.askimed.nf.test.lang.workflow.WorkflowTest -Mar-26 17:10:44.776 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' -Mar-26 17:10:44.806 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'align bwamem2' do not match. Update snapshots flag set. -Mar-26 17:10:44.806 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'align bwamem2' -Mar-26 17:10:44.820 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' -Mar-26 17:10:44.821 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'dfe67d65: align bwamem2' finished. status: PASSED -Mar-26 17:10:44.823 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '6b77a48f: align bwameme'. type: com.askimed.nf.test.lang.workflow.WorkflowTest -Mar-26 17:11:36.424 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots 'align bwameme' do not match. Update snapshots flag set. -Mar-26 17:11:36.425 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot 'align bwameme' -Mar-26 17:11:36.457 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap' -Mar-26 17:11:36.457 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '6b77a48f: align bwameme' finished. status: PASSED -Mar-26 17:11:36.458 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME' finished. snapshot file: true, skipped tests: false, failed tests: false -Mar-26 17:11:36.462 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 2 tests. 0 tests failed. Done! From 0312831bff8b94ac032139dd325a3faf49013368 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Apr 2025 16:18:28 +0200 Subject: [PATCH 012/872] update gitignore --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index c8e6bd9d3..f248858bb 100644 --- a/.gitignore +++ b/.gitignore @@ -10,4 +10,3 @@ null/ .prettierignore .nf-test/ .nf-test.log - From 11fd655a30696929580b1ba54ceeb5b0be4d1d09 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 May 2025 14:29:45 +0200 Subject: [PATCH 013/872] review comments --- nf-test.config | 2 +- subworkflows/local/align/tests/main.nf.test.snap | 4 ++-- subworkflows/local/align/tests/nextflow.config | 2 -- 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/nf-test.config b/nf-test.config index 4e9dd8f4f..46f3ccb92 100644 --- a/nf-test.config +++ b/nf-test.config @@ -10,6 +10,6 @@ config { // Include plugins plugins { - load "nft-bam@0.4.0" + load "nft-bam@0.6.0" } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 728de7e2c..7da80759e 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -93,9 +93,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-08T14:20:31.830991" + "timestamp": "2025-05-23T14:10:29.767866862" }, "align bwameme": { "content": [ diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index d93f81889..48280859b 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -1,7 +1,5 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'BWAMEME_INDEX' { ext.args = '-a meme' } From c9dcfd3cde87eae3080fc532fc22d22705c01e2a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 May 2025 15:31:49 +0200 Subject: [PATCH 014/872] review suggestions --- subworkflows/local/align/tests/main.nf.test | 64 +++++++++---------- .../local/align_MT/tests/main.nf.test | 40 ++++++------ .../tests/main.nf.test | 20 +++--- .../tests/nextflow.config | 2 - .../local/align_sentieon/tests/main.nf.test | 10 +-- .../prepare_references/tests/main.nf.test | 9 ++- .../local/scatter_genome/tests/main.nf.test | 9 +-- tests/nextflow.config | 5 ++ 8 files changed, 81 insertions(+), 78 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index adb028291..09306688a 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -52,7 +52,7 @@ nextflow_workflow { params { aligner = 'bwamem2' mt_aligner = 'bwamem2' - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true analysis_type = "wgs" skip_tools = null @@ -66,37 +66,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = GENOME_MEM2.out.index input[6] = [[:],[]] - input[7] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -138,7 +138,7 @@ nextflow_workflow { params { aligner = 'bwameme' mt_aligner = 'bwamem2' - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true analysis_type = "wgs" skip_tools = null @@ -152,37 +152,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = [[:],[]] input[6] = GENOME_MEME.out.index - input[7] = Channel.of([[id:'genome'], [file(params.testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 4b977279c..87ba3e310 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -26,43 +26,43 @@ nextflow_workflow { params { mt_aligner = 'bwamem2' outdir = "$outputDir" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { """ input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = [[:],[]] input[3] = MT_MEM2.out.index.collect() - input[4] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } @@ -93,43 +93,43 @@ nextflow_workflow { params { mt_aligner = 'bwa' outdir = "$outputDir" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { """ input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = MT_BWA.out.index.collect() input[3] = [[:],[]] - input[4] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index d2084c431..b271ca587 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -26,7 +26,7 @@ nextflow_workflow { when { params { aligner = "bwamem2" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' save_mapped_as_cram = true restrict_to_contigs = "MT192765.1" } @@ -35,15 +35,15 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) input[1] = [[:],[]] input[2] = BWAMEM2_INDEX.out.index input[3] = [[:],[]] - input[4] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 @@ -83,7 +83,7 @@ nextflow_workflow { when { params { aligner = "bwameme" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' save_mapped_as_cram = false restrict_to_contigs = "MT192765.1" } @@ -92,15 +92,15 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) input[1] = [[:],[]] input[2] = [[:],[]] input[3] = BWAMEME_INDEX.out.index - input[4] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config index b1fadfb59..4563b2d78 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config @@ -1,7 +1,5 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'BWAMEME_INDEX' { ext.args = '-a meme' } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index afb866822..e528bf6c4 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -26,7 +26,7 @@ nextflow_workflow { when { params { aligner = "sentieon" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' save_mapped_as_cram = true } workflow { @@ -34,12 +34,12 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[2] = Channel.of([[id:'sarscov2'], [file(params.testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[1] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[2] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[3] = SENTIEON_BWAINDEX.out.index input[4] = "illumina" """ diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 4e1451fa0..897a14e3d 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -13,11 +13,10 @@ nextflow_workflow { mt_aligner = "bwa" variant_caller = "deepvariant" mito_name = "MT" - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/' - fasta = params.testdata_base_path + 'reference.fasta' - fai = params.testdata_base_path + 'reference.fasta.fai' - target_bed = params.testdata_base_path + 'target.bed' - vep_cache = params.testdata_base_path + 'vep_cache_and_plugins.tar.gz' + fasta = params.raredisease_testdata_base_path+ 'reference/reference.fasta' + fai = params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai' + target_bed = params.raredisease_testdata_base_path+ 'reference/target.bed' + vep_cache = params.raredisease_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz' } workflow { diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 6125792f9..bef113c4a 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -9,10 +9,11 @@ nextflow_workflow { when { params { - testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/' - fasta = params.testdata_base_path + 'reference.fasta' - fai = params.testdata_base_path + 'reference.fasta.fai' - dict = params.testdata_base_path + 'reference.dict' + raredisease_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + fasta = params.raredisease_testdata_base_path+ 'reference/reference.fasta' + fai = params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai' + dict = params.raredisease_testdata_base_path+ 'reference/reference.dict' + scatter_count = 20 } workflow { """ diff --git a/tests/nextflow.config b/tests/nextflow.config index 39d3f8ead..f2aa1c8b5 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -5,3 +5,8 @@ process { time: '1.h' ] } + +params { + raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + sarscov_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +} From 67e4226dcbd1f6ead57edca871e45d4fb311e003 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 May 2025 17:26:47 +0200 Subject: [PATCH 015/872] update tests --- .../local/align/tests/main.nf.test.snap | 60 +++++++++---------- .../tests/main.nf.test.snap | 12 ++-- .../align_sentieon/tests/nextflow.config | 4 +- 3 files changed, 38 insertions(+), 38 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 7da80759e..80a8eeb11 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -95,7 +95,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.6" }, - "timestamp": "2025-05-23T14:10:29.767866862" + "timestamp": "2025-05-23T15:53:23.463213506" }, "align bwameme": { "content": [ @@ -104,20 +104,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "51ae634c7bc1b9ddcaaf1e09bb9d7c88", - "hugelymodelbat_sorted_md.bam.bai:md5,64eda414c1177767cd0088ce855de6a1" + "b75a16ff1082ce42e9a9ac046b509181", + "slowlycivilbuck_sorted_md.bam.bai:md5,ff8eb902e42e6aeec775b9b412252ab6" ] ], [ @@ -125,20 +125,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "b18998c8cf7dc417ca9a122ba1c9403d", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,ebc9222d03624e276c0c242e87e6618c" + "a5d6892191a2c8c1f29966448623ca1b", + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" ] ], [ @@ -146,20 +146,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "97e6eaae1cda668da59e5c16a9bbcc1d", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,f9a4e5c7c7ca7c25f365bee4cfcdb3a9" + "427b5e476d84c5277d2d24210800ad60", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,6c663c5661749b25782ac78a3ba1f242" ] ], [ @@ -191,8 +191,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-04-08T15:00:14.317214" + "timestamp": "2025-05-23T15:59:18.726434076" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index eaa46753e..8b6bdcef2 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "25560381cc0aa918291edbe063985a30" + "17f8c2ac941e887d9470f69453c08ea5" ] ], [ @@ -41,9 +41,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-03-26T17:10:44.806666276" + "timestamp": "2025-05-23T16:03:29.762040277" }, "align bwameme": { "content": [ @@ -59,7 +59,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "dc8900ed9754ed2dd3160462d0f8a5fa" + "144054510dda19100c4274a7db41bd8" ] ], [ @@ -87,8 +87,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "24.10.6" }, - "timestamp": "2025-03-26T17:11:36.42521993" + "timestamp": "2025-05-23T16:04:03.379890309" } } \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/nextflow.config b/subworkflows/local/align_sentieon/tests/nextflow.config index 12943e0ac..76615ae41 100644 --- a/subworkflows/local/align_sentieon/tests/nextflow.config +++ b/subworkflows/local/align_sentieon/tests/nextflow.config @@ -1,6 +1,6 @@ env { - // NOTE This is how nf-core/raredisease users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This is how nf-core/raredisease users will use Sentieon in real world use with an IP + // SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" // NOTE This is how nf-core/raredisease users will test out Sentieon in raredisease with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) From e67c45339ac3134f0ccf567c2a856cdd404dfde7 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 13:24:45 +0200 Subject: [PATCH 016/872] bump-version --- .nf-core.yml | 2 +- CHANGELOG.md | 20 ++++++++++++++ assets/multiqc_config.yml | 4 +-- nextflow.config | 2 +- ro-crate-metadata.json | 58 +++++++++++++++++++-------------------- 5 files changed, 53 insertions(+), 33 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 3f5bbbb34..8c0c1203f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 2.6.0 + version: 2.7.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index cb7fb320b..a5ac166e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,26 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 2.7.0dev - Semiautomatix [xxxx-xx-xx] + +### `Added` + +### `Changed` + +### `Fixed` + +### Parameters + +| Old parameter | New parameter | +| ------------- | ------------- | +| | | + +### Tool updates + +| Tool | Old version | New version | +| ---- | ----------- | ----------- | +| | | | + ## 2.6.0 - Cacofonix [2025-06-25] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 98820ad71..034fb00ed 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,9 +2,9 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about - how to interpret these results, please see the documentation. report_section_order: diff --git a/nextflow.config b/nextflow.config index c45672bb0..52bb94ad8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -436,7 +436,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '2.6.0' + version = '2.7.0dev' doi = '10.5281/zenodo.7995798' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 64d0c09af..377193d2d 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2025-06-25T09:02:19+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2025-06-25T11:10:32+00:00", "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#54f4c43c-5277-4feb-87f6-9700f8b38e9c" + "@id": "#5df1d719-3598-49de-a8e6-a937fe09f95c" } ], "name": "nf-core/raredisease" @@ -134,26 +134,26 @@ ], "creator": [ { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "#25568561+projectoriented@users.noreply.github.com" }, { "@id": "https://orcid.org/0000-0002-4100-9963" }, { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0003-1316-2845" }, { - "@id": "https://orcid.org/0000-0003-1316-2845" + "@id": "https://orcid.org/0000-0002-2219-0197" }, { - "@id": "https://orcid.org/0000-0002-5044-7754" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { - "@id": "#25568561+projectoriented@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-5044-7754" } ], "dateCreated": "", - "dateModified": "2025-06-25T11:02:19Z", + "dateModified": "2025-06-25T13:10:32Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,7 +172,7 @@ ], "maintainer": [ { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "#25568561+projectoriented@users.noreply.github.com" }, { "@id": "https://orcid.org/0000-0002-4100-9963" @@ -181,10 +181,10 @@ "@id": "https://orcid.org/0000-0002-2219-0197" }, { - "@id": "https://orcid.org/0000-0002-5044-7754" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { - "@id": "#25568561+projectoriented@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-5044-7754" } ], "name": [ @@ -198,10 +198,10 @@ }, "url": [ "https://github.com/nf-core/raredisease", - "https://nf-co.re/raredisease/2.6.0/" + "https://nf-co.re/raredisease/dev/" ], "version": [ - "2.6.0" + "2.7.0dev" ] }, { @@ -217,11 +217,11 @@ "version": "!>=24.04.2" }, { - "@id": "#54f4c43c-5277-4feb-87f6-9700f8b38e9c", + "@id": "#5df1d719-3598-49de-a8e6-a937fe09f95c", "@type": "TestSuite", "instance": [ { - "@id": "#d8630621-ea14-4767-9e8d-8ab89ed17c30" + "@id": "#98ca337c-0536-4ec5-9593-4c57c4409314" } ], "mainEntity": { @@ -230,7 +230,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#d8630621-ea14-4767-9e8d-8ab89ed17c30", + "@id": "#98ca337c-0536-4ec5-9593-4c57c4409314", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -369,10 +369,10 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0001-7313-3734", + "@id": "#25568561+projectoriented@users.noreply.github.com", "@type": "Person", - "email": "20065894+ramprasadn@users.noreply.github.com", - "name": "Ramprasad Neethiraj" + "email": "25568561+projectoriented@users.noreply.github.com", + "name": "Mei Wu" }, { "@id": "https://orcid.org/0000-0002-4100-9963", @@ -380,6 +380,12 @@ "email": "Gwenna.breton@gu.se", "name": "Gwenna Breton" }, + { + "@id": "https://orcid.org/0000-0003-1316-2845", + "@type": "Person", + "email": "raysloks@gmail.com", + "name": "Emil Bertilsson" + }, { "@id": "https://orcid.org/0000-0002-2219-0197", "@type": "Person", @@ -387,22 +393,16 @@ "name": "Anders Jemt" }, { - "@id": "https://orcid.org/0000-0003-1316-2845", + "@id": "https://orcid.org/0000-0001-7313-3734", "@type": "Person", - "email": "raysloks@gmail.com", - "name": "Emil Bertilsson" + "email": "20065894+ramprasadn@users.noreply.github.com", + "name": "Ramprasad Neethiraj" }, { "@id": "https://orcid.org/0000-0002-5044-7754", "@type": "Person", "email": "lucia.pena.perez@scilifelab.se", "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" - }, - { - "@id": "#25568561+projectoriented@users.noreply.github.com", - "@type": "Person", - "email": "25568561+projectoriented@users.noreply.github.com", - "name": "Mei Wu" } ] } \ No newline at end of file From 71dee5a08c1db4df029a6f149860b99bcafac03d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 14:31:43 +0200 Subject: [PATCH 017/872] update sentieon bwaindex --- .../nf-core/sentieon/bwaindex/environment.yml | 4 +- modules/nf-core/sentieon/bwaindex/main.nf | 6 +- modules/nf-core/sentieon/bwaindex/meta.yml | 2 +- .../sentieon/bwaindex/tests/main.nf.test | 58 ++++++++++++ .../sentieon/bwaindex/tests/main.nf.test.snap | 92 +++++++++++++++++++ .../sentieon/bwaindex/tests/nextflow.config | 11 +++ 6 files changed, 168 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/sentieon/bwaindex/tests/main.nf.test create mode 100644 modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap create mode 100644 modules/nf-core/sentieon/bwaindex/tests/nextflow.config diff --git a/modules/nf-core/sentieon/bwaindex/environment.yml b/modules/nf-core/sentieon/bwaindex/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/bwaindex/environment.yml +++ b/modules/nf-core/sentieon/bwaindex/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/bwaindex/main.nf b/modules/nf-core/sentieon/bwaindex/main.nf index 4372cc04b..010165e47 100644 --- a/modules/nf-core/sentieon/bwaindex/main.nf +++ b/modules/nf-core/sentieon/bwaindex/main.nf @@ -5,14 +5,14 @@ process SENTIEON_BWAINDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(fasta) output: - tuple val(meta), path(bwa), emit: index + tuple val(meta), path("bwa"), emit: index path "versions.yml" , emit: versions when: diff --git a/modules/nf-core/sentieon/bwaindex/meta.yml b/modules/nf-core/sentieon/bwaindex/meta.yml index acbd14d51..f265049d1 100644 --- a/modules/nf-core/sentieon/bwaindex/meta.yml +++ b/modules/nf-core/sentieon/bwaindex/meta.yml @@ -30,7 +30,7 @@ output: description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - - bwa: + - "bwa": type: file description: BWA genome index files pattern: "*.{amb,ann,bwt,pac,sa}" diff --git a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test new file mode 100644 index 000000000..7df044019 --- /dev/null +++ b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process SENTIEON_BWAINDEX" + script "../main.nf" + process "SENTIEON_BWAINDEX" + + tag "modules" + tag "modules_nfcore" + tag "sentieon" + tag "sentieon/bwaindex" + + test("build index - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("build index - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap new file mode 100644 index 000000000..a4672d557 --- /dev/null +++ b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap @@ -0,0 +1,92 @@ +{ + "build index - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:00:00.130499875" + }, + "build index - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "1": [ + "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ] + ] + ], + "versions": [ + "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T07:59:32.96587875" + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/bwaindex/tests/nextflow.config b/modules/nf-core/sentieon/bwaindex/tests/nextflow.config new file mode 100644 index 000000000..47f5ec002 --- /dev/null +++ b/modules/nf-core/sentieon/bwaindex/tests/nextflow.config @@ -0,0 +1,11 @@ +env { + // NOTE This is how nf-core/sarek users will use Sentieon in real world use + SENTIEON_LICENSE = $SENTIEON_LICSRVR_IP + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = $SENTIEON_AUTH_MECH + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat | base64 -w 0) +} +process { +} From 8577e19db04a3f363cf7673a8c7adf3aa13ed809 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 15:39:12 +0200 Subject: [PATCH 018/872] update sentieon modules --- modules.json | 16 +- .../nf-core/sentieon/bwamem/environment.yml | 4 +- modules/nf-core/sentieon/bwamem/main.nf | 4 +- .../sentieon/bwamem/tests/main.nf.test.snap | 74 ++--- .../nf-core/sentieon/bwamem/tests/tags.yml | 2 - .../sentieon/datametrics/environment.yml | 4 +- modules/nf-core/sentieon/datametrics/main.nf | 4 +- modules/nf-core/sentieon/datametrics/meta.yml | 8 +- .../sentieon/datametrics/tests/main.nf.test | 20 +- .../datametrics/tests/main.nf.test.snap | 300 ++++++------------ .../nf-core/sentieon/dedup/environment.yml | 4 +- modules/nf-core/sentieon/dedup/main.nf | 4 +- .../sentieon/dedup/tests/main.nf.test.snap | 78 ++--- .../sentieon/dnamodelapply/environment.yml | 4 +- .../nf-core/sentieon/dnamodelapply/main.nf | 12 +- .../nf-core/sentieon/dnamodelapply/meta.yml | 2 +- .../sentieon/dnamodelapply/tests/main.nf.test | 87 +++++ .../dnamodelapply/tests/main.nf.test.snap | 76 +++++ .../dnamodelapply/tests/nextflow.config | 9 + .../nf-core/sentieon/dnascope/environment.yml | 4 +- modules/nf-core/sentieon/dnascope/main.nf | 35 +- .../sentieon/dnascope/tests/main.nf.test | 155 +++++++++ .../sentieon/dnascope/tests/main.nf.test.snap | 122 +++++++ .../sentieon/dnascope/tests/nextflow.config | 9 + .../sentieon/readwriter/environment.yml | 4 +- modules/nf-core/sentieon/readwriter/main.nf | 4 +- .../readwriter/tests/main.nf.test.snap | 42 +-- .../sentieon/wgsmetrics/environment.yml | 4 +- modules/nf-core/sentieon/wgsmetrics/main.nf | 15 +- .../sentieon/wgsmetrics/tests/main.nf.test | 85 +++++ .../wgsmetrics/tests/main.nf.test.snap | 66 ++++ .../sentieon/wgsmetrics/tests/nextflow.config | 9 + subworkflows/local/call_snv_sentieon/main.nf | 2 +- 33 files changed, 896 insertions(+), 372 deletions(-) delete mode 100644 modules/nf-core/sentieon/bwamem/tests/tags.yml create mode 100644 modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test create mode 100644 modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap create mode 100644 modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config create mode 100644 modules/nf-core/sentieon/dnascope/tests/main.nf.test create mode 100644 modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap create mode 100644 modules/nf-core/sentieon/dnascope/tests/nextflow.config create mode 100644 modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test create mode 100644 modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap create mode 100644 modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config diff --git a/modules.json b/modules.json index edb5cc6dc..39cac7990 100644 --- a/modules.json +++ b/modules.json @@ -410,42 +410,42 @@ }, "sentieon/bwaindex": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/datametrics": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/readwriter": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "sentieon/wgsmetrics": { "branch": "master", - "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d", + "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", "installed_by": ["modules"] }, "smncopynumbercaller": { diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf index c038a857b..2f014d064 100644 --- a/modules/nf-core/sentieon/bwamem/main.nf +++ b/modules/nf-core/sentieon/bwamem/main.nf @@ -5,8 +5,8 @@ process SENTIEON_BWAMEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap index 77070ccc4..88b8f5e0d 100644 --- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap @@ -8,12 +8,12 @@ "id": "test", "single_end": true }, - "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b", - "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18" + "test.bam:md5,dea3fc9d19388fefd3fca90f07b0a1f8", + "test.bam.bai:md5,0cdb1f6a29cf060612b607d9166e4c36" ] ], "1": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ], "bam_and_bai": [ [ @@ -21,20 +21,20 @@ "id": "test", "single_end": true }, - "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b", - "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18" + "test.bam:md5,dea3fc9d19388fefd3fca90f07b0a1f8", + "test.bam.bai:md5,0cdb1f6a29cf060612b607d9166e4c36" ] ], "versions": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:25:33.275731212" + "timestamp": "2025-05-09T08:00:37.715936422" }, "Paired-End - stub": { "content": [ @@ -50,7 +50,7 @@ ] ], "1": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ], "bam_and_bai": [ [ @@ -63,15 +63,15 @@ ] ], "versions": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:26:16.58588651" + "timestamp": "2025-05-09T08:03:07.521348975" }, "Paired-End": { "content": [ @@ -82,12 +82,12 @@ "id": "test", "single_end": false }, - "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268", - "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919" + "test.bam:md5,ee68f972e594b3d1751696eef91f183b", + "test.bam.bai:md5,b22cbbc501adedc7433d2334f631f754" ] ], "1": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ], "bam_and_bai": [ [ @@ -95,20 +95,20 @@ "id": "test", "single_end": false }, - "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268", - "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919" + "test.bam:md5,ee68f972e594b3d1751696eef91f183b", + "test.bam.bai:md5,b22cbbc501adedc7433d2334f631f754" ] ], "versions": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:25:55.068934639" + "timestamp": "2025-05-09T08:01:52.416216804" }, "Single-End - stub": { "content": [ @@ -124,7 +124,7 @@ ] ], "1": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ], "bam_and_bai": [ [ @@ -137,15 +137,15 @@ ] ], "versions": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:26:05.151760076" + "timestamp": "2025-05-09T08:02:30.011453766" }, "Single-End Output CRAM": { "content": [ @@ -156,12 +156,12 @@ "id": "test", "single_end": true }, - "test.cram:md5,817cf0847ae0c89062e2ee4be312101a", - "test.cram.crai:md5,60f801c550a18982e55207adb31ec351" + "test.cram:md5,0922ee1600c3a9bb77547bde94dbe846", + "test.cram.crai:md5,554d760554ce52d5ec269c8949eb3ab2" ] ], "1": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ], "bam_and_bai": [ [ @@ -169,19 +169,19 @@ "id": "test", "single_end": true }, - "test.cram:md5,817cf0847ae0c89062e2ee4be312101a", - "test.cram.crai:md5,60f801c550a18982e55207adb31ec351" + "test.cram:md5,0922ee1600c3a9bb77547bde94dbe846", + "test.cram.crai:md5,554d760554ce52d5ec269c8949eb3ab2" ] ], "versions": [ - "versions.yml:md5,755d24c7416c1408313ec93814cef759" + "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:25:44.360755915" + "timestamp": "2025-05-09T08:01:15.037591768" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/bwamem/tests/tags.yml b/modules/nf-core/sentieon/bwamem/tests/tags.yml deleted file mode 100644 index fbc2bb3cc..000000000 --- a/modules/nf-core/sentieon/bwamem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -sentieon/bwamem: - - "modules/nf-core/sentieon/bwamem/**" diff --git a/modules/nf-core/sentieon/datametrics/environment.yml b/modules/nf-core/sentieon/datametrics/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/datametrics/environment.yml +++ b/modules/nf-core/sentieon/datametrics/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf index 85bf6b507..3a4fce755 100644 --- a/modules/nf-core/sentieon/datametrics/main.nf +++ b/modules/nf-core/sentieon/datametrics/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DATAMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/68/68b1ed28e610d30e71f2941062dd1dddc5ccaa59496442761d0a3579e0ab9d69/data' : + 'community.wave.seqera.io/library/sentieon_gnuplot:be1a7a35856e97bb' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/datametrics/meta.yml b/modules/nf-core/sentieon/datametrics/meta.yml index 2b59da39c..91c60b756 100644 --- a/modules/nf-core/sentieon/datametrics/meta.yml +++ b/modules/nf-core/sentieon/datametrics/meta.yml @@ -122,7 +122,7 @@ output: e.g. `[ id:'test', single_end:false ]` - "*mq_metrics.pdf": type: file - description: "PDF containting plot of mean base quality scores" + description: "PDF containing plot of mean base quality scores" pattern: "*.pdf" - qd_plot: - meta: @@ -132,7 +132,7 @@ output: e.g. `[ id:'test', single_end:false ]` - "*qd_metrics.pdf": type: file - description: "PDF containting plot of specific base quality score" + description: "PDF containing plot of specific base quality score" pattern: "*.pdf" - is_plot: - meta: @@ -142,7 +142,7 @@ output: e.g. `[ id:'test', single_end:false ]` - "*is_metrics.pdf": type: file - description: "PDF containting plot of insert sizes" + description: "PDF containing plot of insert sizes" pattern: "*.pdf" - gc_plot: - meta: @@ -152,7 +152,7 @@ output: e.g. `[ id:'test', single_end:false ]` - "*gc_metrics.pdf": type: file - description: "PDF containting plot of GC bias" + description: "PDF containing plot of GC bias" pattern: "*.pdf" - versions: - versions.yml: diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test b/modules/nf-core/sentieon/datametrics/tests/main.nf.test index a13d68e6e..44f631a61 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test @@ -64,12 +64,26 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.mq_metrics, + process.out.qd_metrics, + process.out.gc_summary, + process.out.gc_metrics, + process.out.aln_metrics, + process.out.is_metrics, + file(process.out.mq_plot[0][1]).name, + file(process.out.qd_plot[0][1]).name, + file(process.out.is_plot[0][1]).name, + file(process.out.gc_plot[0][1]).name, + process.out.versions, + path(process.out.versions[0]).yaml + ).match() + } ) } - + } test("sarscov2 - stub") { diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap index d31612106..b5180833d 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "10": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" + "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" ], "2": [ [ @@ -186,212 +186,90 @@ ] ], "versions": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" + "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:22:45.899449567" + "timestamp": "2025-05-09T08:08:55.410924336" }, "metrics - with plots": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" - ] - ], - "10": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.pdf:md5,c04212fac971c67066082dcb63fa08ce" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.pdf:md5,4edab3779660668a7cfd203196912ace" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.pdf:md5,068232633e0f93ea2b53f4c698bd8a54" - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.pdf:md5,950372106204ff4d2fbe5ca413ac8300" - ] - ], - "aln_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" - ] - ], - "gc_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" - ] - ], - "gc_plot": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.pdf:md5,950372106204ff4d2fbe5ca413ac8300" - ] - ], - "gc_summary": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" - ] - ], - "is_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" - ] - ], - "is_plot": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.pdf:md5,068232633e0f93ea2b53f4c698bd8a54" - ] - ], - "mq_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" - ] - ], - "mq_plot": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.pdf:md5,c04212fac971c67066082dcb63fa08ce" - ] - ], - "qd_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" - ] - ], - "qd_plot": [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.pdf:md5,4edab3779660668a7cfd203196912ace" - ] - ], - "versions": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" + [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" + ] + ], + "test_mq_metrics.pdf", + "test_qd_metrics.pdf", + "test_is_metrics.pdf", + "test_gc_metrics.pdf", + [ + "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" + ], + { + "SENTIEON_DATAMETRICS": { + "sentieon": 202503 + } } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:22:36.981327826" + "timestamp": "2025-05-09T09:59:14.060728182" }, "metrics - no plots": { "content": [ @@ -402,7 +280,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" + "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" ] ], "1": [ @@ -411,11 +289,11 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" + "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" ] ], "10": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" + "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" ], "2": [ [ @@ -423,7 +301,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" + "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" ] ], "3": [ @@ -432,7 +310,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" + "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" ] ], "4": [ @@ -441,7 +319,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" + "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" ] ], "5": [ @@ -450,7 +328,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" + "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" ] ], "6": [ @@ -471,7 +349,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" + "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" ] ], "gc_metrics": [ @@ -480,7 +358,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" + "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" ] ], "gc_plot": [ @@ -492,7 +370,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" + "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" ] ], "is_metrics": [ @@ -501,7 +379,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" + "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" ] ], "is_plot": [ @@ -513,7 +391,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" + "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" ] ], "mq_plot": [ @@ -525,21 +403,21 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" + "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" ] ], "qd_plot": [ ], "versions": [ - "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" + "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:22:26.909097428" + "timestamp": "2025-05-09T08:07:40.668772808" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf index 5735df734..976d0baa1 100644 --- a/modules/nf-core/sentieon/dedup/main.nf +++ b/modules/nf-core/sentieon/dedup/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DEDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap index 26117a7cd..a0c84a503 100644 --- a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.cram:md5,e46e97256846338e1cff32d862105491" + "test.cram:md5,4e01d75d8942343a339f05b71b09c9d3" ] ], "1": [ @@ -15,7 +15,7 @@ { "id": "test" }, - "test.cram.crai:md5,4b7b2152b33c5334f9477cc3650f8c91" + "test.cram.crai:md5,b9ea073c563afd5a7c3239e3051a7a15" ] ], "2": [ @@ -26,7 +26,7 @@ { "id": "test" }, - "test.cram.bai:md5,889503338dc569b24e44e5e3aec815ea" + "test.cram.bai:md5,827bf9e62729b7760290fc27750821c2" ] ], "4": [ @@ -34,7 +34,7 @@ { "id": "test" }, - "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" + "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" ] ], "5": [ @@ -42,7 +42,7 @@ { "id": "test" }, - "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc" + "test.cram.metrics:md5,a082690dac37c795965e86387a7d610f" ] ], "6": [ @@ -50,18 +50,18 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc" + "test.cram.metrics.multiqc.tsv:md5,a082690dac37c795965e86387a7d610f" ] ], "7": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ], "bai": [ [ { "id": "test" }, - "test.cram.bai:md5,889503338dc569b24e44e5e3aec815ea" + "test.cram.bai:md5,827bf9e62729b7760290fc27750821c2" ] ], "bam": [ @@ -72,7 +72,7 @@ { "id": "test" }, - "test.cram.crai:md5,4b7b2152b33c5334f9477cc3650f8c91" + "test.cram.crai:md5,b9ea073c563afd5a7c3239e3051a7a15" ] ], "cram": [ @@ -80,7 +80,7 @@ { "id": "test" }, - "test.cram:md5,e46e97256846338e1cff32d862105491" + "test.cram:md5,4e01d75d8942343a339f05b71b09c9d3" ] ], "metrics": [ @@ -88,7 +88,7 @@ { "id": "test" }, - "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc" + "test.cram.metrics:md5,a082690dac37c795965e86387a7d610f" ] ], "metrics_multiqc_tsv": [ @@ -96,7 +96,7 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc" + "test.cram.metrics.multiqc.tsv:md5,a082690dac37c795965e86387a7d610f" ] ], "score": [ @@ -104,19 +104,19 @@ { "id": "test" }, - "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" + "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" ] ], "versions": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:28:10.570152622" + "timestamp": "2025-05-09T08:09:22.353050455" }, "Test removing duplicates": { "content": [ @@ -126,7 +126,7 @@ { "id": "test" }, - "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4" + "test.cram:md5,0c75659393aefbe720f7d351beae67d6" ] ], "1": [ @@ -134,7 +134,7 @@ { "id": "test" }, - "test.cram.crai:md5,c617398ead281c1339d78d5df0d606e9" + "test.cram.crai:md5,00eaec21ddce36812f449c0fc36d13e1" ] ], "2": [ @@ -145,7 +145,7 @@ { "id": "test" }, - "test.cram.bai:md5,a1ea729eca4732ca3a5dee946a70fbc8" + "test.cram.bai:md5,86d206b627fe39eb667b72dee25ad849" ] ], "4": [ @@ -153,7 +153,7 @@ { "id": "test" }, - "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" + "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" ] ], "5": [ @@ -161,7 +161,7 @@ { "id": "test" }, - "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65" + "test.cram.metrics:md5,ce60af7e91a325b6c720009ac9a68d74" ] ], "6": [ @@ -169,18 +169,18 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65" + "test.cram.metrics.multiqc.tsv:md5,ce60af7e91a325b6c720009ac9a68d74" ] ], "7": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ], "bai": [ [ { "id": "test" }, - "test.cram.bai:md5,a1ea729eca4732ca3a5dee946a70fbc8" + "test.cram.bai:md5,86d206b627fe39eb667b72dee25ad849" ] ], "bam": [ @@ -191,7 +191,7 @@ { "id": "test" }, - "test.cram.crai:md5,c617398ead281c1339d78d5df0d606e9" + "test.cram.crai:md5,00eaec21ddce36812f449c0fc36d13e1" ] ], "cram": [ @@ -199,7 +199,7 @@ { "id": "test" }, - "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4" + "test.cram:md5,0c75659393aefbe720f7d351beae67d6" ] ], "metrics": [ @@ -207,7 +207,7 @@ { "id": "test" }, - "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65" + "test.cram.metrics:md5,ce60af7e91a325b6c720009ac9a68d74" ] ], "metrics_multiqc_tsv": [ @@ -215,7 +215,7 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65" + "test.cram.metrics.multiqc.tsv:md5,ce60af7e91a325b6c720009ac9a68d74" ] ], "score": [ @@ -223,19 +223,19 @@ { "id": "test" }, - "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" + "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" ] ], "versions": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:28:19.377946074" + "timestamp": "2025-05-09T08:09:49.954445693" }, "Test stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "7": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ], "bai": [ [ @@ -346,14 +346,14 @@ ] ], "versions": [ - "versions.yml:md5,763463853476be96846b6da5aecfacf4" + "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:28:28.792696026" + "timestamp": "2025-05-09T08:10:17.139642524" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf index 85fd601b3..acc7edd47 100644 --- a/modules/nf-core/sentieon/dnamodelapply/main.nf +++ b/modules/nf-core/sentieon/dnamodelapply/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DNAMODELAPPLY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(vcf), path(idx) @@ -16,7 +16,7 @@ process SENTIEON_DNAMODELAPPLY { output: tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi"), emit: index + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi path "versions.yml" , emit: versions when: @@ -24,7 +24,7 @@ process SENTIEON_DNAMODELAPPLY { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}_applied" def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : "" @@ -47,9 +47,9 @@ process SENTIEON_DNAMODELAPPLY { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}_applied" """ - touch ${prefix}.vcf.gz + echo | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index 2505aff74..b73064111 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -65,7 +65,7 @@ output: type: file description: INPUT VCF file pattern: "*.{vcf,vcf.gz}" - - index: + - tbi: - meta: type: map description: | diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test new file mode 100644 index 000000000..6d4384168 --- /dev/null +++ b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SENTIEON_DNAMODELAPPLY" + config "./nextflow.config" + script "../main.nf" + process "SENTIEON_DNAMODELAPPLY" + + tag "modules" + tag "modules_nfcore" + tag "sentieon" + tag "sentieon/dnascope" + tag "sentieon/dnamodelapply" + + setup { + run("SENTIEON_DNASCOPE") { + script "../../dnascope/main.nf" + + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true), + []// no intervals + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = [[:],file("https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model", checkIfExists:true)] + input[6] = 'CONSERVATIVE' + input[7] = 'variant' + input[8] = false + """ + } + } + } + + test("apply model") { + + when { + process { + """ + input[0] = SENTIEON_DNASCOPE.out.vcf.join(SENTIEON_DNASCOPE.out.vcf_tbi) + input[1] = [[id:'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'],file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],file("https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model", checkIfExists:true)] + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + file(process.out.tbi[0][1]).name, + path(process.out.versions[0]).yaml + ).match() } + ) + } + } + + + test("apply model -- stub") { + options '-stub' + when { + process { + """ + input[0] = SENTIEON_DNASCOPE.out.vcf.join(SENTIEON_DNASCOPE.out.vcf_tbi) + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],file("https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model", checkIfExists:true)] + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap new file mode 100644 index 000000000..9d5dd67f9 --- /dev/null +++ b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap @@ -0,0 +1,76 @@ +{ + "apply model": { + "content": [ + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", + "test_applied.vcf.gz.tbi", + { + "SENTIEON_DNAMODELAPPLY": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:11:55.349533849" + }, + "apply model -- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_applied.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_applied.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,b14db672791c6252e540cb6404148c5d" + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_applied.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_applied.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,b14db672791c6252e540cb6404148c5d" + ] + }, + { + "SENTIEON_DNAMODELAPPLY": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:12:33.395536554" + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config b/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config new file mode 100644 index 000000000..09a068ee6 --- /dev/null +++ b/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config @@ -0,0 +1,9 @@ +env { + // NOTE This is how nf-core/sarek users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf index bdeb62521..f027783c2 100644 --- a/modules/nf-core/sentieon/dnascope/main.nf +++ b/modules/nf-core/sentieon/dnascope/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DNASCOPE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(bam), path(bai), path(intervals) @@ -30,17 +30,17 @@ process SENTIEON_DNASCOPE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' // options for the driver - def args2 = task.ext.args2 ?: '' // options for the vcf generation - def args3 = task.ext.args3 ?: '' // options for the gvcf generation - def interval = intervals ? "--interval ${intervals}" : '' - def dbsnp_cmd = dbsnp ? "-d ${dbsnp}" : '' - def model_cmd = ml_model ? " --model ${ml_model}" : '' - def pcr_indel_model_cmd = pcr_indel_model ? " --pcr_indel_model ${pcr_indel_model}" : '' - def prefix = task.ext.prefix ?: "${meta.id}" - def vcf_cmd = "" - def gvcf_cmd = "" - def base_cmd = '--algo DNAscope ' + dbsnp_cmd + ' ' + def args = task.ext.args ?: '' // options for the driver + def args2 = task.ext.args2 ?: '' // options for the vcf generation + def args3 = task.ext.args3 ?: '' // options for the gvcf generation + def interval = intervals ? "--interval ${intervals}" : '' + def dbsnp_cmd = dbsnp ? "-d ${dbsnp}" : '' + def model_cmd = ml_model ? " --model ${ml_model}" : '' + def pcr_indel_model_cmd = pcr_indel_model ? " --pcr_indel_model ${pcr_indel_model}" : '' + def prefix = task.ext.prefix ?: "${meta.id}" + def vcf_cmd = "" + def gvcf_cmd = "" + def base_cmd = '--algo DNAscope ' + dbsnp_cmd + ' ' if (emit_vcf) { // emit_vcf can be the empty string, 'variant', 'confident' or 'all' but NOT 'gvcf' vcf_cmd = base_cmd + args2 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode ' + emit_vcf + ' ' + prefix + '.unfiltered.vcf.gz' @@ -65,12 +65,13 @@ process SENTIEON_DNASCOPE { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" + def gvcf_cmd = emit_gvcf ? "echo | gzip > ${prefix}.g.vcf.gz; touch ${prefix}.g.vcf.gz.tbi": "" + """ - touch ${prefix}.unfiltered.vcf.gz + echo | gzip > ${prefix}.unfiltered.vcf.gz touch ${prefix}.unfiltered.vcf.gz.tbi - touch ${prefix}.g.vcf.gz - touch ${prefix}.g.vcf.gz.tbi + $gvcf_cmd cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/sentieon/dnascope/tests/main.nf.test b/modules/nf-core/sentieon/dnascope/tests/main.nf.test new file mode 100644 index 000000000..010266471 --- /dev/null +++ b/modules/nf-core/sentieon/dnascope/tests/main.nf.test @@ -0,0 +1,155 @@ +nextflow_process { + + name "Test Process SENTIEON_DNASCOPE" + config "./nextflow.config" + script "../main.nf" + process "SENTIEON_DNASCOPE" + + tag "modules" + tag "modules_nfcore" + tag "sentieon" + tag "sentieon/dnascope" + config './nextflow.config' + + test("conservative indel model - variant") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true), + []// no intervals + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = [[:],file("https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model", checkIfExists: true)] + input[6] = 'CONSERVATIVE' + input[7] = 'variant' + input[8] = false + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + file(process.out.vcf_tbi[0][1]).name, + path(process.out.versions[0]).yaml + ).match() } + ) + } + } + + + test("conservative indel model - all") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true), + []// no intervals + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = [[:],file("https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model", checkIfExists: true)] + input[6] = 'AGGRESSIVE' + input[7] = 'all' + input[8] = false + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + file(process.out.vcf_tbi[0][1]).name, + process.out.versions, + path(process.out.versions[0]).yaml + ).match() } + ) + } + } + + + test("hostile indel model - confident") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true), + []// no intervals + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = 'HOSTILE' + input[7] = 'confident' + input[8] = true + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + path(process.out.vcf[0][1]).vcf.summary, + file(process.out.vcf_tbi[0][1]).name, + process.out.versions, + path(process.out.versions[0]).yaml + ).match() } + ) + } + } + + + test("conversative indel model - variant - stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true), + []// no intervals + ] + input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)] + input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)] + input[3] = [[:],[]] + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = 'CONSERVATIVE' + input[7] = 'variant' + input[8] = false + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap b/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap new file mode 100644 index 000000000..0720c00e2 --- /dev/null +++ b/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap @@ -0,0 +1,122 @@ +{ + "hostile indel model - confident": { + "content": [ + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", + "test.unfiltered.vcf.gz.tbi", + [ + "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + ], + { + "SENTIEON_DNASCOPE": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:13:57.370693339" + }, + "conservative indel model - variant": { + "content": [ + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", + "test.unfiltered.vcf.gz.tbi", + { + "SENTIEON_DNASCOPE": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:13:01.800860635" + }, + "conversative indel model - variant - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.unfiltered.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + ], + "gvcf": [ + + ], + "gvcf_tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.unfiltered.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test" + }, + "test.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + ] + }, + { + "SENTIEON_DNASCOPE": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:14:24.965334187" + }, + "conservative indel model - all": { + "content": [ + "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=8, phased=false, phasedAutodetect=false]", + "test.unfiltered.vcf.gz.tbi", + [ + "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + ], + { + "SENTIEON_DNASCOPE": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T08:13:30.044864434" + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnascope/tests/nextflow.config b/modules/nf-core/sentieon/dnascope/tests/nextflow.config new file mode 100644 index 000000000..09a068ee6 --- /dev/null +++ b/modules/nf-core/sentieon/dnascope/tests/nextflow.config @@ -0,0 +1,9 @@ +env { + // NOTE This is how nf-core/sarek users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} diff --git a/modules/nf-core/sentieon/readwriter/environment.yml b/modules/nf-core/sentieon/readwriter/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/readwriter/environment.yml +++ b/modules/nf-core/sentieon/readwriter/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/readwriter/main.nf b/modules/nf-core/sentieon/readwriter/main.nf index 7e00b9e98..a785e593d 100644 --- a/modules/nf-core/sentieon/readwriter/main.nf +++ b/modules/nf-core/sentieon/readwriter/main.nf @@ -5,8 +5,8 @@ process SENTIEON_READWRITER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap index 0af607892..f56e17cb9 100644 --- a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap @@ -4,56 +4,56 @@ "2f11e4fe3390b8ad0a1852616fd1da04", "test.bam.bai", [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:32:10.696224516" + "timestamp": "2025-05-09T08:25:19.723258714" }, "cram": { "content": [ "2f11e4fe3390b8ad0a1852616fd1da04", "test.cram.crai", [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:32:23.080911465" + "timestamp": "2025-05-09T08:25:47.849309508" }, "merging - output bam": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.bam.bai", [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:32:36.741074568" + "timestamp": "2025-05-09T08:26:15.337826518" }, "merging - output bam to cram": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.cram.crai", [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:33:50.523887508" + "timestamp": "2025-05-09T08:26:44.414501574" }, "sentieon readwriter - stub": { "content": [ @@ -84,7 +84,7 @@ ] ], "3": [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ], "index": [ [ @@ -112,14 +112,14 @@ ] ], "versions": [ - "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" + "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T10:34:00.856232997" + "timestamp": "2025-05-09T08:27:11.322150361" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/wgsmetrics/environment.yml b/modules/nf-core/sentieon/wgsmetrics/environment.yml index d7abf668e..ec48106f3 100644 --- a/modules/nf-core/sentieon/wgsmetrics/environment.yml +++ b/modules/nf-core/sentieon/wgsmetrics/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.03 + - bioconda::sentieon=202503 diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf index 9f268f5a8..8ccdbe8f4 100644 --- a/modules/nf-core/sentieon/wgsmetrics/main.nf +++ b/modules/nf-core/sentieon/wgsmetrics/main.nf @@ -5,11 +5,11 @@ process SENTIEON_WGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : - 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : + 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" input: - tuple val(meta), path(bam), path(bai) + tuple val(meta) , path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(intervals_list) @@ -22,10 +22,10 @@ process SENTIEON_WGSMETRICS { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def input = bam.sort().collect{"-i $it"}.join(' ') + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def interval = intervals_list ? "--interval ${intervals_list}" : "" + def interval = intervals_list ? "--interval ${intervals_list}" : "" + def input = bam.sort().collect{"-i $it"}.join(' ') def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : "" @@ -39,7 +39,8 @@ process SENTIEON_WGSMETRICS { $input \\ $interval \\ $args \\ - --algo WgsMetricsAlgo ${prefix}.txt + --algo WgsMetricsAlgo \\ + ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test new file mode 100644 index 000000000..ee431a8e9 --- /dev/null +++ b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_process { + + name "Test Process SENTIEON_WGSMETRICS" + config "./nextflow.config" + script "../main.nf" + process "SENTIEON_WGSMETRICS" + + tag "modules" + tag "modules_nfcore" + tag "sentieon" + tag "sentieon/wgsmetrics" + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [[:],[]] + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.wgs_metrics[0][1]).readLines()[1..5], + process.out.versions, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + } + + + test("sarscov2 - bam -- stub") { + options '-stub' + when { + params { + module_args = '' + } + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [[:],[]] + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() + } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap new file mode 100644 index 000000000..dae6dfaeb --- /dev/null +++ b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap @@ -0,0 +1,66 @@ +{ + "sarscov2 - bam -- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" + ], + "versions": [ + "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" + ], + "wgs_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + }, + { + "SENTIEON_WGSMETRICS": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T09:20:45.201824519" + }, + "sarscov2 - bam": { + "content": [ + [ + "GENOME_TERRITORY\tMEAN_COVERAGE\tSD_COVERAGE\tMEDIAN_COVERAGE\tMAD_COVERAGE\tPCT_EXC_MAPQ\tPCT_EXC_DUPE\tPCT_EXC_UNPAIRED\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_CAPPED\tPCT_EXC_TOTAL\tPCT_1X\tPCT_5X\tPCT_10X\tPCT_15X\tPCT_20X\tPCT_25X\tPCT_30X\tPCT_40X\tPCT_50X\tPCT_60X\tPCT_70X\tPCT_80X\tPCT_90X\tPCT_100X\tHET_SNP_SENSITIVITY\tHET_SNP_Q\t", + "29829\t0.63086\t0.94268\t0\t0\t0.0054378\t0\t0.013649\t0.063246\t0.2309\t0\t0.31324\t0.41151\t0.0051963\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.17212\t1\t", + "", + "coverage\thigh_quality_coverage_count\t", + "0\t17554" + ], + [ + "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" + ], + { + "SENTIEON_WGSMETRICS": { + "sentieon": 202503 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-05-09T09:20:17.64441942" + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config b/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config new file mode 100644 index 000000000..09a068ee6 --- /dev/null +++ b/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config @@ -0,0 +1,9 @@ +env { + // NOTE This is how nf-core/sarek users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 6ff570097..e987d26cb 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -53,7 +53,7 @@ workflow CALL_SNV_SENTIEON { SENTIEON_DNAMODELAPPLY ( ch_dnamodelapply_in, ch_genome_fasta, ch_genome_fai, ch_ml_model ) - ch_bcffilterone_in = SENTIEON_DNAMODELAPPLY.out.vcf.join(SENTIEON_DNAMODELAPPLY.out.index, failOnMismatch: true) + ch_bcffilterone_in = SENTIEON_DNAMODELAPPLY.out.vcf.join(SENTIEON_DNAMODELAPPLY.out.tbi, failOnMismatch: true) BCF_FILTER_ONE (ch_bcffilterone_in) ch_bcffiltertwo_in = BCF_FILTER_ONE.out.vcf.join(BCF_FILTER_ONE.out.tbi, failOnMismatch: true) From f8c50b69eea2340aa321635ae411c278c0e9eb12 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 19:22:39 +0200 Subject: [PATCH 019/872] update snaps --- .../local/align/tests/main.nf.test.snap | 58 +++++++++---------- .../align_sentieon/tests/main.nf.test.snap | 48 +++++++-------- .../prepare_references/tests/main.nf.test | 17 ++---- .../tests/main.nf.test.snap | 36 ++++++++++-- 4 files changed, 89 insertions(+), 70 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 80a8eeb11..e6ae1d9ea 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -6,20 +6,20 @@ { "groupSize": 1, "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", "case_id": "justhusky" } }, - "8aa7930105c6aa55f96e3719de968144", - "slowlycivilbuck_sorted_md.bam.bai:md5,b6c5d2736032f5e1cb190853ca366afe" + "5826e0ede26849bd789600cb576607c6", + "hugelymodelbat_sorted_md.bam.bai:md5,60666327a06035997be296c2636c313c" ] ], [ @@ -27,20 +27,20 @@ { "groupSize": 1, "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", "case_id": "justhusky" } }, - "a5d6892191a2c8c1f29966448623ca1b", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" + "b18998c8cf7dc417ca9a122ba1c9403d", + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,ebc9222d03624e276c0c242e87e6618c" ] ], [ @@ -48,20 +48,20 @@ { "groupSize": 1, "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", "case_id": "justhusky" } }, - "427b5e476d84c5277d2d24210800ad60", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,6c663c5661749b25782ac78a3ba1f242" + "97e6eaae1cda668da59e5c16a9bbcc1d", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,f9a4e5c7c7ca7c25f365bee4cfcdb3a9" ] ], [ @@ -93,9 +93,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-23T15:53:23.463213506" + "timestamp": "2025-06-25T17:24:58.017903349" }, "align bwameme": { "content": [ diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index fbaaf1ac7..8bc1129d0 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,0dda7e8e144c07591f06330b07b36071" + "test_dedup.bam:md5,eecb176fcd4ba3862cd8a87584d29d7f" ] ], "1": [ @@ -29,7 +29,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,0458a0ef98b3a86ba28a2bcac628f7d4" + "test_dedup.bam.bai:md5,2c3892c0b7dd38008f812936f19edcfd" ] ], "2": [ @@ -44,7 +44,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_mq_metrics.txt:md5,1ba9b952749ad4e5310598fe23c02085" + "test_datametrics_mq_metrics.txt:md5,d924101f16a609cfe2381fb2904c1157" ] ], "3": [ @@ -59,7 +59,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_qd_metrics.txt:md5,5294d174c6ffaaf47ceb02befbbffc40" + "test_datametrics_qd_metrics.txt:md5,5d823326eaf59b00e31b7a10b8e1a09e" ] ], "4": [ @@ -74,7 +74,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_metrics.txt:md5,96c951444c7f5af19c60d5262e74fb1c" + "test_datametrics_gc_metrics.txt:md5,6d373e38fcaa29620eb2c1c62bd9ece9" ] ], "5": [ @@ -89,7 +89,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_summary.txt:md5,77045bf67dbc251523af0d5bf9b57dbf" + "test_datametrics_gc_summary.txt:md5,123abd2c83e7df6f141a30c7d38bff27" ] ], "6": [ @@ -104,7 +104,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_aln_metrics.txt:md5,f4681d1f08b687f424af70772cfb597a" + "test_datametrics_aln_metrics.txt:md5,609454bf43dd880e347da719e1868432" ] ], "7": [ @@ -119,13 +119,13 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_is_metrics.txt:md5,90bfb2b94b01074d93e6da1b69c4e494" + "test_datametrics_is_metrics.txt:md5,04eb7da7a2b7acea2bf02f860535c2e8" ] ], "8": [ - "versions.yml:md5,01896e6794bd10730ddfe6872631bdde", - "versions.yml:md5,2b8ad96b3aa67e6563e8a05744db6174", - "versions.yml:md5,c0917d5569d12b01718342f7aac5cbbd" + "versions.yml:md5,081d0fd598d1279f3025f39626df5a10", + "versions.yml:md5,9f88074c5a7336a02eeb30461af26fd1", + "versions.yml:md5,f084363cb6d662d82d09a289b6b68346" ], "aln_metrics": [ [ @@ -139,7 +139,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_aln_metrics.txt:md5,f4681d1f08b687f424af70772cfb597a" + "test_datametrics_aln_metrics.txt:md5,609454bf43dd880e347da719e1868432" ] ], "gc_metrics": [ @@ -154,7 +154,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_metrics.txt:md5,96c951444c7f5af19c60d5262e74fb1c" + "test_datametrics_gc_metrics.txt:md5,6d373e38fcaa29620eb2c1c62bd9ece9" ] ], "gc_summary": [ @@ -169,7 +169,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_summary.txt:md5,77045bf67dbc251523af0d5bf9b57dbf" + "test_datametrics_gc_summary.txt:md5,123abd2c83e7df6f141a30c7d38bff27" ] ], "is_metrics": [ @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_is_metrics.txt:md5,90bfb2b94b01074d93e6da1b69c4e494" + "test_datametrics_is_metrics.txt:md5,04eb7da7a2b7acea2bf02f860535c2e8" ] ], "marked_bai": [ @@ -199,7 +199,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,0458a0ef98b3a86ba28a2bcac628f7d4" + "test_dedup.bam.bai:md5,2c3892c0b7dd38008f812936f19edcfd" ] ], "marked_bam": [ @@ -214,7 +214,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,0dda7e8e144c07591f06330b07b36071" + "test_dedup.bam:md5,eecb176fcd4ba3862cd8a87584d29d7f" ] ], "mq_metrics": [ @@ -229,7 +229,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_mq_metrics.txt:md5,1ba9b952749ad4e5310598fe23c02085" + "test_datametrics_mq_metrics.txt:md5,d924101f16a609cfe2381fb2904c1157" ] ], "qd_metrics": [ @@ -244,20 +244,20 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_qd_metrics.txt:md5,5294d174c6ffaaf47ceb02befbbffc40" + "test_datametrics_qd_metrics.txt:md5,5d823326eaf59b00e31b7a10b8e1a09e" ] ], "versions": [ - "versions.yml:md5,01896e6794bd10730ddfe6872631bdde", - "versions.yml:md5,2b8ad96b3aa67e6563e8a05744db6174", - "versions.yml:md5,c0917d5569d12b01718342f7aac5cbbd" + "versions.yml:md5,081d0fd598d1279f3025f39626df5a10", + "versions.yml:md5,9f88074c5a7336a02eeb30461af26fd1", + "versions.yml:md5,f084363cb6d662d82d09a289b6b68346" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.3" }, - "timestamp": "2025-04-09T14:36:45.125659653" + "timestamp": "2025-06-25T17:05:48.914189124" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 897a14e3d..0353d9815 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -13,23 +13,18 @@ nextflow_workflow { mt_aligner = "bwa" variant_caller = "deepvariant" mito_name = "MT" - fasta = params.raredisease_testdata_base_path+ 'reference/reference.fasta' - fai = params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai' - target_bed = params.raredisease_testdata_base_path+ 'reference/target.bed' - vep_cache = params.raredisease_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz' - } workflow { """ - input[0] = Channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() - input[1] = Channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() + input[0] = Channel.of(params.raredisease_testdata_base_path+ 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() + input[1] = Channel.of(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() input[2] = Channel.empty() input[3] = Channel.empty() - input[4] = Channel.value([[:],[]]) - input[5] = Channel.value([[:],[]]) - input[6] = Channel.of(params.target_bed).map {it -> [[id:'genome'], it]}.collect() + input[4] = Channel.of(params.raredisease_testdata_base_path+ 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() + input[5] = Channel.of(params.raredisease_testdata_base_path+ 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() + input[6] = Channel.of(params.raredisease_testdata_base_path+ 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() input[7] = Channel.empty() - input[8] = Channel.of(params.vep_cache).map {it -> [[id:'genome'], it]}.collect() + input[8] = Channel.of(params.raredisease_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 686a1ba92..c7b69f839 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -112,10 +112,20 @@ ], "20": [ - + [ + { + "id": "genome" + }, + "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + ] ], "21": [ - + [ + { + "id": "genome" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + ] ], "22": [ [ @@ -379,6 +389,7 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", + "versions.yml:md5,3e1d1e300c9f1e99a758f5854e226a8c", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", @@ -386,6 +397,7 @@ "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", + "versions.yml:md5,94381c84c4482acd1f7bdb0309eb7d65", "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", @@ -497,10 +509,20 @@ ] ], "gnomad_af_idx": [ - + [ + { + "id": "genome" + }, + "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + ] ], "known_dbsnp_tbi": [ - + [ + { + "id": "genome" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + ] ], "mt_bwa_index": [ [ @@ -862,6 +884,7 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", + "versions.yml:md5,3e1d1e300c9f1e99a758f5854e226a8c", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", @@ -869,6 +892,7 @@ "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", + "versions.yml:md5,94381c84c4482acd1f7bdb0309eb7d65", "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", @@ -880,8 +904,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.3" }, - "timestamp": "2025-03-28T06:30:49.504838" + "timestamp": "2025-06-25T19:15:39.213374312" } } \ No newline at end of file From c5a2f6f7bcf678a8a752884af696d3333acc5a99 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 19:36:16 +0200 Subject: [PATCH 020/872] update sentieon for CI --- .github/actions/nf-test/action.yml | 10 +++ .github/workflows/nf-test.yml | 4 + bin/license_message.py | 113 +++++++++++++++++++++++++++++ tests/nextflow.config | 11 ++- 4 files changed, 137 insertions(+), 1 deletion(-) create mode 100644 bin/license_message.py diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 75abf76c3..53ed069c9 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -59,6 +59,14 @@ runs: conda-solver: libmamba conda-remove-defaults: true + # Set up secrets + - name: Set up Nextflow secrets + if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != '' + shell: bash + run: | + python -m pip install cryptography + nextflow secrets set SENTIEON_AUTH_DATA $(python3 bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") + # TODO Skip failing conda tests and document their failures # https://github.com/nf-core/modules/issues/7017 - name: Run nf-test @@ -67,6 +75,8 @@ runs: NFT_DIFF: ${{ env.NFT_DIFF }} NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }} + SENTIEON_AUTH_MECH: "GitHub Actions - token" run: | nf-test test \ --profile=+${{ inputs.profile }} \ diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 5a604ff24..89254bf72 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -102,6 +102,10 @@ jobs: uses: ./.github/actions/nf-test env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + SENTIEON_AUTH_MECH: "GitHub Actions - token" + SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} + SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} + SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} diff --git a/bin/license_message.py b/bin/license_message.py new file mode 100644 index 000000000..b8281f01b --- /dev/null +++ b/bin/license_message.py @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 + +######################################### +# Author: [DonFreed](https://github.com/DonFreed) +# File: license_message.py +# Source: https://github.com/DonFreed/docker-actions-test/blob/main/.github/scripts/license_message.py +# Source+commit: https://github.com/DonFreed/docker-actions-test/blob/aa1051a9f53b3a1e801953748d062cad74dca9a9/.github/scripts/license_message.py +# Download Date: 2023-07-04, commit: aa1051a +# This source code is licensed under the BSD 2-Clause license +######################################### + +""" +Functions for generating and sending license messages +""" + +# Modified from - https://stackoverflow.com/a/59835994 + +import argparse +import base64 +import calendar +import re +import secrets +import sys + +from cryptography.hazmat.primitives.ciphers.aead import AESGCM +from datetime import datetime as dt + +MESSAGE_TIMEOUT = 60 * 60 * 24 # Messages are valid for 1 day +NONCE_BYTES = 12 + + +class DecryptionTimeout(Exception): + # Decrypting a message that is too old + pass + + +def generate_key(): + key = secrets.token_bytes(32) + return key + + +def handle_generate_key(args): + key = generate_key() + key_b64 = base64.b64encode(key) + print(key_b64.decode("utf-8"), file=args.outfile) + + +def encrypt_message(key, message): + nonce = secrets.token_bytes(NONCE_BYTES) + timestamp = calendar.timegm(dt.now().utctimetuple()) + data = timestamp.to_bytes(10, byteorder="big") + b"__" + message + ciphertext = nonce + AESGCM(key).encrypt(nonce, data, b"") + return ciphertext + + +def handle_encrypt_message(args): + key = base64.b64decode(args.key.encode("utf-8")) + message = args.message.encode("utf-8") + ciphertext = encrypt_message(key, message) + ciphertext_b64 = base64.b64encode(ciphertext) + print(ciphertext_b64.decode("utf-8"), file=args.outfile) + + +def decrypt_message(key, ciphertext, timeout=MESSAGE_TIMEOUT): + nonce, ciphertext = ciphertext[:NONCE_BYTES], ciphertext[NONCE_BYTES:] + message = AESGCM(key).decrypt(nonce, ciphertext, b"") + + msg_timestamp, message = re.split(b"__", message, maxsplit=1) + msg_timestamp = int.from_bytes(msg_timestamp, byteorder="big") + timestamp = calendar.timegm(dt.now().utctimetuple()) + if (timestamp - msg_timestamp) > timeout: + raise DecryptionTimeout("The message has an expired timeout") + return message.decode("utf-8") + + +def handle_decrypt_message(args): + key = base64.b64decode(args.key.encode("utf-8")) + ciphertext = base64.b64decode(args.message.encode("utf-8")) + message = decrypt_message(key, ciphertext, timeout=args.timeout) + print(str(message), file=args.outfile) + + +def parse_args(argv=None): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--outfile", default=sys.stdout, type=argparse.FileType("w"), help="The output file") + + subparsers = parser.add_subparsers(help="Available sub-commands") + + gen_parser = subparsers.add_parser("generate_key", help="Generate a random key string") + gen_parser.set_defaults(func=handle_generate_key) + + encrypt_parser = subparsers.add_parser("encrypt", help="Encrypt a message") + encrypt_parser.add_argument("--key", required=True, help="The encryption key") + encrypt_parser.add_argument("--message", required=True, help="Message to encrypt") + encrypt_parser.set_defaults(func=handle_encrypt_message) + + decrypt_parser = subparsers.add_parser("decrypt", help="Decyrpt a message") + decrypt_parser.add_argument("--key", required=True, help="The encryption key") + decrypt_parser.add_argument("--message", required=True, help="Message to decrypt") + decrypt_parser.add_argument( + "--timeout", + default=MESSAGE_TIMEOUT, + type=int, + help="A message timeout. Decryption will fail for older messages", + ) + decrypt_parser.set_defaults(func=handle_decrypt_message) + + return parser.parse_args(argv) + + +if __name__ == "__main__": + args = parse_args() + args.func(args) \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config index bb12c47de..71ee05da1 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -16,7 +16,16 @@ params { raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' sarscov_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners + +env { + // NOTE This is how pipeline users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how pipeline users will test out Sentieon with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} \ No newline at end of file From c4ddaefad562a8d04c0157fac10837d738c4c43b Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 19:40:37 +0200 Subject: [PATCH 021/872] fix lint --- bin/license_message.py | 2 +- tests/nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/license_message.py b/bin/license_message.py index b8281f01b..9ba2abba3 100644 --- a/bin/license_message.py +++ b/bin/license_message.py @@ -110,4 +110,4 @@ def parse_args(argv=None): if __name__ == "__main__": args = parse_args() - args.func(args) \ No newline at end of file + args.func(args) diff --git a/tests/nextflow.config b/tests/nextflow.config index 71ee05da1..1c6b865f3 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -28,4 +28,4 @@ env { SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA // NOTE This is how pipeline users will test out Sentieon with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} \ No newline at end of file +} From d21e062b6676d9e14703de844c2bbae23ae855fe Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 19:44:59 +0200 Subject: [PATCH 022/872] lint fix --- subworkflows/local/align/tests/main.nf.test | 64 +++++++++---------- .../local/align_MT/tests/main.nf.test | 40 ++++++------ .../prepare_references/tests/main.nf.test | 12 ++-- .../local/scatter_genome/tests/main.nf.test | 8 +-- tests/nextflow.config | 2 +- 5 files changed, 63 insertions(+), 63 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 09306688a..e8a4a1e88 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -52,7 +52,7 @@ nextflow_workflow { params { aligner = 'bwamem2' mt_aligner = 'bwamem2' - raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true analysis_type = "wgs" skip_tools = null @@ -66,37 +66,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = GENOME_MEM2.out.index input[6] = [[:],[]] - input[7] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -138,7 +138,7 @@ nextflow_workflow { params { aligner = 'bwameme' mt_aligner = 'bwamem2' - raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true analysis_type = "wgs" skip_tools = null @@ -152,37 +152,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.raredisease_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = [[:],[]] input[6] = GENOME_MEME.out.index - input[7] = Channel.of([[id:'genome'], [file(params.raredisease_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 87ba3e310..88b2e89d0 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -26,43 +26,43 @@ nextflow_workflow { params { mt_aligner = 'bwamem2' outdir = "$outputDir" - raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { """ input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = [[:],[]] input[3] = MT_MEM2.out.index.collect() - input[4] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } @@ -93,43 +93,43 @@ nextflow_workflow { params { mt_aligner = 'bwa' outdir = "$outputDir" - raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { """ input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.raredisease_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = MT_BWA.out.index.collect() input[3] = [[:],[]] - input[4] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.raredisease_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 0353d9815..6b172037a 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -16,15 +16,15 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of(params.raredisease_testdata_base_path+ 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = Channel.of(params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() + input[0] = Channel.of(params.pipelines_testdata_base_path+ 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() + input[1] = Channel.of(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() input[2] = Channel.empty() input[3] = Channel.empty() - input[4] = Channel.of(params.raredisease_testdata_base_path+ 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() - input[5] = Channel.of(params.raredisease_testdata_base_path+ 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() - input[6] = Channel.of(params.raredisease_testdata_base_path+ 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() + input[4] = Channel.of(params.pipelines_testdata_base_path+ 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() + input[5] = Channel.of(params.pipelines_testdata_base_path+ 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() + input[6] = Channel.of(params.pipelines_testdata_base_path+ 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() input[7] = Channel.empty() - input[8] = Channel.of(params.raredisease_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[8] = Channel.of(params.pipelines_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() """ } } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index bef113c4a..391d66f9b 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -9,10 +9,10 @@ nextflow_workflow { when { params { - raredisease_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - fasta = params.raredisease_testdata_base_path+ 'reference/reference.fasta' - fai = params.raredisease_testdata_base_path+ 'reference/reference.fasta.fai' - dict = params.raredisease_testdata_base_path+ 'reference/reference.dict' + pipelines_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + fasta = params.pipelines_testdata_base_path+ 'reference/reference.fasta' + fai = params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai' + dict = params.pipelines_testdata_base_path+ 'reference/reference.dict' scatter_count = 20 } workflow { diff --git a/tests/nextflow.config b/tests/nextflow.config index 71ee05da1..c5a5c3aed 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -13,7 +13,7 @@ process { } params { - raredisease_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' sarscov_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' } From 62601b5f33e92167ac78eb0d6b60a9bd4df60956 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Jun 2025 20:13:08 +0200 Subject: [PATCH 023/872] update snaps --- tests/default.nf.test.snap | 4 ++-- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a849006bc..4342097b1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -375,7 +375,7 @@ "vcfanno": "0.3.5" }, "Workflow": { - "nf-core/raredisease": "v2.6.0" + "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_ROHCALL": { "tabix": 1.2 @@ -578,6 +578,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-06-16T15:08:20.089341908" + "timestamp": "2025-06-25T20:06:21.438307947" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 5f568670b..1f2fe7825 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -356,7 +356,7 @@ "vcfanno": "0.3.5" }, "Workflow": { - "nf-core/raredisease": "v2.6.0" + "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_ROHCALL": { "tabix": 1.2 @@ -543,6 +543,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-06-16T15:11:10.063786271" + "timestamp": "2025-06-25T20:08:34.973300629" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 13693ae0e..78db775d8 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -357,7 +357,7 @@ "vcfanno": "0.3.5" }, "Workflow": { - "nf-core/raredisease": "v2.6.0" + "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_ROHCALL": { "tabix": 1.2 @@ -466,6 +466,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-06-16T15:14:25.756733004" + "timestamp": "2025-06-25T20:11:32.593010906" } } \ No newline at end of file From 99e3097cb2e137e37f1bbee089554452be25dd06 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 4 Jul 2025 15:38:35 +0200 Subject: [PATCH 024/872] review suggestions --- subworkflows/local/align/tests/main.nf.test | 60 +++++++++---------- .../local/align_MT/tests/main.nf.test | 36 +++++------ .../tests/main.nf.test | 16 ++--- .../local/align_sentieon/tests/main.nf.test | 8 +-- .../prepare_references/tests/main.nf.test | 12 ++-- .../local/scatter_genome/tests/main.nf.test | 6 +- 6 files changed, 69 insertions(+), 69 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index e8a4a1e88..2b334fe14 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -66,37 +66,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = GENOME_MEM2.out.index input[6] = [[:],[]] - input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -152,37 +152,37 @@ nextflow_workflow { input[0] = Channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) ]], [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path+ '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai', checkIfExists: true)]]) + input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) + input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) input[4] = [[:],[]] input[5] = [[:],[]] input[6] = GENOME_MEME.out.index - input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path+ 'reference/reference.dict', checkIfExists: true)]]) + input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) input[8] = [[:],[]] input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[13] = [[:],[]] input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) + input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[18] = 3072 input[19] = "illumina" input[20] = 4 diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 88b2e89d0..0ecf25c52 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -33,36 +33,36 @@ nextflow_workflow { input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = [[:],[]] input[3] = MT_MEM2.out.index.collect() - input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } @@ -100,36 +100,36 @@ nextflow_workflow { input[0] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) input[1] = Channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] ], [ [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] ], [ [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map - [ file(params.pipelines_testdata_base_path+ '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) input[2] = MT_BWA.out.index.collect() input[3] = [[:],[]] - input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path+ 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index b271ca587..ba9b60814 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -35,15 +35,15 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) input[1] = [[:],[]] input[2] = BWAMEM2_INDEX.out.index input[3] = [[:],[]] - input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 @@ -92,15 +92,15 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) input[1] = [[:],[]] input[2] = [[:],[]] input[3] = BWAMEME_INDEX.out.index - input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index e528bf6c4..54ae5efcb 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -34,12 +34,12 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[2] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path+ 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[1] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[2] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[3] = SENTIEON_BWAINDEX.out.index input[4] = "illumina" """ diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 6b172037a..275c86dc7 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -16,15 +16,15 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of(params.pipelines_testdata_base_path+ 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = Channel.of(params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() + input[0] = Channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() + input[1] = Channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() input[2] = Channel.empty() input[3] = Channel.empty() - input[4] = Channel.of(params.pipelines_testdata_base_path+ 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() - input[5] = Channel.of(params.pipelines_testdata_base_path+ 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() - input[6] = Channel.of(params.pipelines_testdata_base_path+ 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() + input[4] = Channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() + input[5] = Channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() + input[6] = Channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() input[7] = Channel.empty() - input[8] = Channel.of(params.pipelines_testdata_base_path+ 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[8] = Channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() """ } } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 391d66f9b..47a55f9fa 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -10,9 +10,9 @@ nextflow_workflow { when { params { pipelines_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - fasta = params.pipelines_testdata_base_path+ 'reference/reference.fasta' - fai = params.pipelines_testdata_base_path+ 'reference/reference.fasta.fai' - dict = params.pipelines_testdata_base_path+ 'reference/reference.dict' + fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' + fai = params.pipelines_testdata_base_path + 'reference/reference.fasta.fai' + dict = params.pipelines_testdata_base_path + 'reference/reference.dict' scatter_count = 20 } workflow { From a61279aa7dd738a1ea3e8cd70cc061196a9bc874 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 5 Jul 2025 11:13:57 +0200 Subject: [PATCH 025/872] update test with sort --- subworkflows/local/align/tests/main.nf.test | 12 ++--- .../local/align/tests/main.nf.test.snap | 50 +++++++++---------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 2b334fe14..def9ab84b 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -108,9 +108,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }, - workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, - workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }.sort { it[0].id }, + workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, + workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, workflow.out.versions ).match() } @@ -194,9 +194,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }, - workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, - workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }.sort { it[0].id }, + workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, + workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id } , workflow.out.versions ).match() } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index e6ae1d9ea..9bf73242b 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -6,20 +6,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "5826e0ede26849bd789600cb576607c6", - "hugelymodelbat_sorted_md.bam.bai:md5,60666327a06035997be296c2636c313c" + "52242c5e2e04e75b0f50c4c13467cfcb", + "earlycasualcaiman_sorted_md.bam.bai:md5,9f4b2ef1c24bd6fd6660b1958aed50ff" ] ], [ @@ -27,20 +27,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "b18998c8cf7dc417ca9a122ba1c9403d", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,ebc9222d03624e276c0c242e87e6618c" + "9beeefe789d896c08d55e8b8d13d9623", + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d8870681672ce9c1b5799bcfc28a8040" ] ], [ @@ -48,20 +48,20 @@ { "groupSize": 1, "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", + "phenotype": 1, + "paternal": 0, + "maternal": 0, "case_id": "justhusky" } }, - "97e6eaae1cda668da59e5c16a9bbcc1d", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,f9a4e5c7c7ca7c25f365bee4cfcdb3a9" + "130fb09f419109e40a6be267bfbd8c88", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai:md5,4d92948adf094d3ddede8b7bd7e6ee3e" ] ], [ @@ -95,7 +95,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-06-25T17:24:58.017903349" + "timestamp": "2025-07-05T11:05:46.341290772" }, "align bwameme": { "content": [ From a2a97af8bc819ee374d0b339938f3af9586b5bdc Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 7 Jul 2025 21:09:29 +0200 Subject: [PATCH 026/872] update test --- subworkflows/local/align/main.nf | 1 + subworkflows/local/align/tests/main.nf.test | 119 ++++---- .../local/align/tests/main.nf.test.snap | 257 +++++++++++++++++- .../local/align_bwa_bwamem2_bwameme/main.nf | 4 +- 4 files changed, 311 insertions(+), 70 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index cba43665f..f1593283d 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -153,6 +153,7 @@ workflow ALIGN { SAMTOOLS_VIEW( ch_genome_bam_bai, ch_genome_fasta, [] ) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } + emit: fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index def9ab84b..46d32168d 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -63,40 +63,46 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.fromList([ - [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + input[0] = Channel.of( [ - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) - ]], - [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ], [ - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) - ]], - [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ], [ - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) - ]] - ]) + [id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ] + ) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) - input[4] = [[:],[]] - input[5] = GENOME_MEM2.out.index - input[6] = [[:],[]] - input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) - input[8] = [[:],[]] - input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[13] = [[:],[]] - input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = Channel.empty() + input[5] = GENOME_MEM2.out.index.collect() + input[6] = Channel.empty() + input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = Channel.empty() + input[9] = MT_MEM2.out.index.collect() + input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = Channel.empty() + input[14] = SHIFTMT_MEM2.out.index.collect() + input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -108,9 +114,12 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }.sort { it[0].id }, - workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, - workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, + workflow.out.genome_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mtshift_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, workflow.out.versions ).match() } @@ -141,7 +150,7 @@ nextflow_workflow { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true analysis_type = "wgs" - skip_tools = null + skip_tools = "fastp" platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -167,22 +176,22 @@ nextflow_workflow { ]] ]) input[1] = Channel.empty() - input[2] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]]) - input[3] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]]) - input[4] = [[:],[]] - input[5] = [[:],[]] - input[6] = GENOME_MEME.out.index - input[7] = Channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]]) - input[8] = [[:],[]] - input[9] = MT_MEM2.out.index - input[10] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[11] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[12] = Channel.of([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[13] = [[:],[]] - input[14] = SHIFTMT_MEM2.out.index - input[15] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[16] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) - input[17] = Channel.of([[id:'shiftmt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = Channel.empty() + input[5] = Channel.empty() + input[6] = GENOME_MEME.out.index.collect() + input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = Channel.empty() + input[9] = MT_MEM2.out.index.collect() + input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = Channel.empty() + input[14] = SHIFTMT_MEM2.out.index.collect() + input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -194,14 +203,16 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getHeaderMD5(), index ] }.sort { it[0].id }, - workflow.out.mt_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id }, - workflow.out.mtshift_bam_bai.collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }.sort { it[0].id } , + workflow.out.genome_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + workflow.out.mtshift_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, workflow.out.versions ).match() } ) } } - } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 9bf73242b..8a77405b0 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -18,8 +18,46 @@ "case_id": "justhusky" } }, - "52242c5e2e04e75b0f50c4c13467cfcb", + "d948b0bd18f6f6526f5d8832465e1542", "earlycasualcaiman_sorted_md.bam.bai:md5,9f4b2ef1c24bd6fd6660b1958aed50ff" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "2530fd24192b09084f45011703bd4954", + "hugelymodelbat_sorted_md.bam.bai:md5,60666327a06035997be296c2636c313c" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "cc1385671a27d394f628d2d7868eba80", + "slowlycivilbuck_sorted_md.bam.bai:md5,b6c5d2736032f5e1cb190853ca366afe" ] ], [ @@ -40,7 +78,45 @@ } }, "9beeefe789d896c08d55e8b8d13d9623", - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d8870681672ce9c1b5799bcfc28a8040" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,9ed95c6e6e2b5610a007ca3cb79653da" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "b18998c8cf7dc417ca9a122ba1c9403d", + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,ebc9222d03624e276c0c242e87e6618c" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "a5d6892191a2c8c1f29966448623ca1b", + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" ] ], [ @@ -62,6 +138,44 @@ }, "130fb09f419109e40a6be267bfbd8c88", "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai:md5,4d92948adf094d3ddede8b7bd7e6ee3e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "97e6eaae1cda668da59e5c16a9bbcc1d", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,2b8cd7306bca24d1af7d3bb7b21337f7" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "427b5e476d84c5277d2d24210800ad60", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,6c663c5661749b25782ac78a3ba1f242" ] ], [ @@ -72,6 +186,8 @@ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", "versions.yml:md5,753dc9d8832a5f5a1e10237d78e157f2", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", @@ -95,11 +211,49 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-07-05T11:05:46.341290772" + "timestamp": "2025-07-07T20:37:01.281209386" }, "align bwameme": { "content": [ [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "9266e8231917cc16ff9845e50ed22801", + "earlycasualcaiman_sorted_md.bam.bai:md5,47dc8ed4c73ff84f81757845c0bd6401" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "1df3c2e109a79ba4e7b8293aefbad8", + "hugelymodelbat_sorted_md.bam.bai:md5,a05a8a744ae157f49fc56fbea4444e77" + ], [ { "groupSize": 1, @@ -116,11 +270,49 @@ "case_id": "justhusky" } }, - "b75a16ff1082ce42e9a9ac046b509181", - "slowlycivilbuck_sorted_md.bam.bai:md5,ff8eb902e42e6aeec775b9b412252ab6" + "645db4b1d55d6d42cba2b55eee1a630", + "slowlycivilbuck_sorted_md.bam.bai:md5,f3689db2144b87ab34d86760b245bdfb" ] ], [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "ae49d126580da2d5a72ada636e1ff358", + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,0408c73d17c90378f9e8ba6c5aa2931d" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "5646035310bba3a507a671aca33ca533", + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,90820ea4c824a2e56b0b35bc00a67fc0" + ], [ { "groupSize": 1, @@ -137,11 +329,49 @@ "case_id": "justhusky" } }, - "a5d6892191a2c8c1f29966448623ca1b", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" + "246a28939c75e40353107bc79b93d494", + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,015540a3bc50f6f89a791d913bbe2ce0" ] ], [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "c96587f3323ea479aebf0a8ba3ee710b", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai:md5,27b8d9a9ecb70a4b96dd34fa01ffb7f8" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "9f79604c77dc54d30daff682a50399bf", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,07f2103399352519b190069322e8d72d" + ], [ { "groupSize": 1, @@ -158,8 +388,8 @@ "case_id": "justhusky" } }, - "427b5e476d84c5277d2d24210800ad60", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,6c663c5661749b25782ac78a3ba1f242" + "8d810d8acecdeadc5a0e7ea159cb1343", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,a098c5077314f0d5e7dbf2cf4f910ce0" ] ], [ @@ -170,11 +400,10 @@ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", "versions.yml:md5,753dc9d8832a5f5a1e10237d78e157f2", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", "versions.yml:md5,9c218b25dd02dc279b1ce6fad9ae182b", @@ -191,8 +420,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-23T15:59:18.726434076" + "timestamp": "2025-07-07T21:08:06.337138956" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 315279666..c4be6a433 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -18,9 +18,9 @@ include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-c workflow ALIGN_BWA_BWAMEM2_BWAMEME { take: ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] - ch_bwa_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] + ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] - ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] + ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] val_mbuffer_mem // integer: [mandatory] default: 3072 From 936bec3d098fb69a37a3b86c0727a2c28655644b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 8 Jul 2025 13:21:55 +0200 Subject: [PATCH 027/872] update test --- subworkflows/local/align/tests/main.nf.test | 12 +++--- .../local/align/tests/main.nf.test.snap | 40 +++++++++---------- 2 files changed, 26 insertions(+), 26 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 46d32168d..f7c51cab6 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -115,11 +115,11 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.genome_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions ).match() } @@ -204,11 +204,11 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.genome_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), index ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions ).match() } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 8a77405b0..d692c61be 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -19,7 +19,7 @@ } }, "d948b0bd18f6f6526f5d8832465e1542", - "earlycasualcaiman_sorted_md.bam.bai:md5,9f4b2ef1c24bd6fd6660b1958aed50ff" + "earlycasualcaiman_sorted_md.bam.bai" ], [ { @@ -38,7 +38,7 @@ } }, "2530fd24192b09084f45011703bd4954", - "hugelymodelbat_sorted_md.bam.bai:md5,60666327a06035997be296c2636c313c" + "hugelymodelbat_sorted_md.bam.bai" ], [ { @@ -57,7 +57,7 @@ } }, "cc1385671a27d394f628d2d7868eba80", - "slowlycivilbuck_sorted_md.bam.bai:md5,b6c5d2736032f5e1cb190853ca366afe" + "slowlycivilbuck_sorted_md.bam.bai" ] ], [ @@ -78,7 +78,7 @@ } }, "9beeefe789d896c08d55e8b8d13d9623", - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,9ed95c6e6e2b5610a007ca3cb79653da" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai" ], [ { @@ -97,7 +97,7 @@ } }, "b18998c8cf7dc417ca9a122ba1c9403d", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,ebc9222d03624e276c0c242e87e6618c" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai" ], [ { @@ -116,7 +116,7 @@ } }, "a5d6892191a2c8c1f29966448623ca1b", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,35373ec0e388ae91025a4eec9897434e" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai" ] ], [ @@ -137,7 +137,7 @@ } }, "130fb09f419109e40a6be267bfbd8c88", - "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai:md5,4d92948adf094d3ddede8b7bd7e6ee3e" + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" ], [ { @@ -156,7 +156,7 @@ } }, "97e6eaae1cda668da59e5c16a9bbcc1d", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,2b8cd7306bca24d1af7d3bb7b21337f7" + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" ], [ { @@ -175,7 +175,7 @@ } }, "427b5e476d84c5277d2d24210800ad60", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,6c663c5661749b25782ac78a3ba1f242" + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" ] ], [ @@ -211,7 +211,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-07-07T20:37:01.281209386" + "timestamp": "2025-07-08T10:47:18.906258299" }, "align bwameme": { "content": [ @@ -233,7 +233,7 @@ } }, "9266e8231917cc16ff9845e50ed22801", - "earlycasualcaiman_sorted_md.bam.bai:md5,47dc8ed4c73ff84f81757845c0bd6401" + "earlycasualcaiman_sorted_md.bam.bai" ], [ { @@ -252,7 +252,7 @@ } }, "1df3c2e109a79ba4e7b8293aefbad8", - "hugelymodelbat_sorted_md.bam.bai:md5,a05a8a744ae157f49fc56fbea4444e77" + "hugelymodelbat_sorted_md.bam.bai" ], [ { @@ -271,7 +271,7 @@ } }, "645db4b1d55d6d42cba2b55eee1a630", - "slowlycivilbuck_sorted_md.bam.bai:md5,f3689db2144b87ab34d86760b245bdfb" + "slowlycivilbuck_sorted_md.bam.bai" ] ], [ @@ -292,7 +292,7 @@ } }, "ae49d126580da2d5a72ada636e1ff358", - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,0408c73d17c90378f9e8ba6c5aa2931d" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai" ], [ { @@ -311,7 +311,7 @@ } }, "5646035310bba3a507a671aca33ca533", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,90820ea4c824a2e56b0b35bc00a67fc0" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai" ], [ { @@ -330,7 +330,7 @@ } }, "246a28939c75e40353107bc79b93d494", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,015540a3bc50f6f89a791d913bbe2ce0" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai" ] ], [ @@ -351,7 +351,7 @@ } }, "c96587f3323ea479aebf0a8ba3ee710b", - "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai:md5,27b8d9a9ecb70a4b96dd34fa01ffb7f8" + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" ], [ { @@ -370,7 +370,7 @@ } }, "9f79604c77dc54d30daff682a50399bf", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai:md5,07f2103399352519b190069322e8d72d" + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" ], [ { @@ -389,7 +389,7 @@ } }, "8d810d8acecdeadc5a0e7ea159cb1343", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai:md5,a098c5077314f0d5e7dbf2cf4f910ce0" + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" ] ], [ @@ -422,6 +422,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.3" }, - "timestamp": "2025-07-07T21:08:06.337138956" + "timestamp": "2025-07-08T10:54:20.418307597" } } \ No newline at end of file From 569af722e889884b3ad4604f0efddfe13eeb06a1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 8 Jul 2025 11:39:44 +0000 Subject: [PATCH 028/872] Template update for nf-core/tools version 3.3.2 --- .github/actions/nf-test/action.yml | 4 - .github/workflows/linting.yml | 2 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/nf-test.yml | 45 +++---- .github/workflows/release-announcements.yml | 2 +- .nf-core.yml | 4 +- .pre-commit-config.yaml | 2 +- CHANGELOG.md | 2 +- README.md | 6 +- assets/schema_input.json | 4 +- conf/base.config | 1 + modules.json | 4 +- modules/nf-core/fastqc/environment.yml | 2 + modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/fastqc/meta.yml | 23 ++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/meta.yml | 110 ++++++++++-------- .../nf-core/multiqc/tests/main.nf.test.snap | 18 +-- nextflow.config | 7 +- nf-test.config | 2 +- ro-crate-metadata.json | 18 +-- .../tests/nextflow.config | 2 +- tests/.nftignore | 1 + tests/nextflow.config | 6 +- 25 files changed, 150 insertions(+), 127 deletions(-) diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 243e78238..bf44d9612 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -54,13 +54,9 @@ runs: conda-solver: libmamba conda-remove-defaults: true - # TODO Skip failing conda tests and document their failures - # https://github.com/nf-core/modules/issues/7017 - name: Run nf-test shell: bash env: - NFT_DIFF: ${{ env.NFT_DIFF }} - NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} NFT_WORKDIR: ${{ env.NFT_WORKDIR }} run: | nf-test test \ diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index f2d7d1dd7..8b0f88c36 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - name: Set up Python 3.12 + - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: python-version: "3.13" diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 7e8050fb8..d43797d9d 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f03aea0c0..e7b58449b 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -1,12 +1,5 @@ name: Run nf-test on: - push: - paths-ignore: - - "docs/**" - - "**/meta.yml" - - "**/*.md" - - "**/*.png" - - "**/*.svg" pull_request: paths-ignore: - "docs/**" @@ -35,7 +28,7 @@ jobs: nf-test-changes: name: nf-test-changes runs-on: # use self-hosted runners - - runs-on=$-nf-test-changes + - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 outputs: shard: ${{ steps.set-shards.outputs.shard }} @@ -69,7 +62,7 @@ jobs: needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} runs-on: # use self-hosted runners - - runs-on=$-nf-test + - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 strategy: fail-fast: false @@ -85,7 +78,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.04.2" + - "24.10.5" - "latest-everything" env: NXF_ANSI_LOG: false @@ -97,23 +90,39 @@ jobs: fetch-depth: 0 - name: Run nf-test + id: run_nf_test uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: - NFT_DIFF: ${{ env.NFT_DIFF }} - NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} NFT_WORKDIR: ${{ env.NFT_WORKDIR }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + confirm-pass: needs: [nf-test] if: always() runs-on: # use self-hosted runners - - runs-on=$-confirm-pass + - runs-on=${{ github.run_id }}-confirm-pass - runner=2cpu-linux-x64 steps: - - name: One or more tests failed + - name: One or more tests failed (excluding latest-everything) if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 @@ -132,11 +141,3 @@ jobs: echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" - - - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner - if: always() - run: | - ls -la ./ - rm -rf ./* || true - rm -rf ./.??* || true - ls -la ./ diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 4abaf4843..0f7324956 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -30,7 +30,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0 + - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.nf-core.yml b/.nf-core.yml index 226339ce2..b259be0e2 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,7 +8,7 @@ lint: - docs/images/nf-core-raredisease_logo_light.png - assets/nf-core-raredisease_logo_light.png modules_config: false -nf_core_version: 3.3.1 +nf_core_version: 3.3.2 repository_type: pipeline template: author: Clinical Genomics Stockholm @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 2.6.0dev + version: 2.7.0dev diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9d0b248d3..bb41beec1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.5.0 + - prettier@3.6.2 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v5.0.0 hooks: diff --git a/CHANGELOG.md b/CHANGELOG.md index bc3cb98b9..2b323f37f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.6.0dev - [date] +## v2.7.0dev - [date] Initial release of nf-core/raredisease, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index c3b4ba7c4..2d0769292 100644 --- a/README.md +++ b/README.md @@ -5,12 +5,12 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/assets/schema_input.json b/assets/schema_input.json index e661c9e55..10431a018 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -17,14 +17,14 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, diff --git a/conf/base.config b/conf/base.config index 608a5a799..ce5ceb0d3 100644 --- a/conf/base.config +++ b/conf/base.config @@ -61,5 +61,6 @@ process { } withLabel: process_gpu { ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } } } diff --git a/modules.json b/modules.json index 7bb10cda6..8f82d56f3 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c763..f9f54ee9b 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 033f4154a..23e16634c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,7 @@ process FASTQC { // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null + def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 2b2e62b8a..c8d9d025a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -29,9 +29,10 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] output: - - html: - - meta: + html: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,8 +41,9 @@ output: type: file description: FastQC report pattern: "*_{fastqc.html}" - - zip: - - meta: + ontologies: [] + zip: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,11 +52,14 @@ output: type: file description: FastQC report archive pattern: "*_{fastqc.zip}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122ce1..812fc4c5e 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.27 + - bioconda::multiqc=1.29 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 58d9313c6..0ac3c3699 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : - 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : + 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index b16c18792..ce30eb732 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -15,57 +15,71 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:multiqc input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV +output: + report: + - "*multiqc_report.html": type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: + description: MultiQC report file + pattern: "multiqc_report.html" + ontologies: [] + data: + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - "*_plots": type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: + description: Plots created by MultiQC + pattern: "*_data" + ontologies: [] + versions: + - versions.yml: type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c13220..88e90571c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:29:57.631982377" + "timestamp": "2025-05-22T11:50:41.182332996" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:34.743726958" + "timestamp": "2025-05-22T11:51:22.448739369" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:21.44383553" + "timestamp": "2025-05-22T11:51:06.198928424" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 1ab47de4e..017317ead 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,7 +235,6 @@ dag { manifest { name = 'nf-core/raredisease' - author = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ @@ -251,14 +250,14 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.04.2' - version = '2.6.0dev' + nextflowVersion = '!>=24.10.5' + version = '2.7.0dev' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nf-test.config b/nf-test.config index 889df7601..3a1fff59f 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,7 +9,7 @@ config { configFile "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*' + ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' // run all test with defined profile(s) from the main nextflow.config profile "test" diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 2021c4ea5..8475ce38b 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-06-03T11:02:35+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-07-08T11:39:40+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#33dfa1f4-93d2-4404-b035-3125a923ec66" + "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75" } ], "name": "nf-core/raredisease" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-06-03T11:02:35Z", + "dateModified": "2025-07-08T11:39:40Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -146,7 +146,7 @@ "@id": "https://nf-co.re/" }, "url": ["https://github.com/nf-core/raredisease", "https://nf-co.re/raredisease/dev/"], - "version": ["2.6.0dev"] + "version": ["2.7.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -158,14 +158,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.04.2" + "version": "!>=24.10.5" }, { - "@id": "#33dfa1f4-93d2-4404-b035-3125a923ec66", + "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75", "@type": "TestSuite", "instance": [ { - "@id": "#0c77e713-7c32-406d-90f8-cc8a76b9e01a" + "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05" } ], "mainEntity": { @@ -174,7 +174,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#0c77e713-7c32-406d-90f8-cc8a76b9e01a", + "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac58f..09ef842ae 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.4.2" } validation { diff --git a/tests/.nftignore b/tests/.nftignore index c10bc1f11..158c83c59 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,5 +1,6 @@ .DS_Store multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt +multiqc/multiqc_data/BETA-multiqc.parquet multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_sources.txt diff --git a/tests/nextflow.config b/tests/nextflow.config index 8a838141a..f46754286 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -6,7 +6,9 @@ // TODO nf-core: Specify any additional parameters here // Or any resources requirements -params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' -params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease' +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease' +} aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 5d09619168565590dff15d82b0e564d9b8525195 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 8 Jul 2025 14:13:18 +0200 Subject: [PATCH 029/872] lint --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bd1537c56..a5ac166e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - ## 2.7.0dev - Semiautomatix [xxxx-xx-xx] ### `Added` From dde24ab6e5180829a905605fff392b302e69019e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 8 Jul 2025 14:18:05 +0200 Subject: [PATCH 030/872] update lint --- docs/output.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index 519de7ef6..5c5d0401a 100644 --- a/docs/output.md +++ b/docs/output.md @@ -607,7 +607,6 @@ Provided a truth set, SNVs can be evaluated using RTG Tools' vcfeval engine. Out Output files - `rtgvcfeval/` - - `_vcfeval.fn.vcf.gz`: contains variants from the baseline VCF which were not correctly called. - `_vcfeval.fn.vcf.gz.tbi`: index of the \*fn.vcf file - `_vcfeval.fp.vcf.gz`: contains variants from the calls VCF which do not agree with baseline variants. @@ -635,7 +634,6 @@ The sequencing data can be prepared for visualization of CNVs in [Gens](https:// Output files - `gens/` - - `_gens.baf.bed.gz`: contains sample b-allele frequencies in bed format. - `_gens.baf.bed.gz.tbi`: index of the \*baf.bed.gz file. - `_gens.cov.bed.gz`: contains sample coverage in bed format. From 04f6fa782c2bbfb383226e7d9f827ac61917859f Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 8 Jul 2025 14:27:34 +0200 Subject: [PATCH 031/872] update rocrate --- ro-crate-metadata.json | 65 +++++++++++++++++++++++------------------- 1 file changed, 35 insertions(+), 30 deletions(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 6528524f6..4c02cb37f 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T11:39:40+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-07-08T12:27:15+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75" + "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067" } ], "name": "nf-core/raredisease" @@ -134,26 +134,26 @@ ], "creator": [ { - "@id": "#25568561+projectoriented@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-2219-0197" }, { "@id": "https://orcid.org/0000-0002-4100-9963" }, { - "@id": "https://orcid.org/0000-0003-1316-2845" + "@id": "https://orcid.org/0000-0002-5044-7754" }, { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0003-1316-2845" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0002-5044-7754" + "@id": "https://orcid.org/0000-0001-7313-3734" } ], "dateCreated": "", - "dateModified": "2025-07-08T11:39:40Z", + "dateModified": "2025-07-08T14:27:15Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,19 +172,19 @@ ], "maintainer": [ { - "@id": "#25568561+projectoriented@users.noreply.github.com" + "@id": "https://orcid.org/0000-0002-2219-0197" }, { "@id": "https://orcid.org/0000-0002-4100-9963" }, { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0002-5044-7754" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0002-5044-7754" + "@id": "https://orcid.org/0000-0001-7313-3734" } ], "name": [ @@ -196,8 +196,13 @@ "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/raredisease", "https://nf-co.re/raredisease/dev/"], - "version": ["2.7.0dev"] + "url": [ + "https://github.com/nf-core/raredisease", + "https://nf-co.re/raredisease/dev/" + ], + "version": [ + "2.7.0dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -212,11 +217,11 @@ "version": "!>=24.10.5" }, { - "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75", + "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067", "@type": "TestSuite", "instance": [ { - "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05" + "@id": "#34b99e0d-03ba-4190-be8d-081702d44958" } ], "mainEntity": { @@ -225,7 +230,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05", + "@id": "#34b99e0d-03ba-4190-be8d-081702d44958", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -364,10 +369,10 @@ "url": "https://nf-co.re/" }, { - "@id": "#25568561+projectoriented@users.noreply.github.com", + "@id": "https://orcid.org/0000-0002-2219-0197", "@type": "Person", - "email": "25568561+projectoriented@users.noreply.github.com", - "name": "Mei Wu" + "email": "jemten@users.noreply.github.com", + "name": "Anders Jemt" }, { "@id": "https://orcid.org/0000-0002-4100-9963", @@ -375,6 +380,12 @@ "email": "Gwenna.breton@gu.se", "name": "Gwenna Breton" }, + { + "@id": "https://orcid.org/0000-0002-5044-7754", + "@type": "Person", + "email": "lucia.pena.perez@scilifelab.se", + "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" + }, { "@id": "https://orcid.org/0000-0003-1316-2845", "@type": "Person", @@ -382,22 +393,16 @@ "name": "Emil Bertilsson" }, { - "@id": "https://orcid.org/0000-0002-2219-0197", + "@id": "#25568561+projectoriented@users.noreply.github.com", "@type": "Person", - "email": "jemten@users.noreply.github.com", - "name": "Anders Jemt" + "email": "25568561+projectoriented@users.noreply.github.com", + "name": "Mei Wu" }, { "@id": "https://orcid.org/0000-0001-7313-3734", "@type": "Person", "email": "20065894+ramprasadn@users.noreply.github.com", "name": "Ramprasad Neethiraj" - }, - { - "@id": "https://orcid.org/0000-0002-5044-7754", - "@type": "Person", - "email": "lucia.pena.perez@scilifelab.se", - "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" } ] } \ No newline at end of file From f18767dc367b6fc74702cbc97925c10d33c866b3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Jul 2025 12:58:44 +0200 Subject: [PATCH 032/872] move qc bam to folder --- subworkflows/local/{ => qc_bam}/qc_bam.nf | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename subworkflows/local/{ => qc_bam}/qc_bam.nf (100%) diff --git a/subworkflows/local/qc_bam.nf b/subworkflows/local/qc_bam/qc_bam.nf similarity index 100% rename from subworkflows/local/qc_bam.nf rename to subworkflows/local/qc_bam/qc_bam.nf From 3b1edbf5cb418574e53903f7b0e322754834e080 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Jul 2025 12:59:54 +0200 Subject: [PATCH 033/872] move call_repeat_expansions to a folder --- .../local/{ => call_repeat_expansions}/call_repeat_expansions.nf | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename subworkflows/local/{ => call_repeat_expansions}/call_repeat_expansions.nf (100%) diff --git a/subworkflows/local/call_repeat_expansions.nf b/subworkflows/local/call_repeat_expansions/call_repeat_expansions.nf similarity index 100% rename from subworkflows/local/call_repeat_expansions.nf rename to subworkflows/local/call_repeat_expansions/call_repeat_expansions.nf From 761a80c45e293ca27c06e8190fc559a6e97cd952 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Jul 2025 13:00:31 +0200 Subject: [PATCH 034/872] rename to main.nf --- .../call_repeat_expansions/{call_repeat_expansions.nf => main.nf} | 0 subworkflows/local/qc_bam/{qc_bam.nf => main.nf} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename subworkflows/local/call_repeat_expansions/{call_repeat_expansions.nf => main.nf} (100%) rename subworkflows/local/qc_bam/{qc_bam.nf => main.nf} (100%) diff --git a/subworkflows/local/call_repeat_expansions/call_repeat_expansions.nf b/subworkflows/local/call_repeat_expansions/main.nf similarity index 100% rename from subworkflows/local/call_repeat_expansions/call_repeat_expansions.nf rename to subworkflows/local/call_repeat_expansions/main.nf diff --git a/subworkflows/local/qc_bam/qc_bam.nf b/subworkflows/local/qc_bam/main.nf similarity index 100% rename from subworkflows/local/qc_bam/qc_bam.nf rename to subworkflows/local/qc_bam/main.nf From e7bd07172aa811ee69ecc0e8a08604c5e5e2c729 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Jul 2025 13:22:30 +0200 Subject: [PATCH 035/872] update modules --- modules.json | 38 ++--- modules/nf-core/bcftools/norm/environment.yml | 4 +- modules/nf-core/bcftools/norm/main.nf | 18 ++- modules/nf-core/bcftools/norm/meta.yml | 30 ++-- .../bcftools/norm/tests/main.nf.test.snap | 152 +++++++++--------- modules/nf-core/bcftools/norm/tests/tags.yml | 2 - .../nf-core/bcftools/reheader/environment.yml | 4 +- modules/nf-core/bcftools/reheader/main.nf | 4 +- modules/nf-core/bcftools/reheader/meta.yml | 26 +-- .../bcftools/reheader/tests/main.nf.test.snap | 112 ++++++------- .../nf-core/bcftools/reheader/tests/tags.yml | 2 - modules/nf-core/chromograph/environment.yml | 2 + modules/nf-core/chromograph/meta.yml | 24 ++- modules/nf-core/chromograph/tests/tags.yml | 2 - .../nf-core/expansionhunter/environment.yml | 2 + modules/nf-core/expansionhunter/meta.yml | 35 ++-- .../nf-core/expansionhunter/tests/tags.yml | 2 - modules/nf-core/mosdepth/environment.yml | 4 +- modules/nf-core/mosdepth/main.nf | 4 +- modules/nf-core/mosdepth/meta.yml | 76 +++++---- .../nf-core/mosdepth/tests/main.nf.test.snap | 132 +++++++-------- modules/nf-core/mosdepth/tests/tags.yml | 2 - .../ngsbits/samplegender/environment.yml | 4 +- modules/nf-core/ngsbits/samplegender/main.nf | 6 +- modules/nf-core/ngsbits/samplegender/meta.yml | 34 ++-- .../ngsbits/samplegender/tests/main.nf.test | 2 +- .../samplegender/tests/main.nf.test.snap | 10 +- .../ngsbits/samplegender/tests/tags.yml | 2 - .../picard/collecthsmetrics/environment.yml | 2 + .../nf-core/picard/collecthsmetrics/meta.yml | 24 ++- .../picard/collecthsmetrics/tests/tags.yml | 2 - .../collectmultiplemetrics/environment.yml | 2 + .../picard/collectmultiplemetrics/meta.yml | 26 +-- .../picard/collectwgsmetrics/environment.yml | 2 + .../nf-core/picard/collectwgsmetrics/meta.yml | 30 ++-- .../picard/renamesampleinvcf/environment.yml | 2 + .../nf-core/picard/renamesampleinvcf/meta.yml | 18 ++- .../nf-core/qualimap/bamqc/environment.yml | 2 + modules/nf-core/qualimap/bamqc/meta.yml | 26 +-- modules/nf-core/qualimap/bamqc/tests/tags.yml | 2 - modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/index/meta.yml | 28 ++-- modules/nf-core/samtools/index/tests/tags.yml | 2 - modules/nf-core/samtools/sort/meta.yml | 34 ++-- modules/nf-core/samtools/sort/tests/tags.yml | 3 - modules/nf-core/sentieon/wgsmetrics/meta.yml | 26 +-- modules/nf-core/svdb/merge/meta.yml | 49 +++--- modules/nf-core/svdb/merge/tests/tags.yml | 2 - modules/nf-core/tabix/tabix/environment.yml | 4 +- modules/nf-core/tabix/tabix/main.nf | 4 +- modules/nf-core/tabix/tabix/meta.yml | 23 +-- .../nf-core/tabix/tabix/tests/main.nf.test | 2 +- .../tabix/tabix/tests/main.nf.test.snap | 50 +++--- modules/nf-core/tabix/tabix/tests/tags.yml | 2 - modules/nf-core/tiddit/cov/environment.yml | 2 + modules/nf-core/tiddit/cov/meta.yml | 24 +-- modules/nf-core/tiddit/cov/tests/tags.yml | 2 - .../nf-core/ucsc/wigtobigwig/environment.yml | 2 + modules/nf-core/ucsc/wigtobigwig/meta.yml | 26 +-- .../nf-core/verifybamid/verifybamid2/meta.yml | 75 +++++---- 60 files changed, 699 insertions(+), 536 deletions(-) delete mode 100644 modules/nf-core/bcftools/norm/tests/tags.yml delete mode 100644 modules/nf-core/bcftools/reheader/tests/tags.yml delete mode 100644 modules/nf-core/chromograph/tests/tags.yml delete mode 100644 modules/nf-core/expansionhunter/tests/tags.yml delete mode 100644 modules/nf-core/mosdepth/tests/tags.yml delete mode 100644 modules/nf-core/ngsbits/samplegender/tests/tags.yml delete mode 100644 modules/nf-core/picard/collecthsmetrics/tests/tags.yml delete mode 100644 modules/nf-core/qualimap/bamqc/tests/tags.yml delete mode 100644 modules/nf-core/samtools/index/tests/tags.yml delete mode 100644 modules/nf-core/samtools/sort/tests/tags.yml delete mode 100644 modules/nf-core/svdb/merge/tests/tags.yml delete mode 100644 modules/nf-core/tabix/tabix/tests/tags.yml delete mode 100644 modules/nf-core/tiddit/cov/tests/tags.yml diff --git a/modules.json b/modules.json index 0024877ca..f9b8d3819 100644 --- a/modules.json +++ b/modules.json @@ -27,12 +27,12 @@ }, "bcftools/norm": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "bcftools/roh": { @@ -102,7 +102,7 @@ }, "chromograph": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "cnvnator/cnvnator": { @@ -139,7 +139,7 @@ }, "expansionhunter": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "fastp": { @@ -295,7 +295,7 @@ }, "mosdepth": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "multiqc": { @@ -305,7 +305,7 @@ }, "ngsbits/samplegender": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "peddy": { @@ -320,17 +320,17 @@ }, "picard/collecthsmetrics": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/liftovervcf": { @@ -345,7 +345,7 @@ }, "picard/renamesampleinvcf": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "picard/sortvcf": { @@ -355,7 +355,7 @@ }, "qualimap/bamqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "rhocall/annotate": { @@ -385,7 +385,7 @@ }, "samtools/index": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "samtools/merge": { @@ -395,7 +395,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "samtools/stats": { @@ -445,7 +445,7 @@ }, "sentieon/wgsmetrics": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "smncopynumbercaller": { @@ -465,7 +465,7 @@ }, "svdb/merge": { "branch": "master", - "git_sha": "95185f269ec10a33cde61d294fcd4ba7c66bc6b8", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "svdb/query": { @@ -485,12 +485,12 @@ }, "tabix/tabix": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "tiddit/sv": { @@ -500,7 +500,7 @@ }, "ucsc/wigtobigwig": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "untar": { @@ -525,7 +525,7 @@ }, "verifybamid/verifybamid2": { "branch": "master", - "git_sha": "33278f733f3452dc77bde5c1a45db3a5f9278ac0", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 5c00b116a..557488607 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + - bioconda::bcftools=1.21 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index bd7a25012..3ad9b35cc 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_NORM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': + 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" input: tuple val(meta), path(vcf), path(tbi) @@ -51,12 +51,16 @@ process BCFTOOLS_NORM { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf.gz" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def index = '' + if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) { + if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') { + index = 'tbi' + } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) { + index = 'csi' + } + } def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" - def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + def create_index = index ? "touch ${prefix}.${extension}.${index}" : "" """ ${create_cmd} ${prefix}.${extension} diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index b6edeb4aa..bda91258c 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -26,11 +26,13 @@ input: The vcf file to be normalized e.g. 'file1.vcf' pattern: "*.{vcf,vcf.gz}" + ontologies: [] - tbi: type: file description: | An optional index of the VCF file (for when the VCF is compressed) pattern: "*.vcf.gz.tbi" + ontologies: [] - - meta2: type: map description: | @@ -40,9 +42,10 @@ input: type: file description: FASTA reference file pattern: "*.{fasta,fa}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -52,8 +55,9 @@ output: description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -62,8 +66,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -72,11 +77,14 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap index 3be52116a..b71721a73 100644 --- a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap @@ -17,7 +17,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -34,15 +34,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:38:42.639095032" + "timestamp": "2025-04-01T14:02:35.039667679" }, "sarscov2 - [ vcf, [] ], fasta - stub": { "content": [ @@ -62,7 +62,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -79,15 +79,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:38:05.448449893" + "timestamp": "2025-04-01T14:02:19.531714933" }, "sarscov2 - [ vcf, tbi ], fasta - vcf output": { "content": [ @@ -107,7 +107,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -124,15 +124,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:37:12.741719961" + "timestamp": "2025-04-01T14:01:53.57043182" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub": { "content": [ @@ -157,7 +157,7 @@ ] ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ [ @@ -179,15 +179,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:39:22.875147941" + "timestamp": "2025-04-01T14:02:53.457953524" }, "sarscov2 - [ vcf, tbi ], fasta - vcf_gz output": { "content": [ @@ -206,14 +206,14 @@ ], [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-05T08:15:23.38765384" + "timestamp": "2025-04-01T14:02:00.719886153" }, "sarscov2 - [ vcf, [] ], fasta": { "content": [ @@ -233,7 +233,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -250,15 +250,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:36:21.519977754" + "timestamp": "2025-04-01T14:01:23.75323253" }, "sarscov2 - [ vcf, tbi ], fasta - vcf output -stub": { "content": [ @@ -278,7 +278,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -295,15 +295,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:38:27.8230994" + "timestamp": "2025-04-01T14:02:30.863210572" }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output": { "content": [ @@ -313,7 +313,7 @@ { "id": "test" }, - "test_norm.bcf:md5,f35545c26a788b5eb697d9c0490339d9" + "test_norm.bcf:md5,bf88706ef69c44ca9e287bc953ba3593" ] ], "1": [ @@ -323,7 +323,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -336,19 +336,19 @@ { "id": "test" }, - "test_norm.bcf:md5,f35545c26a788b5eb697d9c0490339d9" + "test_norm.bcf:md5,bf88706ef69c44ca9e287bc953ba3593" ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:37:53.942403192" + "timestamp": "2025-04-01T14:02:12.325415263" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub": { "content": [ @@ -373,7 +373,7 @@ ] ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ [ @@ -395,15 +395,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-05T13:56:05.3799488" + "timestamp": "2025-04-01T14:03:00.652023677" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi": { "content": [ @@ -443,7 +443,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -460,15 +460,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:36:58.39445154" + "timestamp": "2025-04-01T14:01:46.207313323" }, "sarscov2 - [ vcf, tbi ], fasta -stub": { "content": [ @@ -488,7 +488,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -505,15 +505,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:38:16.259516142" + "timestamp": "2025-04-01T14:02:26.686137644" }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub": { "content": [ @@ -533,7 +533,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -550,15 +550,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:39:10.503208929" + "timestamp": "2025-04-01T14:02:46.406125297" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index": { "content": [ @@ -603,7 +603,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -620,15 +620,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:38:59.121377258" + "timestamp": "2025-04-01T14:02:39.213092385" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub": { "content": [ @@ -653,7 +653,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -675,15 +675,15 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-05T13:56:16.404380471" + "timestamp": "2025-04-01T14:03:07.888046412" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi": { "content": [ @@ -728,7 +728,7 @@ ], "3": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ], "csi": [ @@ -745,14 +745,14 @@ ] ], "versions": [ - "versions.yml:md5,ff760495922469e56d0fc3372773000d" + "versions.yml:md5,cb38669b7069800497b0706a09932aec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-04T14:37:42.141945244" + "timestamp": "2025-04-01T14:02:04.993236789" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/norm/tests/tags.yml b/modules/nf-core/bcftools/norm/tests/tags.yml deleted file mode 100644 index f6f5e3561..000000000 --- a/modules/nf-core/bcftools/norm/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/norm: - - "modules/nf-core/bcftools/norm/**" diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 5c00b116a..557488607 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + - bioconda::bcftools=1.21 diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 9cf6d0d38..37062ab14 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': + 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" input: tuple val(meta), path(vcf), path(header), path(samples) diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index 47e5344cd..4bc15ad65 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -23,14 +23,17 @@ input: type: file description: VCF/BCF file pattern: "*.{vcf.gz,vcf,bcf}" + ontologies: [] - header: type: file description: New header to add to the VCF pattern: "*.{header.txt}" + ontologies: [] - samples: type: file description: File containing sample names to update (one sample per line) pattern: "*.{samples.txt}" + ontologies: [] - - meta2: type: map description: | @@ -40,9 +43,10 @@ input: type: file description: Fasta index to update header sequences with pattern: "*.{fai}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,8 +55,9 @@ output: type: file description: VCF with updated header, bgzipped per default pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - index: - - meta: + ontologies: [] + index: + - - meta: type: map description: | Groovy Map containing sample information @@ -61,11 +66,14 @@ output: type: file description: Index of VCF with updated header pattern: "*.{csi,tbi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap index 87a3654a5..fc8dfd58b 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T10:09:05.955833763" + "timestamp": "2025-04-01T14:09:50.163995386" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": { "content": [ @@ -51,7 +51,7 @@ ] ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ [ @@ -72,15 +72,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:52:41.444952182" + "timestamp": "2025-04-01T14:10:22.786980419" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": { "content": [ @@ -104,7 +104,7 @@ ] ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ [ @@ -125,15 +125,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:53:04.314827944" + "timestamp": "2025-04-01T14:10:30.908145496" }, "sarscov2 - [vcf, [], []], fai - vcf output": { "content": [ @@ -151,7 +151,7 @@ ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ @@ -166,15 +166,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:50:41.983008108" + "timestamp": "2025-04-01T14:09:27.878225575" }, "sarscov2 - [vcf, [], []], fai - bcf output": { "content": [ @@ -192,7 +192,7 @@ ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ @@ -207,15 +207,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:51:43.072513252" + "timestamp": "2025-04-01T14:09:57.340213283" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output": { "content": [ @@ -233,7 +233,7 @@ ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ @@ -248,15 +248,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:50:53.055630152" + "timestamp": "2025-04-01T14:09:32.00582809" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": { "content": [ @@ -279,14 +279,14 @@ ] ], [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T10:08:37.999924355" + "timestamp": "2025-04-01T14:09:38.993337881" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": { "content": [ @@ -310,7 +310,7 @@ ] ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ [ @@ -331,28 +331,28 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:52:52.512269206" + "timestamp": "2025-04-01T14:10:26.882028182" }, "sarscov2 - [vcf, [], []], fai - stub": { "content": [ "tested.vcf", [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-05-31T15:16:36.337112514" + "timestamp": "2025-04-01T14:10:15.695515447" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": { "content": [ @@ -375,14 +375,14 @@ ] ], [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T10:08:55.434831174" + "timestamp": "2025-04-01T14:09:43.054413402" }, "sarscov2 - [vcf, [], samples], fai": { "content": [ @@ -400,7 +400,7 @@ ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ @@ -415,15 +415,15 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:52:12.216002665" + "timestamp": "2025-04-01T14:10:11.620196263" }, "sarscov2 - [vcf, header, []], []": { "content": [ @@ -441,7 +441,7 @@ ], "2": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ], "index": [ @@ -456,14 +456,14 @@ ] ], "versions": [ - "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-09-03T09:51:54.062386022" + "timestamp": "2025-04-01T14:10:04.588597619" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/tests/tags.yml b/modules/nf-core/bcftools/reheader/tests/tags.yml deleted file mode 100644 index c252941e0..000000000 --- a/modules/nf-core/bcftools/reheader/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/reheader: - - modules/nf-core/bcftools/reheader/** diff --git a/modules/nf-core/chromograph/environment.yml b/modules/nf-core/chromograph/environment.yml index 47881b1fb..cc931c767 100644 --- a/modules/nf-core/chromograph/environment.yml +++ b/modules/nf-core/chromograph/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/chromograph/meta.yml b/modules/nf-core/chromograph/meta.yml index 4a986dbbb..c61482807 100644 --- a/modules/nf-core/chromograph/meta.yml +++ b/modules/nf-core/chromograph/meta.yml @@ -24,6 +24,7 @@ input: - autozyg: type: file description: Bed file containing the regions of autozygosity + ontologies: [] - - meta2: type: map description: | @@ -32,6 +33,7 @@ input: - coverage: type: file description: Wig file containing the coverage information + ontologies: [] - - meta3: type: map description: | @@ -40,6 +42,7 @@ input: - exome: type: file description: Bed file containing the coverage for exome. + ontologies: [] - - meta4: type: map description: | @@ -48,6 +51,7 @@ input: - fracsnp: type: file description: Wig file containing the fraction of homozygous SNPs + ontologies: [] - - meta5: type: map description: | @@ -58,6 +62,7 @@ input: description: | Bed file containing information necessary for ideogram plots. Format ['chrom', 'start', 'end', 'name', 'gStain'] + ontologies: [] - - meta6: type: map description: | @@ -66,6 +71,7 @@ input: - regions: type: file description: Bed file containing UPD regions + ontologies: [] - - meta7: type: map description: | @@ -74,9 +80,10 @@ input: - sites: type: file description: Bed file containing UPD sites + ontologies: [] output: - - plots: - - meta: + plots: + - - meta: type: map description: | Groovy Map containing sample information @@ -85,11 +92,14 @@ output: type: file description: Directory containing the plots in png format pattern: "*.png" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/chromograph/tests/tags.yml b/modules/nf-core/chromograph/tests/tags.yml deleted file mode 100644 index e60ad9db2..000000000 --- a/modules/nf-core/chromograph/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -chromograph: - - "modules/nf-core/chromograph/**" diff --git a/modules/nf-core/expansionhunter/environment.yml b/modules/nf-core/expansionhunter/environment.yml index 07db4374d..951de76c0 100644 --- a/modules/nf-core/expansionhunter/environment.yml +++ b/modules/nf-core/expansionhunter/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml index 4d55fe260..44ca3361c 100644 --- a/modules/nf-core/expansionhunter/meta.yml +++ b/modules/nf-core/expansionhunter/meta.yml @@ -25,10 +25,12 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - bai: type: file description: Index of BAM/CRAM file pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -38,6 +40,7 @@ input: type: file description: Reference genome pattern: "*.{fna,fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -47,6 +50,7 @@ input: type: file description: Reference genome index pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -56,9 +60,11 @@ input: type: file description: JSON file with repeat expansion sites to genotype pattern: "*.json" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +73,10 @@ output: type: file description: VCF with repeat expansions pattern: "*.vcf.gz" - - json: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + json: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,8 +85,10 @@ output: type: file description: JSON with repeat expansions pattern: "*.json.gz" - - bam: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -87,11 +97,14 @@ output: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@jemten" maintainers: diff --git a/modules/nf-core/expansionhunter/tests/tags.yml b/modules/nf-core/expansionhunter/tests/tags.yml deleted file mode 100644 index 032663519..000000000 --- a/modules/nf-core/expansionhunter/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -expansionhunter: - - "modules/nf-core/expansionhunter/**" diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index e93798738..f871e054e 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.8 + - mosdepth=0.3.10 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 6f4a83834..3bf945f90 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.10--h4e814b3_1' : + 'biocontainers/mosdepth:0.3.10--h4e814b3_1'}" input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index dc783c900..af1ea44ad 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -23,14 +23,17 @@ input: type: file description: Input BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - bai: type: file description: Index for BAM/CRAM file pattern: "*.{bai,crai}" + ontologies: [] - bed: type: file description: BED file with intersected intervals pattern: "*.{bed}" + ontologies: [] - - meta2: type: map description: | @@ -40,9 +43,10 @@ input: type: file description: Reference genome FASTA file pattern: "*.{fa,fasta}" + ontologies: [] output: - - global_txt: - - meta: + global_txt: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,8 +55,9 @@ output: type: file description: Text file with global cumulative coverage distribution pattern: "*.{global.dist.txt}" - - summary_txt: - - meta: + ontologies: [] + summary_txt: + - - meta: type: map description: | Groovy Map containing sample information @@ -61,8 +66,9 @@ output: type: file description: Text file with summary mean depths per chromosome and regions pattern: "*.{summary.txt}" - - regions_txt: - - meta: + ontologies: [] + regions_txt: + - - meta: type: map description: | Groovy Map containing sample information @@ -71,8 +77,9 @@ output: type: file description: Text file with region cumulative coverage distribution pattern: "*.{region.dist.txt}" - - per_base_d4: - - meta: + ontologies: [] + per_base_d4: + - - meta: type: map description: | Groovy Map containing sample information @@ -81,8 +88,9 @@ output: type: file description: D4 file with per-base coverage pattern: "*.{per-base.d4}" - - per_base_bed: - - meta: + ontologies: [] + per_base_bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -91,8 +99,9 @@ output: type: file description: BED file with per-base coverage pattern: "*.{per-base.bed.gz}" - - per_base_csi: - - meta: + ontologies: [] + per_base_csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -101,8 +110,9 @@ output: type: file description: Index file for BED file with per-base coverage pattern: "*.{per-base.bed.gz.csi}" - - regions_bed: - - meta: + ontologies: [] + regions_bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -111,8 +121,9 @@ output: type: file description: BED file with per-region coverage pattern: "*.{regions.bed.gz}" - - regions_csi: - - meta: + ontologies: [] + regions_csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -121,8 +132,9 @@ output: type: file description: Index file for BED file with per-region coverage pattern: "*.{regions.bed.gz.csi}" - - quantized_bed: - - meta: + ontologies: [] + quantized_bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -131,8 +143,9 @@ output: type: file description: BED file with binned coverage pattern: "*.{quantized.bed.gz}" - - quantized_csi: - - meta: + ontologies: [] + quantized_csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -141,8 +154,9 @@ output: type: file description: Index file for BED file with binned coverage pattern: "*.{quantized.bed.gz.csi}" - - thresholds_bed: - - meta: + ontologies: [] + thresholds_bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -152,8 +166,9 @@ output: description: BED file with the number of bases in each region that are covered at or above each threshold pattern: "*.{thresholds.bed.gz}" - - thresholds_csi: - - meta: + ontologies: [] + thresholds_csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -162,11 +177,14 @@ output: type: file description: Index file for BED file with threshold coverage pattern: "*.{thresholds.bed.gz.csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index c604540b0..67e16562b 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -222,15 +222,15 @@ ] ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:16.953408231" + "timestamp": "2025-01-17T14:57:12.350279421" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -260,7 +260,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -289,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -367,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -395,15 +395,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:50.160217828" + "timestamp": "2025-01-17T14:56:12.528228123" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -433,7 +433,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -456,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -480,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" + "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" ] ], "global_txt": [ @@ -507,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -528,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" + "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" ] ], "regions_bed": [ @@ -556,15 +556,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:01.164885111" + "timestamp": "2025-01-17T14:56:38.422491251" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -594,7 +594,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -623,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -641,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -674,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -701,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -729,15 +729,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:39.071657456" + "timestamp": "2025-01-17T14:55:43.01015749" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -767,7 +767,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -796,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -814,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" + "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" ] ], "8": [ @@ -847,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -874,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" + "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" ] ], "regions_txt": [ @@ -902,15 +902,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:55.631776118" + "timestamp": "2025-01-17T14:56:27.10647246" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -940,7 +940,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -963,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1002,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1039,15 +1039,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:33.642125299" + "timestamp": "2025-01-17T14:55:30.449110281" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -1077,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -1100,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1139,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1176,15 +1176,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:44.704920941" + "timestamp": "2025-01-17T14:55:55.244274402" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -1222,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" + "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" ] ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -1255,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1273,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -1306,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1333,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -1369,18 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" + "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" ] ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:06.737266831" + "timestamp": "2025-01-17T14:56:49.888375978" } } \ No newline at end of file diff --git a/modules/nf-core/mosdepth/tests/tags.yml b/modules/nf-core/mosdepth/tests/tags.yml deleted file mode 100644 index 5cd2e08e2..000000000 --- a/modules/nf-core/mosdepth/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mosdepth: - - "modules/nf-core/mosdepth/**" diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml index 932d1556a..906277c5d 100644 --- a/modules/nf-core/ngsbits/samplegender/environment.yml +++ b/modules/nf-core/ngsbits/samplegender/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::ngs-bits=2023_02 + - bioconda::ngs-bits=2024_11 diff --git a/modules/nf-core/ngsbits/samplegender/main.nf b/modules/nf-core/ngsbits/samplegender/main.nf index 3562238df..655149084 100644 --- a/modules/nf-core/ngsbits/samplegender/main.nf +++ b/modules/nf-core/ngsbits/samplegender/main.nf @@ -4,13 +4,13 @@ process NGSBITS_SAMPLEGENDER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ngs-bits:2023_02--py311ha0b7adc_2': - 'biocontainers/ngs-bits:2023_02--py311ha0b7adc_2' }" + 'https://depot.galaxyproject.org/singularity/ngs-bits:2024_11--py312hd80e9a6_0': + 'biocontainers/ngs-bits:2024_11--py312hd80e9a6_0' }" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) - tuple val(meta2), path(fai) + tuple val(meta3), path(fai) val method output: diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml index 54a611812..4b79dfca3 100644 --- a/modules/nf-core/ngsbits/samplegender/meta.yml +++ b/modules/nf-core/ngsbits/samplegender/meta.yml @@ -23,10 +23,12 @@ input: type: file description: One or more BAM/CRAM files to determine the gender of pattern: "*.{bam,cram}" + ontologies: [] - bai: type: file description: The index file(s) from the input BAM/CRAM file(s) pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -36,7 +38,8 @@ input: type: file description: The reference FASTA to use (mandatory when CRAM files are used) pattern: "*.{fasta,fa,fna}" - - - meta2: + ontologies: [] + - - meta3: type: map description: | Groovy Map containing reference fasta information @@ -45,14 +48,15 @@ input: type: file description: The index file from the reference FASTA pattern: "*.fai" - - - method: - type: string - description: The method to use to define the gender (posibilities are 'xy', - 'hetx' and 'sry') - pattern: "(xy|hetx|sry)" + ontologies: [] + - method: + type: string + description: The method to use to define the gender (possibilities are 'xy', 'hetx' + and 'sry') + pattern: "(xy|hetx|sry)" output: - - tsv: - - meta: + tsv: + - - meta: type: map description: | Groovy Map containing sample information @@ -61,11 +65,15 @@ output: type: file description: An output TSV file containing the results of the gender prediction pattern: "*.tsv" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test index 4f8379b40..0917b7dde 100644 --- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test +++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "ngsbits" tag "ngsbits/samplegender" - // Only a stub test here because the modules needs the full chrX and chrY + // Only a stub test here because the module needs the full chrX and chrY test("homo_sapiens - bam, bai, [], [], sry - stub") { options "-stub" diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap index 48fd8af9c..cb493a2c2 100644 --- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap +++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b" + "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" ], "tsv": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,72f3e70be3e6a734bf39d1a6bf6d604b" + "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.1", + "nextflow": "24.10.1" }, - "timestamp": "2024-03-18T15:36:37.639882564" + "timestamp": "2024-12-10T13:36:08.650020628" } } \ No newline at end of file diff --git a/modules/nf-core/ngsbits/samplegender/tests/tags.yml b/modules/nf-core/ngsbits/samplegender/tests/tags.yml deleted file mode 100644 index 8b7a0da9e..000000000 --- a/modules/nf-core/ngsbits/samplegender/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -ngsbits/samplegender: - - "modules/nf-core/ngsbits/samplegender/**" diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index 1d715d564..8f34e975c 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index ea6deda3e..68549f7a0 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -28,18 +28,22 @@ input: type: file description: An aligned BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - bai: type: file description: Optional aligned BAM/CRAM/SAM file index pattern: "*.{bai,crai,sai}" + ontologies: [] - bait_intervals: type: file description: An interval file that contains the locations of the baits used. pattern: "*.{interval_list,bed,bed.gz}" + ontologies: [] - target_intervals: type: file description: An interval file that contains the locations of the targets. pattern: "*.{interval_list,bed,bed.gz}" + ontologies: [] - - meta2: type: map description: | @@ -51,6 +55,7 @@ input: A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input. pattern: "*.{fa,fasta,fna}" + ontologies: [] - - meta3: type: map description: | @@ -60,6 +65,7 @@ input: type: file description: Index of FASTA file. Only needed when fasta is supplied. pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -70,9 +76,10 @@ input: description: Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied. pattern: "*.dict" + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -81,11 +88,14 @@ output: type: file description: Alignment metrics files generated by picard pattern: "*_{metrics}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/picard/collecthsmetrics/tests/tags.yml b/modules/nf-core/picard/collecthsmetrics/tests/tags.yml deleted file mode 100644 index b353f95ec..000000000 --- a/modules/nf-core/picard/collecthsmetrics/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -picard/collecthsmetrics: - - "modules/nf-core/picard/collecthsmetrics/**" diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index 1d715d564..8f34e975c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 2b7981ac6..3f0bf6103 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -26,10 +26,12 @@ input: type: file description: SAM/BAM/CRAM file pattern: "*.{sam,bam,cram}" + ontologies: [] - bai: type: file description: Optional SAM/BAM/CRAM file index pattern: "*.{sai,bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -38,6 +40,7 @@ input: - fasta: type: file description: Genome fasta file + ontologies: [] - - meta3: type: map description: | @@ -47,9 +50,10 @@ input: type: file description: Index of FASTA file. Only needed when fasta is supplied. pattern: "*.fai" + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -58,8 +62,9 @@ output: type: file description: Alignment metrics files generated by picard pattern: "*_{metrics}" - - pdf: - - meta: + ontologies: [] + pdf: + - - meta: type: map description: | Groovy Map containing sample information @@ -68,11 +73,14 @@ output: type: file description: PDF plots of metrics pattern: "*.{pdf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 13265842f..5f2dfc031 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index bb7480809..a27e0a88c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -26,10 +26,12 @@ input: type: file description: Aligned reads file pattern: "*.{bam, cram}" + ontologies: [] - bai: type: file description: (Optional) Aligned reads file index pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -39,6 +41,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta,fna}" + ontologies: [] - - meta3: type: map description: | @@ -48,13 +51,15 @@ input: type: file description: Genome fasta file index pattern: "*.{fai}" - - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be - generated from a BED file with GATK BedToIntervalList. + ontologies: [] + - intervallist: + type: file + description: Picard Interval List. Defines which contigs to include. Can be generated + from a BED file with GATK BedToIntervalList. + ontologies: [] output: - - metrics: - - meta: + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -63,11 +68,14 @@ output: type: file description: Alignment metrics files generated by picard pattern: "*_{metrics}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index 1d715d564..8f34e975c 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 7c279fe1e..8af62051e 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -24,9 +24,10 @@ input: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -35,11 +36,14 @@ output: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/qualimap/bamqc/environment.yml b/modules/nf-core/qualimap/bamqc/environment.yml index 4fa5f4e8e..4574291d3 100644 --- a/modules/nf-core/qualimap/bamqc/environment.yml +++ b/modules/nf-core/qualimap/bamqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 8be33c00a..6a563fa4c 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -26,13 +26,15 @@ input: type: file description: BAM file pattern: "*.{bam}" - - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" + ontologies: [] + - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" + ontologies: [] output: - - results: - - meta: + results: + - - meta: type: map description: | Groovy Map containing sample information @@ -41,11 +43,13 @@ output: type: directory description: Qualimap results dir pattern: "*/*" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@phue" maintainers: diff --git a/modules/nf-core/qualimap/bamqc/tests/tags.yml b/modules/nf-core/qualimap/bamqc/tests/tags.yml deleted file mode 100644 index b2b5eb6fc..000000000 --- a/modules/nf-core/qualimap/bamqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -qualimap/bamqc: - - modules/nf-core/qualimap/bamqc/** diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 311756102..7019a72e4 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -24,7 +24,7 @@ process SAMTOOLS_INDEX { """ samtools \\ index \\ - -@ ${task.cpus-1} \\ + -@ ${task.cpus} \\ $args \\ $input diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index db8df0d50..1bed6bca6 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -25,9 +25,10 @@ input: - input: type: file description: input file + ontologies: [] output: - - bai: - - meta: + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -36,8 +37,9 @@ output: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -46,8 +48,9 @@ output: type: file description: CSI index file pattern: "*.{csi}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -56,11 +59,14 @@ output: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml deleted file mode 100644 index e0f58a7a3..000000000 --- a/modules/nf-core/samtools/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/index: - - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index a9dbec5a8..ab2b3b280 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -26,6 +26,7 @@ input: type: file description: BAM/CRAM/SAM file(s) pattern: "*.{bam,cram,sam}" + ontologies: [] - - meta2: type: map description: | @@ -36,9 +37,10 @@ input: description: Reference genome FASTA file pattern: "*.{fa,fasta,fna}" optional: true + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -47,8 +49,9 @@ output: type: file description: Sorted BAM file pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -57,8 +60,9 @@ output: type: file description: Sorted CRAM file pattern: "*.{cram}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +71,9 @@ output: type: file description: CRAM index file (optional) pattern: "*.crai" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,11 +82,14 @@ output: type: file description: BAM index file (optional) pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml deleted file mode 100644 index cd63ea208..000000000 --- a/modules/nf-core/samtools/sort/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -samtools/sort: - - modules/nf-core/samtools/sort/** - - tests/modules/nf-core/samtools/sort/** diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml index a8b647277..7e04bfd8f 100644 --- a/modules/nf-core/sentieon/wgsmetrics/meta.yml +++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml @@ -22,10 +22,12 @@ input: type: file description: Sorted BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - bai: type: file description: Index of th sorted BAM/CRAM/SAM file pattern: "*.{bai,crai,sai}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +37,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -44,6 +47,7 @@ input: type: file description: Index of the genome fasta file pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -52,23 +56,27 @@ input: - intervals_list: type: file description: intervals + ontologies: [] output: - - wgs_metrics: - - meta: + wgs_metrics: + - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - "*.txt": type: file - description: File containing the information about mean base quality score for - each sequencing cycle + description: File containing the information about mean base quality score + for each sequencing cycle pattern: "*.txt" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index c34a9cb15..574fbad16 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -23,20 +23,20 @@ input: One or more VCF files. The order and number of files should correspond to the order and number of tags in the `priority` input channel. pattern: "*.{vcf,vcf.gz}" - - - input_priority: - type: list - description: | - Prioritize the input VCF files according to this list, - e.g ['tiddit','cnvnator']. The order and number of tags should correspond to - the order and number of VCFs in the `vcfs` input channel. - - - sort_inputs: - type: boolean - description: | - Should the input files be sorted by name. The priority tag will be sorted - together with it's corresponding VCF file. + - input_priority: + type: list + description: | + Prioritize the input VCF files according to this list, + e.g ['tiddit','cnvnator']. The order and number of tags should correspond to + the order and number of VCFs in the `vcfs` input channel. + - sort_inputs: + type: boolean + description: | + Should the input files be sorted by name. The priority tag will be sorted + together with it's corresponding VCF file. output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -45,8 +45,9 @@ output: type: file description: VCF output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,8 +56,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -65,11 +67,14 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/svdb/merge/tests/tags.yml b/modules/nf-core/svdb/merge/tests/tags.yml deleted file mode 100644 index 8501d9072..000000000 --- a/modules/nf-core/svdb/merge/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -svdb/merge: - - modules/nf-core/svdb/merge/** diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 017c259da..6221bb53a 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,7 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 13acd670e..325b8bbff 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : - 'biocontainers/htslib:1.20--h5efdd21_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' : + 'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }" input: tuple val(meta), path(tab) diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index 7864832d9..c172968d8 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -22,9 +22,10 @@ input: type: file description: TAB-delimited genome position file compressed with bgzip pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + ontologies: [] output: - - tbi: - - meta: + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -33,8 +34,9 @@ output: type: file description: tabix index file pattern: "*.{tbi}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -43,11 +45,14 @@ output: type: file description: coordinate sorted index file pattern: "*.{csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index 102b0d7bf..e74afd926 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test Process TABIX_TABIX" - script "modules/nf-core/tabix/tabix/main.nf" + script "../main.nf" process "TABIX_TABIX" tag "modules" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index c2b9ed0b8..67b8e3c2f 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -14,7 +14,7 @@ ], "2": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ], "csi": [ @@ -28,16 +28,16 @@ ] ], "versions": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] }, "genome.gff3.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-07-19T12:06:25.653807564" + "timestamp": "2025-03-26T13:52:48.638506004" }, "sarscov2_bedgz_tbi": { "content": [ @@ -54,7 +54,7 @@ ], "2": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ], "csi": [ @@ -68,16 +68,16 @@ ] ], "versions": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] }, "test.bed.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-07-19T12:06:09.754082161" + "timestamp": "2025-03-26T13:52:44.910707349" }, "sarscov2_vcf_tbi": { "content": [ @@ -94,7 +94,7 @@ ], "2": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ], "csi": [ @@ -108,16 +108,16 @@ ] ], "versions": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] }, "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-07-19T12:06:40.042648294" + "timestamp": "2025-03-26T13:52:52.405662623" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -139,7 +139,7 @@ ] ], "2": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ], "csi": [ [ @@ -158,16 +158,16 @@ ] ], "versions": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] }, "test.vcf.gz.csi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-07-19T12:07:08.700367261" + "timestamp": "2025-03-26T13:52:59.633992323" }, "sarscov2_vcf_csi": { "content": [ @@ -184,7 +184,7 @@ ] ], "2": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ], "csi": [ [ @@ -198,15 +198,15 @@ ], "versions": [ - "versions.yml:md5,07064637fb8a217174052be8e40234e2" + "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] }, "test.vcf.gz.csi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-07-19T12:06:55.362067748" + "timestamp": "2025-03-26T13:52:56.083553332" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml deleted file mode 100644 index 6eda06537..000000000 --- a/modules/nf-core/tabix/tabix/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tabix/tabix: - - "modules/nf-core/tabix/tabix/**" diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index 2fd01cfd4..a33b14c85 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml index 88b72641d..71bbf7864 100644 --- a/modules/nf-core/tiddit/cov/meta.yml +++ b/modules/nf-core/tiddit/cov/meta.yml @@ -23,6 +23,7 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - - meta2: type: map description: | @@ -34,9 +35,10 @@ input: Reference genome file. Only needed when passing in CRAM instead of BAM. If not using CRAM, please pass an empty file instead. pattern: "*.fasta" + ontologies: [] output: - - cov: - - meta: + cov: + - - meta: type: map description: | Groovy Map containing sample information @@ -45,8 +47,9 @@ output: type: file description: The coverage of different regions in bed format. Optional. pattern: "*.bed" - - wig: - - meta: + ontologies: [] + wig: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,11 +58,14 @@ output: type: file description: The coverage of different regions in WIG format. Optional. pattern: "*.wig" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/tiddit/cov/tests/tags.yml b/modules/nf-core/tiddit/cov/tests/tags.yml deleted file mode 100644 index d5831f1d1..000000000 --- a/modules/nf-core/tiddit/cov/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tiddit/cov: - - "modules/nf-core/tiddit/cov/**" diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml index 331ad3b27..e80eb6d09 100644 --- a/modules/nf-core/ucsc/wigtobigwig/environment.yml +++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml index 97bf98b16..bc82734da 100644 --- a/modules/nf-core/ucsc/wigtobigwig/meta.yml +++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml @@ -22,24 +22,30 @@ input: type: file description: wig file pattern: "*.{wig}" - - - sizes: - type: file - description: Chromosome sizes file + ontologies: [] + - sizes: + type: file + description: Chromosome sizes file + ontologies: [] output: - - bw: - - meta: + bw: + - - meta: type: file description: bigwig file pattern: "*.{bw}" + ontologies: [] - "*.bw": type: file description: bigwig file pattern: "*.{bw}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@jianhong" - "@projectoriented" diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index b511fc3cd..8b6f2bdf8 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -27,34 +27,41 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - bai: type: file description: BAI/CRAI/CSI index file pattern: "*.{bai,crai,csi}" + ontologies: [] - - svd_ud: type: file description: .UD matrix file from SVD result of genotype matrix pattern: "*.UD" + ontologies: [] - svd_mu: type: file description: .mu matrix file of genotype matrix pattern: "*.mu" + ontologies: [] - svd_bed: type: file description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] pattern: "*.bed" - - - refvcf: - type: file - description: Reference panel VCF with genotype information, for generation of - .UD .mu .bed files [Optional] - pattern: "*.vcf" - - - references: - type: file - description: reference file [Required] - pattern: "*.fasta" + ontologies: [] + - refvcf: + type: file + description: Reference panel VCF with genotype information, for generation of + .UD .mu .bed files [Optional] + pattern: "*.vcf" + ontologies: [] + - references: + type: file + description: reference file [Required] + pattern: "*.fasta" + ontologies: [] output: - - log: - - meta: + log: + - - meta: type: map description: | Groovy Map containing sample information @@ -63,8 +70,9 @@ output: type: file description: Detailed summary of the VerifyBamId2 results pattern: "*.log" - - ud: - - meta: + ontologies: [] + ud: + - - meta: type: map description: | Groovy Map containing sample information @@ -73,8 +81,9 @@ output: type: file description: .UD matrix file from customized reference vcf input pattern: "*.UD" - - bed: - - meta: + ontologies: [] + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -83,30 +92,33 @@ output: type: file description: .Bed file from customized reference marker vcf input pattern: "*.bed" - - mu: - - meta: + ontologies: [] + mu: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.mu": type: file - description: .mu matrix file of genotype matrix from customized reference vcf - input + description: .mu matrix file of genotype matrix from customized reference + vcf input pattern: "*.mu" - - self_sm: - - meta: + ontologies: [] + self_sm: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.selfSM": type: file - description: Shares the same format as legacy VB1 and the key information FREEMIX - indicates the estimated contamination level. + description: Shares the same format as legacy VB1 and the key information + FREEMIX indicates the estimated contamination level. pattern: "*.selfSM" - - ancestry: - - meta: + ontologies: [] + ancestry: + - - meta: type: map description: | Groovy Map containing sample information @@ -115,11 +127,14 @@ output: type: file description: Ancestry information pattern: "*.Ancestry" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@manifestoso" maintainers: From 7ab61c282763b0aa4979f0d9890eaecd83467088 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 10 Jul 2025 16:21:44 +0200 Subject: [PATCH 036/872] add test for qc bam --- conf/modules/qc_bam.config | 1 + .../local/call_repeat_expansions/main.nf | 16 +- subworkflows/local/qc_bam/main.nf | 27 +-- subworkflows/local/qc_bam/tests/main.nf.test | 168 ++++++++++++++++++ .../local/qc_bam/tests/main.nf.test.snap | 160 +++++++++++++++++ .../local/qc_bam/tests/nextflow.config | 64 +++++++ 6 files changed, 415 insertions(+), 21 deletions(-) create mode 100644 subworkflows/local/qc_bam/tests/main.nf.test create mode 100644 subworkflows/local/qc_bam/tests/main.nf.test.snap create mode 100644 subworkflows/local/qc_bam/tests/nextflow.config diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index ef8603419..bd38111a2 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -55,6 +55,7 @@ process { } withName: '.*QC_BAM:MOSDEPTH' { + ext.args = "--d4" ext.prefix = { "${meta.id}_mosdepth" } } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index fb364aac5..7d62025bf 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -2,14 +2,14 @@ // Run ExpansionHunter and Stranger // -include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_EXP } from '../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_EXP } from '../../modules/nf-core/bcftools/reheader/main' -include { EXPANSIONHUNTER } from '../../modules/nf-core/expansionhunter/main' -include { PICARD_RENAMESAMPLEINVCF as RENAMESAMPLE_EXP } from '../../modules/nf-core/picard/renamesampleinvcf/main' -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { SVDB_MERGE as SVDB_MERGE_REPEATS } from '../../modules/nf-core/svdb/merge/main' -include { TABIX_TABIX as TABIX_EXP_RENAME } from '../../modules/nf-core/tabix/tabix/main' +include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_EXP } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_EXP } from '../../../modules/nf-core/bcftools/reheader/main' +include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main' +include { PICARD_RENAMESAMPLEINVCF as RENAMESAMPLE_EXP } from '../../../modules/nf-core/picard/renamesampleinvcf/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { SVDB_MERGE as SVDB_MERGE_REPEATS } from '../../../modules/nf-core/svdb/merge/main' +include { TABIX_TABIX as TABIX_EXP_RENAME } from '../../../modules/nf-core/tabix/tabix/main' workflow CALL_REPEAT_EXPANSIONS { take: diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index b1750b88a..3ee0817fc 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -2,19 +2,19 @@ // A quality check subworkflow for processed bams. // -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../modules/nf-core/picard/collectmultiplemetrics/main' -include { PICARD_COLLECTHSMETRICS } from '../../modules/nf-core/picard/collecthsmetrics/main' -include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../modules/nf-core/chromograph/main' -include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' -include { TIDDIT_COV } from '../../modules/nf-core/tiddit/cov/main' -include { MOSDEPTH } from '../../modules/nf-core/mosdepth/main' -include { UCSC_WIGTOBIGWIG } from '../../modules/nf-core/ucsc/wigtobigwig/main' -include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG } from '../../modules/nf-core/picard/collectwgsmetrics/main' -include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../modules/nf-core/picard/collectwgsmetrics/main' -include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG } from '../../modules/nf-core/sentieon/wgsmetrics/main' -include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../modules/nf-core/sentieon/wgsmetrics/main' -include { NGSBITS_SAMPLEGENDER } from '../../modules/nf-core/ngsbits/samplegender/main' -include { VERIFYBAMID_VERIFYBAMID2 } from '../../modules/nf-core/verifybamid/verifybamid2/main' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' +include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' +include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../../modules/nf-core/chromograph/main' +include { QUALIMAP_BAMQC } from '../../../modules/nf-core/qualimap/bamqc/main' +include { TIDDIT_COV } from '../../../modules/nf-core/tiddit/cov/main' +include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' +include { UCSC_WIGTOBIGWIG } from '../../../modules/nf-core/ucsc/wigtobigwig/main' +include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG } from '../../../modules/nf-core/sentieon/wgsmetrics/main' +include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../../modules/nf-core/sentieon/wgsmetrics/main' +include { NGSBITS_SAMPLEGENDER } from '../../../modules/nf-core/ngsbits/samplegender/main' +include { VERIFYBAMID_VERIFYBAMID2 } from '../../../modules/nf-core/verifybamid/verifybamid2/main' workflow QC_BAM { @@ -53,6 +53,7 @@ workflow QC_BAM { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) } + TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_chrom_sizes) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test new file mode 100644 index 000000000..b3326074e --- /dev/null +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -0,0 +1,168 @@ +nextflow_workflow { + + name "Test Workflow QC_BAM" + script "subworkflows/local/qc_bam/main.nf" + workflow "QC_BAM" + tag "subworkflows" + tag "qc_bam" + config "./nextflow.config" + + test("QC_BAM - test, bwamem2") { + + when { + params { + aligner = "bwamem2" + skip_tools = null + outdir = "tests/results" + } + workflow { + """ + input[0] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[6] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[7] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[8] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[9] = Channel.empty() + input[10] = Channel.empty() + input[11] = Channel.empty() + input[12] = Channel.empty() + input[13] = 'xy' + """ + } + } + + then { + assertAll ( + { assert workflow.success }, + { assert snapshot( + workflow.out.multiple_metrics + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.hs_metrics + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.d4 + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.cov + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.tiddit_wig, + workflow.out.bigwig, + workflow.out.global_dist + ).match() + } + ) + } + + } + + test("QC_BAM - test, sentieon") { + + when { + params { + aligner = "sentieon" + skip_tools = null + outdir = "tests/results" + } + workflow { + """ + input[0] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[6] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[7] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[8] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[9] = Channel.empty() + input[10] = Channel.empty() + input[11] = Channel.empty() + input[12] = Channel.empty() + input[13] = 'xy' + """ + } + } + + then { + assertAll ( + { assert workflow.success }, + { assert workflow.success }, + { assert snapshot( + workflow.out.multiple_metrics + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.hs_metrics + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.d4 + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.cov + .collect {it[1]} + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.tiddit_wig, + workflow.out.bigwig, + workflow.out.global_dist + ).match() + } + ) + } + } + + + +} diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap new file mode 100644 index 000000000..74762c958 --- /dev/null +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -0,0 +1,160 @@ +{ + "QC_BAM - test, bwamem2": { + "content": [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-07-10T16:16:06.053312997" + }, + "QC_BAM - test, sentieon": { + "content": [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ + "earlycasualcaiman_wgsmetrics.txt" + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-07-10T16:17:02.204969887" + } +} \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config new file mode 100644 index 000000000..3a48ae572 --- /dev/null +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -0,0 +1,64 @@ +process { + + withName: '.*QC_BAM:PICARD_COLLECTMULTIPLEMETRICS' { + ext.args = "--TMP_DIR ." + ext.prefix = { "${meta.id}_multiplemetrics" } + } + + withName: '.*QC_BAM:PICARD_COLLECTHSMETRICS' { + ext.args = "--TMP_DIR ." + ext.prefix = { "${meta.id}_hsmetrics" } + } + + withName: '.*QC_BAM:QUALIMAP_BAMQC' { + ext.prefix = { "${meta.id}_qualimap" } + } + + withName: '.*QC_BAM:TIDDIT_COV' { + ext.args = '-z 500 -w' + ext.prefix = { "${meta.id}_tidditcov" } + } + + withName: '.*QC_BAM:UCSC_WIGTOBIGWIG' { + ext.args = '-clip' + ext.prefix = { "${meta.id}_tidditcov" } + } + + withName: '.*QC_BAM:CHROMOGRAPH_COV' { + ext.args = '--euploid --step 500' + ext.prefix = { "${meta2.id}_chromographcov" } + } + + withName: '.*QC_BAM:MOSDEPTH' { + ext.args = "--d4" + ext.prefix = { "${meta.id}_mosdepth" } + } + + withName: '.*QC_BAM:NGSBITS_SAMPLEGENDER' { + // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.prefix = { "${meta.id}_ngsbits_sex" } + } + + withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' { + ext.args = "--TMP_DIR ." + ext.when = { !params.aligner.equals("sentieon") } + ext.prefix = { "${meta.id}_wgsmetrics" } + } + + withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' { + ext.args = "--TMP_DIR ." + ext.when = { !params.aligner.equals("sentieon") } + ext.prefix = { "${meta.id}_wgsmetrics_y" } + } + + withName: '.*QC_BAM:SENTIEON_WGSMETRICS_WG' { + ext.when = { params.aligner.equals("sentieon") } + ext.prefix = { "${meta.id}_wgsmetrics" } + } + + withName: '.*QC_BAM:SENTIEON_WGSMETRICS_Y' { + ext.when = { params.aligner.equals("sentieon") } + ext.prefix = { "${meta.id}_wgsmetrics_y" } + } +} \ No newline at end of file From c68b73ce88fd601275b6e5e353466c34e2f28603 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 10 Jul 2025 16:33:11 +0200 Subject: [PATCH 037/872] add test for call repeat expansions --- .../call_repeat_expansions/tests/main.nf.test | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 subworkflows/local/call_repeat_expansions/tests/main.nf.test diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test new file mode 100644 index 000000000..ae82b1367 --- /dev/null +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -0,0 +1,40 @@ +nextflow_workflow { + + name "Test Workflow CALL_REPEAT_EXPANSIONS" + script "subworkflows/local/call_repeat_expansions/main.nf" + workflow "CALL_REPEAT_EXPANSIONS" + tag "subworkflows" + tag "call_repeat_expansions" + config "./nextflow.config" + + test("CALL_REPEAT_EXPANSIONS") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + input[0] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[1] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() + input[2] = "justhusky" + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + +} From 6138d6799e51497b08b6a02dbe6d632f73653458 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 10 Jul 2025 19:58:09 +0200 Subject: [PATCH 038/872] repeat expansions test --- nf-test.config | 1 + .../call_repeat_expansions/tests/main.nf.test | 6 ++- .../tests/main.nf.test.snap | 12 ++++++ .../tests/nextflow.config | 43 +++++++++++++++++++ 4 files changed, 60 insertions(+), 2 deletions(-) create mode 100644 subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap create mode 100644 subworkflows/local/call_repeat_expansions/tests/nextflow.config diff --git a/nf-test.config b/nf-test.config index 7b52f1313..0374f50f2 100644 --- a/nf-test.config +++ b/nf-test.config @@ -21,6 +21,7 @@ config { plugins { load "nft-utils@0.0.3" load "nft-bam@0.6.0" + load "nft-vcf@1.0.7" } } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index ae82b1367..9f90750f5 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_workflow { ] ) input[1] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() - input[2] = "justhusky" + input[2] = Channel.of([id:'justhusky']) input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() """ @@ -32,7 +32,9 @@ nextflow_workflow { then { assert workflow.success - assert snapshot(workflow.out).match() + assert snapshot( + path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5 + ).match() } } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap new file mode 100644 index 000000000..35360c9bd --- /dev/null +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -0,0 +1,12 @@ +{ + "CALL_REPEAT_EXPANSIONS": { + "content": [ + "5f06dccb7fc4ad3758bc23e3232f9abb" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-07-10T19:44:19.538636651" + } +} \ No newline at end of file diff --git a/subworkflows/local/call_repeat_expansions/tests/nextflow.config b/subworkflows/local/call_repeat_expansions/tests/nextflow.config new file mode 100644 index 000000000..916cff868 --- /dev/null +++ b/subworkflows/local/call_repeat_expansions/tests/nextflow.config @@ -0,0 +1,43 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +// +// Repeat expansion calling options +// + +process { + withName: '.*CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER' { + ext.args = { ("${meta.sex}" == '1') ? '--sex male' : '--sex female' } + ext.prefix = { "${meta.id}_exphunter" } + } + + withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}_exphunter_sorted" } + } + + withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' { + ext.args = "--temp-prefix ." + ext.args2 = "-O v" + ext.prefix = { "${meta.id}_repeat_expansion" } + } + + withName: '.*CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP' { + ext.args = '--output-type z --multiallelics -both' + ext.prefix = { "${meta.id}_split_exp" } + } + + withName: '.*CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS' { + ext.args = {"--notag"} + } + +} From 8abca7df63d4847b92032cb357ffc61465bb71c7 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 10 Jul 2025 20:21:10 +0200 Subject: [PATCH 039/872] fix lint --- .../call_repeat_expansions/tests/main.nf.test | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 14 ++++++-------- subworkflows/local/qc_bam/tests/nextflow.config | 2 +- 3 files changed, 8 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 9f90750f5..d6f4967bd 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index b3326074e..ee76b76bb 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -17,19 +17,19 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = Channel.of( + input[2] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], @@ -95,19 +95,19 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = Channel.of( + input[2] = Channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], @@ -163,6 +163,4 @@ nextflow_workflow { } } - - } diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config index 3a48ae572..72c51555d 100644 --- a/subworkflows/local/qc_bam/tests/nextflow.config +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -61,4 +61,4 @@ process { ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics_y" } } -} \ No newline at end of file +} From 986f6adda4ae914fbb6113d5f1d7ac74515fd0fd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 10 Jul 2025 23:03:05 +0200 Subject: [PATCH 040/872] update snaps --- .../tests/main.nf.test.snap | 12 +++--- tests/default.nf.test.snap | 40 +++++++++--------- tests/test_bam.nf.test.snap | 42 +++++++++---------- tests/test_singleton.nf.test.snap | 40 +++++++++--------- 4 files changed, 67 insertions(+), 67 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index c7b69f839..fe5c7e7d8 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -389,15 +389,15 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", - "versions.yml:md5,3e1d1e300c9f1e99a758f5854e226a8c", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", + "versions.yml:md5,4e8ef14026e5c035dd4c36c30fe76e0e", "versions.yml:md5,6a0d25217268ed42e4cfe4f77972ba9b", "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", + "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", - "versions.yml:md5,94381c84c4482acd1f7bdb0309eb7d65", "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", @@ -884,15 +884,15 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", - "versions.yml:md5,3e1d1e300c9f1e99a758f5854e226a8c", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", + "versions.yml:md5,4e8ef14026e5c035dd4c36c30fe76e0e", "versions.yml:md5,6a0d25217268ed42e4cfe4f77972ba9b", "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", + "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", - "versions.yml:md5,94381c84c4482acd1f7bdb0309eb7d65", "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", @@ -904,8 +904,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-25T19:15:39.213374312" + "timestamp": "2025-07-10T22:52:01.91651849" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4342097b1..1dcb4e545 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -24,7 +24,7 @@ "bcftools": 1.2 }, "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "BCFTOOLS_ROH": { "bcftools": 1.2 @@ -199,7 +199,7 @@ "picard": "3.3.0" }, "MOSDEPTH": { - "mosdepth": "0.3.8" + "mosdepth": "0.3.10" }, "MT_DELETION": { "samtools": "1.19.2" @@ -226,10 +226,10 @@ "picard": "3.3.0" }, "REMOVE_DUPLICATES_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "REMOVE_DUPLICATES_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "RENAMESAMPLE_EXP": { "picard": "3.3.0" @@ -277,13 +277,13 @@ "SMNCopyNumberCaller": "1.1.2" }, "SPLIT_MULTIALLELICS_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPRING_DECOMPRESS_TO_FQ_PAIR": { "spring": "1.1.1" @@ -309,10 +309,10 @@ "bcftools": 1.21 }, "TABIX_ANNOTATE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BGZIP": { "tabix": 1.2 @@ -324,34 +324,34 @@ "tabix": 1.2 }, "TABIX_DBSNP": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_EXP_RENAME": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GL": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GNOMAD_AF": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_PBT": { "tabix": 1.2 }, "TABIX_TABIX": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MERGE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT2": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_VEP": { - "tabix": 1.2 + "tabix": 1.21 }, "TIDDIT_COV": { "tiddit": "3.6.1" @@ -576,8 +576,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-25T20:06:21.438307947" + "timestamp": "2025-07-10T20:55:24.657588384" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 1f2fe7825..1cd707669 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -24,7 +24,7 @@ "bcftools": 1.2 }, "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "BCFTOOLS_ROH": { "bcftools": 1.2 @@ -189,13 +189,13 @@ "manta": "1.6.0" }, "MOSDEPTH": { - "mosdepth": "0.3.8" + "mosdepth": "0.3.10" }, "MT_DELETION": { "samtools": "1.19.2" }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202302 + "ngs-bits": 202411 }, "PICARD_ADDORREPLACEREADGROUPS_MT": { "picard": "3.3.0" @@ -219,10 +219,10 @@ "picard": "3.3.0" }, "REMOVE_DUPLICATES_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "REMOVE_DUPLICATES_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "RENAMESAMPLE_EXP": { "picard": "3.3.0" @@ -261,13 +261,13 @@ "SMNCopyNumberCaller": "1.1.2" }, "SPLIT_MULTIALLELICS_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "STRANGER": { "stranger": "0.9.4", @@ -290,10 +290,10 @@ "bcftools": 1.21 }, "TABIX_ANNOTATE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BGZIP": { "tabix": 1.2 @@ -305,34 +305,34 @@ "tabix": 1.2 }, "TABIX_DBSNP": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_EXP_RENAME": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GL": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GNOMAD_AF": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_PBT": { "tabix": 1.2 }, "TABIX_TABIX": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MERGE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT2": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_VEP": { - "tabix": 1.2 + "tabix": 1.21 }, "TIDDIT_COV": { "tiddit": "3.6.1" @@ -541,8 +541,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-25T20:08:34.973300629" + "timestamp": "2025-07-10T20:58:45.788245796" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 78db775d8..54a27d0d9 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -21,7 +21,7 @@ "bcftools": 1.2 }, "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "BCFTOOLS_ROH": { "bcftools": 1.2 @@ -190,7 +190,7 @@ "picard": "3.3.0" }, "MOSDEPTH": { - "mosdepth": "0.3.8" + "mosdepth": "0.3.10" }, "MT_DELETION": { "samtools": "1.19.2" @@ -217,10 +217,10 @@ "picard": "3.3.0" }, "REMOVE_DUPLICATES_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "REMOVE_DUPLICATES_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "RENAMESAMPLE_EXP": { "picard": "3.3.0" @@ -268,13 +268,13 @@ "SMNCopyNumberCaller": "1.1.2" }, "SPLIT_MULTIALLELICS_EXP": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_GL": { - "bcftools": 1.2 + "bcftools": 1.21 }, "SPLIT_MULTIALLELICS_MT": { - "bcftools": 1.2 + "bcftools": 1.21 }, "STRANGER": { "stranger": "0.9.4", @@ -297,10 +297,10 @@ "bcftools": 1.21 }, "TABIX_ANNOTATE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_BGZIP": { "tabix": 1.2 @@ -312,34 +312,34 @@ "tabix": 1.2 }, "TABIX_DBSNP": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_EXP_RENAME": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GL": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_GNOMAD_AF": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_PBT": { "tabix": 1.2 }, "TABIX_TABIX": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MERGE": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT2": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_TABIX_MT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_VEP": { - "tabix": 1.2 + "tabix": 1.21 }, "TIDDIT_COV": { "tiddit": "3.6.1" @@ -464,8 +464,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-25T20:11:32.593010906" + "timestamp": "2025-07-10T21:02:39.028101546" } } \ No newline at end of file From b86dc06ad63d989349d4faabffa618092aecf369 Mon Sep 17 00:00:00 2001 From: alexiandra97 Date: Tue, 19 Aug 2025 16:24:14 +0200 Subject: [PATCH 041/872] Resolve inconsistencies in schema JSON definitions --- assets/rtg_truthvcfs_schema.json | 2 +- assets/sample_id_map.json | 2 +- assets/svdb_query_bedpe_schema.json | 2 +- assets/svdb_query_vcf_schema.json | 2 +- assets/vep_plugin_files_schema.json | 2 +- nextflow_schema.json | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/assets/rtg_truthvcfs_schema.json b/assets/rtg_truthvcfs_schema.json index e0630455a..5695ad566 100644 --- a/assets/rtg_truthvcfs_schema.json +++ b/assets/rtg_truthvcfs_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/rtg_truthvcfs_schema.json", "title": "Schema for RTGTOOLS/VCFEVAL VCFs", "description": "Schema for the vcfeval's vcf input", "type": "array", diff --git a/assets/sample_id_map.json b/assets/sample_id_map.json index c69fa645e..1110f959f 100644 --- a/assets/sample_id_map.json +++ b/assets/sample_id_map.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/sample_id_map.json", "title": "Schema for customerid_internalid_map", "description": "Schema for the file provided with params.customerid_internalid_map", "type": "array", diff --git a/assets/svdb_query_bedpe_schema.json b/assets/svdb_query_bedpe_schema.json index b220bce5b..a9fbedbe8 100644 --- a/assets/svdb_query_bedpe_schema.json +++ b/assets/svdb_query_bedpe_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/svdb_query_bedpe_schema.json", "title": "Schema for SVDB query - BEDPE", "description": "Schema for the SVDB query database input, bedpe version", "type": "array", diff --git a/assets/svdb_query_vcf_schema.json b/assets/svdb_query_vcf_schema.json index a927a1f38..1176fccf0 100644 --- a/assets/svdb_query_vcf_schema.json +++ b/assets/svdb_query_vcf_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/svdb_query_vcf_schema.json", "title": "Schema for SVDB query - VCF", "description": "Schema for the SVDB query database input, VCF version", "type": "array", diff --git a/assets/vep_plugin_files_schema.json b/assets/vep_plugin_files_schema.json index 34fe41983..65ba49342 100644 --- a/assets/vep_plugin_files_schema.json +++ b/assets/vep_plugin_files_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/mobile_element_references_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/raredisease/master/assets/vep_plugin_files_schema.json", "title": "Schema for VEP plugin files and their indices", "description": "Schema for VEP plugin files and their indices", "type": "array", diff --git a/nextflow_schema.json b/nextflow_schema.json index 8ece884bf..e134ede5b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -174,7 +174,7 @@ "exists": true, "format": "path", "fa_icon": "fas fa-file", - "pattern": "^\\S+\\.bed(\\.gz)?\\.idx$", + "pattern": "^\\S+\\.tab(\\.gz)?\\.tbi$", "description": "Path to the index file for the gnomad tab file with allele frequencies.", "help_text": "Path to the index of gnomad tab file with CHR/START/REF,ALT/AF" }, From 49b06f2fb4c56b10f747a3e223e4d8fa2d390ba5 Mon Sep 17 00:00:00 2001 From: alexiandra97 Date: Tue, 19 Aug 2025 17:07:40 +0200 Subject: [PATCH 042/872] Use distinct output filenames for bcfools and svdb --- conf/modules/call_mobile_elements.config | 2 +- conf/modules/call_sv_tiddit.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules/call_mobile_elements.config b/conf/modules/call_mobile_elements.config index fd6bf61c2..6a35bd075 100644 --- a/conf/modules/call_mobile_elements.config +++ b/conf/modules/call_mobile_elements.config @@ -49,7 +49,7 @@ process { withName: '.*CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME' { ext.args = { '--bnd_distance 150 --overlap 0.5' } - ext.prefix = { "${meta.id}_mobile_elements" } + ext.prefix = { "${meta.id}_mobile_elements_merged" } publishDir = [ path: { "${params.outdir}/call_mobile_elements" }, mode: params.publish_dir_mode, diff --git a/conf/modules/call_sv_tiddit.config b/conf/modules/call_sv_tiddit.config index ab2cd646e..99cd42c9b 100644 --- a/conf/modules/call_sv_tiddit.config +++ b/conf/modules/call_sv_tiddit.config @@ -21,7 +21,7 @@ process { } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT" { - ext.prefix = { "${meta.id}_tiddit" } + ext.prefix = { "${meta.id}_tiddit_bcftools" } ext.args = { '--apply-filters .,PASS --output-type z' } } From 23be89e290fc2acb3d70fadc602f91992503a101 Mon Sep 17 00:00:00 2001 From: alexiandra97 Date: Wed, 20 Aug 2025 15:31:46 +0200 Subject: [PATCH 043/872] Add interval parameter to RetroSeq --- conf/modules/call_mobile_elements.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/call_mobile_elements.config b/conf/modules/call_mobile_elements.config index fd6bf61c2..445e07da7 100644 --- a/conf/modules/call_mobile_elements.config +++ b/conf/modules/call_mobile_elements.config @@ -27,7 +27,7 @@ process { } withName: '.*CALL_MOBILE_ELEMENTS:RETROSEQ_CALL' { - ext.args = { '--soft' } + ext.args = { "--soft --region ${meta.interval}" } ext.prefix = { "${meta.id}_${meta.interval}_retroseq_call" } } From d3af98763b21c17d6916895ff813e13aef9c162c Mon Sep 17 00:00:00 2001 From: Aleksandra Vitkovac <113299638+alexiandra97@users.noreply.github.com> Date: Fri, 22 Aug 2025 12:17:53 +0200 Subject: [PATCH 044/872] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a5ac166e1..18715048a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` + - Fixed inconsistencies in JSON schema #714 + ### Parameters | Old parameter | New parameter | From f7613a3c444a058993387b76c6c941433bcf1a7b Mon Sep 17 00:00:00 2001 From: peterpru Date: Wed, 1 Oct 2025 09:06:21 +0200 Subject: [PATCH 045/872] initial commit --- modules.json | 11 +- .../vcf_filter_bcftools_ensemblvep/main.nf | 54 +++++++ .../vcf_filter_bcftools_ensemblvep/meta.yml | 56 ++++++++ .../nextflow.config | 9 ++ .../tests/main.nf.test | 136 ++++++++++++++++++ .../tests/main.nf.test.snap | 103 +++++++++++++ .../tests/nextflow.config | 10 ++ workflows/raredisease.nf | 8 +- 8 files changed, 380 insertions(+), 7 deletions(-) create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config diff --git a/modules.json b/modules.json index 0024877ca..20912feaf 100644 --- a/modules.json +++ b/modules.json @@ -48,7 +48,7 @@ "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bedtools/genomecov": { "branch": "master", @@ -129,7 +129,7 @@ "ensemblvep/filtervep": { "branch": "master", "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", - "installed_by": ["modules"] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { "branch": "master", @@ -481,7 +481,7 @@ "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules"] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", @@ -546,6 +546,11 @@ "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] + }, + "vcf_filter_bcftools_ensemblvep": { + "branch": "master", + "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf new file mode 100644 index 000000000..39b8aafc2 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -0,0 +1,54 @@ +include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' +// Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config +workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { + + take: + ch_vcf // channel: [ val(meta), path(vcf) ] + ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] + filter_with_bcftools // bool: should bcftools view be run + filter_with_filter_vep // bool: should filter_vep be run + + main: + ch_versions = Channel.empty() + ch_tbi = Channel.empty() + + // Since bcftools is likely much faster than filter_vep, + // we run it first to reduce the number of variants that filter_vep has to process. + if(filter_with_bcftools) { + + BCFTOOLS_VIEW ( + ch_vcf.map { meta, vcf -> [ meta, vcf, [] ] }, + [], + [], + [] + ) + ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) + + ch_vcf = BCFTOOLS_VIEW.out.vcf + ch_tbi = BCFTOOLS_VIEW.out.tbi + } + + if(filter_with_filter_vep) { + + ENSEMBLVEP_FILTERVEP ( + ch_vcf, + ch_filter_vep_feature_file.map { _meta, file -> file } + ) + ch_versions = ch_versions.mix(ENSEMBLVEP_FILTERVEP.out.versions) + + TABIX_BGZIPTABIX ( + ENSEMBLVEP_FILTERVEP.out.output + ) + ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) + + ch_vcf = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, _tbi -> [ meta, vcf ] } + ch_tbi = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, _vcf, tbi -> [ meta, tbi ] } + } + + emit: + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml new file mode 100644 index 000000000..b9d3d7c40 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml @@ -0,0 +1,56 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "vcf_filter_bcftools_ensemblvep" +description: Filter VCF file with bcftools and filter_vep +keywords: + - filter + - vcf + - bcftools + - filter_vep +components: + - bcftools/view + - ensemblvep/filtervep + - tabix/bgziptabix +input: + - ch_vcf: + type: file + description: | + The input channel containing the VCF files + Structure: [ val(meta), path(vcf) ] + pattern: "*.{vcf/vcf.gz}" + - ch_filter_vep_file: + type: file + description: | + File to pass to filter_vep, containing e.g. HGNC IDs to filter on + Structure: [ val(meta), path(txt) ] + - filter_with_bcftools: + type: boolean + description: | + Whether to filter the VCF file with bcftools before passing it to filter_vep + - filter_with_filter_vep: + type: boolean + description: | + Whether to filter the VCF file with filter_vep +output: + - vcf: + type: file + description: | + Channel containing VCF files + Structure: [ val(meta), path(bam) ] + pattern: "*.vcf.gz" + - bai: + type: file + description: | + Channel containing indexed VCF (TBI) files + Structure: [ val(meta), path(bai) ] + pattern: "*.tbi" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@fellen31" +maintainers: + - "@fellen31" + - "@ramprasadn" diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config new file mode 100644 index 000000000..3c9c895a2 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config @@ -0,0 +1,9 @@ +// IMPORTANT: This config file should be included to ensure that the subworkflow works properly. +process { + withName: '.*VCF_FILTER_BCFTOOLS_FILTERVEP:BCFTOOLS_VIEW' { + ext.args = { [ + '--output-type z', + '--write-index=tbi', + ].join(" ") } + } +} diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test new file mode 100644 index 000000000..811929877 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_workflow { + + name "Test Subworkflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP" + script "../main.nf" + workflow "VCF_FILTER_BCFTOOLS_ENSEMBLVEP" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/vcf_filter_bcftools_ensemblvep" + tag "bcftools/view" + tag "ensemblvep/filtervep" + tag "tabix/bgziptabix" + + test("vcf, hgnc_ids - filter on expression") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz') + ]) + input[1] = Channel.of('3084') + .collectFile(name: 'hgnc_ids.txt') + .map { file -> [ [ id: 'hgnc_ids' ], file ] } + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.versions, + file(workflow.out.tbi.get(0).get(1)).name, + path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, + path(workflow.out.vcf.get(0).get(1)).vcf.summary, + ).match() } + ) + } + } + + test("vcf, hgnc_ids - filter on hgnc ids") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz') + ]) + input[1] = Channel.of('3084') + .collectFile(name: 'hgnc_ids.txt') + .map { file -> [ [ id: 'hgnc_ids' ], file ] } + input[2] = false + input[3] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.versions, + file(workflow.out.tbi.get(0).get(1)).name, + path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, + path(workflow.out.vcf.get(0).get(1)).vcf.summary, + ).match() } + ) + } + } + + test("vcf, hgnc_ids - filter on hgnc ids and expression") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz') + ]) + input[1] = Channel.of('3084') + .collectFile(name: 'hgnc_ids.txt') + .map { file -> [ [ id: 'hgnc_ids' ], file ] } + input[2] = true + input[3] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.versions, + file(workflow.out.tbi.get(0).get(1)).name, + path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, + path(workflow.out.vcf.get(0).get(1)).vcf.summary, + ).match() } + ) + } + } + + test("vcf, hgnc_ids - filter on hgnc ids and expression - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz') + ]) + input[1] = Channel.of('3084') + .collectFile(name: 'hgnc_ids.txt') + .map { file -> [ [ id: 'hgnc_ids' ], file ] } + input[2] = true + input[3] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + +} \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap new file mode 100644 index 000000000..731a41068 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap @@ -0,0 +1,103 @@ +{ + "vcf, hgnc_ids - filter on hgnc ids": { + "content": [ + [ + "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", + "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f" + ], + "test.vcf.gz.tbi", + "18e010447bd23a05a202d44daf66bcd2", + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-29T09:51:55.795875" + }, + "vcf, hgnc_ids - filter on hgnc ids and expression": { + "content": [ + [ + "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", + "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", + "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + ], + "test.vcf.gz.tbi", + "18e010447bd23a05a202d44daf66bcd2", + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-29T09:52:06.507756" + }, + "vcf, hgnc_ids - filter on expression": { + "content": [ + [ + "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + ], + "test_filtered.vcf.gz.tbi", + "9236236d782191442193a20355604927", + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=37, phased=false, phasedAutodetect=false]" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-19T16:47:44.418033098" + }, + "vcf, hgnc_ids - filter on hgnc ids and expression - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", + "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", + "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", + "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", + "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-29T09:52:17.525437" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config new file mode 100644 index 000000000..49d12aa8f --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: 'ENSEMBLVEP_FILTERVEP' { + ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } + } + + withName: 'BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_filtered" } + ext.args = '-e "swegenAF>0.1" --no-version --output-type z --write-index=tbi' + } +} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 531dc27ec..04c20c22d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -54,10 +54,6 @@ include { CALL_MOBILE_ELEMENTS } from '../subworkf include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' include { CALL_SNV } from '../subworkflows/local/call_snv' include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_ME } from '../subworkflows/local/generate_clinical_set.nf' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_MT } from '../subworkflows/local/generate_clinical_set' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/local/generate_clinical_set' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_SV } from '../subworkflows/local/generate_clinical_set' include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' include { GENS } from '../subworkflows/local/gens' include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' @@ -68,6 +64,10 @@ include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkf include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 0c6a8439ed5c90558b29ffc09d7ae7ccc2f2c602 Mon Sep 17 00:00:00 2001 From: peterpru Date: Tue, 7 Oct 2025 08:25:32 +0200 Subject: [PATCH 046/872] add to workflow and conf --- .../vcf_filter_bcftools_ensemblvep.config | 100 ++++++++++++++++++ subworkflows/local/generate_clinical_set.nf | 40 ------- workflows/raredisease.nf | 54 +++++----- 3 files changed, 129 insertions(+), 65 deletions(-) create mode 100644 conf/modules/vcf_filter_bcftools_ensemblvep.config delete mode 100644 subworkflows/local/generate_clinical_set.nf diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_ensemblvep.config new file mode 100644 index 000000000..a2322976f --- /dev/null +++ b/conf/modules/vcf_filter_bcftools_ensemblvep.config @@ -0,0 +1,100 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +// +// Filter out clinical and research variants +// + +// SNVs + +process { + withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_sv_${meta.set}" } + ext.args = { [ + '--output-type z', + '--write-index=tbi', + ].join(" ") } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:ENSEMBLVEP_FILTERVEP' { + ext.prefix = { "${meta.id}_snv_${meta.set}" } + ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:TABIX_BGZIPTABIX' { + ext.prefix = { "${meta.id}_snv_${meta.set}" } + ext.args2 = = { "--tbi -p vcf" } + } +} + +// SVs + +process { + withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_sv_${meta.set}" } + ext.args = { [ + '--output-type z', + '--write-index=tbi', + ].join(" ") } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:ENSEMBLVEP_FILTERVEP' { + ext.prefix = { "${meta.id}_sv_${meta.set}" } + ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:TABIX_BGZIPTABIX' { + ext.prefix = { "${meta.id}_sv_${meta.set}" } + ext.args2 = = { "--tbi -p vcf" } + } +} + +// MT variants + +process { + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_mt_${meta.set}" } + ext.args = { "-Oz -i 'AF>0.05'" } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:ENSEMBLVEP_FILTERVEP' { + ext.prefix = { "${meta.id}_mt_filtervep_${meta.set}" } + ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:TABIX_BGZIPTABIX' { + ext.prefix = { "${meta.id}_mt_${meta.set}" } + ext.args2 = = { "--tbi -p vcf" } + } +} + +// ME variants +process { + withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_me_${meta.set}" } + ext.args = { [ + '--output-type z', + '--write-index=tbi', + ].join(" ") } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:ENSEMBLVEP_FILTERVEP' { + ext.prefix = { "${meta.id}_me_${meta.set}" } + ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } + } + + withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:TABIX_BGZIPTABIX' { + ext.prefix = { "${meta.id}_me_${meta.set}" } + ext.args2 = = { "--tbi -p vcf" } + } +} diff --git a/subworkflows/local/generate_clinical_set.nf b/subworkflows/local/generate_clinical_set.nf deleted file mode 100644 index 3ed94ad63..000000000 --- a/subworkflows/local/generate_clinical_set.nf +++ /dev/null @@ -1,40 +0,0 @@ -// -// Generarte clinical set of variants -// - -include { ENSEMBLVEP_FILTERVEP } from '../../modules/nf-core/ensemblvep/filtervep' -include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip' -include { BCFTOOLS_FILTER } from '../../modules/nf-core/bcftools/filter' - -workflow GENERATE_CLINICAL_SET { - take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_hgnc_ids // channel: [mandatory] [ val(hgnc_ids) ] - val_ismt // value: if mitochondria, set to true - - main: - ch_versions = Channel.empty() - - ENSEMBLVEP_FILTERVEP( - ch_vcf, - ch_hgnc_ids - ) - .output - .set { ch_filtervep_out } - - if (val_ismt) { - BCFTOOLS_FILTER (ch_filtervep_out.map { meta, vcf -> return [meta, vcf, []]}) - ch_clinical = BCFTOOLS_FILTER.out.vcf - ch_versions = ch_versions.mix( BCFTOOLS_FILTER.out.versions ) - } else { - TABIX_BGZIP( ch_filtervep_out ) - ch_clinical = TABIX_BGZIP.out.output - ch_versions = ch_versions.mix( TABIX_BGZIP.out.versions ) - } - - ch_versions = ch_versions.mix( ENSEMBLVEP_FILTERVEP.out.versions ) - - emit: - vcf = ch_clinical // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] -} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 04c20c22d..123756cd3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -64,10 +64,10 @@ include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkf include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -514,15 +514,15 @@ workflow RAREDISEASE { .set { ch_clin_research_snv_vcf } ch_clinical_snv_vcf = Channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { - GENERATE_CLINICAL_SET_SNV( + if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('vcf_filter_bcftools_ensemblvep'))) { ch_clin_research_snv_vcf.clinical, ch_hgnc_ids, - false + true, + true ) - .vcf + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV.out.vcf .set { ch_clinical_snv_vcf } - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions) + ch_versions = ch_versions.mix(VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV.out.versions) } ch_ann_csq_snv_in = ch_clinical_snv_vcf.mix(ch_clin_research_snv_vcf.research) @@ -581,15 +581,17 @@ workflow RAREDISEASE { .set { ch_clin_research_mt_vcf } ch_clinical_mtsnv_vcf = Channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { - GENERATE_CLINICAL_SET_MT( + if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('vcf_filter_bcftools_ensemblvep'))) { + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT( ch_clin_research_mt_vcf.clinical, ch_hgnc_ids, - true + true, + false ) - .vcf - .set { ch_clinical_mtsnv_vcf } - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions) + VCF_FILTER_BCFTOOLS_ENSEMBLVEP.out.vcf + .set { ch_clinical_mtsnv_vcf } + + ch_versions = ch_versions.mix( VCF_FILTER_BCFTOOLS_ENSEMBLVEP.out.versions ) } ch_ann_csq_mtsnv_in = ch_clinical_mtsnv_vcf.mix(ch_clin_research_mt_vcf.research) @@ -671,15 +673,16 @@ workflow RAREDISEASE { .set { ch_clin_research_sv_vcf } ch_clinical_sv_vcf = Channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { - GENERATE_CLINICAL_SET_SV( + if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('vcf_filter_bcftools_ensemblvep'))) { + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV( ch_clin_research_sv_vcf.clinical, ch_hgnc_ids, - false + true, + true ) - .vcf + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV.out.vcf .set { ch_clinical_sv_vcf } - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SV.out.versions) + ch_versions = ch_versions.mix(VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV.out.versions) } ch_ann_csq_sv_in = ch_clinical_sv_vcf.mix(ch_clin_research_sv_vcf.research) @@ -747,15 +750,16 @@ workflow RAREDISEASE { .set { ch_clin_research_me_vcf } ch_clinical_me_vcf = Channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { - GENERATE_CLINICAL_SET_ME( + if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('vcf_filter_bcftools_ensemblvep'))) { + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME( ch_clin_research_me_vcf.clinical, ch_hgnc_ids, - false + true, + true ) - .vcf + VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME.out.vcf .set { ch_clinical_me_vcf } - ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_ME.out.versions ) + ch_versions = ch_versions.mix( VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME.out.versions ) } ch_ann_csq_me_in = ch_clinical_me_vcf.mix(ch_clin_research_me_vcf.research) From db43d593769b0b50ed3838360a7ed2685585f8af Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:59:54 +0200 Subject: [PATCH 047/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 18715048a..590eb4aa7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - - Fixed inconsistencies in JSON schema #714 + - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) ### Parameters From 173090822dfa6363e46db93ab1b445bbc1db55aa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:21:42 +0200 Subject: [PATCH 048/872] prettier fix --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 590eb4aa7..0e9fc4def 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - +- Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) + ### Parameters | Old parameter | New parameter | From c27e556dba681f14ea809eeac0ad1399801986a2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:54:35 +0200 Subject: [PATCH 049/872] keep the suffix of the published file constant --- conf/modules/call_mobile_elements.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules/call_mobile_elements.config b/conf/modules/call_mobile_elements.config index 6a35bd075..b3ab67cd0 100644 --- a/conf/modules/call_mobile_elements.config +++ b/conf/modules/call_mobile_elements.config @@ -44,12 +44,12 @@ process { withName: '.*CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME' { ext.args = { '--output-type z --allow-overlaps' } - ext.prefix = { "${meta.id}_mobile_elements" } + ext.prefix = { "${meta.id}_mobile_elements_concat" } } withName: '.*CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME' { ext.args = { '--bnd_distance 150 --overlap 0.5' } - ext.prefix = { "${meta.id}_mobile_elements_merged" } + ext.prefix = { "${meta.id}_mobile_elements" } publishDir = [ path: { "${params.outdir}/call_mobile_elements" }, mode: params.publish_dir_mode, From 05af526a29a6b643fc816126632573508e43533a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 9 Oct 2025 13:58:54 +0200 Subject: [PATCH 050/872] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e9fc4def..8a7d0378c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) + ### `Fixed` - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) From 77959c3ded61177e1bbcc156745d2deeb5785d5e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 10 Oct 2025 13:40:32 +0200 Subject: [PATCH 051/872] nf-core mscsq mspli --- conf/modules/annotate_consequence_pli.config | 34 ++++------ modules.json | 10 +++ .../local/add_most_severe_consequence/main.nf | 44 ------------- modules/local/add_most_severe_pli/main.nf | 43 ------------ .../custom/addmostsevereconsequence/main.nf | 61 +++++++++++++++++ .../custom/addmostsevereconsequence/meta.yml | 66 +++++++++++++++++++ .../usr/bin}/add_most_severe_consequence.py | 1 + .../nf-core/custom/addmostseverepli/main.nf | 58 ++++++++++++++++ .../nf-core/custom/addmostseverepli/meta.yml | 56 ++++++++++++++++ .../resources/usr/bin}/add_most_severe_pli.py | 1 + nextflow.config | 3 + .../local/annotate_consequence_pli.nf | 26 ++++---- workflows/raredisease.nf | 20 +++--- 13 files changed, 296 insertions(+), 127 deletions(-) delete mode 100644 modules/local/add_most_severe_consequence/main.nf delete mode 100644 modules/local/add_most_severe_pli/main.nf create mode 100644 modules/nf-core/custom/addmostsevereconsequence/main.nf create mode 100644 modules/nf-core/custom/addmostsevereconsequence/meta.yml rename {bin => modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin}/add_most_severe_consequence.py (99%) create mode 100644 modules/nf-core/custom/addmostseverepli/main.nf create mode 100644 modules/nf-core/custom/addmostseverepli/meta.yml rename {bin => modules/nf-core/custom/addmostseverepli/resources/usr/bin}/add_most_severe_pli.py (99%) diff --git a/conf/modules/annotate_consequence_pli.config b/conf/modules/annotate_consequence_pli.config index 21e2e8358..4175691d0 100644 --- a/conf/modules/annotate_consequence_pli.config +++ b/conf/modules/annotate_consequence_pli.config @@ -14,61 +14,55 @@ process { - withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_CSQ' { + withName: '.*ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE' { ext.prefix = { "${meta.id}_sv_csq_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_SV:ADD_MOST_SEVERE_PLI' { + withName: '.*ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI' { ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_SV:TABIX_BGZIPTABIX' { - ext.prefix = { "${meta.id}_sv_csq_pli_${meta.set}" } - } } process { - withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_CSQ' { + withName: '.*ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE' { ext.prefix = { "${meta.id}_snv_csq_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_SNV:ADD_MOST_SEVERE_PLI' { + withName: '.*ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI' { ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_SNV:TABIX_BGZIPTABIX' { - ext.prefix = { "${meta.id}_snv_csq_pli_${meta.set}" } - } } process { - withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_CSQ' { + withName: '.*ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE' { ext.prefix = { "${meta.id}_mt_csq_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_MT:ADD_MOST_SEVERE_PLI' { + withName: '.*ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI' { ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_MT:TABIX_BGZIPTABIX' { - ext.prefix = { "${meta.id}_mt_csq_pli_${meta.set}" } - } } process { - withName: '.*ANN_CSQ_PLI_ME:ADD_MOST_SEVERE_CSQ' { + withName: '.*ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE' { ext.prefix = { "${meta.id}_me_csq_${meta.set}" } } - withName: '.*ANN_CSQ_PLI_ME:ADD_MOST_SEVERE_PLI' { + withName: '.*ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI' { ext.prefix = { "${meta.id}_me_pli_${meta.set}" } + publishDir = [ + path: { "${params.outdir}/annotate_mobile_elements" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } - - withName: '.*ANN_CSQ_PLI_ME:TABIX_BGZIPTABIX' { - ext.prefix = { "${meta.id}_me_annotated_${meta.set}" } + withName: '.*ANN_CSQ_PLI_ME:TABIX_TABIX' { publishDir = [ path: { "${params.outdir}/annotate_mobile_elements" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 0024877ca..6d793a17b 100644 --- a/modules.json +++ b/modules.json @@ -116,6 +116,16 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "custom/addmostsevereconsequence": { + "branch": "master", + "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "installed_by": ["modules"] + }, + "custom/addmostseverepli": { + "branch": "master", + "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "installed_by": ["modules"] + }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69", diff --git a/modules/local/add_most_severe_consequence/main.nf b/modules/local/add_most_severe_consequence/main.nf deleted file mode 100644 index dd9975219..000000000 --- a/modules/local/add_most_severe_consequence/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process ADD_MOST_SEVERE_CSQ { - tag "$meta.id" - label 'process_low' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - tuple val(meta), path(vcf) - path (variant_consequences) - - output: - tuple val(meta), path("*.vcf") , emit: vcf - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - add_most_severe_consequence.py --file_in ${vcf} --file_out ${prefix}.vcf --variant_csq ${variant_consequences} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: v1.1 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}_csq.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: v1.1 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/local/add_most_severe_pli/main.nf b/modules/local/add_most_severe_pli/main.nf deleted file mode 100644 index e1bfe67db..000000000 --- a/modules/local/add_most_severe_pli/main.nf +++ /dev/null @@ -1,43 +0,0 @@ -process ADD_MOST_SEVERE_PLI { - tag "$meta.id" - label 'process_low' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - tuple val(meta), path(vcf) - - output: - tuple val(meta), path("*.vcf") , emit: vcf - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - add_most_severe_pli.py --file_in ${vcf} --file_out ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: v1.1 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}_pli.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: v1.1 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/addmostsevereconsequence/main.nf b/modules/nf-core/custom/addmostsevereconsequence/main.nf new file mode 100644 index 000000000..c4dacf3e9 --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/main.nf @@ -0,0 +1,61 @@ +process CUSTOM_ADDMOSTSEVERECONSEQUENCE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cbeb20c898a76bec809629320ece9e1f84a3e355e96568bfbe14b9f411bdf3e7/data': + 'community.wave.seqera.io/library/htslib_python:9c6265e98ef06930' }" + + input: + tuple val(meta), path(vcf) + tuple val(meta2), path(variant_consequences) + + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. + + """ + add_most_severe_consequence.py \\ + $args \\ + --file_in $vcf \\ + --file_out ${prefix}.vcf \\ + --variant_csq $variant_consequences + + bgzip \\ + $args2 \\ + --threads ${task.cpus} \\ + ${prefix}.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_consequence: $VERSION + bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. + """ + echo | gzip > ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_consequence: $VERSION + bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/custom/addmostsevereconsequence/meta.yml b/modules/nf-core/custom/addmostsevereconsequence/meta.yml new file mode 100644 index 000000000..07f69da7e --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/meta.yml @@ -0,0 +1,66 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_addmostsevereconsequence" +description: Annotate a VEP annotated VCF with the most severe consequence field +keywords: + - annotation + - vep + - consequence + - vcf +tools: + - "custom": + description: "Custom module to annotate a VEP annotated VCF with the most severe + consequence field" + tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostsevereconsequence/main.nf" + licence: ["MIT"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: VEP annotated VCF file + pattern: "*.{vcf,vcf.gz}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - variant_consequences: + type: file + description: File with VEP variant consequences, one per line. + pattern: "*" + + ontologies: [] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Annotated VCF file + pattern: "*.vcf.gz" + + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@ramprasadn" + - "@fellen31" +maintainers: + - "@ramprasadn" + - "@fellen31" diff --git a/bin/add_most_severe_consequence.py b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py similarity index 99% rename from bin/add_most_severe_consequence.py rename to modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py index 78dcfb947..b3aa22a0c 100755 --- a/bin/add_most_severe_consequence.py +++ b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py @@ -68,6 +68,7 @@ def construct_most_severe_consequence_info( columns = line.strip().split() info_fields = columns[7].split(";") + transcripts = [] for field in info_fields: if field.startswith("CSQ="): transcripts = field.split("CSQ=")[1].split(",") diff --git a/modules/nf-core/custom/addmostseverepli/main.nf b/modules/nf-core/custom/addmostseverepli/main.nf new file mode 100644 index 000000000..0d252c046 --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/main.nf @@ -0,0 +1,58 @@ +process CUSTOM_ADDMOSTSEVEREPLI { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cb/cbeb20c898a76bec809629320ece9e1f84a3e355e96568bfbe14b9f411bdf3e7/data': + 'community.wave.seqera.io/library/htslib_python:9c6265e98ef06930' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. + + """ + add_most_severe_pli.py \\ + $args \\ + --file_in $vcf \\ + --file_out ${prefix}.vcf + + bgzip \\ + $args2 \\ + --threads ${task.cpus} \\ + ${prefix}.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_pli: $VERSION + bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. + """ + echo | gzip > ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + add_most_severe_pli: $VERSION + bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/custom/addmostseverepli/meta.yml b/modules/nf-core/custom/addmostseverepli/meta.yml new file mode 100644 index 000000000..f69423822 --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/meta.yml @@ -0,0 +1,56 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_addmostseverepli" +description: Annotate a VEP annotated VCF with the most severe pLi field +keywords: + - annotation + - vep + - pli + - vcf +tools: + - "custom": + description: "Custom module to annotate a VEP annotated VCF with the most severe + pLi field" + tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostseverepli/main.nf" + licence: ["MIT"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: VEP annotated VCF file + pattern: "*.{vcf,vcf.gz}" + + ontologies: [] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Annotated VCF file + pattern: "*.vcf.gz" + + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@ramprasadn" + - "@fellen31" +maintainers: + - "@ramprasadn" + - "@fellen31" diff --git a/bin/add_most_severe_pli.py b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py similarity index 99% rename from bin/add_most_severe_pli.py rename to modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py index abb1f5b7b..6ef40515a 100755 --- a/bin/add_most_severe_pli.py +++ b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py @@ -46,6 +46,7 @@ def construct_most_severe_pli_info(line: str, pli_ind: int) -> list: columns = line.strip().split() info_fields = columns[7].split(";") + transcripts = [] for field in info_fields: if field.startswith("CSQ="): transcripts = field.split("CSQ=")[1].split(",") diff --git a/nextflow.config b/nextflow.config index 6baef5753..02aa007f1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -272,6 +272,9 @@ profiles { } } +// Stage locally scoped binary scripts +nextflow.enable.moduleBinaries = true + // Load nf-core custom profiles from different institutions // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index 5b625a7b2..333be66b7 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -2,30 +2,32 @@ // A subworkflow to add most severe consequence and pli to a vep annotated vcf // -include { ADD_MOST_SEVERE_CSQ } from '../../modules/local/add_most_severe_consequence' -include { ADD_MOST_SEVERE_PLI } from '../../modules/local/add_most_severe_pli' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { CUSTOM_ADDMOSTSEVERECONSEQUENCE } from '../../modules/nf-core/custom/addmostsevereconsequence' +include { CUSTOM_ADDMOSTSEVEREPLI } from '../../modules/nf-core/custom/addmostseverepli' +include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CSQ_PLI { take: ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_variant_consequences // channel: [mandatory] [ path(consequences) ] + val_index // bool main: ch_versions = Channel.empty() - ADD_MOST_SEVERE_CSQ (ch_vcf, ch_variant_consequences) + CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) - ADD_MOST_SEVERE_PLI (ADD_MOST_SEVERE_CSQ.out.vcf) + CUSTOM_ADDMOSTSEVEREPLI (CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.vcf) - TABIX_BGZIPTABIX (ADD_MOST_SEVERE_PLI.out.vcf) + if (val_index) { + TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) + ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) + } - ch_versions = ch_versions.mix(ADD_MOST_SEVERE_CSQ.out.versions) - ch_versions = ch_versions.mix(ADD_MOST_SEVERE_PLI.out.versions) - ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) + ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.versions) + ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVEREPLI.out.versions) emit: - vcf_ann = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, vcf ] } // channel: [ val(meta), path(vcf) ] - tbi_ann = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, tbi -> return [ meta, tbi ] } // channel: [ val(meta), path(tbi) ] - versions = ch_versions // channel: [ path(versions.yml) ] + vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 531dc27ec..535386e35 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -221,10 +221,10 @@ workflow RAREDISEASE { ch_target_intervals = ch_references.target_intervals ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() : Channel.value([[],[]]) - ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).collect() - : Channel.value([]) - ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).collect() - : Channel.value([]) + ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() + : Channel.value([[],[]]) + ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() + : Channel.value([[],[]]) ch_vcfanno_extra = ch_references.vcfanno_extra ch_vcfanno_resources = params.vcfanno_resources ? Channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() : Channel.value([]) @@ -529,7 +529,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SNV ( ch_ann_csq_snv_in, - ch_variant_consequences_snv + ch_variant_consequences_snv, + false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) @@ -596,7 +597,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_MT( ch_ann_csq_mtsnv_in, - ch_variant_consequences_snv + ch_variant_consequences_snv, + false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions) @@ -686,7 +688,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SV ( ch_ann_csq_sv_in, - ch_variant_consequences_sv + ch_variant_consequences_sv, + false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions) @@ -762,7 +765,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_ME( ch_ann_csq_me_in, - ch_variant_consequences_sv + ch_variant_consequences_sv, + true ) ch_versions = ch_versions.mix( ANN_CSQ_PLI_ME.out.versions ) From 65a6964fea309a21d4bab9d9098c2d8f65fa02e3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 10 Oct 2025 13:44:53 +0200 Subject: [PATCH 052/872] update changelog --- CHANGELOG.md | 1 + conf/test.config | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a7d0378c..4f3abd9f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) +- Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) ### `Fixed` diff --git a/conf/test.config b/conf/test.config index 7958cf363..0c01b1035 100644 --- a/conf/test.config +++ b/conf/test.config @@ -37,7 +37,7 @@ params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' - skip_subworkflows = "mt_annotation,mt_subsample,me_calling,me_annotation,sv_annotation" + skip_subworkflows = "mt_annotation,mt_subsample,sv_annotation" input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' From 092def21f645927947c94db36d0f1fd1487d2947 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 10 Oct 2025 14:13:01 +0200 Subject: [PATCH 053/872] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a5ac166e1..25e4bfa92 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717) + ### `Changed` ### `Fixed` From f26b8d7ceff267f7505bdde286bd78c5d08ddfb2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 10 Oct 2025 19:06:09 +0200 Subject: [PATCH 054/872] update snaps --- tests/default.nf.test.snap | 81 +++++++++++++++++++++++++------ tests/test_bam.nf.test.snap | 27 +++++------ tests/test_singleton.nf.test.snap | 27 +++++------ 3 files changed, 90 insertions(+), 45 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4342097b1..6801a9508 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,16 +1,8 @@ { "-profile test": { "content": [ - 298, + 817, { - "ADD_MOST_SEVERE_CSQ": { - "add_most_severe_consequence": "v1.1", - "python": "3.8.3" - }, - "ADD_MOST_SEVERE_PLI": { - "add_most_severe_pli": "v1.1", - "python": "3.8.3" - }, "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, @@ -20,21 +12,33 @@ "BCFTOOLS_CONCAT": { "bcftools": 1.2 }, + "BCFTOOLS_CONCAT_ME": { + "bcftools": 1.2 + }, "BCFTOOLS_MERGE_MT": { "bcftools": 1.2 }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.2 }, + "BCFTOOLS_REHEADER_ME": { + "bcftools": 1.2 + }, "BCFTOOLS_ROH": { "bcftools": 1.2 }, + "BCFTOOLS_SORT_ME": { + "bcftools": 1.2 + }, "BCFTOOLS_VIEW": { "bcftools": 1.2 }, "BCFTOOLS_VIEW_CNVNATOR": { "bcftools": 1.2 }, + "BCFTOOLS_VIEW_FILTER": { + "bcftools": 1.2 + }, "BCFTOOLS_VIEW_MANTA": { "bcftools": 1.2 }, @@ -107,12 +111,23 @@ "create_pedigree_file": "v1.0", "python": "3.8.3" }, + "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { + "add_most_severe_consequence": 1.1, + "bgzip": 1.21 + }, + "CUSTOM_ADDMOSTSEVEREPLI": { + "add_most_severe_pli": 1.1, + "bgzip": 1.21 + }, "DEEPVARIANT": { "deepvariant": "1.8.0" }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, + "ENSEMBLVEP_ME": { + "ensemblvep": 110.0 + }, "ENSEMBLVEP_SNV": { "ensemblvep": 110.0 }, @@ -198,6 +213,12 @@ "MARKDUPLICATES": { "picard": "3.3.0" }, + "ME_INDEX_SPLIT_ALIGNMENT": { + "samtools": 1.21 + }, + "ME_SPLIT_ALIGNMENT": { + "samtools": 1.21 + }, "MOSDEPTH": { "mosdepth": "0.3.8" }, @@ -225,6 +246,9 @@ "PICARD_MARKDUPLICATES_MT": { "picard": "3.3.0" }, + "PICARD_SORTVCF": { + "picard": "3.3.0" + }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.2 }, @@ -240,6 +264,12 @@ "RENAME_BAM": { "coreutils": 8.31 }, + "RETROSEQ_CALL": { + "retroseq_call": 1.5 + }, + "RETROSEQ_DISCOVER": { + "retroseq_discover": 1.5 + }, "RHOCALL_ANNOTATE": { "rhocall": "0.5.1" }, @@ -300,6 +330,10 @@ "svdb": "2.8.2", "bcftools": 1.21 }, + "SVDB_MERGE_ME": { + "svdb": "2.8.2", + "bcftools": 1.21 + }, "SVDB_MERGE_REPEATS": { "svdb": "2.8.2", "bcftools": 1.21 @@ -308,6 +342,9 @@ "svdb": "2.8.2", "bcftools": 1.21 }, + "SVDB_QUERY_DB": { + "svdb": "2.8.2" + }, "TABIX_ANNOTATE": { "tabix": 1.2 }, @@ -320,9 +357,6 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, - "TABIX_BGZIPTABIX": { - "tabix": 1.2 - }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -335,6 +369,12 @@ "TABIX_GNOMAD_AF": { "tabix": 1.2 }, + "TABIX_ME": { + "tabix": 1.2 + }, + "TABIX_ME_SPLIT": { + "tabix": 1.2 + }, "TABIX_PBT": { "tabix": 1.2 }, @@ -395,6 +435,13 @@ "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", "alignment/slowlycivilbuck_sorted_md.bam", "alignment/slowlycivilbuck_sorted_md.bam.bai", + "annotate_mobile_elements", + "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", + "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", + "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", + "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz", + "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.csi", + "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", "annotate_snv/genome/earlycasualcaiman_rhocallviz", @@ -417,6 +464,10 @@ "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.csi", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", "call_snv", "call_snv/genome", "call_snv/genome/justhusky_snv.vcf.gz", @@ -575,9 +626,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-06-25T20:06:21.438307947" + "timestamp": "2025-10-10T18:52:51.501264357" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 1f2fe7825..884ca1953 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,16 +1,8 @@ { "-profile test_bam": { "content": [ - 282, + 280, { - "ADD_MOST_SEVERE_CSQ": { - "add_most_severe_consequence": "v1.1", - "python": "3.8.3" - }, - "ADD_MOST_SEVERE_PLI": { - "add_most_severe_pli": "v1.1", - "python": "3.8.3" - }, "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, @@ -103,6 +95,14 @@ "create_pedigree_file": "v1.0", "python": "3.8.3" }, + "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { + "add_most_severe_consequence": 1.1, + "bgzip": 1.21 + }, + "CUSTOM_ADDMOSTSEVEREPLI": { + "add_most_severe_pli": 1.1, + "bgzip": 1.21 + }, "DEEPVARIANT": { "deepvariant": "1.8.0" }, @@ -301,9 +301,6 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, - "TABIX_BGZIPTABIX": { - "tabix": 1.2 - }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -540,9 +537,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-06-25T20:08:34.973300629" + "timestamp": "2025-10-10T18:57:59.891726639" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 78db775d8..fbe513850 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,16 +1,8 @@ { "-profile test_singleton": { "content": [ - 152, + 150, { - "ADD_MOST_SEVERE_CSQ": { - "add_most_severe_consequence": "v1.1", - "python": "3.8.3" - }, - "ADD_MOST_SEVERE_PLI": { - "add_most_severe_pli": "v1.1", - "python": "3.8.3" - }, "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, @@ -98,6 +90,14 @@ "create_pedigree_file": "v1.0", "python": "3.8.3" }, + "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { + "add_most_severe_consequence": 1.1, + "bgzip": 1.21 + }, + "CUSTOM_ADDMOSTSEVEREPLI": { + "add_most_severe_pli": 1.1, + "bgzip": 1.21 + }, "DEEPVARIANT": { "deepvariant": "1.8.0" }, @@ -308,9 +308,6 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, - "TABIX_BGZIPTABIX": { - "tabix": 1.2 - }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -463,9 +460,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-06-25T20:11:32.593010906" + "timestamp": "2025-10-10T19:03:47.493506549" } } \ No newline at end of file From 7ccdccfe8e7ba7324dec3027f4b293943fb8a29c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Oct 2025 10:57:03 +0200 Subject: [PATCH 055/872] review suggestions --- CHANGELOG.md | 1 + .../local/call_repeat_expansions/tests/main.nf.test | 6 ++---- subworkflows/local/qc_bam/tests/main.nf.test | 2 -- subworkflows/local/qc_bam/tests/nextflow.config | 2 +- 4 files changed, 4 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa1e12440..5e296f367 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717) +- Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) ### `Changed` diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index d6f4967bd..f797174c5 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -10,9 +10,6 @@ nextflow_workflow { test("CALL_REPEAT_EXPANSIONS") { when { - params { - outdir = "tests/results" - } workflow { """ input[0] = Channel.of( @@ -33,7 +30,8 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5 + path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, + path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index ee76b76bb..673c3d669 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -13,7 +13,6 @@ nextflow_workflow { params { aligner = "bwamem2" skip_tools = null - outdir = "tests/results" } workflow { """ @@ -91,7 +90,6 @@ nextflow_workflow { params { aligner = "sentieon" skip_tools = null - outdir = "tests/results" } workflow { """ diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config index 72c51555d..bd4ae2d5d 100644 --- a/subworkflows/local/qc_bam/tests/nextflow.config +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -36,7 +36,7 @@ process { withName: '.*QC_BAM:NGSBITS_SAMPLEGENDER' { // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) } ext.prefix = { "${meta.id}_ngsbits_sex" } } From 4bec5e8da078f7344b2f371ac60b59ad9497ad0a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Oct 2025 14:08:36 +0200 Subject: [PATCH 056/872] update snaps --- .../local/call_repeat_expansions/tests/main.nf.test.snap | 9 +++++---- subworkflows/local/qc_bam/tests/main.nf.test.snap | 6 +++--- tests/default.nf.test.snap | 8 ++++---- 3 files changed, 12 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 35360c9bd..da37ecae6 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -1,12 +1,13 @@ { "CALL_REPEAT_EXPANSIONS": { "content": [ - "5f06dccb7fc4ad3758bc23e3232f9abb" + "5f06dccb7fc4ad3758bc23e3232f9abb", + "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-07-10T19:44:19.538636651" + "timestamp": "2025-10-14T14:06:58.984015651" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 74762c958..0f597d1c6 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -152,9 +152,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-07-10T16:17:02.204969887" + "timestamp": "2025-10-14T14:04:26.353165287" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b9479928a..50e6e9a7e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -22,7 +22,7 @@ "bcftools": 1.21 }, "BCFTOOLS_REHEADER_ME": { - "bcftools": 1.2 + "bcftools": 1.21 }, "BCFTOOLS_ROH": { "bcftools": 1.2 @@ -370,10 +370,10 @@ "tabix": 1.21 }, "TABIX_ME": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_ME_SPLIT": { - "tabix": 1.2 + "tabix": 1.21 }, "TABIX_PBT": { "tabix": 1.2 @@ -629,6 +629,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-10T18:52:51.501264357" + "timestamp": "2025-10-14T11:10:17.686286914" } } \ No newline at end of file From 667a36a9c89b49253a5342dff59c946a6c8c0a64 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Oct 2025 14:18:56 +0200 Subject: [PATCH 057/872] update declaration --- CHANGELOG.md | 1 + modules/local/add_varcallername_to_bed/main.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa1e12440..c00b219ec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) +- Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) ### Parameters diff --git a/modules/local/add_varcallername_to_bed/main.nf b/modules/local/add_varcallername_to_bed/main.nf index 11190c2ac..566402559 100644 --- a/modules/local/add_varcallername_to_bed/main.nf +++ b/modules/local/add_varcallername_to_bed/main.nf @@ -2,7 +2,7 @@ process ADD_VARCALLER_TO_BED { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" + conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : 'biocontainers/tabix:1.11--hdfd78af_0' }" From bc39b94f9b9384e145269a94cea533af27f4503f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Oct 2025 14:21:36 +0200 Subject: [PATCH 058/872] change to dev From f1ffabaa7dace02b5ac36691b60d31a6880f58bd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Oct 2025 21:20:29 +0200 Subject: [PATCH 059/872] draft --- conf/modules/generate_clinical_set.config | 72 ------------------- .../vcf_filter_bcftools_ensemblvep.config | 37 ++-------- modules/local/create_hgncids_file/main.nf | 2 +- nextflow.config | 2 +- nextflow_schema.json | 2 +- workflows/raredisease.nf | 7 +- 6 files changed, 11 insertions(+), 111 deletions(-) delete mode 100644 conf/modules/generate_clinical_set.config diff --git a/conf/modules/generate_clinical_set.config b/conf/modules/generate_clinical_set.config deleted file mode 100644 index 143e0a6d8..000000000 --- a/conf/modules/generate_clinical_set.config +++ /dev/null @@ -1,72 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. - ext.when = Conditional clause ----------------------------------------------------------------------------------------- -*/ - -// -// Filter out clinical and research variants -// - -// SNVs - -process { - withName: '.*:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP' { - ext.prefix = { "${meta.id}_snv_${meta.set}" } - ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } - } - - withName: '.*:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIP' { - ext.prefix = { "${meta.id}_snv_${meta.set}" } - } -} - -// SVs - -process { - withName: '.*:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP' { - ext.prefix = { "${input.simpleName}_sv_${meta.set}" } - ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } - } - - withName: '.*:GENERATE_CLINICAL_SET_SV:TABIX_BGZIP' { - ext.prefix = { "${meta.id}_sv_${meta.set}" } - } -} - -// MT variants - -process { - withName: '.*:GENERATE_CLINICAL_SET_MT:ENSEMBLVEP_FILTERVEP' { - ext.prefix = { "${meta.id}_mt_filtervep_${meta.set}" } - ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } - } - - withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_FILTER' { - ext.prefix = { "${meta.id}_mt_${meta.set}" } - ext.args = { "-Oz -i 'AF>0.05'" } - } - - withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIP' { - ext.prefix = { "${meta.id}_mt_${meta.set}" } - } -} - -// ME variants -process{ - withName: '.*:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP' { - ext.prefix = { "${meta.id}_me_${meta.set}" } - ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } - } - - withName: '.*:GENERATE_CLINICAL_SET_ME:TABIX_BGZIP' { - ext.prefix = { "${meta.id}_me_${meta.set}" } - } -} diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_ensemblvep.config index a2322976f..43517b7b6 100644 --- a/conf/modules/vcf_filter_bcftools_ensemblvep.config +++ b/conf/modules/vcf_filter_bcftools_ensemblvep.config @@ -18,14 +18,6 @@ // SNVs process { - withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:BCFTOOLS_VIEW' { - ext.prefix = { "${meta.id}_sv_${meta.set}" } - ext.args = { [ - '--output-type z', - '--write-index=tbi', - ].join(" ") } - } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_snv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } @@ -33,21 +25,13 @@ process { withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_snv_${meta.set}" } - ext.args2 = = { "--tbi -p vcf" } + ext.args2 = { "-p vcf" } } } // SVs process { - withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:BCFTOOLS_VIEW' { - ext.prefix = { "${meta.id}_sv_${meta.set}" } - ext.args = { [ - '--output-type z', - '--write-index=tbi', - ].join(" ") } - } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_sv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } @@ -55,7 +39,7 @@ process { withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_sv_${meta.set}" } - ext.args2 = = { "--tbi -p vcf" } + ext.args2 = { "-p vcf" } } } @@ -67,27 +51,14 @@ process { ext.args = { "-Oz -i 'AF>0.05'" } } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:ENSEMBLVEP_FILTERVEP' { - ext.prefix = { "${meta.id}_mt_filtervep_${meta.set}" } - ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } - } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_mt_${meta.set}" } - ext.args2 = = { "--tbi -p vcf" } + ext.args2 = { "-p vcf" } } } // ME variants process { - withName: '.*VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:BCFTOOLS_VIEW' { - ext.prefix = { "${meta.id}_me_${meta.set}" } - ext.args = { [ - '--output-type z', - '--write-index=tbi', - ].join(" ") } - } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_me_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } @@ -95,6 +66,6 @@ process { withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_me_${meta.set}" } - ext.args2 = = { "--tbi -p vcf" } + ext.args2 = { "-p vcf" } } } diff --git a/modules/local/create_hgncids_file/main.nf b/modules/local/create_hgncids_file/main.nf index a6e1abdb3..f842d6a2c 100644 --- a/modules/local/create_hgncids_file/main.nf +++ b/modules/local/create_hgncids_file/main.nf @@ -11,7 +11,7 @@ process CREATE_HGNCIDS_FILE { tuple val(meta), path(input) output: - path("*_reformatted.txt"), emit: txt + tuple val(meta), path("*_reformatted.txt"), emit: txt path "versions.yml" , emit: versions when: diff --git a/nextflow.config b/nextflow.config index 6baef5753..b114497d5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -472,7 +472,7 @@ includeConfig 'conf/modules/call_sv_tiddit.config' includeConfig 'conf/modules/postprocess_MT_calls.config' includeConfig 'conf/modules/call_mobile_elements.config' includeConfig 'conf/modules/annotate_mobile_elements.config' -includeConfig 'conf/modules/generate_clinical_set.config' +includeConfig 'conf/modules/vcf_filter_bcftools_ensemblvep.config' includeConfig 'conf/modules/variant_evaluation.config' includeConfig 'conf/modules/subsample_mt.config' includeConfig 'conf/modules/annotate_rhocallviz.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 8ece884bf..b1c8208a6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -585,7 +585,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified subworkflows.", "help_text": "Multiple subworkflows can be specified, separated by commas.", - "pattern": "^((me_calling|me_annotation|mt_annotation|mt_subsample|repeat_annotation|repeat_calling|snv_annotation|snv_calling|sv_annotation|sv_calling|generate_clinical_set)?,?)*(? Date: Wed, 15 Oct 2025 09:43:35 +0200 Subject: [PATCH 060/872] update snaps --- tests/default.nf.test.snap | 5 ++++- tests/test_bam.nf.test.snap | 5 ++++- tests/test_singleton.nf.test.snap | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6801a9508..6d6725b74 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -357,6 +357,9 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, + "TABIX_BGZIPTABIX": { + "tabix": 1.2 + }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -629,6 +632,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-10T18:52:51.501264357" + "timestamp": "2025-10-15T09:35:18.332397339" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 884ca1953..eacfe17bd 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -301,6 +301,9 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, + "TABIX_BGZIPTABIX": { + "tabix": 1.2 + }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -540,6 +543,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-10T18:57:59.891726639" + "timestamp": "2025-10-15T09:40:09.030137924" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index fbe513850..92133a9bf 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -308,6 +308,9 @@ "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, + "TABIX_BGZIPTABIX": { + "tabix": 1.2 + }, "TABIX_DBSNP": { "tabix": 1.2 }, @@ -463,6 +466,6 @@ "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-10T19:03:47.493506549" + "timestamp": "2025-10-15T09:43:13.720671267" } } \ No newline at end of file From 9fd8bb099b2e4f882b4fc7d4bc2d3bf04cba1a65 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 16 Oct 2025 13:39:02 +0000 Subject: [PATCH 061/872] Template update for nf-core/tools version 3.4.1 --- .devcontainer/devcontainer.json | 28 ++++---- .devcontainer/setup.sh | 13 ++++ .github/actions/nf-test/action.yml | 6 +- .github/workflows/awsfulltest.yml | 12 ++-- .github/workflows/awstest.yml | 12 ++-- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 6 +- .github/workflows/fix_linting.yml | 16 ++--- .github/workflows/linting.yml | 14 ++-- .github/workflows/linting_comment.yml | 2 +- .github/workflows/nf-test.yml | 9 +-- .github/workflows/release-announcements.yml | 7 ++ .../workflows/template-version-comment.yml | 2 +- .gitpod.yml | 10 --- .nf-core.yml | 2 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + README.md | 5 +- docs/usage.md | 2 +- main.nf | 5 +- modules.json | 8 +-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 18 +++--- modules/nf-core/multiqc/tests/tags.yml | 2 - nextflow.config | 64 ++++++------------- nextflow_schema.json | 12 ++++ ro-crate-metadata.json | 16 ++--- .../utils_nfcore_raredisease_pipeline/main.nf | 31 ++++++++- .../utils_nextflow_pipeline/tests/tags.yml | 2 - .../utils_nfcore_pipeline/tests/tags.yml | 2 - .../nf-core/utils_nfschema_plugin/main.nf | 40 ++++++++++-- .../utils_nfschema_plugin/tests/main.nf.test | 56 ++++++++++++++++ .../tests/nextflow.config | 4 +- tests/.nftignore | 3 +- tests/default.nf.test | 2 - 36 files changed, 267 insertions(+), 155 deletions(-) create mode 100755 .devcontainer/setup.sh delete mode 100644 .gitpod.yml delete mode 100644 modules/nf-core/multiqc/tests/tags.yml delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml delete mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b290e0901..97c8c97fe 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,20 +1,20 @@ { "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh new file mode 100755 index 000000000..e0b37e0cd --- /dev/null +++ b/.devcontainer/setup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +# Customise the terminal command prompt +echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc +echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc +export PROMPT_DIRTRIM=2 +export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] ' + +# Update Nextflow +nextflow self-update + +# Update welcome message +echo "Welcome to the nf-core/raredisease devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index bf44d9612..3b9724c76 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -25,9 +25,9 @@ runs: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install nf-test uses: nf-core/setup-nf-test@v1 @@ -52,6 +52,8 @@ runs: with: auto-update-conda: true conda-solver: libmamba + channels: conda-forge + channel-priority: strict conda-remove-defaults: true - name: Run nf-test diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index dca279852..213c6afbe 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,15 +28,15 @@ jobs: # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/raredisease/work-${{ steps.revision.outputs.revision }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/raredisease/work-${{ steps.revision.outputs.revision }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/raredisease/results-${{ steps.revision.outputs.revision }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/raredisease/results-${{ steps.revision.outputs.revision }}" } profiles: test_full @@ -44,5 +44,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 78f48f475..cae8521ca 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -14,14 +14,14 @@ jobs: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/raredisease/work-${{ github.sha }} + workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/raredisease/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/raredisease/results-test-${{ github.sha }}" + "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/raredisease/results-test-${{ github.sha }}" } profiles: test @@ -29,5 +29,5 @@ jobs: with: name: Seqera Platform debug log file path: | - seqera_platform_action_*.log - seqera_platform_action_*.json + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index ac030fd58..6adb0fff4 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9 + - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 999bcc382..6d94bcbf9 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -44,9 +44,9 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: Setup Apptainer @@ -57,7 +57,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install git+https://github.com/nf-core/tools.git - name: Make a cache directory for the container images run: | diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index b5f9f22f3..75c24ba1c 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,13 +13,13 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} # indication that the linting is being fixed - name: React on comment - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: eyes @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -47,7 +47,7 @@ jobs: # indication that the linting has finished - name: react if linting finished succesfully if: steps.pre-commit.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: "+1" @@ -67,21 +67,21 @@ jobs: - name: react if linting errors were fixed id: react-if-fixed if: steps.commit-and-push.outcome == 'success' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: hooray - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} reactions: confused - name: react if linting errors were not fixed if: steps.commit-and-push.outcome == 'failure' - uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: issue-number: ${{ github.event.issue.number }} body: | diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8b0f88c36..30e66026f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,12 +11,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - - name: Set up Python 3.13 - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - name: Set up Python 3.14 + uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" - name: Install pre-commit run: pip install pre-commit @@ -28,14 +28,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.13" + python-version: "3.14" architecture: "x64" - name: read .nf-core.yml diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index d43797d9d..e6e9bc269 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index e7b58449b..e20bf6d0c 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -18,7 +18,7 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.2" + NFT_VER: "0.9.3" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.10.5" + - "25.04.0" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: fetch-depth: 0 @@ -95,6 +95,7 @@ jobs: continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + NXF_VERSION: ${{ matrix.NXF_VER }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 0f7324956..e64cebd6a 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -14,6 +14,11 @@ jobs: run: | echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT + - name: get description + id: get_topics + run: | + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -23,6 +28,8 @@ jobs: message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + ${{ steps.get_topics.outputs.description }} + Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index beb5c77fb..c5988af90 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 83599f633..000000000 --- a/.gitpod.yml +++ /dev/null @@ -1,10 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - -vscode: - extensions: - - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index b259be0e2..b09fc4c3d 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,7 +8,7 @@ lint: - docs/images/nf-core-raredisease_logo_light.png - assets/nf-core-raredisease_logo_light.png modules_config: false -nf_core_version: 3.3.2 +nf_core_version: 3.4.1 repository_type: pipeline template: author: Clinical Genomics Stockholm diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bb41beec1..d06777a8f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: additional_dependencies: - prettier@3.6.2 - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v5.0.0 + rev: v6.0.0 hooks: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] diff --git a/.prettierignore b/.prettierignore index edd29f01e..2255e3e36 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,4 +10,5 @@ testing/ testing* *.pyc bin/ +.nf-test/ ro-crate-metadata.json diff --git a/README.md b/README.md index 2d0769292..757211705 100644 --- a/README.md +++ b/README.md @@ -5,12 +5,13 @@ +[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease) [![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/docs/usage.md b/docs/usage.md index bc7f56264..4d6a6b2d4 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -149,7 +149,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `shifter` - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) + - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` diff --git a/main.nf b/main.nf index c98fc2620..68e9a1bd2 100644 --- a/main.nf +++ b/main.nf @@ -74,7 +74,10 @@ workflow { params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.help, + params.help_full, + params.show_hidden ) // diff --git a/modules.json b/modules.json index 8f82d56f3..4d6e14640 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 812fc4c5e..dd513cbd1 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.29 + - bioconda::multiqc=1.31 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 0ac3c3699..5288f5ccf 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : - 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' : + 'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 88e90571c..17881d15c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:50:41.182332996" + "timestamp": "2025-09-08T20:57:36.139055243" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:51:22.448739369" + "timestamp": "2025-09-08T20:59:15.142230631" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-22T11:51:06.198928424" + "timestamp": "2025-09-08T20:58:29.629087066" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d37..000000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index 017317ead..af8d0c396 100644 --- a/nextflow.config +++ b/nextflow.config @@ -32,13 +32,15 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = null + hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + + // Config options config_profile_name = null config_profile_description = null @@ -91,7 +93,18 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { + arm64 { + process.arch = 'arm64' + // TODO https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { @@ -148,18 +161,6 @@ profiles { wave.freeze = true wave.strategy = 'conda,container' } - gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB - process { - resourceLimits = [ - memory: 8.GB, - cpus : 4, - time : 1.h - ] - } - } gpu { docker.runOptions = '-u $(id -u):$(id -g) --gpus all' apptainer.runOptions = '--nv' @@ -169,6 +170,8 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set AWS client to anonymous when using the default igenomes_base +aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false // Load nf-core custom profiles from different institutions // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. @@ -250,46 +253,19 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.10.5' + nextflowVersion = '!>=25.04.0' version = '2.7.0dev' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs - help { - enabled = true - command = "nextflow run nf-core/raredisease -profile --input samplesheet.csv --outdir " - fullParameter = "help_full" - showHiddenParameter = "show_hidden" - beforeText = """ --\033[2m----------------------------------------------------\033[0m- - \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m -\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m -\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m -\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m - \033[0;32m`._,._,\'\033[0m -\033[0;35m nf-core/raredisease ${manifest.version}\033[0m --\033[2m----------------------------------------------------\033[0m- -""" - afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md -""" - } - summary { - beforeText = validation.help.beforeText - afterText = validation.help.afterText - } } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index 5177d7598..365fd7129 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -224,6 +224,18 @@ "fa_icon": "far calendar", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true + }, + "help": { + "type": ["boolean", "string"], + "description": "Display the help message." + }, + "help_full": { + "type": "boolean", + "description": "Display the full detailed help message." + }, + "show_hidden": { + "type": "boolean", + "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." } } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8475ce38b..bb924f5cc 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T11:39:40+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-10-16T13:38:58+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75" + "@id": "#fb488ede-d306-43ef-bc44-527dc8f10111" } ], "name": "nf-core/raredisease" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-07-08T11:39:40Z", + "dateModified": "2025-10-16T13:38:58Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -158,14 +158,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.10.5" + "version": "!>=25.04.0" }, { - "@id": "#0b623809-34f0-46cc-a0c9-506e2fe49f75", + "@id": "#fb488ede-d306-43ef-bc44-527dc8f10111", "@type": "TestSuite", "instance": [ { - "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05" + "@id": "#e7b1a59e-d93b-4d46-b065-e5b00376601c" } ], "mainEntity": { @@ -174,7 +174,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#db67e69b-8d62-4cd4-830c-0b198aacfc05", + "@id": "#e7b1a59e-d93b-4d46-b065-e5b00376601c", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index d0e7152e5..b8517ea7d 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -11,6 +11,7 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' @@ -32,6 +33,9 @@ workflow PIPELINE_INITIALISATION { nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + help // boolean: Display help message and exit + help_full // boolean: Show the full help message + show_hidden // boolean: Show hidden parameters in the help message main: @@ -50,10 +54,35 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + before_text = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m nf-core/raredisease ${workflow.manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md +""" + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFSCHEMA_PLUGIN ( workflow, validate_params, - null + null, + help, + help_full, + show_hidden, + before_text, + after_text, + command ) // diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f84761125..000000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c9a..000000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 4994303ea..ee4738c8d 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -4,6 +4,7 @@ include { paramsSummaryLog } from 'plugin/nf-schema' include { validateParameters } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' workflow UTILS_NFSCHEMA_PLUGIN { @@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN { // when this input is empty it will automatically use the configured schema or // "${projectDir}/nextflow_schema.json" as default. This input should not be empty // for meta pipelines + help // boolean: show help message + help_full // boolean: show full help message + show_hidden // boolean: show hidden parameters in help message + before_text // string: text to show before the help message and parameters summary + after_text // string: text to show after the help message and parameters summary + command // string: an example command of the pipeline main: + if(help || help_full) { + help_options = [ + beforeText: before_text, + afterText: after_text, + command: command, + showHidden: show_hidden, + fullHelp: help_full, + ] + if(parameters_schema) { + help_options << [parametersSchema: parameters_schema] + } + log.info paramsHelp( + help_options, + params.help instanceof String ? params.help : "", + ) + exit 0 + } + // // Print parameter summary to stdout. This will display the parameters // that differ from the default given in the JSON schema // + + summary_options = [:] if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) + summary_options << [parametersSchema: parameters_schema] } + log.info before_text + log.info paramsSummaryLog(summary_options, input_workflow) + log.info after_text // // Validate the parameters using nextflow_schema.json or the schema // given via the validation.parametersSchema configuration option // if(validate_params) { + validateOptions = [:] if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() + validateOptions << [parametersSchema: parameters_schema] } + validateParameters(validateOptions) } emit: diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 8fb301648..c977917aa 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -25,6 +25,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -51,6 +57,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -77,6 +89,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -103,6 +121,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -114,4 +138,36 @@ nextflow_workflow { ) } } + + test("Should create a help message") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = true + input[4] = false + input[5] = false + input[6] = "Before" + input[7] = "After" + input[8] = "nextflow run test/test" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 09ef842ae..8d8c73718 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,8 +1,8 @@ plugins { - id "nf-schema@2.4.2" + id "nf-schema@2.5.1" } validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} \ No newline at end of file +} diff --git a/tests/.nftignore b/tests/.nftignore index 158c83c59..e128a1284 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,10 +1,11 @@ .DS_Store multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt -multiqc/multiqc_data/BETA-multiqc.parquet +multiqc/multiqc_data/multiqc.parquet multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/llms-full.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} diff --git a/tests/default.nf.test b/tests/default.nf.test index 2ed612c5d..c1bc745ca 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -20,8 +20,6 @@ nextflow_pipeline { assertAll( { assert workflow.success}, { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_raredisease_software_mqc_versions.yml"), // All stable path name, with a relative path From 9590a6e1d98d5c7e9dc1e0342b745b894b9000c4 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Oct 2025 14:07:31 +0100 Subject: [PATCH 062/872] update rocrate --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 60143179c..3d7375ebd 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-07-08T12:27:15+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" From c80d75eb5f778fbd9ce907233e94451ba911ee0c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Oct 2025 14:39:35 +0100 Subject: [PATCH 063/872] add tool updates --- CHANGELOG.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e296f367..b9d8cdf48 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,9 +27,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| ---- | ----------- | ----------- | -| | | | +| Tool | Old version | New version | +| -------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| htslib | 1.20 | 1.21 | +| mosdepth | 0.3.8 | 0.3.10 | +| ngs-bits | 2023_02 | 2024_11 | ## 2.6.0 - Cacofonix [2025-06-25] From ce6138c54ec5b559f7a59b2406d4ae2b1b530ed9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Oct 2025 16:10:46 +0100 Subject: [PATCH 064/872] update snap --- tests/default.nf.test.snap | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6801a9508..c57e2f4ea 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,6 @@ { "-profile test": { "content": [ - 817, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -627,8 +626,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-10T18:52:51.501264357" + "timestamp": "2025-10-27T15:59:49.765279594" } } \ No newline at end of file From 632991e2d1399e6360f2e3d6ca683bf97f289fa6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Oct 2025 21:32:21 +0100 Subject: [PATCH 065/872] review suggestions --- .../vcf_filter_bcftools_ensemblvep.config | 20 ++++------ nextflow_schema.json | 2 +- workflows/raredisease.nf | 40 +++++++++---------- 3 files changed, 29 insertions(+), 33 deletions(-) diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_ensemblvep.config index 43517b7b6..c152b5836 100644 --- a/conf/modules/vcf_filter_bcftools_ensemblvep.config +++ b/conf/modules/vcf_filter_bcftools_ensemblvep.config @@ -18,54 +18,50 @@ // SNVs process { - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_snv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SNV:TABIX_BGZIPTABIX' { + withName: '.*:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_snv_${meta.set}" } - ext.args2 = { "-p vcf" } } } // SVs process { - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_sv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_SV:TABIX_BGZIPTABIX' { + withName: '.*:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_sv_${meta.set}" } - ext.args2 = { "-p vcf" } } } // MT variants process { - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:BCFTOOLS_VIEW' { + withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW' { ext.prefix = { "${meta.id}_mt_${meta.set}" } ext.args = { "-Oz -i 'AF>0.05'" } } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_MT:TABIX_BGZIPTABIX' { + withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_mt_${meta.set}" } - ext.args2 = { "-p vcf" } } } // ME variants process { - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP' { ext.prefix = { "${meta.id}_me_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } - withName: '.*:VCF_FILTER_BCFTOOLS_ENSEMBLVEP_ME:TABIX_BGZIPTABIX' { + withName: '.*:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX' { ext.prefix = { "${meta.id}_me_${meta.set}" } - ext.args2 = { "-p vcf" } } } diff --git a/nextflow_schema.json b/nextflow_schema.json index 6b2fe370a..384f9a4e4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -585,7 +585,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified subworkflows.", "help_text": "Multiple subworkflows can be specified, separated by commas.", - "pattern": "^((me_calling|me_annotation|mt_annotation|mt_subsample|repeat_annotation|repeat_calling|snv_annotation|snv_calling|sv_annotation|sv_calling|vcf_filter_bcftools_ensemblvep)?,?)*(? Date: Mon, 27 Oct 2025 22:09:34 +0100 Subject: [PATCH 066/872] remove space --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e59c220e3..700068196 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -593,7 +593,7 @@ workflow RAREDISEASE { GENERATE_CLINICAL_SET_MT.out.vcf .set { ch_clinical_mtsnv_vcf } - ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_MT.out.versions ) + ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions) } ch_ann_csq_mtsnv_in = ch_clinical_mtsnv_vcf.mix(ch_clin_research_mt_vcf.research) From 202c341e927b3850b2fc3763fe63098abbef0378 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 29 Oct 2025 09:58:55 +0100 Subject: [PATCH 067/872] add changelog --- CHANGELOG.md | 1 + workflows/raredisease.nf | 46 ++++++++++++++++++++-------------------- 2 files changed, 24 insertions(+), 23 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc3cd155a..4e890c575 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) +- Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) ### `Fixed` diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 700068196..75bc0d56c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -41,29 +41,29 @@ include { CREATE_PEDIGREE_FILE } from '../modules/local/create_pedig // SUBWORKFLOWS // -include { ALIGN } from '../subworkflows/local/align' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli.nf' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_MT } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SV } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_GENOME_SNVS } from '../subworkflows/local/annotate_genome_snvs' -include { ANNOTATE_MOBILE_ELEMENTS } from '../subworkflows/local/annotate_mobile_elements' -include { ANNOTATE_MT_SNVS } from '../subworkflows/local/annotate_mt_snvs' -include { ANNOTATE_STRUCTURAL_VARIANTS } from '../subworkflows/local/annotate_structural_variants' -include { CALL_MOBILE_ELEMENTS } from '../subworkflows/local/call_mobile_elements' -include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' -include { CALL_SNV } from '../subworkflows/local/call_snv' -include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' -include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' -include { GENS } from '../subworkflows/local/gens' -include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' -include { QC_BAM } from '../subworkflows/local/qc_bam' -include { RANK_VARIANTS as RANK_VARIANTS_MT } from '../subworkflows/local/rank_variants' -include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' -include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' -include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' -include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' -include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' +include { ALIGN } from '../subworkflows/local/align' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli.nf' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_MT } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_GENOME_SNVS } from '../subworkflows/local/annotate_genome_snvs' +include { ANNOTATE_MOBILE_ELEMENTS } from '../subworkflows/local/annotate_mobile_elements' +include { ANNOTATE_MT_SNVS } from '../subworkflows/local/annotate_mt_snvs' +include { ANNOTATE_STRUCTURAL_VARIANTS } from '../subworkflows/local/annotate_structural_variants' +include { CALL_MOBILE_ELEMENTS } from '../subworkflows/local/call_mobile_elements' +include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' +include { CALL_SNV } from '../subworkflows/local/call_snv' +include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' +include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' +include { GENS } from '../subworkflows/local/gens' +include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' +include { QC_BAM } from '../subworkflows/local/qc_bam' +include { RANK_VARIANTS as RANK_VARIANTS_MT } from '../subworkflows/local/rank_variants' +include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' +include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' +include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' +include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' +include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' From c1b036f8d76e69e161dbb2bde00e449d7ecf3117 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 29 Oct 2025 10:06:48 +0100 Subject: [PATCH 068/872] lint --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e890c575..e8c2b99b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) -- Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) +- Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) ### `Fixed` From 8b024b6ba241aed2dd5284e1e8dcdfbc44edf0f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 3 Nov 2025 16:40:32 +0100 Subject: [PATCH 069/872] Update to new runner size syntax See https://nfcore.slack.com/archives/C050DNB6K5H/p1762184179238379 for details --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 7de079a6c..2ca6252a8 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -64,7 +64,7 @@ jobs: runs-on: # use self-hosted runners - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 - - disk=large + - volume=80gb strategy: fail-fast: false matrix: From bf8139b61353955615203ba7c348be19b0719271 Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Mon, 10 Nov 2025 08:14:06 +0100 Subject: [PATCH 070/872] Ref and alt allele should be in the same column separated by comma --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index fec7d4fe7..a406550ff 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -288,7 +288,7 @@ The mandatory and optional parameters for each category are tabulated below. VEP plugins may be installed in the cache directory, and the plugin pLI is mandatory to install. To supply files required by VEP plugins, use `vep_plugin_files` parameter. See example cache [here](https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz).
    5 GnomAD VCF files can be downloaded from [here](https://gnomad.broadinstitute.org/downloads). The option `gnomad_af` expects a tab-delimited file with -no header and the following columns: `CHROM POS REF_ALLELE ALT_ALLELE AF`. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/gnomad_reformated.tab.gz).
    +no header and the following columns: `CHROM POS REF_ALLELE,ALT_ALLELE AF`. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/gnomad_reformated.tab.gz).
    6Used by GENMOD for ranking the variants. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/rank_model_snv.ini).
    7File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html). 8A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv).
    From 5f9ab4afc55e8fee3e9ac736f946454dd5992044 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 14 Nov 2025 15:35:40 +0100 Subject: [PATCH 071/872] turn off me calling in MT --- CHANGELOG.md | 1 + subworkflows/local/call_mobile_elements.nf | 5 ++--- workflows/raredisease.nf | 3 +-- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e8c2b99b4..b0b8d7ecb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) +- Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741) ### `Fixed` diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 9def4ccd3..cc9c1ee51 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -21,15 +21,14 @@ workflow CALL_MOBILE_ELEMENTS { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_me_references // channel: [mandatory] [path(tsv)] ch_case_info // channel: [mandatory] [ val(case_info) ] - val_genome_build // string: [mandatory] GRCh37 or GRCh38 main: ch_versions = Channel.empty() // Building chromosome channels based on fasta index ch_genome_fai - .splitCsv( sep: "\t", elem: 1, limit: 25 ) - .map { meta, fai -> [ fai.first() ] } + .splitCsv( sep: "\t", elem: 1, limit: 24 ) + .map { _meta, fai -> [ fai.first() ] } .collect() .map { chr -> [ chr, chr.size() ] } .transpose() diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 75bc0d56c..6bbfda779 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -728,8 +728,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai, ch_me_references, - ch_case_info, - params.genome + ch_case_info ) ch_versions = ch_versions.mix(CALL_MOBILE_ELEMENTS.out.versions) From 64a4a5adcd61e2ebbec35b6caa34cd20fb0d3523 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 14 Nov 2025 15:45:37 +0100 Subject: [PATCH 072/872] Call SVs in mitochondria using mitochondrial alignments --- CHANGELOG.md | 1 + subworkflows/local/align/main.nf | 45 +++++++++---------- .../local/call_structural_variants.nf | 2 - .../local/convert_mt_bam_to_fastq/main.nf | 6 ++- workflows/raredisease.nf | 6 +-- 5 files changed, 30 insertions(+), 30 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e8c2b99b4..e6af0181a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) +- Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742) ### `Fixed` diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f1593283d..9c1ab6fa9 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -120,7 +120,7 @@ workflow ALIGN { ALIGN_MT ( CONVERT_MT_BAM_TO_FASTQ.out.fastq, - CONVERT_MT_BAM_TO_FASTQ.out.bam, + CONVERT_MT_BAM_TO_FASTQ.out.ubam, ch_mt_bwaindex, ch_mt_bwamem2index, ch_mt_fasta, @@ -130,7 +130,7 @@ workflow ALIGN { ALIGN_MT_SHIFT ( CONVERT_MT_BAM_TO_FASTQ.out.fastq, - CONVERT_MT_BAM_TO_FASTQ.out.bam, + CONVERT_MT_BAM_TO_FASTQ.out.ubam, ch_mtshift_bwaindex, ch_mtshift_bwamem2index, ch_mtshift_fasta, @@ -138,15 +138,17 @@ workflow ALIGN { ch_mtshift_fai ) - ch_mt_marked_bam = ALIGN_MT.out.marked_bam - ch_mt_marked_bai = ALIGN_MT.out.marked_bai - ch_mt_bam_bai = ch_mt_marked_bam.join(ch_mt_marked_bai, failOnMismatch:true, failOnDuplicate:true) - ch_mtshift_marked_bam = ALIGN_MT_SHIFT.out.marked_bam - ch_mtshift_marked_bai = ALIGN_MT_SHIFT.out.marked_bai - ch_mtshift_bam_bai = ch_mtshift_marked_bam.join(ch_mtshift_marked_bai, failOnMismatch:true, failOnDuplicate:true) - ch_versions = ch_versions.mix(ALIGN_MT.out.versions, - ALIGN_MT_SHIFT.out.versions, - CONVERT_MT_BAM_TO_FASTQ.out.versions) + ch_mt_bam_bai = CONVERT_MT_BAM_TO_FASTQ.out.bam_bai // Used for subsampling and SV calling + ch_mt_marked_bam = ALIGN_MT.out.marked_bam + ch_mt_marked_bai = ALIGN_MT.out.marked_bai + ch_mt_bam_bai_mtsub = ch_mt_marked_bam + .join(ch_mt_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling + ch_mtshift_marked_bam = ALIGN_MT_SHIFT.out.marked_bam + ch_mtshift_marked_bai = ALIGN_MT_SHIFT.out.marked_bai + ch_mtshift_bam_bai_mtsub = ch_mtshift_marked_bam + .join(ch_mtshift_marked_bai, failOnMismatch:true, failOnDuplicate:true) + ch_versions = ch_versions + .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) } if (params.save_mapped_as_cram) { @@ -155,16 +157,13 @@ workflow ALIGN { } emit: - fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] - genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] - genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] - genome_bam_bai = ch_genome_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] - mt_marked_bam = ch_mt_marked_bam // channel: [ val(meta), path(bam) ] - mt_marked_bai = ch_mt_marked_bai // channel: [ val(meta), path(bai) ] - mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - mtshift_marked_bam = ch_mtshift_marked_bam // channel: [ val(meta), path(bam) ] - mtshift_marked_bai = ch_mtshift_marked_bai // channel: [ val(meta), path(bai) ] - mtshift_bam_bai = ch_mtshift_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - versions = ch_versions // channel: [ path(versions.yml) ] + fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] + genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] + genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] + genome_bam_bai = ch_genome_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] + mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + mt_bam_bai_mtsub = ch_mt_bam_bai_mtsub // channel: [ val(meta), path(bam), path(bai) ] + mtshift_bam_bai_mtsub = ch_mtshift_bam_bai_mtsub // channel: [ val(meta), path(bam), path(bai) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index ae0a4ae71..311cfdc9c 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -17,11 +17,9 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_mtshift_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_case_info // channel: [mandatory] [ val(case_info) ] ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] ch_genome_dictionary // channel: [optional; used by mandatory for GATK's cnvcaller][ val(meta), path(dict) ] diff --git a/subworkflows/local/convert_mt_bam_to_fastq/main.nf b/subworkflows/local/convert_mt_bam_to_fastq/main.nf index 156f71bb4..50bd6fd6a 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/main.nf +++ b/subworkflows/local/convert_mt_bam_to_fastq/main.nf @@ -5,6 +5,7 @@ include { GATK4_PRINTREADS as GATK4_PRINTREADS_MT } from '../../../modules/nf-core/gatk4/printreads/main' include { GATK4_REVERTSAM as GATK4_REVERTSAM_MT } from '../../../modules/nf-core/gatk4/revertsam/main' include { GATK4_SAMTOFASTQ as GATK4_SAMTOFASTQ_MT } from '../../../modules/nf-core/gatk4/samtofastq/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MT } from '../../../modules/nf-core/samtools/index/main' workflow CONVERT_MT_BAM_TO_FASTQ { take: @@ -18,7 +19,9 @@ workflow CONVERT_MT_BAM_TO_FASTQ { // Outputs bam containing only MT GATK4_PRINTREADS_MT ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_genome_dict ) + SAMTOOLS_INDEX_MT (GATK4_PRINTREADS_MT.out.bam) + ch_bam_bai = GATK4_PRINTREADS_MT.out.bam.join(SAMTOOLS_INDEX_MT.out.bai) // Removes alignment information GATK4_REVERTSAM_MT ( GATK4_PRINTREADS_MT.out.bam ) @@ -31,6 +34,7 @@ workflow CONVERT_MT_BAM_TO_FASTQ { emit: fastq = GATK4_SAMTOFASTQ_MT.out.fastq // channel: [ val(meta), [ path(fastq) ] ] - bam = GATK4_REVERTSAM_MT.out.bam // channel: [ val(meta), path(bam) ] + bam_bai = ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + ubam = GATK4_REVERTSAM_MT.out.bam // channel: [ val(meta), path(bam) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 75bc0d56c..347ff228e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -452,8 +452,8 @@ workflow RAREDISEASE { if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_calling'))) { CALL_SNV ( ch_mapped.genome_bam_bai, - ch_mapped.mt_bam_bai, - ch_mapped.mtshift_bam_bai, + ch_mapped.mt_bam_bai_mtsub, + ch_mapped.mtshift_bam_bai_mtsub, ch_genome_chrsizes, ch_genome_fasta, ch_genome_fai, @@ -636,11 +636,9 @@ workflow RAREDISEASE { ch_mapped.genome_marked_bai, ch_mapped.genome_bam_bai, ch_mapped.mt_bam_bai, - ch_mapped.mtshift_bam_bai, ch_genome_bwaindex, ch_genome_fasta, ch_genome_fai, - ch_mtshift_fasta, ch_case_info, ch_target_bed, ch_genome_dictionary, From 17afe9006dc3efefd03e9946822322d22499868e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 15 Nov 2025 12:36:43 +0100 Subject: [PATCH 073/872] update snap --- .../local/align/tests/main.nf.test.snap | 152 +++--------------- .../local/qc_bam/tests/main.nf.test.snap | 4 +- tests/test_bam.nf.test.snap | 6 +- tests/test_singleton.nf.test.snap | 6 +- 4 files changed, 28 insertions(+), 140 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index d692c61be..b220fb7e5 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -77,8 +77,8 @@ "case_id": "justhusky" } }, - "9beeefe789d896c08d55e8b8d13d9623", - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + "df4054395a0ae4588719c34560b4e26f", + "earlycasualcaiman.bam.bai" ], [ { @@ -96,8 +96,8 @@ "case_id": "justhusky" } }, - "b18998c8cf7dc417ca9a122ba1c9403d", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai" + "601871c90e6b0a1f805d19ea8b60a7e5", + "hugelymodelbat.bam.bai" ], [ { @@ -115,68 +115,12 @@ "case_id": "justhusky" } }, - "a5d6892191a2c8c1f29966448623ca1b", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + "35da26a8d2d56b62e01b2e879cd8addd", + "slowlycivilbuck.bam.bai" ] ], [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "130fb09f419109e40a6be267bfbd8c88", - "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "97e6eaae1cda668da59e5c16a9bbcc1d", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "427b5e476d84c5277d2d24210800ad60", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] + ], [ "versions.yml:md5,04cb590a101237e8d8726039ee466819", @@ -208,10 +152,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-07-08T10:47:18.906258299" + "timestamp": "2025-11-14T16:54:07.946917784" }, "align bwameme": { "content": [ @@ -291,8 +235,8 @@ "case_id": "justhusky" } }, - "ae49d126580da2d5a72ada636e1ff358", - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + "c55f8bf7b7c42ad8dcef6565eff4440b", + "earlycasualcaiman.bam.bai" ], [ { @@ -310,8 +254,8 @@ "case_id": "justhusky" } }, - "5646035310bba3a507a671aca33ca533", - "hugelymodelbat_sorted_merged_md_sorted.bam.bai" + "7fc6a7a47e90fb46daeff00093c7c498", + "hugelymodelbat.bam.bai" ], [ { @@ -329,68 +273,12 @@ "case_id": "justhusky" } }, - "246a28939c75e40353107bc79b93d494", - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + "f0b3fe7d566ae0db56bb85e17d8ec28f", + "slowlycivilbuck.bam.bai" ] ], [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "c96587f3323ea479aebf0a8ba3ee710b", - "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "9f79604c77dc54d30daff682a50399bf", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "8d810d8acecdeadc5a0e7ea159cb1343", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] + ], [ "versions.yml:md5,04cb590a101237e8d8726039ee466819", @@ -419,9 +307,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-07-08T10:54:20.418307597" + "timestamp": "2025-11-14T17:16:13.633955179" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 0f597d1c6..28d846441 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -153,8 +153,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-14T14:04:26.353165287" + "timestamp": "2025-11-15T10:54:27.243271854" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9a2eb045b..c38b510d1 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 280, + 283, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -541,8 +541,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-15T09:40:09.030137924" + "timestamp": "2025-11-15T12:06:37.106816288" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index c912baf8d..3d92421f7 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 150, + 151, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -464,8 +464,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-15T09:43:13.720671267" + "timestamp": "2025-11-15T12:11:02.492935999" } } \ No newline at end of file From e93f1067f16cb2b6ba24203b29d0fc9e9e7ba2bf Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 18 Nov 2025 10:10:54 +0100 Subject: [PATCH 074/872] mitosalt test --- bin/MitoSAlt1.1.1.pl | 1045 +++++++++++++++++ conf/modules/call_sv_MT.config | 2 +- conf/test.config | 10 +- modules.json | 452 +++++-- modules/local/mitosalt/environment.yml | 16 + modules/local/mitosalt/main.nf | 34 + modules/local/saltshaker/call/main.nf | 6 + modules/nf-core/seqtk/sample/environment.yml | 7 + modules/nf-core/seqtk/sample/main.nf | 58 + modules/nf-core/seqtk/sample/meta.yml | 56 + .../nf-core/seqtk/sample/tests/main.nf.test | 102 ++ .../seqtk/sample/tests/main.nf.test.snap | 126 ++ .../seqtk/sample/tests/standard.config | 6 + nextflow.config | 7 + nextflow_schema.json | 2 +- .../local/call_structural_variants.nf | 6 - subworkflows/local/call_sv_MT/main.nf | 40 +- tests/nextflow.config | 2 +- workflows/raredisease.nf | 25 + 19 files changed, 1861 insertions(+), 141 deletions(-) create mode 100755 bin/MitoSAlt1.1.1.pl create mode 100644 modules/local/mitosalt/environment.yml create mode 100644 modules/local/mitosalt/main.nf create mode 100644 modules/local/saltshaker/call/main.nf create mode 100644 modules/nf-core/seqtk/sample/environment.yml create mode 100644 modules/nf-core/seqtk/sample/main.nf create mode 100644 modules/nf-core/seqtk/sample/meta.yml create mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test create mode 100644 modules/nf-core/seqtk/sample/tests/main.nf.test.snap create mode 100644 modules/nf-core/seqtk/sample/tests/standard.config diff --git a/bin/MitoSAlt1.1.1.pl b/bin/MitoSAlt1.1.1.pl new file mode 100755 index 000000000..e8300bf78 --- /dev/null +++ b/bin/MitoSAlt1.1.1.pl @@ -0,0 +1,1045 @@ +#!/usr/bin/env perl +use strict; +use warnings; +use List::Util qw(first min max sum); +use Data::Dumper; + +#INPUT +my $config_file = $ARGV[0]; +my $p1 = $ARGV[1]; +my $p2 = $ARGV[2]; +my $tag = $ARGV[3]; + +#CREATE DIRECTORIES -- added by ID +mkdir "log" unless -d "log"; +mkdir "indel" unless -d "indel"; +mkdir "bam" unless -d "bam"; +mkdir "tab" unless -d "tab"; +mkdir "bw" unless -d "bw"; +mkdir "plot" unless -d "plot"; + +#LOG +open (STDOUT, "| tee -ai log/$tag.log"); + +my $usage = "usage: perl mitopoint.pl "; +die "Configuration file missing, $usage" unless $config_file; +die "Pair 1 file missing, $usage" unless $p1; +die "Pair 2 file missing, $usage" unless $p2; +die "Study name not given, $usage" unless $tag; + +die "check path to fastq 1, script exit.\n" unless -e $p1; +die "check path to fastq 2, script exit.\n" unless -e $p2; + + +#LOAD CONFIGURATION FILE +open(CONFIG, "<$config_file"); +my $User_Preferences; +while () { + chomp; # no newline + s/#.*//; # no comments + s/^\s+//; # no leading white + s/\s+$//; # no trailing white + next unless length; # anything left? + my ($var, $value) = split(/\s*=\s*/, $_, 2); + $User_Preferences->{$var} = $value; + my $line = $_; + print $line."\n"; +} + +#PROGRAMS +my $hisat2 = $User_Preferences->{hisat2}; +my $lastal = $User_Preferences->{lastal}; +my $lastsp = $User_Preferences->{lastsp}; +my $mfcv = $User_Preferences->{mfcv}; +my $b2fq = $User_Preferences->{b2fq}; +my $reformat = $User_Preferences->{reformat}; +my $samtools = $User_Preferences->{samtools}; +my $sambamba = $User_Preferences->{sambamba}; +my $gcov = $User_Preferences->{gcov}; +my $intersectBed = $User_Preferences->{intersectBed}; +my $sortBed = $User_Preferences->{sortBed}; +my $clusterBed = $User_Preferences->{clusterBed}; +my $randomBed = $User_Preferences->{randomBed}; +my $groupBy = $User_Preferences->{groupBy}; +my $bg2bw = $User_Preferences->{bg2bw}; + +#DATABASES +my $hsindex = $User_Preferences->{hsindex}; +my $faindex = $User_Preferences->{faindex}; +my $lastindex = $User_Preferences->{lastindex}; +my $mtfaindex = $User_Preferences->{mtfaindex}; +my $gsize = $User_Preferences->{gsize}; +my $MT_fasta = $User_Preferences->{MT_fasta}; + +#COMPUTATION +my $threads = $User_Preferences->{threads}; + +#MITOCHONDRIA FEATURES +my $refchr = $User_Preferences->{refchr}; +my $msize = $User_Preferences->{msize}; +my $orihs = $User_Preferences->{orihs}; +my $orihe = $User_Preferences->{orihe}; +my $orils = $User_Preferences->{orils}; +my $orile = $User_Preferences->{orile}; +my $exclude = $User_Preferences->{exclude}; +my $dloop1 = $exclude; +my $dloop2 = $msize - $exclude; +my $hash; + +#SCORING AND FILTERING FEATURES +my $score_threshold = $User_Preferences->{score_threshold}; +my $evalue_threshold = $User_Preferences->{evalue_threshold}; +my $split_length = $User_Preferences->{split_length}; +my $paired_distance = $User_Preferences->{paired_distance}; +my $deletion_threshold_min = $User_Preferences->{deletion_threshold_min}; +my $deletion_threshold_max = $User_Preferences->{deletion_threshold_max}; +my $breakthreshold = $User_Preferences->{breakthreshold}; +my $cluster_threshold = $User_Preferences->{cluster_threshold}; +my $breakspan = $User_Preferences->{breakspan}; +my $sizelimit = $User_Preferences->{sizelimit}; +my $hplimit = $User_Preferences->{hplimit}; +my $flank = $User_Preferences->{flank}; +my $split_distance_threshold = $User_Preferences->{split_distance_threshold}; + +#STEPS +my $dna = $User_Preferences->{dna}; #USE SPECIFIC HISAT PARAMETERS FOR DNA AND RNA SEQUENCING +my $enriched = $User_Preferences->{enriched}; #IF THE SEQUENCING IS MITOCHONDRIAL DNA ENRICHED THEN SKIP THE INITIAL NUCLEAR GENOME ALIGNMENT STEP +my $nu_mt = $User_Preferences->{nu_mt}; #MAPPING TO NUCLEAR AND MITOCHONDRIAL GENOME WITH BOWTIE2 +my $rmtmp = $User_Preferences->{rmtmp}; #REMOVE TEMPORARY FILES +my $o_mt = $User_Preferences->{o_mt}; #MITOCHONDRIAL READ EXTRACTION AND REMAPPING TO ONLY MITOCHONDRIAL GENOME WITH LASTAL +my $i_del = $User_Preferences->{i_del}; #IDENTIFICATION AND CLUSTERING OF DELETIONS/DUPLICATIONS +my $cn_mt = $User_Preferences->{cn_mt}; #ESTIMATION OF MT DNA COPY NUMBER + +#EXIT IF THE CONFIGURATION STEPS DO NOT MATCH +if(($nu_mt eq 'yes' && $enriched eq 'yes')||($nu_mt eq 'no' && $o_mt eq 'no' && $i_del eq 'no')||($cn_mt eq 'yes' && $nu_mt eq 'no')||($cn_mt eq 'yes' && $o_mt eq 'no')||($i_del eq 'yes' && $o_mt eq 'no' && $nu_mt eq 'yes')){ + print scalar(localtime).": Check config file for correct STEP combination\n"; + die; +} + +#MAP TO NU+MT GENOME +if($nu_mt eq 'yes' && $enriched eq 'no'){ + print scalar(localtime).": Map to NU+MT genome\n"; + if($dna eq 'yes'){system("$hisat2 -p $threads -x $hsindex --no-temp-splicesite --no-spliced-alignment --max-intronlen 5000 -1 $p1 -2 $p2 -S tmp_$tag.sam 2>> log/$tag.log");} + if($dna eq 'no'){system("$hisat2 -p $threads -x $hsindex -1 $p1 -2 $p2 -S tmp_$tag.sam 2>> log/$tag.log");} + + #EXTRACT READS + print scalar(localtime).": Extract reads\n"; + system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); + system("$samtools index tmp_$tag.bam"); + system("$samtools idxstats tmp_$tag.bam > indel/$tag.count.txt"); + system("$samtools view -u -@ $threads -f 12 tmp_$tag.bam > tmp1_$tag.bam"); #flag to extract unmapped reads with mate also unmapped + system("$samtools view -u -@ $threads tmp_$tag.bam $refchr> tmp2_$tag.bam"); + system("$samtools merge -@ $threads tmp_final_$tag.bam tmp1_$tag.bam tmp2_$tag.bam"); + + #EXTRACT FASTQ + print scalar(localtime).": Create FASTQ\n"; + system("$samtools fastq tmp_final_$tag.bam > tmp_$tag.fq"); #ADDS PAIR /1, /2 TO THE READ NAMES HENCE BBMAP REFORMAT NOT REQUIRED + #system("$reformat in=tmp.fq out=tmp1.fq overwrite=true -uniquenames -Xmx100g &>> log/$tag.log"); +} + +if($nu_mt eq 'yes' && $o_mt eq 'yes' && $enriched eq 'no'){ + #REMAP ON MT GENOME + print scalar(localtime).": Map to MT genome\n"; + system("$lastal -Q1 -e80 -P$threads $lastindex tmp_$tag.fq|$lastsp > tmp_$tag.maf"); + system("$mfcv sam -d tmp_$tag.maf|$samtools view -@ $threads -bt $mtfaindex -|$samtools sort -@ $threads -o bam/$tag.bam -"); + system("$samtools index bam/$tag.bam"); + system("$mfcv tab tmp_$tag.maf > tab/$tag.tab"); + + #COMPRESS TAB + system("gzip -f tab/$tag.tab"); + + #GENERATE BIGWIG + print scalar(localtime).": Generate Bigwig\n"; + system("$gcov -split -ibam bam/$tag.bam -bg|sort -k1,1 -k2,2n > tmp_$tag.bg"); + system("$bg2bw tmp_$tag.bg $mtfaindex bw/$tag.bw"); + #unlink("tmp_$tag.bg"); +} + +if($nu_mt eq 'no' && $o_mt eq 'yes' && $enriched eq 'yes'){ + #REMAP ON MT GENOME + print scalar(localtime).": Map to MT genome\n"; + system("$reformat in=$p1 in2=$p2 out=tmp_$tag.fq overwrite=true addslash=t trimreaddescription=t spaceslash=f -Xmx100g"); #2>> log/$tag.log"); + system("$lastal -Q1 -e80 -P$threads $lastindex tmp_$tag.fq|$lastsp > tmp_$tag.maf"); + system("$mfcv sam -d tmp_$tag.maf|$samtools view -@ $threads -bt $mtfaindex -|$samtools sort -@ $threads -o bam/$tag.bam -"); + system("$samtools index bam/$tag.bam"); + system("$mfcv tab tmp_$tag.maf > tab/$tag.tab"); + + #COMPRESS TAB + system("gzip -f tab/$tag.tab"); + + #GENERATE BIGWIG + print scalar(localtime).": Generate Bigwig\n"; + system("$gcov -split -ibam bam/$tag.bam -bg|sort -k1,1 -k2,2n > tmp_$tag.bg"); + system("$bg2bw tmp_$tag.bg $mtfaindex bw/$tag.bw"); + #unlink("tmp_$tag.bg"); +} + +if($cn_mt eq 'yes' && $enriched eq 'no' && $o_mt eq 'yes' && $nu_mt eq 'yes'){ + system("$sambamba depth window -w $msize bam/$tag.bam|cut -f 1,5 > indel/$tag.cnmt.txt"); + system("$randomBed -l 1000 -n 3000 -g $gsize > tmp_random_$tag.bed"); + system("$sambamba depth region -L tmp_random_$tag.bed -t $threads -o tmp_random_$tag.cov tmp_$tag.bam"); + system("$groupBy -g 5 -c 8 -o mean -i tmp_random_$tag.cov >> indel/$tag.cnmt.txt"); +} + +#IDENTIFY DELETIONS/DUPLICATIONS +if($i_del eq 'yes'){ + my $infile = "tab/$tag.tab"; + my $bedfile = "indel/$tag.bed"; + my $breakpointfile = "indel/$tag.breakpoint"; + my $clusterfile = "indel/$tag.cluster"; + + my $check_paired = &check_paired($infile); + print scalar(localtime).": Build split read hash\n"; + $hash = &build_hash($infile,$check_paired); + &remove_duplicates(); + + print scalar(localtime).": Generate non-split read BED\n"; + my $nosplitbed_file = &print_bed($hash,$tag,$refchr); + + print scalar(localtime).": Process hash to get best deletion/duplication candidates\n"; + my $delhash = &process_hash($hash,$bedfile,$breakpointfile,$msize,$tag); + + print scalar(localtime).": Build split read clusters\n"; + my $clusterhash = &get_cluster($delhash,$breakthreshold,$tag); + + print scalar(localtime).": Generate and print results\n"; + my $clustercount = &build_results($hash,$clusterhash,$infile,$refchr,$cluster_threshold,$tag); + &print_result($clustercount,$clusterfile); + + #PLOT DELETIONS + print scalar(localtime).":Plot deletions/duplications\n"; + system("R CMD BATCH --no-save --no-restore \'--args $msize $orihs $orihe $orils $orile $sizelimit indel/$tag.cluster indel/$tag.breakpoint $tag $hplimit $MT_fasta $flank\' delplot.R"); +} + +if($rmtmp eq 'yes'){ + if($nu_mt eq 'yes'){system("rm tmp_$tag* tmp1_$tag* tmp2_$tag* tmp_final_$tag*");} + if($o_mt eq 'yes' && $enriched eq 'yes'){if(glob("tmp_$tag*")){system("rm tmp_$tag*");}} + if($i_del eq 'yes'){if(glob("tmp_$tag*")){system("rm tmp_$tag*");}} + if($cn_mt eq 'yes'){system("rm tmp_random_$tag*");} +} + +print scalar(localtime).":Finished\n"; +###########################################################SUBROUTINES################################################################ +sub check_paired{ + my $check_paired = 0; + my $path = shift; + my $line = `zcat $path|tail -n 1`; + my @elements = split(/\t/, $line); + + $check_paired = 1 if $elements[6]=~m/\/.$/; + return $check_paired; +} + +sub build_hash{ + my $file = shift; + my $check_paired = shift; + + open(IN, "gunzip -c $file |") || die "can’t open pipe to $file"; + my $hash; + my $check_hash; + while(){ + my $line = $_; + chomp($line); + next if $line=~m/^\#/; + + my @elements = split(" ",$line); + my $score = $elements[0]; + my $chr = $elements[1]; + + my $start = $elements[2]; + my $length = $elements[3]; + my $end = $start + $length; + + my $read_start = $elements[7]; + my $id; + my $mate = 1; + + if($check_paired==0){ + $id = $elements[6]; + if($id=~m/\_.$/){ + $mate = $id; + $mate =~s/.*\_(.)$/$1/; + $id =~s/\_.$//; + } + } + elsif($check_paired == 1){ + my @name = split(/\//,$elements[6]); $id = $name[0]; + $mate = $name[1]; + } + + my $strand = $elements[9]; + my $evalue = $elements[12]; + $evalue=~s/.*\=//; + next if exists $check_hash->{$id}->{$start.$length}; + $check_hash->{$id}->{$start.$length}++; + $mate = 2 if $mate > 1; + #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; + + #FILTER BY SCORE AND MAP EVALUE + next if $score < $score_threshold; + next if $evalue > $evalue_threshold; + + push(@{$hash->{$id}->{$mate}->{starts}},$start); + push(@{$hash->{$id}->{$mate}->{ends}},$end); + push(@{$hash->{$id}->{$mate}->{rstarts}},$read_start); + push(@{$hash->{$id}->{$mate}->{strands}},$strand); + push(@{$hash->{$id}->{$mate}->{scores}},$score); + push(@{$hash->{$id}->{$mate}->{evalue}},$evalue); + push(@{$hash->{$id}->{$mate}->{lengths}},$length); + } + undef $check_hash; + close(IN); + return $hash; +} + +sub remove_duplicates{ + my $check_duplicates; + + for my $id (keys %{$hash}){ + my $starts1='NULL'; + my $ends1='NULL'; + my $lengths1='NULL'; + my $starts2='NULL'; + my $ends2='NULL'; + my $lengths2='NULL'; + my $count1 = 0; + my $count2 = 0; + + if(exists $hash->{$id}->{1}){ + $starts1 = join("",@{$hash->{$id}->{1}->{starts}}); + $ends1 = join("",@{$hash->{$id}->{1}->{ends}}); + $lengths1 = join("",@{$hash->{$id}->{1}->{lengths}}); + $count1 = @{$hash->{$id}->{1}->{starts}}; + + } + if(exists $hash->{$id}->{2}){ + $starts2 = join("",@{$hash->{$id}->{2}->{starts}}); + $ends2 = join("",@{$hash->{$id}->{2}->{ends}}); + $lengths2 = join("",@{$hash->{$id}->{2}->{lengths}}); + $count2 = @{$hash->{$id}->{2}->{starts}}; + } + + my $signature1 = $starts1.":".$ends1.":".$lengths1; + my $signature2 = $starts2.":".$ends2.":".$lengths2; + + my @signatures = ($signature1,$signature2); + @signatures = sort @signatures; + my $signature = join("",@signatures); + + + if(exists $check_duplicates->{$signature} && $count1>0 && $count2>0){ + delete $hash->{$id}; + } + else{ + $check_duplicates->{$signature}++; + } + } +} + +#PRINT NON-SPLIT BED +sub print_bed{ + my $hash = shift; + my $tag = shift; + my $refchr = shift; + my $filename = "tmp_".$tag."_nosplit.bed"; + open(ABED,">$filename"); + for my $id (keys %{$hash}){ + #print $id."\n"; + + for my $read(keys %{$hash->{$id}}){ + my $name = $id."_".$read; + + #CHECK IF READ IS SPLIT ALIGNED + my $count = @{$hash->{$id}->{$read}->{starts}}; + next if $count > 1; + my $start = @{$hash->{$id}->{$read}->{starts}}[0]; + my $end = @{$hash->{$id}->{$read}->{ends}}[0]; + print ABED "$refchr\t$start\t$end\t$name\n"; + } + } + system("sort -k2,2n $filename -o $filename"); + close(ABED); + return $filename; +} + +sub process_hash{ + my $hash = shift; + my $bedfile = shift; + my $breakpointfile = shift; + my $size = shift; + my $tag = shift; + my $bps = "tmp_".$tag."_bps.bed"; + my $bpe = "tmp_".$tag."_bpe.bed"; + my $delhash=&process_hash1($hash,$bedfile,$breakpointfile,$msize,$bps,$bpe); + + for my $id (keys %{$hash}){ + #print $id."\n"; + for my $read(keys %{$hash->{$id}}){ + #CHECK IF READ IS SPLIT ALIGNED + my $name = $id."_".$read; + my $count = @{$hash->{$id}->{$read}->{starts}}; + next unless $count == 2; + #next unless $name eq 'C1LUFACXX130228:4:1312:19820:41898_1'; + #CHECK IF THE SPLIT READ FRAGMENTS ARE ABOVE LENGTH THRESHOLD + my $min_len = min @{$hash->{$id}->{$read}->{lengths}}; + next unless $min_len >= $split_length; + + #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_ends = @{$hash->{$id}->{$read}->{ends}}; + my @read_strands = @{$hash->{$id}->{$read}->{strands}}; + my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; + my @read_local_starts = @{$hash->{$id}->{$read}->{rstarts}}; + + #LOOK FOR SPLIT READS WHICH MAP INVERSELY SPANNING THE D'LOOP + my $read_check = 'no'; + if($read_starts[0]<$read_starts[1] && $read_local_starts[0]>$read_local_starts[1]){$read_check = 'yes';} + elsif($read_starts[0]>$read_starts[1] && $read_local_starts[0]<$read_local_starts[1]){$read_check = 'yes';} + elsif($read_starts[0]<=$read_starts[1] && $read_local_starts[0]<$read_local_starts[1] && $read_starts[1]<$read_ends[0] ){$read_check = 'yes';} + elsif($read_starts[0]>=$read_starts[1] && $read_local_starts[0]>$read_local_starts[1] && $read_ends[1]>$read_starts[0] ){$read_check = 'yes';} + + #CHECK IF THE SPLIT READ FRAGMENTS SPAN THE DLOOP + my $min_start = min @{$hash->{$id}->{$read}->{starts}}; + my $max_end = max @{$hash->{$id}->{$read}->{ends}}; + next if $min_start <= $dloop1 && $max_end >= $dloop2; + + my ($size,$start,$end) = &get_frag_distance(\@read_starts,\@read_ends,$read_check,$msize); + next if $size < $deletion_threshold_min; + next if $size > $deletion_threshold_max; + next if $read_strands[0] ne $read_strands[1];#SPLIT READS IN OPPOSITE STRANDS MAY INDICATE INVERSION + #print "$name\t$start\t$end\t$size\n"; + + $start = 1 if $start == 0; + $end = 1 if $end == 0; + + #CHECK IF PAIRED READ EXISTS AND ITS ALIGNMENT POSITION SUPPORTS THE SPLIT READ + my $pair = 1 if $read == 2; + $pair = 2 if $read == 1; + my $paired_support = 'no'; + my $distance_paired_support = &paired_support($hash,$id,$read,$pair); + $paired_support = 'yes' if $distance_paired_support <= $paired_distance; + + #LOOK FOR SPLIT READS WITH LARGE UNMAPPED AREA + my ($split_distance) = &get_split_distance(\@read_local_starts,\@read_lengths); + next if $split_distance > $split_distance_threshold; + + #PRINT SPLIT READ IN BED FORMAT + my @read_scores = @{$hash->{$id}->{$read}->{scores}}; + my @len = &generate_bed($id,$read,\@read_starts,\@read_ends,\@read_lengths,\@read_scores,$read_strands[0]); + + my $readid = $id."_".$read; + my $clusterid = "cluster_".$count; + $delhash->{$readid}->{breakstart}=$len[2]; + $delhash->{$readid}->{breakend}=$len[3]; + $delhash->{$readid}->{breaksize}=$len[4]; + $delhash->{$readid}->{readcheck}=$read_check; + $delhash->{$readid}->{lenstart}=$len[0]; + $delhash->{$readid}->{lenend}=$len[1]; + + $start = $len[2]; + $end = $len[3]; + $size = $len[4]; + + print BP "$refchr\t$name\t$size\t$start\t$end\t$read_lengths[0]\t$read_lengths[1]\t$paired_support\t$distance_paired_support\t$read_check\n"; + print BPS "$refchr\t$start\t$start\t$name\t0\t+\n" if $read_check eq 'no'; + print BPS "$refchr\t$start\t$start\t$name\t0\t-\n" if $read_check eq 'yes'; + print BPE "$refchr\t$end\t$end\t$name\t0\t+\n" if $read_check eq 'no'; + print BPE "$refchr\t$end\t$end\t$name\t0\t-\n" if $read_check eq 'yes'; + } + } + close(BP); + close(BED); + close(BPS); + close(BPE); + return $delhash; +} + +sub process_hash1{ + my $hash = shift; + my $bedfile = shift; + my $breakpointfile = shift; + my $size = shift; + my $bps = shift; + my $bpe = shift; + + my $delhash; + + open(BP,">$breakpointfile"); + open(BED,">$bedfile"); + open(BPS,">$bps"); + open(BPE,">$bpe"); + + for my $id (keys %{$hash}){ + #print $id."\n"; + for my $read(keys %{$hash->{$id}}){ + #CHECK IF READ IS SPLIT ALIGNED + my $name = $id."_".$read; + my $count = @{$hash->{$id}->{$read}->{starts}}; + next unless $count == 3; + + #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_ends = @{$hash->{$id}->{$read}->{ends}}; + my @read_strands = @{$hash->{$id}->{$read}->{strands}}; + my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; + my @read_scores = @{$hash->{$id}->{$read}->{scores}}; + my @read_local_starts = @{$hash->{$id}->{$read}->{rstarts}}; + + + my %strands=map {$_ => 1} @read_strands; + my $count_read_strands = keys(%strands); + next unless $count_read_strands == 1; + + my $as=join(';',@read_starts);my $ae=join(';',@read_ends);my $asr=join(';',@read_strands);my $als=join(';',@read_local_starts); + my @pos = (1000,1000,1000,1000); + #CHECK FOR FALSE SPLITS AT ORIGIN WITH A REAL DELETION + $pos[0] = 0 if grep {$_ == 0} @read_starts; + $pos[1] = $msize if grep {$_ == $msize} @read_starts; + $pos[2] = 0 if grep {$_ == 0} @read_ends; + $pos[3] = $msize if grep {$_ == $msize} @read_ends; + + #print "$name\t$as\t$ae\t$asr\t$als\t$pos[0]\t$pos[1]\t$pos[2]\t$pos[3]\n"; + if(($pos[0] != 1000||$pos[1] != 1000)&&($pos[2] != 1000||$pos[3] != 1000)){ + my $sort_hash; + for(my $i=0;$i<3;$i++){ + $sort_hash->{$read_local_starts[$i]}->{start}=$read_starts[$i]; + $sort_hash->{$read_local_starts[$i]}->{end}=$read_ends[$i]; + $sort_hash->{$read_local_starts[$i]}->{strand}=$read_strands[$i]; + $sort_hash->{$read_local_starts[$i]}->{length}=$read_lengths[$i]; + $sort_hash->{$read_local_starts[$i]}->{score}=$read_scores[$i]; + } + my $order_count=1; + foreach my $local_start (sort { $a <=> $b } keys %{$sort_hash}){ + my $start_check=$sort_hash->{$local_start}->{start}; + my $end_check=$sort_hash->{$local_start}->{end}; + my $pos_check='no'; + $pos_check='yes' unless($start_check==0||$start_check==$msize||$end_check==0||$end_check==$msize); + if($pos_check eq 'yes'){last;} + $order_count++; + } + + my $delete_count=3 if $order_count==1; + $delete_count=1 if $order_count==3; + $order_count=1; + foreach my $local_start (sort { $a <=> $b } keys %{$sort_hash}){ + delete $sort_hash->{$local_start} if($order_count==$delete_count); + $order_count++; + } + my @read_startsN; + my @read_endsN; + my @read_strandsN; + my @read_local_startsN; + my @read_scoresN; + my @read_lengthsN; + foreach my $local_start (sort { $a <=> $b } keys %{$sort_hash}){ + my $start = $sort_hash->{$local_start}->{start}; + my $end = $sort_hash->{$local_start}->{end}; + my $score = $sort_hash->{$local_start}->{score}; + my $length = $sort_hash->{$local_start}->{length}; + my $strand = $sort_hash->{$local_start}->{strand}; + push @read_startsN,$start; + push @read_endsN,$end; + push @read_local_startsN,$local_start; + push @read_strandsN,$strand; + push @read_scoresN,$score; + push @read_lengthsN,$length; + } + + #CHECK IF THE SPLIT READ FRAGMENTS ARE ABOVE LENGTH THRESHOLD + my $min_len = min @read_lengthsN; + next unless $min_len >= $split_length; + + + #LOOK FOR SPLIT READS WHICH MAP INVERSELY SPANNING THE D'LOOP + my $read_check = 'no'; + if($read_startsN[0]<$read_startsN[1] && $read_local_startsN[0]>$read_local_startsN[1]){$read_check = 'yes';} + elsif($read_startsN[0]>$read_startsN[1] && $read_local_startsN[0]<$read_local_startsN[1]){$read_check = 'yes';} + my ($size,$start,$end) = &get_frag_distance(\@read_startsN,\@read_endsN,$read_check,$msize); + next if $size < $deletion_threshold_min; + next if $size > $deletion_threshold_max; + + #CHECK IF PAIRED READ EXISTS AND ITS ALIGNMENT POSITION SUPPORTS THE SPLIT READ + my $pair = 1 if $read == 2; + $pair = 2 if $read == 1; + my $paired_support = 'no'; + my $distance_paired_support = &paired_support($hash,$id,$read,$pair); + $paired_support = 'yes' if $distance_paired_support <= $paired_distance; + + $start = 1 if $start == 0; + $end = 1 if $end == 0; + + #LOOK FOR SPLIT READS WITH LARGE UNMAPPED AREA + my ($split_distance) = &get_split_distance(\@read_local_startsN,\@read_lengthsN); + next if $split_distance > 5; + + #PRINT SPLIT READ IN BED FORMAT + my @len = &generate_bed1($id,$read,\@read_startsN,\@read_endsN,\@read_lengthsN,\@read_scoresN,$read_strandsN[0]); + my $readid = $id."_".$read; + my $clusterid = "cluster_".$count; + $delhash->{$readid}->{breakstart}=$start; + $delhash->{$readid}->{breakend}=$end; + $delhash->{$readid}->{breaksize}=$size; + $delhash->{$readid}->{readcheck}=$read_check; + $delhash->{$readid}->{lenstart}=$len[0]; + $delhash->{$readid}->{lenend}=$len[1]; + + #$start = $len[2]; + #$end = $len[3]; + #$size = $len[4]; + + print BP "$refchr\t$name\t$size\t$start\t$end\t$read_lengths[0]\t$read_lengths[1]\t$paired_support\t$distance_paired_support\t$read_check\n"; + print BPS "$refchr\t$start\t$start\t$name\t0\t+\n" if $read_check eq 'no'; + print BPS "$refchr\t$start\t$start\t$name\t0\t-\n" if $read_check eq 'yes'; + print BPE "$refchr\t$end\t$end\t$name\t0\t+\n" if $read_check eq 'no'; + print BPE "$refchr\t$end\t$end\t$name\t0\t-\n" if $read_check eq 'yes'; + + } + } + } + return $delhash; +} + +#CHECK IF THE PAIR OF A SPLIT READ LIES WITHIN A GIVEN THRESHOLD DISTANCE TO A FRAGMENT OF THE SPLIT READ +sub paired_support{ + my $hash = shift; + my $id = shift; + my $read = shift; + my $pair = shift; + my $distance = 1000; + + if(exists $hash->{$id}->{$pair}){ + my $distance1 = 0; + my $distance2=0; + + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_ends = @{$hash->{$id}->{$read}->{ends}}; + + my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; + my $pair_end = @{$hash->{$id}->{$pair}->{ends}}[0]; + + $distance1 = $read_starts[0] - $pair_end if $read_starts[0] > $pair_end; + $distance1 = $pair_start - $read_ends[0] if $pair_start > $read_ends[0]; + + $distance2 = $read_starts[1] - $pair_end if $read_starts[1] > $pair_end; + $distance2 = $pair_start - $read_ends[1] if $pair_start > $read_ends[1]; + $distance = min ($distance1,$distance2); + } + return $distance; +} + +#GET THE SIZE OF PUTATIVE DELETION AND THE BREAKPOINTS +sub get_frag_distance{ + my $starts = shift; + my $ends = shift; + my $read_check = shift; + my $msize = shift; + my @res; + + my $frag1_start = @{$starts}[0]; + my $frag2_start = @{$starts}[1]; + + my $frag1_end = @{$ends}[0]; + my $frag2_end = @{$ends}[1]; + + if($read_check eq 'no'){ + if($frag1_start > $frag2_end){ + my $size = $frag1_start - $frag2_end; + @res = ($size,$frag2_end,$frag1_start); + } + elsif($frag2_start > $frag1_end){ + my $size = $frag2_start - $frag1_end; + @res = ($size,$frag1_end,$frag2_start); + } + elsif($frag1_start < $frag2_start && $frag2_end <= $frag1_end){ + my $size = $msize - $frag2_end + $frag1_start; + @res = ($size,$frag1_start,$frag2_end); + } + elsif($frag2_start < $frag1_start && $frag1_end <= $frag2_end){ + my $size = $msize - $frag2_end + $frag1_start; + @res = ($size,$frag1_start,$frag2_end); + } + elsif($frag1_start <= $frag2_start && $frag1_end <= $frag2_end){ + my $size = $msize - $frag2_start + $frag1_end ; + @res = ($size,$frag1_end,$frag2_start); + } + elsif($frag2_start <= $frag1_start && $frag2_end <= $frag1_end){ + my $size = $msize - $frag1_end + $frag2_start ; + @res = ($size,$frag2_start,$frag1_end); + } + } + + if($read_check eq 'yes'){ + if($frag1_start > $frag2_end){ + my $size = ($msize -$frag1_end) + $frag2_start; + @res = ($size,$frag2_start,$frag1_end); + } + elsif($frag2_start > $frag1_end){ + my $size = ($msize-$frag2_end) + $frag1_start; + @res = ($size,$frag1_start,$frag2_end); + } + elsif($frag1_start <= $frag2_start && $frag1_end <= $frag2_end){ + my $size = $msize - $frag2_start + $frag1_end ; + @res = ($size,$frag1_end,$frag2_start); + } + elsif($frag2_start <= $frag1_start && $frag2_end <= $frag1_end){ + my $size = $msize - $frag1_end + $frag2_start ; + @res = ($size,$frag2_start,$frag1_end); + } + elsif($frag1_start < $frag2_start && $frag2_end <= $frag1_end){ + my $size = $msize - $frag2_end + $frag1_start; + @res = ($size,$frag1_start,$frag2_end); + } + elsif($frag2_start < $frag1_start && $frag1_end <= $frag2_end){ + my $size = $msize - $frag2_end + $frag1_start; + @res = ($size,$frag1_start,$frag2_end); + } + } + return @res; +} + +#GET THE DISTANCE BETWEEN SPLIT READS +sub get_split_distance{ + my $starts = shift; + my $lengths = shift; + my @res; + + my $local1_start = @{$starts}[0]; + my $local2_start = @{$starts}[1]; + + my $local1_length = @{$lengths}[0]; + my $local2_length = @{$lengths}[1]; + + if($local1_start>$local2_start){ + my $distance = $local1_start - $local2_start - $local2_length; + @res = ($distance); + } + if($local2_start>$local1_start){ + my $distance = $local2_start - $local1_start - $local1_length; + @res = ($distance); + } + return @res; +} + +#GENERATE A BED FILE FOR THE SPLIT READS FOR IGV VISUALIZATION +sub generate_bed{ + my $id = shift; + my $read = shift; + my $starts = shift; + my $ends = shift; + my $lengths = shift; + my $scores = shift; + my $strand = shift; + + my $size = shift; + my $bstart = shift; + my $bend = shift; + my @len; + + my $start; + my $end; + + my $frag1_start = @{$starts}[0]; + my $frag2_start = @{$starts}[1]; + + my $frag1_end = @{$ends}[0]; + my $frag2_end = @{$ends}[1]; + + my $frag1_length = @{$lengths}[0]; + my $frag2_length = @{$lengths}[1]; + + my $frag1_score = @{$scores}[0]; + my $frag2_score = @{$scores}[1]; + my $score = int(($frag1_score+$frag2_score)/2); + + if($frag1_start > $frag2_end && $strand eq '-'){ + $start = $frag2_start; + $end = $frag1_end; + $bstart = $frag2_end; + $bend = $frag1_start; + $size = $frag1_start - $frag2_end; + my $block_start=$frag1_start-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); + } + elsif($frag1_start > $frag2_end && $strand eq '+'){ + $start = $frag2_start; + $end = $frag1_end; + $bstart = $frag2_start; + $bend = $frag1_end; + $size = 1 + $msize- $frag1_end + $frag2_start; + my $block_start=$frag1_start-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); + } + elsif($frag2_start > $frag1_end && $strand eq '+'){ + $start = $frag1_start; + $end = $frag2_end; + $bstart = $frag1_end; + $bend = $frag2_start; + $size = $frag2_start - $frag1_end; + my $block_start=$frag2_start-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); + } + elsif($frag2_start > $frag1_end && $strand eq '-'){ + $start = $frag1_start; + $end = $frag2_end; + $bstart = $frag1_start; + $bend = $frag2_end; + $size = 1 + $msize - $frag2_end + $frag1_start; + my $block_start=$frag2_start-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); + } + elsif($frag2_start < $frag1_end && $strand eq '+'){ + $start = $frag1_start; + $end = $frag2_end; + $bstart = $frag2_start; + $bend = $frag1_end; + $size = $msize - $frag1_end + $frag2_start; + my $block_start=$frag1_end-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); + } + elsif($frag1_start < $frag2_end && $strand eq '-'){ + $start = $frag2_start; + $end = $frag1_end; + $bstart = $frag1_start; + $bend = $frag2_end; + $size = $msize - $frag2_end + $frag1_start; + my $block_start=$frag2_end-$start; + $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); + } + + return @len; +} + +#GENERATE A BED FILE FOR THE SPLIT READS FOR IGV VISUALIZATION (reads which split twice, once due to deletion/duplication and once due to genome circularity) +sub generate_bed1{ + my $id = shift; + my $read = shift; + my $starts = shift; + my $ends = shift; + my $lengths = shift; + my $scores = shift; + my $strand = shift; + my @len; + + my $start; + my $end; + + my $frag1_start = @{$starts}[0]; + my $frag2_start = @{$starts}[1]; + + my $frag1_end = @{$ends}[0]; + my $frag2_end = @{$ends}[1]; + + my $frag1_length = @{$lengths}[0]; + my $frag2_length = @{$lengths}[1]; + + my $frag1_score = @{$scores}[0]; + my $frag2_score = @{$scores}[1]; + my $score = int(($frag1_score+$frag2_score)/2); + + if($frag1_start > $frag2_end){ + $start = $frag2_start; + $end = $frag1_end; + my $block_start=$frag1_start-$start; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + @len = ($frag2_length,$frag1_length); + } + elsif($frag2_start > $frag1_end){ + $start = $frag1_start; + $end = $frag2_end; + my $block_start=$frag2_start-$start; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + @len = ($frag1_length,$frag2_length); + } + return @len; +} + +sub get_cluster{ + my $delhash = shift; + my $breakthreshold = shift; + my $tag = shift; + my $bps = "tmp_".$tag."_bps.bed"; + my $bpe = "tmp_".$tag."_bpe.bed"; + my $bpsc = "tmp_".$tag."_bps.cls"; + my $bpec = "tmp_".$tag."_bpe.cls"; + my $clusterhash; + + system("$sortBed -i $bps|$clusterBed -s -d $breakthreshold -i stdin > $bpsc"); + system("$sortBed -i $bpe|$clusterBed -s -d $breakthreshold -i stdin > $bpec"); + + open(BPS, "<$bpsc"); + my @bps=; + my $bps_hash; + foreach my $line(@bps){ + chomp $line; + my @fields=split(/\t/,$line); + my $readid=$fields[3]; + my $clusterid=$fields[6]; + $bps_hash->{$readid} = $clusterid; + } + close(BPS); + + open(BPE, "<$bpec"); + my @bpe=; + my $bpe_hash; + foreach my $line(@bpe){ + chomp $line; + my @fields=split(/\t/,$line); + my $readid=$fields[3]; + my $clusterid=$fields[6]; + $bpe_hash->{$readid} = $clusterid; + } + close(BPE); + + for my $readid(keys %{$delhash}){ + next unless exists $bps_hash->{$readid}; + next unless exists $bpe_hash->{$readid}; + my $clusterids = $bps_hash->{$readid}; + my $clusteride = $bpe_hash->{$readid}; + my $clusterid="cluster".$clusterids.$clusteride; + $clusterhash->{$clusterid}->{$readid} = $delhash->{$readid}; + } + return $clusterhash; +} + +sub build_results{ + my $hash = shift; + my $clusterhash = shift; + my $infile = shift; + my $refchr = shift; + my $cluster_read_count_threshold = shift; + my $tag = shift; + my $clustercount; + + my $nosplitbed_file = "tmp_".$tag."_nosplit.bed";; + for my $clusterid (keys %{$clusterhash}){ + my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; + next if $cluster_read_count < $cluster_read_count_threshold; + + print "Check $clusterid\n"; + my $clustercheck; + $clustercount->{$clusterid}->{wt} = 0; + $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; + + my $splitbed_fileS = "tmp_".$tag.".split.start.bed"; + my $splitbed_fileE = "tmp_".$tag.".split.end.bed"; + + open(SBEDS,">$splitbed_fileS"); + open(SBEDE,">$splitbed_fileE"); + + for my $readid (keys %{$clusterhash->{$clusterid}}){ + my $breakstart = $clusterhash->{$clusterid}->{$readid}->{breakstart}; + my $breakend = $clusterhash->{$clusterid}->{$readid}->{breakend}; + my $lenstart = $clusterhash->{$clusterid}->{$readid}->{lenstart}; + my $lenend = $clusterhash->{$clusterid}->{$readid}->{lenend}; + + push(@{$clustercount->{$clusterid}->{starts}},$breakstart); + push(@{$clustercount->{$clusterid}->{ends}},$breakend); + push(@{$clustercount->{$clusterid}->{names}},$readid); + push(@{$clustercount->{$clusterid}->{lenstarts}},$lenstart); + push(@{$clustercount->{$clusterid}->{lenends}},$lenend); + + print SBEDS "$refchr\t$breakstart\t$breakstart\n"; + print SBEDE "$refchr\t$breakend\t$breakend\n"; + } + + system("sort -u -k2,2n -k3 $splitbed_fileS -o $splitbed_fileS"); + system("sort -u -k2,2n -k3 $splitbed_fileE -o $splitbed_fileE"); + + my $intersectbed_fileS = "tmp_".$tag.".intersect.start.bed"; + my $intersectbed_fileE = "tmp_".$tag.".intersect.end.bed"; + + + system("$intersectBed -wo -sorted -a $nosplitbed_file -b $splitbed_fileS > $intersectbed_fileS"); + open(IS,"<$intersectbed_fileS"); + while(){ + my $line = $_; + chomp($line); + my @crd = split(/\t/,$line); + my $start = $crd[1]; + my $end = $crd[2]; + my $name = $crd[3]; + my $breakstart = $crd[5]; + next if exists $clustercheck->{$name}; + my $diffstart = $breakstart - $start; + my $diffend = $end - $breakstart; + next if $diffstart <= $breakspan || $diffend <= $breakspan; + $clustercount->{$clusterid}->{wt1}++; + $clustercheck->{$name}++; + } + close(SBEDS); + close(IS); + unlink $splitbed_fileS,$intersectbed_fileS; + + system("$intersectBed -wo -sorted -a $nosplitbed_file -b $splitbed_fileE > $intersectbed_fileE"); + open(IE,"<$intersectbed_fileE"); + while(){ + my $line = $_; + chomp($line); + my @crd = split(/\t/,$line); + my $start = $crd[1]; + my $end = $crd[2]; + my $name = $crd[3]; + my $breakend = $crd[5]; + next if exists $clustercheck->{$name}; + my $diffstart = $breakend - $start; + my $diffend = $end - $breakend; + next if $diffstart <= $breakspan || $diffend <= $breakspan; + $clustercount->{$clusterid}->{wt2}++; + $clustercheck->{$name}++; + } + close(SBEDE); + close(IE); + unlink $splitbed_fileE,$intersectbed_fileE; + } + return $clustercount; +} + +sub print_result{ + my $clustercount = shift; + my $clusterfile = shift; + open(CF,">$clusterfile"); + + for my $clusterid(keys %{$clustercount}){ + my $names = $clustercount->{$clusterid}->{names}; + my $starts = $clustercount->{$clusterid}->{starts}; + my $ends = $clustercount->{$clusterid}->{ends}; + my $lenstarts = $clustercount->{$clusterid}->{lenstarts}; + my $lenends = $clustercount->{$clusterid}->{lenends}; + my $mt = $clustercount->{$clusterid}->{mt}; + my $wt1 = 0; + $wt1 = $clustercount->{$clusterid}->{wt1} if exists $clustercount->{$clusterid}->{wt1}; + my $wt2 = 0; + $wt2 = $clustercount->{$clusterid}->{wt2} if exists $clustercount->{$clusterid}->{wt2}; + my $sum_wt = $wt1 + $wt2; + my $mean_wt = sprintf "%.0f",$sum_wt/2; + + my $names_print = join("\,",@$names); + my $starts_print = join("\,",@$starts); + my $ends_print = join("\,",@$ends); + + #if fragments overlap, then lenstart and and lenend are committed to NA + my $lenstarts_print = "NA"; + my $lenends_print = "NA"; + if(defined(@$lenstarts[0])){$lenstarts_print = join("\,",@$lenstarts);} + if(defined(@$lenends[0])){$lenends_print = join("\,",@$lenends);} + + my $perc_hp = $mt*100/($mt+$mean_wt); + + print CF "$clusterid\t$names_print\t$starts_print\t$ends_print\t$lenstarts_print\t$lenends_print\t$mt\t$mean_wt\t$perc_hp\n"; + } + close(CF); +} + + diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index a220615f4..4bbd5101b 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -27,7 +27,7 @@ process { ] } - withName: '.*CALL_SV_MT:EKLIPSE' { + withName: '.*CALL_SV_MT:MITOSALT' { ext.args = "-tmp ." publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, diff --git a/conf/test.config b/conf/test.config index 0c01b1035..1a98fa730 100644 --- a/conf/test.config +++ b/conf/test.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '2.h' ] withName: 'ENSEMBLVEP.*' { @@ -36,8 +36,8 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' - skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' - skip_subworkflows = "mt_annotation,mt_subsample,sv_annotation" + skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,ngsbits' + skip_subworkflows = "sv_annotation,snv_calling" input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' @@ -65,5 +65,7 @@ params { vep_filters = params.pipelines_testdata_base_path + '/reference/hgnc.txt' vep_cache_version = 107 vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' - + mitosalt_config = 'data/config_human.txt' + mitosalt_reference = 'data/genome' + mitosalt_depth = '1000000' } diff --git a/modules.json b/modules.json index c16b71bf0..f6ebeb8d4 100644 --- a/modules.json +++ b/modules.json @@ -8,535 +8,757 @@ "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "chromograph": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostseverepli": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "eklipse": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/filtervep": { "branch": "master", "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "expansionhunter": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + 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"b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwamem": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/datametrics": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dedup": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnascope": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/readwriter": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] + }, + "seqtk/sample": { + "branch": "master", + "git_sha": "af2861c63a6db77168f039ac265d84cfecd9efc2", + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "ffe458cbd1208b82e33e607fa43fbe80df191047", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -545,25 +767,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/local/mitosalt/environment.yml b/modules/local/mitosalt/environment.yml new file mode 100644 index 000000000..fb034f855 --- /dev/null +++ b/modules/local/mitosalt/environment.yml @@ -0,0 +1,16 @@ +channels: +- conda-forge +- bioconda +dependencies: +- bioconda::bbmap=39.37 +- bioconda::bedtools=2.31.1 +- bioconda::bioconductor-biostrings=2.74.0 +- bioconda::bioconductor-pwalign=1.2.0 +- bioconda::hisat2=2.2.1 +- bioconda::last=1648 +- bioconda::sambamba=1.0.1 +- bioconda::samtools=1.22.1 +- bioconda::ucsc-bedgraphtobigwig=482 +- bioconda::ucsc-fasize=482 +- bioconda::ucsc-fasomerecords=482 +- conda-forge::r-rcolorbrewer=1.1_3 diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf new file mode 100644 index 000000000..007c0102e --- /dev/null +++ b/modules/local/mitosalt/main.nf @@ -0,0 +1,34 @@ +#!/usr/bin/env nextflow + +process MITOSALT { + tag "MITOSALT" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': + 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" + + input: + tuple val(meta), path(reads) + path config + path genome + + output: + tuple val(meta), path("*breakpoint") , emit: breakpoint + tuple val(meta), path("*cluster") , emit: cluster + path "versions.yml" , emit: versions + + script: + def VERSION = "1.1.1" // from perl script, unlikely to be updated + def prefix = task.ext.prefix ?: "${meta.id}" + """ + MitoSAlt1.1.1.pl $config $reads $prefix + mv indel/*.breakpoint mitosalt_${prefix}.breakpoint + mv indel/*.cluster mitosalt_${prefix}.cluster + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mitosalt: $VERSION + END_VERSIONS + """ +} diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf new file mode 100644 index 000000000..59cf6461a --- /dev/null +++ b/modules/local/saltshaker/call/main.nf @@ -0,0 +1,6 @@ +process SS_CALL { + tag "$meta.id" + label 'process_single' + + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + ' diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml new file mode 100644 index 000000000..b1d11cbd2 --- /dev/null +++ b/modules/nf-core/seqtk/sample/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf new file mode 100644 index 000000000..0c2aaeda2 --- /dev/null +++ b/modules/nf-core/seqtk/sample/main.nf @@ -0,0 +1,58 @@ +process SEQTK_SAMPLE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' : + 'biocontainers/seqtk:1.4--he4a0461_1' }" + + input: + tuple val(meta), path(reads), val(sample_size) + + output: + tuple val(meta), path("*.fastq.gz"), emit: reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if (!(args ==~ /.*\ -s\ ?[0-9]+.*/)) { + args += " -s100" + } + if ( !sample_size ) { + error "SEQTK/SAMPLE must have a sample_size value included" + } + """ + printf "%s\\n" $reads | while read f; + do + seqtk \\ + sample \\ + $args \\ + \$f \\ + $sample_size \\ + | gzip --no-name > ${prefix}_\$(basename \$f) + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo "" | gzip > ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + +} diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml new file mode 100644 index 000000000..ed1f3325c --- /dev/null +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -0,0 +1,56 @@ +name: seqtk_sample +description: Subsample reads from FASTQ files +keywords: + - sample + - fastx + - reads +tools: + - seqtk: + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk sample command subsamples sequences. + homepage: https://github.com/lh3/seqtk + documentation: https://docs.csc.fi/apps/seqtk/ + tool_dev_url: https://github.com/lh3/seqtk + licence: ["MIT"] + identifier: biotools:seqtk +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files + pattern: "*.{fastq.gz}" + ontologies: [] + - sample_size: + type: float + description: Fraction (<1.0) or number (>=1) of reads to sample. +output: + reads: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Subsampled FastQ files + pattern: "*.{fastq.gz}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@kaurravneet4123" + - "@sidorov-si" + - "@adamrtalbot" +maintainers: + - "@kaurravneet4123" + - "@sidorov-si" + - "@adamrtalbot" diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test b/modules/nf-core/seqtk/sample/tests/main.nf.test new file mode 100644 index 000000000..2152ecd41 --- /dev/null +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test @@ -0,0 +1,102 @@ +nextflow_process { + + name "Test Process SEQTK_SAMPLE" + script "modules/nf-core/seqtk/sample/main.nf" + process "SEQTK_SAMPLE" + config "./standard.config" + + tag "modules" + tag "modules_nfcore" + tag "seqtk" + tag "seqtk/sample" + + test("sarscov2_sample_singleend_fqgz") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + 50 + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2_sample_pairedend_fqgz") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + 50 + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2_sample_singlend_fqgz_stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + 50 + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2_sample_singleend_frac") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + 0.5 + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap new file mode 100644 index 000000000..aa6991e6c --- /dev/null +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap @@ -0,0 +1,126 @@ +{ + "sarscov2_sample_singlend_fqgz_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ] + } + ], + "timestamp": "2024-02-22T15:58:45.902956" + }, + "sarscov2_sample_pairedend_fqgz": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" + ] + ], + "1": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" + ] + ], + "versions": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ] + } + ], + "timestamp": "2024-02-22T15:58:37.679954" + }, + "sarscov2_sample_singleend_fqgz": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" + ] + ], + "1": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" + ] + ], + "versions": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ] + } + ], + "timestamp": "2024-02-22T15:58:29.474491" + }, + "sarscov2_sample_singleend_frac": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" + ] + ], + "1": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" + ] + ], + "versions": [ + "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + ] + } + ], + "timestamp": "2025-07-15T09:48:30.275951" + } +} \ No newline at end of file diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config new file mode 100644 index 000000000..b2dd4b9f9 --- /dev/null +++ b/modules/nf-core/seqtk/sample/tests/standard.config @@ -0,0 +1,6 @@ +process { + withName: SEQTK_SAMPLE { + ext.args = '-s100' + ext.prefix = { "${meta.id}.sampled" } + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index a94922be6..2fa4d94e9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -216,6 +216,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + singularity.pullTimeout = '50 min' } podman { podman.enabled = true @@ -492,3 +493,9 @@ validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } + +singularity { + autoMounts = true + runOptions = '-B /home/irene.duba/tmp' +} + diff --git a/nextflow_schema.json b/nextflow_schema.json index 384f9a4e4..459e1bee9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -592,7 +592,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified tools.", "help_text": "Multiple tools can be specified, separated by commas.", - "pattern": "^((fastp|gens|germlinecnvcaller|haplogrep3|peddy|smncopynumbercaller|vcf2cytosure|fastqc|qualimap|ngsbits|eklipse)?,?)*(? [meta, reads, ch_subdepth] } - if (!(params.skip_tools && params.skip_tools.split(',').contains('eklipse'))) { - EKLIPSE(ch_bam_bai,[]) - ch_eklipse_del = EKLIPSE.out.deletions - ch_eklipse_genes = EKLIPSE.out.genes - ch_eklipse_circos = EKLIPSE.out.circos - ch_versions = ch_versions.mix(EKLIPSE.out.versions.first()) + if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { + SEQTK_SAMPLE(ch_reads_subdepth) + ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) + + MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_genome) + ch_mitosalt_breakpoint = MITOSALT.out.breakpoint + ch_mitosalt_cluster = MITOSALT.out.cluster + ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } MT_DELETION(ch_bam_bai, ch_fasta) ch_versions = ch_versions.mix(MT_DELETION.out.versions.first()) emit: - eklipse_del = ch_eklipse_del // channel: [ val(meta), path(csv) ] - eklipse_genes = ch_eklipse_genes // channel: [ val(meta), path(csv) ] - eklipse_circos = ch_eklipse_circos // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - versions = ch_versions // channel: [ path(versions.yml) ] + mitosalt_breakpoint = ch_mitosalt_breakpoint // channel: [ val(meta), path(breakpoint) ] + mitosalt_cluster = ch_mitosalt_cluster // channel: [ val(meta), path(cluster) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/tests/nextflow.config b/tests/nextflow.config index fef7084f8..559ae7a9e 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '2.h' ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 75bc0d56c..9f65bf17a 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -54,6 +54,7 @@ include { CALL_MOBILE_ELEMENTS } from '.. include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' include { CALL_SNV } from '../subworkflows/local/call_snv' include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' +include { CALL_SV_MT } from '../subworkflows/local/call_sv_MT' include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' include { GENS } from '../subworkflows/local/gens' include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' @@ -715,6 +716,30 @@ workflow RAREDISEASE { ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) } } +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CALL MITOCHONDRIAL SVs +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + // + // Initialize file channels for mitosalt input + // + ch_msconfig = params.mitosalt_config ? channel.fromPath(params.mitosalt_config) + : channel.empty() + ch_msref = params.mitosalt_reference ? channel.fromPath(params.mitosalt_reference) + : channel.empty() + + // + // Call mitochondrial SVs + // + CALL_SV_MT( + ch_reads, + ch_mapped.genome_bam_bai, + ch_genome_fasta, + ch_msconfig, + ch_msref + ) + ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 2770144bf3de396c6bdb56ce200fc7adc03de23d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 20 Nov 2025 09:32:00 +0000 Subject: [PATCH 075/872] Template update for nf-core/tools version 3.5.1 --- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/fix_linting.yml | 2 +- .github/workflows/linting.yml | 6 +-- .github/workflows/nf-test.yml | 4 +- .github/workflows/release-announcements.yml | 9 ++--- .../workflows/template-version-comment.yml | 2 +- .nf-core.yml | 2 +- .prettierignore | 2 + README.md | 4 +- modules.json | 4 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 24 ++++++------ nextflow.config | 2 - ro-crate-metadata.json | 14 +++---- .../utils_nfcore_raredisease_pipeline/main.nf | 6 +-- .../nf-core/utils_nfcore_pipeline/main.nf | 2 +- workflows/raredisease.nf | 38 ++++++++++++++----- 20 files changed, 74 insertions(+), 59 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 213c6afbe..5cc5ff209 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -40,7 +40,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index cae8521ca..ce658b626 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 6d94bcbf9..45884ff90 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -127,7 +127,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 75c24ba1c..ebf4b81c9 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 30e66026f..7a527a346 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,7 +11,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Set up Python 3.14 uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -71,7 +71,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: linting-logs path: | diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index e20bf6d0c..c98d76ec7 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: fetch-depth: 0 @@ -85,7 +85,7 @@ jobs: TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index e64cebd6a..431d3d445 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -15,10 +15,9 @@ jobs: echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - name: get description - id: get_topics + id: get_description run: | - echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT - + echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -27,9 +26,7 @@ jobs: # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release message: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - ${{ steps.get_topics.outputs.description }} - + ${{ steps.get_description.outputs.description }} Please see the changelog: ${{ github.event.release.html_url }} ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index c5988af90..e8560fc7c 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.nf-core.yml b/.nf-core.yml index b09fc4c3d..c30136f84 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,7 +8,7 @@ lint: - docs/images/nf-core-raredisease_logo_light.png - assets/nf-core-raredisease_logo_light.png modules_config: false -nf_core_version: 3.4.1 +nf_core_version: 3.5.1 repository_type: pipeline template: author: Clinical Genomics Stockholm diff --git a/.prettierignore b/.prettierignore index 2255e3e36..dd749d43d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -12,3 +12,5 @@ testing* bin/ .nf-test/ ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/README.md b/README.md index 757211705..69f34e906 100644 --- a/README.md +++ b/README.md @@ -5,13 +5,13 @@ -[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease) +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease) [![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/modules.json b/modules.json index 4d6e14640..618ec0652 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b", + "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", "installed_by": ["modules"] } } @@ -26,7 +26,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index dd513cbd1..d02016a00 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.31 + - bioconda::multiqc=1.32 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 5288f5ccf..c1158fb08 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' : - 'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : + 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 17881d15c..a88bafd67 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:57:36.139055243" + "timestamp": "2025-10-27T13:33:24.356715" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:59:15.142230631" + "timestamp": "2025-10-27T13:34:11.103619" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "24.10.4" }, - "timestamp": "2025-09-08T20:58:29.629087066" + "timestamp": "2025-10-27T13:34:04.615233" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index af8d0c396..670d8aea1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -170,8 +170,6 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set AWS client to anonymous when using the default igenomes_base -aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false // Load nf-core custom profiles from different institutions // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index bb924f5cc..f4579141e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-10-16T13:38:58+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-11-20T09:31:56+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#fb488ede-d306-43ef-bc44-527dc8f10111" + "@id": "#6f2bb14f-9d35-4e7a-bdb2-b3f8a0952d05" } ], "name": "nf-core/raredisease" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-10-16T13:38:58Z", + "dateModified": "2025-11-20T09:31:56Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -161,11 +161,11 @@ "version": "!>=25.04.0" }, { - "@id": "#fb488ede-d306-43ef-bc44-527dc8f10111", + "@id": "#6f2bb14f-9d35-4e7a-bdb2-b3f8a0952d05", "@type": "TestSuite", "instance": [ { - "@id": "#e7b1a59e-d93b-4d46-b065-e5b00376601c" + "@id": "#7f2b0b84-cc76-45e2-964b-48cad7249f4f" } ], "mainEntity": { @@ -174,7 +174,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#e7b1a59e-d93b-4d46-b065-e5b00376601c", + "@id": "#7f2b0b84-cc76-45e2-964b-48cad7249f4f", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index b8517ea7d..d02b07c24 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION { main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // // Print version and exit if required and dump pipeline parameters to JSON file @@ -64,7 +64,7 @@ workflow PIPELINE_INITIALISATION { \033[0;35m nf-core/raredisease ${workflow.manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} + after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> " https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x @@ -101,7 +101,7 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // - Channel + channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index bfd258760..2f30e9a46 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -98,7 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a2905be29..16b2f11ba 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -22,8 +22,8 @@ workflow RAREDISEASE { ch_samplesheet // channel: samplesheet read in from --input main: - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() // // MODULE: Run FastQC // @@ -36,7 +36,25 @@ workflow RAREDISEASE { // // Collate and save software versions // - softwareVersionsToYAML(ch_versions) + def topic_versions = Channel.topic("versions") + .distinct() + .branch { entry -> + versions_file: entry instanceof Path + versions_tuple: true + } + + def topic_versions_string = topic_versions.versions_tuple + .map { process, tool, version -> + [ process[process.lastIndexOf(':')+1..-1], " ${tool}: ${version}" ] + } + .groupTuple(by:0) + .map { process, tool_versions -> + tool_versions.unique().sort() + "${process}:\n${tool_versions.join('\n')}" + } + + softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + .mix(topic_versions_string) .collectFile( storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_' + 'raredisease_software_' + 'mqc_' + 'versions.yml', @@ -48,24 +66,24 @@ workflow RAREDISEASE { // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath( + ch_multiqc_config = channel.fromPath( "$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_config, checkIfExists: true) : + channel.empty() ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() + channel.fromPath(params.multiqc_logo, checkIfExists: true) : + channel.empty() summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( + ch_methods_description = channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) From ed968a20602b84d3b983dca13fabc01cc40cad15 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 25 Nov 2025 13:43:48 +0100 Subject: [PATCH 076/872] add mitosalt references --- conf/modules/call_sv_MT.config | 1 - conf/test.config | 2 +- modules.json | 14 ++ modules/local/mitosalt/main.nf | 21 ++- modules/nf-core/hisat2/build/environment.yml | 8 + modules/nf-core/hisat2/build/main.nf | 74 +++++++++ modules/nf-core/hisat2/build/meta.yml | 72 +++++++++ .../nf-core/hisat2/build/tests/main.nf.test | 98 ++++++++++++ .../hisat2/build/tests/main.nf.test.snap | 90 +++++++++++ modules/nf-core/last/lastdb/environment.yml | 8 + modules/nf-core/last/lastdb/main.nf | 55 +++++++ modules/nf-core/last/lastdb/meta.yml | 51 ++++++ .../nf-core/last/lastdb/tests/main.nf.test | 80 ++++++++++ .../last/lastdb/tests/main.nf.test.snap | 149 ++++++++++++++++++ .../nf-core/last/lastdb/tests/nextflow.config | 7 + nextflow.config | 7 +- subworkflows/local/call_sv_MT/main.nf | 39 ++--- subworkflows/local/prepare_references/main.nf | 10 ++ workflows/raredisease.nf | 28 ++-- 19 files changed, 775 insertions(+), 39 deletions(-) create mode 100644 modules/nf-core/hisat2/build/environment.yml create mode 100644 modules/nf-core/hisat2/build/main.nf create mode 100644 modules/nf-core/hisat2/build/meta.yml create mode 100644 modules/nf-core/hisat2/build/tests/main.nf.test create mode 100644 modules/nf-core/hisat2/build/tests/main.nf.test.snap create mode 100644 modules/nf-core/last/lastdb/environment.yml create mode 100644 modules/nf-core/last/lastdb/main.nf create mode 100644 modules/nf-core/last/lastdb/meta.yml create mode 100644 modules/nf-core/last/lastdb/tests/main.nf.test create mode 100644 modules/nf-core/last/lastdb/tests/main.nf.test.snap create mode 100644 modules/nf-core/last/lastdb/tests/nextflow.config diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 4bbd5101b..4fa1a01e5 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -28,7 +28,6 @@ process { } withName: '.*CALL_SV_MT:MITOSALT' { - ext.args = "-tmp ." publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, mode: params.publish_dir_mode, diff --git a/conf/test.config b/conf/test.config index 1a98fa730..2bef0f6fa 100644 --- a/conf/test.config +++ b/conf/test.config @@ -67,5 +67,5 @@ params { vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' mitosalt_config = 'data/config_human.txt' mitosalt_reference = 'data/genome' - mitosalt_depth = '1000000' + mitosalt_depth = '100000' } diff --git a/modules.json b/modules.json index f6ebeb8d4..edc23cb80 100644 --- a/modules.json +++ b/modules.json @@ -408,6 +408,13 @@ "modules" ] }, + "hisat2/build": { + "branch": "master", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "installed_by": [ + "modules" + ] + }, "hmtnote/annotate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", @@ -416,6 +423,13 @@ ], "patch": "modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff" }, + "last/lastdb": { + "branch": "master", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "installed_by": [ + "modules" + ] + }, "manta/germline": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 007c0102e..04da24b62 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -1,17 +1,30 @@ #!/usr/bin/env nextflow process MITOSALT { - tag "MITOSALT" + tag "$meta.id" + label "process_low" conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" +// container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +// 'https://depot.galaxyproject.org/singularity/mitosalt:1.1.1--hdfd78af_2': +// 'quay.io/biocontainers/mitosalt:1.1.1--hdfd78af_2' }" + +// container 'docker://ieduba/mitosalt:latest' + input: tuple val(meta), path(reads) path config path genome +// tuple val(meta2), path(hisat2index) +// tuple val(meta3), path(genomefai) +// tuple val(meta4), path(lastindex) +// tuple val(meta5), path(mtfai) +// path chrsizes +// tuple val(meta6), path(mtfasta) output: tuple val(meta), path("*breakpoint") , emit: breakpoint @@ -22,9 +35,11 @@ process MITOSALT { def VERSION = "1.1.1" // from perl script, unlikely to be updated def prefix = task.ext.prefix ?: "${meta.id}" """ + mkdir -p log indel bam tab bw plot + MitoSAlt1.1.1.pl $config $reads $prefix - mv indel/*.breakpoint mitosalt_${prefix}.breakpoint - mv indel/*.cluster mitosalt_${prefix}.cluster + mv indel/*.breakpoint ${prefix}.breakpoint + mv indel/*.cluster ${prefix}.cluster cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml new file mode 100644 index 000000000..cbf12eadc --- /dev/null +++ b/modules/nf-core/hisat2/build/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::hisat2=2.2.1 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf new file mode 100644 index 000000000..1d9370107 --- /dev/null +++ b/modules/nf-core/hisat2/build/main.nf @@ -0,0 +1,74 @@ +process HISAT2_BUILD { + tag "${fasta}" + label 'process_high' + label 'process_high_memory' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d2/d2ec9b73c6b92e99334c6500b1b622edaac316315ac1708f0b425df3131d0a83/data' : + 'community.wave.seqera.io/library/hisat2_samtools:6be64e12472a7b75' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) + tuple val(meta3), path(splicesites) + + output: + tuple val(meta), path("hisat2"), emit: index + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def avail_mem = 0 + if (!task.memory) { + log.info("[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this.") + } + else { + log.info("[HISAT2 index build] Available memory: ${task.memory}") + avail_mem = task.memory.toGiga() + } + + def ss = '' + def exon = '' + def extract_exons = '' + def hisat2_build_memory = params.hisat2_build_memory ? (params.hisat2_build_memory as MemoryUnit).toGiga() : 0 + if (avail_mem >= hisat2_build_memory) { + log.info("[HISAT2 index build] At least ${hisat2_build_memory} GB available, so using splice sites and exons to build HISAT2 index") + extract_exons = gtf ? "hisat2_extract_exons.py ${gtf} > ${gtf.baseName}.exons.txt" : "" + ss = splicesites ? "--ss ${splicesites}" : "" + exon = gtf ? "--exon ${gtf.baseName}.exons.txt" : "" + } + else { + log.info("[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index.") + log.info("[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check.") + } + """ + mkdir hisat2 + ${extract_exons} + hisat2-build \\ + -p ${task.cpus} \\ + ${ss} \\ + ${exon} \\ + ${args} \\ + ${fasta} \\ + hisat2/${fasta.baseName} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) + END_VERSIONS + """ + + stub: + """ + mkdir hisat2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) + END_VERSIONS + """ +} diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml new file mode 100644 index 000000000..ede99d0cc --- /dev/null +++ b/modules/nf-core/hisat2/build/meta.yml @@ -0,0 +1,72 @@ +name: hisat2_build +description: Builds HISAT2 index for reference genome +keywords: + - build + - index + - fasta + - genome + - reference +tools: + - hisat2: + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. + homepage: https://daehwankimlab.github.io/hisat2/ + documentation: https://daehwankimlab.github.io/hisat2/manual/ + doi: "10.1038/s41587-019-0201-4" + licence: ["MIT"] + identifier: biotools:hisat2 +input: + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fa,fasta,fna}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" + ontologies: [] +output: + index: + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - hisat2: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@ntoda03" +maintainers: + - "@ntoda03" diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test new file mode 100644 index 000000000..948f98eae --- /dev/null +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -0,0 +1,98 @@ +nextflow_process { + + name "Test Process HISAT2_BUILD" + script "../main.nf" + process "HISAT2_BUILD" + tag "modules" + tag "modules_nfcore" + tag "hisat2" + tag "hisat2/build" + tag "hisat2/extractsplicesites" + + test("Should run without failures") { + + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Should run without failures - stub") { + + options "-stub" + + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap new file mode 100644 index 000000000..68fc7ffba --- /dev/null +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -0,0 +1,90 @@ +{ + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + [ + + ] + ] + ], + "1": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ], + "index": [ + [ + { + "id": "genome" + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-20T18:18:08.896422" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + [ + "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", + "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", + "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", + "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" + ] + ] + ], + "1": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ], + "index": [ + [ + { + "id": "genome" + }, + [ + "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", + "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", + "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", + "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", + "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", + "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", + "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" + ] + ] + ], + "versions": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-16T14:42:22.381609786" + } +} \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml new file mode 100644 index 000000000..f8d361e0b --- /dev/null +++ b/modules/nf-core/last/lastdb/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::last=1611 diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf new file mode 100644 index 000000000..ae1df8b42 --- /dev/null +++ b/modules/nf-core/last/lastdb/main.nf @@ -0,0 +1,55 @@ +process LAST_LASTDB { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0d27a2649f1291ff817dc8f73357ffac206424cd972d3855421e4258acc600f7/data' + : 'community.wave.seqera.io/library/last:1611--e1193b3871fa0975'}" + + input: + tuple val(meta), path(fastx) + + output: + tuple val(meta), path("lastdb"), emit: index + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir lastdb + lastdb \\ + $args \\ + -P $task.cpus \\ + lastdb/${prefix} \\ + $fastx + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + last: \$(lastdb --version 2>&1 | sed 's/lastdb //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir lastdb + touch lastdb/${prefix}.bck + touch lastdb/${prefix}.des + touch lastdb/${prefix}.prj + touch lastdb/${prefix}.sds + touch lastdb/${prefix}.ssp + touch lastdb/${prefix}.suf + touch lastdb/${prefix}.tis + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + last: \$(lastdb --version 2>&1 | sed 's/lastdb //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/last/lastdb/meta.yml b/modules/nf-core/last/lastdb/meta.yml new file mode 100644 index 000000000..9a5bcbb0a --- /dev/null +++ b/modules/nf-core/last/lastdb/meta.yml @@ -0,0 +1,51 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "last_lastdb" +description: Prepare sequences for subsequent alignment with lastal. +keywords: + - LAST + - index + - fasta + - fastq +tools: + - "last": + description: "LAST finds & aligns related regions of sequences." + homepage: "https://gitlab.com/mcfrith/last" + documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst" + tool_dev_url: "https://gitlab.com/mcfrith/last" + licence: ["GPL v3-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: > + Sequence file in FASTA or FASTQ format. May be compressed with gzip. + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ +output: + index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - lastdb: + type: directory + description: directory containing the files of the LAST index + pattern: "lastdb/" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@charles-plessy" +maintainers: + - "@charles-plessy" diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test b/modules/nf-core/last/lastdb/tests/main.nf.test new file mode 100644 index 000000000..1d5d40329 --- /dev/null +++ b/modules/nf-core/last/lastdb/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process LAST_LASTDB" + script "../main.nf" + process "LAST_LASTDB" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "last" + tag "last/lastdb" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fastq gzipped") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta stub") { + + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap new file mode 100644 index 000000000..382b364ba --- /dev/null +++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap @@ -0,0 +1,149 @@ +{ + "sarscov2 - fasta stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.des:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.prj:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sds:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.ssp:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.suf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tis:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.des:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.prj:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sds:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.ssp:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.suf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tis:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-10T10:48:34.761783" + }, + "sarscov2 - fastq gzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", + "test.des:md5,26ab49015cc572172b9efa50fc5190bc", + "test.prj:md5,a90d0d376caa024349b452d3d6d51676", + "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", + "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", + "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", + "test.tis:md5,d57a3a5f7e3e036807356c15bd3aad97" + ] + ] + ], + "1": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,05b14d8ac418b3193d9cc921086cea05", + "test.des:md5,26ab49015cc572172b9efa50fc5190bc", + "test.prj:md5,a90d0d376caa024349b452d3d6d51676", + "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b", + "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da", + "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0", + "test.tis:md5,d57a3a5f7e3e036807356c15bd3aad97" + ] + ] + ], + "versions": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-10T10:48:20.038195" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,157526d333b88523cb15ac4efe00738f", + "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", + "test.prj:md5,bb7b997633125f0310d02114b8531449", + "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", + "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", + "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", + "test.tis:md5,b7c40f06b1309dc6f37849eeb86dfd22" + ] + ] + ], + "1": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "test.bck:md5,157526d333b88523cb15ac4efe00738f", + "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc", + "test.prj:md5,bb7b997633125f0310d02114b8531449", + "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015", + "test.ssp:md5,53524efdea3d8989201419a29e81ec1f", + "test.suf:md5,ef7482260705bb8146acbbbdce6c0068", + "test.tis:md5,b7c40f06b1309dc6f37849eeb86dfd22" + ] + ] + ], + "versions": [ + "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-10T10:48:04.861781" + } +} \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/tests/nextflow.config b/modules/nf-core/last/lastdb/tests/nextflow.config new file mode 100644 index 000000000..50628ecdb --- /dev/null +++ b/modules/nf-core/last/lastdb/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: LAST_LASTDB { + ext.args = '-Q0' + } + +} diff --git a/nextflow.config b/nextflow.config index 2fa4d94e9..f904a8954 100644 --- a/nextflow.config +++ b/nextflow.config @@ -51,6 +51,7 @@ params { gens_gnomad_pos = null gnomad_af = null gnomad_af_idx = null + hisat2 = null intervals_wgs = null intervals_y = null known_dbsnp = null @@ -216,7 +217,6 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - singularity.pullTimeout = '50 min' } podman { podman.enabled = true @@ -494,8 +494,3 @@ validation { monochromeLogs = params.monochrome_logs } -singularity { - autoMounts = true - runOptions = '-B /home/irene.duba/tmp' -} - diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 25fb8354d..64562b2ea 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -8,35 +8,38 @@ include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' workflow CALL_SV_MT { take: - ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_msconfig // channel: [mandatory] [ path(msconfig) ] - ch_genome // channel: [mandatory] [ path(genome) ] + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_msconfig // channel: [mandatory] [ path(msconfig) ] + ch_msref // channel: [mandatory] [ path(genome) ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] main: ch_versions = Channel.empty() - ch_mitosalt_breakpoint = Channel.empty() - ch_mitosalt_cluster = Channel.empty() - ch_subdepth = params.mitosalt_depth - ch_reads_subdepth = ch_reads.map { meta, reads -> [meta, reads, ch_subdepth] } if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { - SEQTK_SAMPLE(ch_reads_subdepth) - ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) + ch_reads_subdepth = ch_reads.map { meta, reads -> [meta, reads, '1000000'] } + SEQTK_SAMPLE (ch_reads_subdepth) + ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_genome) - ch_mitosalt_breakpoint = MITOSALT.out.breakpoint - ch_mitosalt_cluster = MITOSALT.out.cluster - ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) +// MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta) + MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref) + ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } - MT_DELETION(ch_bam_bai, ch_fasta) + MT_DELETION(ch_bam_bai, ch_genome_fasta) ch_versions = ch_versions.mix(MT_DELETION.out.versions.first()) emit: - mitosalt_breakpoint = ch_mitosalt_breakpoint // channel: [ val(meta), path(breakpoint) ] - mitosalt_cluster = ch_mitosalt_cluster // channel: [ val(meta), path(cluster) ] + mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] + mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 61557e7a1..33d489906 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -17,6 +17,8 @@ include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../../mo include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../../modules/nf-core/gatk4/intervallisttools/main' include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../../modules/nf-core/gatk4/shiftfasta/main' include { GET_CHROM_SIZES } from '../../../modules/local/get_chrom_sizes' +include { HISAT2_BUILD as HISAT2_INDEX_GENOME } from '../../../modules/nf-core/hisat2/build' +include { LAST_LASTDB as LAST_INDEX_MT } from '../../../modules/nf-core/last/lastdb' include { RTGTOOLS_FORMAT } from '../../../modules/nf-core/rtgtools/format/main' include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../../modules/nf-core/samtools/faidx/main' include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../../modules/nf-core/samtools/faidx/main' @@ -54,6 +56,8 @@ workflow PREPARE_REFERENCES { ch_vcfanno_extra = Channel.empty() ch_vcfanno_bgzip = Channel.empty() ch_vcfanno_index = Channel.empty() + ch_gtf = Channel.empty() + ch_splicesites = Channel.empty() // Genome indices SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]) @@ -67,6 +71,7 @@ workflow PREPARE_REFERENCES { BWAMEM2_INDEX_GENOME(ch_genome_fasta) BWAMEME_INDEX_GENOME(ch_genome_fasta) SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} + HISAT2_INDEX_GENOME(ch_genome_fasta,ch_gtf,ch_splicesites) // MT genome indices SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) @@ -80,6 +85,7 @@ workflow PREPARE_REFERENCES { BWA_INDEX_MT(ch_mt_fasta_in) SENTIEON_BWAINDEX_MT(ch_mt_fasta_in) ch_bwa_mt = Channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() + LAST_INDEX_MT(ch_mt_fasta_in) BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) @@ -166,6 +172,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) + ch_versions = ch_versions.mix(HISAT2_INDEX_GENOME.out.versions) ch_versions = ch_versions.mix(GATK_SD.out.versions) ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) @@ -174,6 +181,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(GATK_SHIFTFASTA.out.versions) ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions) ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions) + ch_versions = ch_versions.mix(LAST_INDEX_MT.out.versions) ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions) ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT_SHIFT.out.versions) ch_versions = ch_versions.mix(BWA_INDEX_MT_SHIFT.out.versions) @@ -196,6 +204,7 @@ workflow PREPARE_REFERENCES { genome_bwa_index = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] genome_bwamem2_index = BWAMEM2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_bwameme_index = BWAMEME_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] + genome_hisat2_index = HISAT2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] genome_fai = ch_fai // channel: [ val(meta), path(fai) ] genome_dict = ch_dict // channel: [ val(meta), path(dict) ] @@ -203,6 +212,7 @@ workflow PREPARE_REFERENCES { mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] mt_bwa_index = ch_bwa_mt // channel: [ val(meta), path(index) ] mt_bwamem2_index = BWAMEM2_INDEX_MT.out.index.collect() // channel: [ val(meta), path(index) ] + mt_last_index = LAST_INDEX_MT.out.index // channel: [ val(meta), path(index) ] mt_dict = GATK_SD_MT.out.dict.collect() // channel: [ val(meta), path(dict) ] mt_fasta = ch_mt_fasta_in.collect() // channel: [ val(meta), path(fasta) ] mt_fai = SAMTOOLS_FAIDX_MT.out.fai.collect() // channel: [ val(meta), path(fai) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 9f65bf17a..209b69c74 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -153,6 +153,8 @@ workflow RAREDISEASE { ch_genome_chrsizes = ch_references.genome_chrom_sizes ch_genome_fai = ch_references.genome_fai ch_genome_dictionary = ch_references.genome_dict + ch_genome_hisat2index = params.hisat2 ? Channel.fromPath(params.hisat2).map {it -> [[id:it.simpleName], it]}.collect() + : ch_references.genome_hisat2_index ch_gens_gnomad_pos = params.gens_gnomad_pos ? Channel.fromPath(params.gens_gnomad_pos).collect() : Channel.empty() ch_gens_interval_list = params.gens_interval_list ? Channel.fromPath(params.gens_interval_list).collect() @@ -175,12 +177,17 @@ workflow RAREDISEASE { : Channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) + ch_msconfig = params.mitosalt_config ? channel.fromPath(params.mitosalt_config) + : channel.empty() + ch_msref = params.mitosalt_reference ? channel.fromPath(params.mitosalt_reference) + : channel.empty() ch_mt_intervals = ch_references.mt_intervals ch_mt_bwaindex = ch_references.mt_bwa_index ch_mt_bwamem2index = ch_references.mt_bwamem2_index ch_mt_dictionary = ch_references.mt_dict ch_mt_fai = ch_references.mt_fai ch_mt_fasta = ch_references.mt_fasta + ch_mt_lastdb = ch_references.mt_last_index ch_mtshift_backchain = ch_references.mtshift_backchain ch_mtshift_bwaindex = ch_references.mtshift_bwa_index ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index @@ -208,6 +215,8 @@ workflow RAREDISEASE { : Channel.value([]) ch_sdf = params.sdf ? Channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf + ch_subdepth = params.mitosalt_depth ? channel.fromPath(params.mitosalt_depth) + : channel.empty() ch_sv_dbs = params.svdb_query_dbs ? Channel.fromPath(params.svdb_query_dbs) : Channel.empty() ch_sv_bedpedbs = params.svdb_query_bedpedbs ? Channel.fromPath(params.svdb_query_bedpedbs) @@ -244,7 +253,7 @@ workflow RAREDISEASE { ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? Channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() : Channel.empty() ch_versions = ch_versions.mix(ch_references.versions) - + // // SV caller priority // @@ -721,14 +730,6 @@ workflow RAREDISEASE { CALL MITOCHONDRIAL SVs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - // - // Initialize file channels for mitosalt input - // - ch_msconfig = params.mitosalt_config ? channel.fromPath(params.mitosalt_config) - : channel.empty() - ch_msref = params.mitosalt_reference ? channel.fromPath(params.mitosalt_reference) - : channel.empty() - // // Call mitochondrial SVs // @@ -736,8 +737,15 @@ workflow RAREDISEASE { ch_reads, ch_mapped.genome_bam_bai, ch_genome_fasta, + ch_genome_hisat2index, + ch_genome_fai, + ch_mt_lastdb, + ch_mt_fai, + ch_genome_chrsizes, + ch_mt_fasta, ch_msconfig, - ch_msref + ch_msref, + ch_subdepth ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) From 28173b57e5ee5c994bfb4bc56ad7dd86f70ce6a3 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 09:37:46 +0100 Subject: [PATCH 077/872] add handling for chr prefix --- .nf-test.log | 180 ++++++++++++++++ .../meta/mock.nf | 86 ++++++++ .../meta/nextflow.log | 155 ++++++++++++++ .../meta/params.json | 1 + .../meta/std.err | 0 .../meta/std.out | 3 + .../meta/trace.csv | 1 + .../meta/mock.nf | 86 ++++++++ .../meta/nextflow.log | 155 ++++++++++++++ .../meta/params.json | 1 + .../meta/std.err | 0 .../meta/std.out | 3 + .../meta/trace.csv | 1 + .../meta/mock.nf | 86 ++++++++ .../meta/nextflow.log | 155 ++++++++++++++ .../meta/params.json | 1 + .../meta/std.err | 0 .../meta/std.out | 3 + .../meta/trace.csv | 1 + .../meta/mock.nf | 86 ++++++++ .../meta/nextflow.log | 155 ++++++++++++++ .../meta/params.json | 1 + .../meta/std.err | 0 .../meta/std.out | 3 + .../meta/trace.csv | 1 + conf/modules/annotate_cadd.config | 6 + modules.json | 5 + modules/nf-core/gawk/environment.yml | 7 + modules/nf-core/gawk/main.nf | 70 ++++++ modules/nf-core/gawk/meta.yml | 68 ++++++ modules/nf-core/gawk/tests/main.nf.test | 198 +++++++++++++++++ modules/nf-core/gawk/tests/main.nf.test.snap | 200 ++++++++++++++++++ modules/nf-core/gawk/tests/nextflow.config | 6 + modules/nf-core/tabix/bgziptabix/.nf-test.log | 80 +++++++ modules/nf-core/tabix/bgziptabix/main.nf | 2 +- .../tabix/bgziptabix/tests/.nf-test.log | 80 +++++++ subworkflows/local/annotate_cadd/main.nf | 44 +++- subworkflows/local/annotate_genome_snvs.nf | 13 +- subworkflows/local/annotate_mt_snvs.nf | 14 +- workflows/raredisease.nf | 7 +- 40 files changed, 1941 insertions(+), 23 deletions(-) create mode 100644 .nf-test.log create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out create mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out create mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out create mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out create mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv create mode 100644 modules/nf-core/gawk/environment.yml create mode 100644 modules/nf-core/gawk/main.nf create mode 100644 modules/nf-core/gawk/meta.yml create mode 100644 modules/nf-core/gawk/tests/main.nf.test create mode 100644 modules/nf-core/gawk/tests/main.nf.test.snap create mode 100644 modules/nf-core/gawk/tests/nextflow.config create mode 100644 modules/nf-core/tabix/bgziptabix/.nf-test.log create mode 100644 modules/nf-core/tabix/bgziptabix/tests/.nf-test.log diff --git a/.nf-test.log b/.nf-test.log new file mode 100644 index 000000000..7f02d1750 --- /dev/null +++ b/.nf-test.log @@ -0,0 +1,180 @@ +Nov-15 13:31:09.616 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 +Nov-15 13:31:09.652 [main] INFO com.askimed.nf.test.App - Arguments: [test, modules/nf-core/tabix/bgziptabix/tests/main.nf.test] +Nov-15 13:31:11.675 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 +Nov-15 13:31:11.688 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. +Nov-15 13:31:12.517 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 332 files from directory /Users/annick.renevey/Projects/raredisease in 0.824 sec +Nov-15 13:31:12.536 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. +Nov-15 13:31:12.536 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] +Nov-15 13:31:12.536 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. +Nov-15 13:31:13.837 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan +Nov-15 13:31:13.838 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. +Nov-15 13:31:13.838 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:31:30.599 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED +org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed + at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) + at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) + at main_nf$_run_closure1$_closure2$_closure7.doCall(main.nf.test:27) + at main_nf$_run_closure1$_closure2$_closure7.doCall(main.nf.test) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) + at groovy.lang.Closure.call(Closure.java:427) + at groovy.lang.Closure.call(Closure.java:406) + at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:31:30.621 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:31:47.247 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED +org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed + at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) + at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) + at main_nf$_run_closure1$_closure3$_closure13.doCall(main.nf.test:53) + at main_nf$_run_closure1$_closure3$_closure13.doCall(main.nf.test) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) + at groovy.lang.Closure.call(Closure.java:427) + at groovy.lang.Closure.call(Closure.java:406) + at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:31:47.248 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:32:06.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED +org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed + at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) + at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) + at main_nf$_run_closure1$_closure4$_closure19.doCall(main.nf.test:82) + at main_nf$_run_closure1$_closure4$_closure19.doCall(main.nf.test) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) + at groovy.lang.Closure.call(Closure.java:427) + at groovy.lang.Closure.call(Closure.java:406) + at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:32:06.215 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:32:24.189 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED +org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed + at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) + at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) + at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) + at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) + at main_nf$_run_closure1$_closure5$_closure25.doCall(main.nf.test:111) + at main_nf$_run_closure1$_closure5$_closure25.doCall(main.nf.test) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) + at groovy.lang.Closure.call(Closure.java:427) + at groovy.lang.Closure.call(Closure.java:406) + at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:32:24.190 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true +Nov-15 13:32:24.191 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf new file mode 100644 index 000000000..688cc1328 --- /dev/null +++ b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf @@ -0,0 +1,86 @@ +import groovy.json.JsonGenerator +import groovy.json.JsonGenerator.Converter + +nextflow.enable.dsl=2 + +// comes from nf-test to store json files +params.nf_test_output = "" + +// include dependencies + + +// include test process +include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' + +// define custom rules for JSON that will be generated. +def jsonOutput = + new JsonGenerator.Options() + .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename + .build() + +def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() + + +workflow { + + // run dependencies + + + // process mapping + def input = [] + + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + + //---- + + //run process + TABIX_BGZIPTABIX(*input) + + if (TABIX_BGZIPTABIX.output){ + + // consumes all named output channels and stores items in a json file + for (def name in TABIX_BGZIPTABIX.out.getNames()) { + serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) + } + + // consumes all unnamed output channels and stores items in a json file + def array = TABIX_BGZIPTABIX.out as Object[] + for (def i = 0; i < array.length ; i++) { + serializeChannel(i, array[i], jsonOutput) + } + + } + +} + +def serializeChannel(name, channel, jsonOutput) { + def _name = name + def list = [ ] + channel.subscribe( + onNext: { + list.add(it) + }, + onComplete: { + def map = new HashMap() + map[_name] = list + def filename = "${params.nf_test_output}/output_${_name}.json" + new File(filename).text = jsonOutput.toJson(map) + } + ) +} + + +workflow.onComplete { + + def result = [ + success: workflow.success, + exitStatus: workflow.exitStatus, + errorMessage: workflow.errorMessage, + errorReport: workflow.errorReport + ] + new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) + +} diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log new file mode 100644 index 000000000..f6d032e40 --- /dev/null +++ b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log @@ -0,0 +1,155 @@ +Nov-15 13:32:09.018 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/work -stub +Nov-15 13:32:09.207 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 +Nov-15 13:32:09.267 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 +Nov-15 13:32:09.313 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +Nov-15 13:32:09.315 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +Nov-15 13:32:09.321 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +Nov-15 13:32:09.348 [main] INFO org.pf4j.AbstractPluginManager - No plugins +Nov-15 13:32:09.436 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:32:09.445 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:32:09.446 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config +Nov-15 13:32:09.447 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:32:09.448 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:32:09.448 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config +Nov-15 13:32:09.552 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json +Nov-15 13:32:09.560 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5b69d40d] - activable => nextflow.secret.LocalSecretsProvider@5b69d40d +Nov-15 13:32:09.637 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:32:17.762 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:32:21.455 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:32:21.694 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration +Nov-15 13:32:21.714 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf` [gloomy_hopper] DSL2 - revision: bc38ccaa64 +Nov-15 13:32:21.717 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] +Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] +Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 +Nov-15 13:32:21.736 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved +Nov-15 13:32:21.737 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' +Nov-15 13:32:21.765 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 +Nov-15 13:32:21.861 [main] DEBUG nextflow.Session - Session UUID: 7ba3b48d-c6af-4074-a135-275ae065d882 +Nov-15 13:32:21.862 [main] DEBUG nextflow.Session - Run name: gloomy_hopper +Nov-15 13:32:21.862 [main] DEBUG nextflow.Session - Executor pool size: 8 +Nov-15 13:32:21.878 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +Nov-15 13:32:21.890 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Nov-15 13:32:21.928 [main] DEBUG nextflow.cli.CmdRun - + Version: 24.10.0 build 5928 + Created: 27-10-2024 18:36 UTC (19:36 CEST) + System: Mac OS X 15.0.1 + Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS + Encoding: UTF-8 (UTF-8) + Process: 47561@annickrmbp [130.229.165.9] + CPUs: 8 - Mem: 16 GB (13.9 MB) - Swap: 13 GB (1 GB) +Nov-15 13:32:21.968 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/work [Mac OS X] +Nov-15 13:32:22.038 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +Nov-15 13:32:22.051 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory +Nov-15 13:32:22.152 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +Nov-15 13:32:22.194 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 +Nov-15 13:32:22.311 [main] DEBUG nextflow.Session - Session start +Nov-15 13:32:22.328 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv +Nov-15 13:32:22.381 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:32:22.523 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:32:23.439 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +Nov-15 13:32:24.080 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` +Nov-15 13:32:24.098 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf + Script_2f4fa37490aa9602: /Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf +Nov-15 13:32:24.098 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed +Nov-15 13:32:24.104 [main] DEBUG nextflow.Session - +Thread[Finalizer,8,system] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) + java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) + +Thread[Common-Cleaner,8,InnocuousThreadGroup] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) + +Thread[Signal Dispatcher,9,system] + +Thread[Notification Thread,9,system] + +Thread[Actor Thread 1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) + java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Reference Handler,10,system] + java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) + java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) + java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) + +Thread[main,5,main] + java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) + java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) + app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) + app//nextflow.Session.abort(Session.groovy:800) + app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) + app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) + app//nextflow.cli.Launcher.run(Launcher.groovy:503) + app//nextflow.cli.Launcher.main(Launcher.groovy:658) + +Thread[Thread-1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) + java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) + app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) + app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + app//groovy.lang.Closure.call(Closure.java:433) + app//groovy.lang.Closure.call(Closure.java:412) + app//groovy.lang.Closure.run(Closure.java:505) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Nov-15 13:32:24.124 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed +java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed + at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.Nextflow.file(Nextflow.groovy:123) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_2f4fa37490aa9602$_runScript_closure4$_closure6.doCall(Script_2f4fa37490aa9602:34) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run0(BaseScript.groovy:198) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run(BaseScript.groovy:209) + at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) + at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) + at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) + at nextflow.cli.CmdRun.run(CmdRun.groovy:376) + at nextflow.cli.Launcher.run(Launcher.groovy:503) + at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json new file mode 100644 index 000000000..858f09524 --- /dev/null +++ b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json @@ -0,0 +1 @@ +{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta"} \ No newline at end of file diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err new file mode 100644 index 000000000..e69de29bb diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out new file mode 100644 index 000000000..54dfb492d --- /dev/null +++ b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out @@ -0,0 +1,3 @@ +ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed + + -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv new file mode 100644 index 000000000..6b739acdf --- /dev/null +++ b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf new file mode 100644 index 000000000..d789b2961 --- /dev/null +++ b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf @@ -0,0 +1,86 @@ +import groovy.json.JsonGenerator +import groovy.json.JsonGenerator.Converter + +nextflow.enable.dsl=2 + +// comes from nf-test to store json files +params.nf_test_output = "" + +// include dependencies + + +// include test process +include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' + +// define custom rules for JSON that will be generated. +def jsonOutput = + new JsonGenerator.Options() + .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename + .build() + +def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() + + +workflow { + + // run dependencies + + + // process mapping + def input = [] + + input[0] = [ + [ id:'tbi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + + //---- + + //run process + TABIX_BGZIPTABIX(*input) + + if (TABIX_BGZIPTABIX.output){ + + // consumes all named output channels and stores items in a json file + for (def name in TABIX_BGZIPTABIX.out.getNames()) { + serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) + } + + // consumes all unnamed output channels and stores items in a json file + def array = TABIX_BGZIPTABIX.out as Object[] + for (def i = 0; i < array.length ; i++) { + serializeChannel(i, array[i], jsonOutput) + } + + } + +} + +def serializeChannel(name, channel, jsonOutput) { + def _name = name + def list = [ ] + channel.subscribe( + onNext: { + list.add(it) + }, + onComplete: { + def map = new HashMap() + map[_name] = list + def filename = "${params.nf_test_output}/output_${_name}.json" + new File(filename).text = jsonOutput.toJson(map) + } + ) +} + + +workflow.onComplete { + + def result = [ + success: workflow.success, + exitStatus: workflow.exitStatus, + errorMessage: workflow.errorMessage, + errorReport: workflow.errorReport + ] + new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) + +} diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log new file mode 100644 index 000000000..7b12db494 --- /dev/null +++ b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log @@ -0,0 +1,155 @@ +Nov-15 13:31:16.857 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/work +Nov-15 13:31:17.034 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 +Nov-15 13:31:17.095 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 +Nov-15 13:31:17.143 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +Nov-15 13:31:17.144 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +Nov-15 13:31:17.152 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +Nov-15 13:31:17.181 [main] INFO org.pf4j.AbstractPluginManager - No plugins +Nov-15 13:31:17.278 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:17.294 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:17.296 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config +Nov-15 13:31:17.303 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:17.305 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:17.306 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config +Nov-15 13:31:17.419 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json +Nov-15 13:31:17.428 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@78d39a69] - activable => nextflow.secret.LocalSecretsProvider@78d39a69 +Nov-15 13:31:17.488 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:25.071 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:27.680 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:28.003 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration +Nov-15 13:31:28.057 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf` [marvelous_celsius] DSL2 - revision: be2d57c639 +Nov-15 13:31:28.074 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] +Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] +Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 +Nov-15 13:31:28.194 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved +Nov-15 13:31:28.196 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' +Nov-15 13:31:28.293 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 +Nov-15 13:31:28.534 [main] DEBUG nextflow.Session - Session UUID: 33b7f0a5-cbf7-4a4c-8ee0-6ac139ead31d +Nov-15 13:31:28.535 [main] DEBUG nextflow.Session - Run name: marvelous_celsius +Nov-15 13:31:28.537 [main] DEBUG nextflow.Session - Executor pool size: 8 +Nov-15 13:31:28.553 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +Nov-15 13:31:28.564 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Nov-15 13:31:28.615 [main] DEBUG nextflow.cli.CmdRun - + Version: 24.10.0 build 5928 + Created: 27-10-2024 18:36 UTC (19:36 CEST) + System: Mac OS X 15.0.1 + Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS + Encoding: UTF-8 (UTF-8) + Process: 46100@annickrmbp [130.229.165.9] + CPUs: 8 - Mem: 16 GB (32.3 MB) - Swap: 12 GB (784.6 MB) +Nov-15 13:31:28.692 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/work [Mac OS X] +Nov-15 13:31:28.772 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +Nov-15 13:31:28.785 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory +Nov-15 13:31:28.906 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +Nov-15 13:31:28.927 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 +Nov-15 13:31:28.994 [main] DEBUG nextflow.Session - Session start +Nov-15 13:31:29.001 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv +Nov-15 13:31:29.016 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:31:29.021 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:31:29.939 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +Nov-15 13:31:30.457 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` +Nov-15 13:31:30.473 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf + Script_21322127a7e32787: /Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf +Nov-15 13:31:30.473 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed +Nov-15 13:31:30.477 [main] DEBUG nextflow.Session - +Thread[Actor Thread 1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) + java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Reference Handler,10,system] + java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) + java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) + java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) + +Thread[main,5,main] + java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) + java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) + app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) + app//nextflow.Session.abort(Session.groovy:800) + app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) + app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) + app//nextflow.cli.Launcher.run(Launcher.groovy:503) + app//nextflow.cli.Launcher.main(Launcher.groovy:658) + +Thread[Finalizer,8,system] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) + java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) + +Thread[Common-Cleaner,8,InnocuousThreadGroup] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) + +Thread[Thread-1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) + java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) + app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) + app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + app//groovy.lang.Closure.call(Closure.java:433) + app//groovy.lang.Closure.call(Closure.java:412) + app//groovy.lang.Closure.run(Closure.java:505) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Notification Thread,9,system] + +Thread[Signal Dispatcher,9,system] + +Nov-15 13:31:30.497 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed +java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed + at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.Nextflow.file(Nextflow.groovy:123) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_21322127a7e32787$_runScript_closure4$_closure6.doCall(Script_21322127a7e32787:34) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run0(BaseScript.groovy:198) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run(BaseScript.groovy:209) + at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) + at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) + at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) + at nextflow.cli.CmdRun.run(CmdRun.groovy:376) + at nextflow.cli.Launcher.run(Launcher.groovy:503) + at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json new file mode 100644 index 000000000..11b8863fc --- /dev/null +++ b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json @@ -0,0 +1 @@ +{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta"} \ No newline at end of file diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err new file mode 100644 index 000000000..e69de29bb diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out new file mode 100644 index 000000000..9ec48ae7b --- /dev/null +++ b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out @@ -0,0 +1,3 @@ +ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed + + -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv new file mode 100644 index 000000000..6b739acdf --- /dev/null +++ b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf new file mode 100644 index 000000000..f3d4619b1 --- /dev/null +++ b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf @@ -0,0 +1,86 @@ +import groovy.json.JsonGenerator +import groovy.json.JsonGenerator.Converter + +nextflow.enable.dsl=2 + +// comes from nf-test to store json files +params.nf_test_output = "" + +// include dependencies + + +// include test process +include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' + +// define custom rules for JSON that will be generated. +def jsonOutput = + new JsonGenerator.Options() + .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename + .build() + +def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() + + +workflow { + + // run dependencies + + + // process mapping + def input = [] + + input[0] = [ + [ id:'csi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + + //---- + + //run process + TABIX_BGZIPTABIX(*input) + + if (TABIX_BGZIPTABIX.output){ + + // consumes all named output channels and stores items in a json file + for (def name in TABIX_BGZIPTABIX.out.getNames()) { + serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) + } + + // consumes all unnamed output channels and stores items in a json file + def array = TABIX_BGZIPTABIX.out as Object[] + for (def i = 0; i < array.length ; i++) { + serializeChannel(i, array[i], jsonOutput) + } + + } + +} + +def serializeChannel(name, channel, jsonOutput) { + def _name = name + def list = [ ] + channel.subscribe( + onNext: { + list.add(it) + }, + onComplete: { + def map = new HashMap() + map[_name] = list + def filename = "${params.nf_test_output}/output_${_name}.json" + new File(filename).text = jsonOutput.toJson(map) + } + ) +} + + +workflow.onComplete { + + def result = [ + success: workflow.success, + exitStatus: workflow.exitStatus, + errorMessage: workflow.errorMessage, + errorReport: workflow.errorReport + ] + new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) + +} diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log new file mode 100644 index 000000000..81708986c --- /dev/null +++ b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log @@ -0,0 +1,155 @@ +Nov-15 13:31:33.365 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/work +Nov-15 13:31:33.544 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 +Nov-15 13:31:33.607 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 +Nov-15 13:31:33.647 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +Nov-15 13:31:33.648 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +Nov-15 13:31:33.654 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +Nov-15 13:31:33.679 [main] INFO org.pf4j.AbstractPluginManager - No plugins +Nov-15 13:31:33.780 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:33.805 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:33.806 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config +Nov-15 13:31:33.809 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:33.810 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:33.810 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config +Nov-15 13:31:33.903 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json +Nov-15 13:31:33.910 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@78d39a69] - activable => nextflow.secret.LocalSecretsProvider@78d39a69 +Nov-15 13:31:33.983 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:41.776 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:44.297 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:44.788 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration +Nov-15 13:31:44.882 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf` [awesome_church] DSL2 - revision: 059c08dd97 +Nov-15 13:31:44.896 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] +Nov-15 13:31:44.900 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +Nov-15 13:31:44.900 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] +Nov-15 13:31:44.901 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 +Nov-15 13:31:44.942 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved +Nov-15 13:31:44.943 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' +Nov-15 13:31:45.023 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 +Nov-15 13:31:45.185 [main] DEBUG nextflow.Session - Session UUID: 0379aa71-7989-470e-87e9-7a052f6d84a1 +Nov-15 13:31:45.186 [main] DEBUG nextflow.Session - Run name: awesome_church +Nov-15 13:31:45.187 [main] DEBUG nextflow.Session - Executor pool size: 8 +Nov-15 13:31:45.200 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +Nov-15 13:31:45.210 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Nov-15 13:31:45.253 [main] DEBUG nextflow.cli.CmdRun - + Version: 24.10.0 build 5928 + Created: 27-10-2024 18:36 UTC (19:36 CEST) + System: Mac OS X 15.0.1 + Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS + Encoding: UTF-8 (UTF-8) + Process: 46566@annickrmbp [130.229.165.9] + CPUs: 8 - Mem: 16 GB (43.7 MB) - Swap: 12 GB (792.6 MB) +Nov-15 13:31:45.303 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/work [Mac OS X] +Nov-15 13:31:45.382 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +Nov-15 13:31:45.406 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory +Nov-15 13:31:45.498 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +Nov-15 13:31:45.516 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 +Nov-15 13:31:45.583 [main] DEBUG nextflow.Session - Session start +Nov-15 13:31:45.595 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv +Nov-15 13:31:45.607 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:31:45.612 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:31:46.452 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +Nov-15 13:31:47.152 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` +Nov-15 13:31:47.172 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_d7f74ea11eca7966: /Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf + Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf +Nov-15 13:31:47.173 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed +Nov-15 13:31:47.179 [main] DEBUG nextflow.Session - +Thread[Actor Thread 1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) + java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Reference Handler,10,system] + java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) + java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) + java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) + +Thread[main,5,main] + java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) + java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) + app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) + app//nextflow.Session.abort(Session.groovy:800) + app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) + app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) + app//nextflow.cli.Launcher.run(Launcher.groovy:503) + app//nextflow.cli.Launcher.main(Launcher.groovy:658) + +Thread[Finalizer,8,system] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) + java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) + +Thread[Common-Cleaner,8,InnocuousThreadGroup] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) + +Thread[Thread-1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) + java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) + app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) + app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + app//groovy.lang.Closure.call(Closure.java:433) + app//groovy.lang.Closure.call(Closure.java:412) + app//groovy.lang.Closure.run(Closure.java:505) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Notification Thread,9,system] + +Thread[Signal Dispatcher,9,system] + +Nov-15 13:31:47.199 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed +java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed + at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.Nextflow.file(Nextflow.groovy:123) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_d7f74ea11eca7966$_runScript_closure4$_closure6.doCall(Script_d7f74ea11eca7966:34) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run0(BaseScript.groovy:198) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run(BaseScript.groovy:209) + at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) + at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) + at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) + at nextflow.cli.CmdRun.run(CmdRun.groovy:376) + at nextflow.cli.Launcher.run(Launcher.groovy:503) + at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json new file mode 100644 index 000000000..afb274ded --- /dev/null +++ b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json @@ -0,0 +1 @@ +{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta"} \ No newline at end of file diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err new file mode 100644 index 000000000..e69de29bb diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out new file mode 100644 index 000000000..4b45dfd73 --- /dev/null +++ b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out @@ -0,0 +1,3 @@ +ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed + + -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv new file mode 100644 index 000000000..6b739acdf --- /dev/null +++ b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf new file mode 100644 index 000000000..688cc1328 --- /dev/null +++ b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf @@ -0,0 +1,86 @@ +import groovy.json.JsonGenerator +import groovy.json.JsonGenerator.Converter + +nextflow.enable.dsl=2 + +// comes from nf-test to store json files +params.nf_test_output = "" + +// include dependencies + + +// include test process +include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' + +// define custom rules for JSON that will be generated. +def jsonOutput = + new JsonGenerator.Options() + .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename + .build() + +def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() + + +workflow { + + // run dependencies + + + // process mapping + def input = [] + + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + + //---- + + //run process + TABIX_BGZIPTABIX(*input) + + if (TABIX_BGZIPTABIX.output){ + + // consumes all named output channels and stores items in a json file + for (def name in TABIX_BGZIPTABIX.out.getNames()) { + serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) + } + + // consumes all unnamed output channels and stores items in a json file + def array = TABIX_BGZIPTABIX.out as Object[] + for (def i = 0; i < array.length ; i++) { + serializeChannel(i, array[i], jsonOutput) + } + + } + +} + +def serializeChannel(name, channel, jsonOutput) { + def _name = name + def list = [ ] + channel.subscribe( + onNext: { + list.add(it) + }, + onComplete: { + def map = new HashMap() + map[_name] = list + def filename = "${params.nf_test_output}/output_${_name}.json" + new File(filename).text = jsonOutput.toJson(map) + } + ) +} + + +workflow.onComplete { + + def result = [ + success: workflow.success, + exitStatus: workflow.exitStatus, + errorMessage: workflow.errorMessage, + errorReport: workflow.errorReport + ] + new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) + +} diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log new file mode 100644 index 000000000..0ba3b2d33 --- /dev/null +++ b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log @@ -0,0 +1,155 @@ +Nov-15 13:31:50.087 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/work -stub +Nov-15 13:31:50.264 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 +Nov-15 13:31:50.324 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 +Nov-15 13:31:50.357 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +Nov-15 13:31:50.358 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +Nov-15 13:31:50.364 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +Nov-15 13:31:50.389 [main] INFO org.pf4j.AbstractPluginManager - No plugins +Nov-15 13:31:50.502 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:50.513 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:50.513 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config +Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config +Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config +Nov-15 13:31:50.601 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json +Nov-15 13:31:50.607 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5b69d40d] - activable => nextflow.secret.LocalSecretsProvider@5b69d40d +Nov-15 13:31:50.685 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:31:59.820 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:32:03.237 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +Nov-15 13:32:03.493 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration +Nov-15 13:32:03.514 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf` [kickass_angela] DSL2 - revision: bc38ccaa64 +Nov-15 13:32:03.516 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] +Nov-15 13:32:03.517 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +Nov-15 13:32:03.517 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] +Nov-15 13:32:03.518 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 +Nov-15 13:32:03.537 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved +Nov-15 13:32:03.537 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' +Nov-15 13:32:03.565 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 +Nov-15 13:32:03.670 [main] DEBUG nextflow.Session - Session UUID: 44b6788f-5f43-45f7-8b39-2e10b1e5efa6 +Nov-15 13:32:03.671 [main] DEBUG nextflow.Session - Run name: kickass_angela +Nov-15 13:32:03.672 [main] DEBUG nextflow.Session - Executor pool size: 8 +Nov-15 13:32:03.681 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +Nov-15 13:32:03.693 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Nov-15 13:32:03.793 [main] DEBUG nextflow.cli.CmdRun - + Version: 24.10.0 build 5928 + Created: 27-10-2024 18:36 UTC (19:36 CEST) + System: Mac OS X 15.0.1 + Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS + Encoding: UTF-8 (UTF-8) + Process: 47032@annickrmbp [130.229.165.9] + CPUs: 8 - Mem: 16 GB (50 MB) - Swap: 13 GB (1021.2 MB) +Nov-15 13:32:03.865 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/work [Mac OS X] +Nov-15 13:32:04.071 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +Nov-15 13:32:04.091 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory +Nov-15 13:32:04.223 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +Nov-15 13:32:04.266 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 +Nov-15 13:32:04.384 [main] DEBUG nextflow.Session - Session start +Nov-15 13:32:04.404 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv +Nov-15 13:32:04.449 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:32:04.463 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib +Nov-15 13:32:05.317 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +Nov-15 13:32:06.097 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` +Nov-15 13:32:06.115 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf + Script_2f4fa37490aa9602: /Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf +Nov-15 13:32:06.115 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed +Nov-15 13:32:06.120 [main] DEBUG nextflow.Session - +Thread[Thread-1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) + java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) + java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) + app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) + app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) + app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) + app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + app//groovy.lang.Closure.call(Closure.java:433) + app//groovy.lang.Closure.call(Closure.java:412) + app//groovy.lang.Closure.run(Closure.java:505) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Common-Cleaner,8,InnocuousThreadGroup] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) + +Thread[Actor Thread 1,5,main] + java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) + java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) + java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) + java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) + java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) + java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) + java.base@17.0.3/java.lang.Thread.run(Thread.java:833) + +Thread[Reference Handler,10,system] + java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) + java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) + java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) + +Thread[Signal Dispatcher,9,system] + +Thread[Finalizer,8,system] + java.base@17.0.3/java.lang.Object.wait(Native Method) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) + java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) + java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) + +Thread[main,5,main] + java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) + java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) + app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) + app//nextflow.Session.abort(Session.groovy:800) + app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) + app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) + app//nextflow.cli.Launcher.run(Launcher.groovy:503) + app//nextflow.cli.Launcher.main(Launcher.groovy:658) + +Thread[Notification Thread,9,system] + +Nov-15 13:32:06.140 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed +java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed + at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.Nextflow.file(Nextflow.groovy:123) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_2f4fa37490aa9602$_runScript_closure4$_closure6.doCall(Script_2f4fa37490aa9602:34) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:568) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run0(BaseScript.groovy:198) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.script.BaseScript.run(BaseScript.groovy:209) + at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) + at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) + at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) + at nextflow.cli.CmdRun.run(CmdRun.groovy:376) + at nextflow.cli.Launcher.run(Launcher.groovy:503) + at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json new file mode 100644 index 000000000..b44558174 --- /dev/null +++ b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json @@ -0,0 +1 @@ +{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta"} \ No newline at end of file diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err new file mode 100644 index 000000000..e69de29bb diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out new file mode 100644 index 000000000..459aa58bc --- /dev/null +++ b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out @@ -0,0 +1,3 @@ +ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed + + -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv new file mode 100644 index 000000000..6b739acdf --- /dev/null +++ b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index 9034887fc..46d170304 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -38,4 +38,10 @@ process { ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z" } ext.prefix = { "${input.simpleName}_ann" } } + + withName: '.*:ANNOTATE_CADD:REFERENCE_TO_CADD_CHRNAMES' { + ext.args2 = '\'{original=$1; sub("chr","",$1); print original, $1}\'' + ext.prefix = "reference_to_cadd" + ext.suffix = "txt" + } } diff --git a/modules.json b/modules.json index 938938441..4c7996444 100644 --- a/modules.json +++ b/modules.json @@ -257,6 +257,11 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "gawk": { + "branch": "master", + "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", + "installed_by": ["modules"] + }, "genmod/annotate": { "branch": "master", "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml new file mode 100644 index 000000000..f52109e83 --- /dev/null +++ b/modules/nf-core/gawk/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf new file mode 100644 index 000000000..da79a0ed3 --- /dev/null +++ b/modules/nf-core/gawk/main.nf @@ -0,0 +1,70 @@ +process GAWK { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : + 'biocontainers/gawk:5.3.0' }" + + input: + tuple val(meta), path(input, arity: '0..*') + path(program_file) + val(disable_redirect_output) + + output: + tuple val(meta), path("*.${suffix}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' // args is used for the main arguments of the tool + def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.collect{ file -> file.getExtension()}.get(0)}" // use the first extension of the input files + + program = program_file ? "-f ${program_file}" : "${args2}" + lst_gz = input.findResults{ file -> file.getExtension().endsWith("gz") ? file.toString() : null } + unzip = lst_gz ? "gunzip -q -f ${lst_gz.join(" ")}" : "" + input_cmd = input.collect { file -> file.toString() - ~/\.gz$/ }.join(" ") + output_cmd = suffix.endsWith("gz") ? "| gzip > ${prefix}.${suffix}" : "> ${prefix}.${suffix}" + output = disable_redirect_output ? "" : output_cmd + cleanup = lst_gz ? "rm ${lst_gz.collect{ file -> file - ~/\.gz$/ }.join(" ")}" : "" + + input.collect{ file -> + assert file.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!" + } + + """ + ${unzip} + + awk \\ + ${args} \\ + ${program} \\ + ${input_cmd} \\ + ${output} + + ${cleanup} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" + + """ + ${create_cmd} ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml new file mode 100644 index 000000000..732e18a97 --- /dev/null +++ b/modules/nf-core/gawk/meta.yml @@ -0,0 +1,68 @@ +name: "gawk" +description: | + If you are like many computer users, you would frequently like to make changes in various text files + wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. + The job is easy with awk, especially the GNU implementation gawk. +keywords: + - gawk + - awk + - txt + - text + - file parsing +tools: + - "gawk": + description: "GNU awk" + homepage: "https://www.gnu.org/software/gawk/" + documentation: "https://www.gnu.org/software/gawk/manual/" + tool_dev_url: "https://www.gnu.org/prep/ftp.html" + licence: ["GPL v3"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on + this file on the `ext.args2` or in the program file. If the files have a `.gz` + extension, they will be unzipped using `zcat`. + pattern: "*" + ontologies: [] + - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't wish + to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" + ontologies: [] + - disable_redirect_output: + type: boolean + description: Disable the redirection of awk output to a given file. This is useful + if you want to use awk's built-in redirect to write files instead of the shell's + redirect. +output: + output: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: The output file - if using shell redirection, specify the name + of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, + ensure the awk program produces files with the extension in `ext.suffix`. + pattern: "*" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test new file mode 100644 index 000000000..fc6e240fd --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -0,0 +1,198 @@ +nextflow_process { + + name "Test Process GAWK" + script "../main.nf" + process "GAWK" + + tag "modules" + tag "modules_nfcore" + tag "gawk" + + config "./nextflow.config" + + test("Convert fasta to bed") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Convert fasta to bed with program file") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = Channel.of('BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Convert fasta to bed using awk redirect instead of shell redirect") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 > "test.bed" }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Extract first column from multiple files") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Unzip files before processing") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] + ] + input[1] = Channel.of('/^#CHROM/ { print \$1, \$10 }').collectFile(name:"column_header.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Compress after processing") { + when { + params { + gawk_suffix = "txt.gz" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Input and output files are similar") { + when { + params { + gawk_suffix = "txt" + gawk_args = "" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'hello' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } + ) + } + } +} diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap new file mode 100644 index 000000000..d8e8ac755 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -0,0 +1,200 @@ +{ + "Compress after processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-27T17:11:20.054143406" + }, + "Convert fasta to bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T13:14:02.347809811" + }, + "Convert fasta to bed with program file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T13:14:11.894616209" + }, + "Extract first column from multiple files": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:04:47.729300129" + }, + "Unzip files before processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:08:19.533527657" + }, + "Convert fasta to bed using awk redirect instead of shell redirect": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T08:31:09.88842854" + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config new file mode 100644 index 000000000..895709a76 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GAWK { + ext.suffix = params.gawk_suffix + ext.args2 = params.gawk_args2 + } +} diff --git a/modules/nf-core/tabix/bgziptabix/.nf-test.log b/modules/nf-core/tabix/bgziptabix/.nf-test.log new file mode 100644 index 000000000..38da65725 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/.nf-test.log @@ -0,0 +1,80 @@ +Nov-15 13:30:26.128 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 +Nov-15 13:30:26.161 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/main.nf.test] +Nov-15 13:30:28.875 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 +Nov-15 13:30:28.889 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. +Nov-15 13:30:28.920 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 3 files from directory /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix in 0.026 sec +Nov-15 13:30:28.926 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. +Nov-15 13:30:28.927 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] +Nov-15 13:30:28.927 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. +Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan +Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. +Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:30.152 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:30.168 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:30.169 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:30.170 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:30.171 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:30.171 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true +Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 22f37a773..d2e497fd7 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -23,7 +23,7 @@ process TABIX_BGZIPTABIX { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz + bgzip --threads ${task.cpus} -c $args $input -o ${prefix}.${input.getExtension()}.gz tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log b/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log new file mode 100644 index 000000000..8dfc5fb52 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log @@ -0,0 +1,80 @@ +Nov-15 13:30:10.079 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 +Nov-15 13:30:10.114 [main] INFO com.askimed.nf.test.App - Arguments: [test, main.nf.test] +Nov-15 13:30:12.342 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 +Nov-15 13:30:12.348 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. +Nov-15 13:30:12.375 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 2 files from directory /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests in 0.021 sec +Nov-15 13:30:12.380 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. +Nov-15 13:30:12.381 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] +Nov-15 13:30:12.381 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. +Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan +Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. +Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:13.613 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:13.627 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:13.628 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:13.629 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:13.630 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:13.630 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest +Nov-15 13:30:13.631 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED +java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. + at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) + at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) + at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) + at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) + at picocli.CommandLine.executeUserObject(CommandLine.java:1953) + at picocli.CommandLine.access$1300(CommandLine.java:145) + at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) + at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) + at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + at picocli.CommandLine.execute(CommandLine.java:2078) + at com.askimed.nf.test.App.run(App.java:39) + at com.askimed.nf.test.App.main(App.java:46) +Nov-15 13:30:13.632 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true +Nov-15 13:30:13.632 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 1b5821228..ab43ef12e 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -2,12 +2,15 @@ // A subworkflow to annotate snvs // -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { CADD } from '../../../modules/nf-core/cadd/main' -include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_VIEW } from '../../../modules/nf-core/tabix/tabix/main' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { BCFTOOLS_ANNOTATE as RENAME_CHRNAMES } from '../../../modules/nf-core/bcftools/annotate/main' +include { CADD } from '../../../modules/nf-core/cadd/main' +include { GAWK as REFERENCE_TO_CADD_CHRNAMES } from '../../../modules/nf-core/gawk/main' +include { GAWK as CADD_TO_REFERENCE_CHRNAMES } from '../../../modules/nf-core/gawk/main' +include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_VIEW } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CADD { @@ -15,9 +18,36 @@ workflow ANNOTATE_CADD { ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] ch_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(dir) ] + ch_fai // channel: [optional] [ path(fai) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() + + + if (params.genome_build == 'GRCh38') { + + REFERENCE_TO_CADD_CHRNAMES ( ch_fai , [], false ) + ch_versions = ch_versions.mix(REFERENCE_TO_CADD_CHRNAMES.out.versions) + + CADD_TO_REFERENCE_CHRNAMES ( ch_fai , [], false ) + ch_versions = ch_versions.mix(CADD_TO_REFERENCE_CHRNAMES.out.versions) + + ch_vcf + .map { meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ] } + .set { rename_chrnames_in } + + RENAME_CHRNAMES ( + rename_chrnames_in, + REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt } + ) + ch_versions = ch_versions.mix(RENAME_CHRNAMES.out.versions) + + + RENAME_CHRNAMES.out.vcf + .map { meta, vcf -> [ meta, vcf, [] ] } + .set { ch_vcf } + } + BCFTOOLS_VIEW(ch_vcf, [], [], []) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 62d3808ee..c02558d09 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -25,7 +25,6 @@ workflow ANNOTATE_GENOME_SNVS { take: ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - analysis_type // string: [mandatory] 'wgs' or 'wes' ch_cadd_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(annotation) ] ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] @@ -40,13 +39,14 @@ workflow ANNOTATE_GENOME_SNVS { ch_samples // channel: [mandatory] [ val(sample_meta) ] ch_split_intervals // channel: [mandatory] [ path(intervals) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] + ch_genome_fai // channel: [mandatory] [ path(fai) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] main: - ch_cadd_vcf = Channel.empty() - ch_versions = Channel.empty() - ch_vcf_scatter_in = Channel.empty() - ch_vep_in = Channel.empty() + ch_cadd_vcf = channel.empty() + ch_versions = channel.empty() + ch_vcf_scatter_in = channel.empty() + ch_vep_in = channel.empty() BCFTOOLS_ROH (ch_vcf, ch_gnomad_af, [], [], [], []) @@ -90,7 +90,8 @@ workflow ANNOTATE_GENOME_SNVS { ANNOTATE_CADD ( ch_cadd_in, ch_cadd_header, - ch_cadd_resources + ch_cadd_resources, + ch_genome_fai ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index b1fba8b09..8b35797e7 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -27,10 +27,11 @@ workflow ANNOTATE_MT_SNVS { val_vep_cache_version // string: [mandatory] 107 ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] + ch_fai // channel: [mandatory] [ path(fai) ] main: - ch_versions = Channel.empty() - ch_haplog = Channel.empty() + ch_versions = channel.empty() + ch_haplog = channel.empty() // add prefix to meta ch_mt_vcf @@ -53,20 +54,21 @@ workflow ANNOTATE_MT_SNVS { VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) ZIP_TABIX_VCFANNO_MT(VCFANNO_MT.out.vcf) - ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, tbi -> return [meta, vcf]} - ch_vcfanno_tbi = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, tbi -> return [meta, tbi]} + ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, _tbi -> return [meta, vcf]} + ch_vcfanno_tbi = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, _vcf, tbi -> return [meta, tbi]} // Annotating with CADD if (params.cadd_resources != null) { ANNOTATE_CADD ( ZIP_TABIX_VCFANNO_MT.out.gz_tbi, ch_cadd_header, - ch_cadd_resources + ch_cadd_resources, + ch_fai ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) } else { - ch_cadd_vcf = Channel.empty() + ch_cadd_vcf = channel.empty() } // Pick input for vep diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2bb1485fc..7b3dad0a9 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -487,7 +487,6 @@ workflow RAREDISEASE { ANNOTATE_GENOME_SNVS ( CALL_SNV.out.genome_vcf_tabix, - params.analysis_type, ch_cadd_header, ch_cadd_resources, ch_vcfanno_extra, @@ -502,6 +501,7 @@ workflow RAREDISEASE { ch_samples, ch_scatter_split_intervals, ch_vep_extra_files, + ch_genome_fai, ch_genome_chrsizes ).set { ch_snv_annotate } ch_versions = ch_versions.mix(ch_snv_annotate.versions) @@ -571,7 +571,8 @@ workflow RAREDISEASE { params.genome, params.vep_cache_version, ch_vep_cache, - ch_vep_extra_files + ch_vep_extra_files, + ch_genome_fai ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) @@ -582,7 +583,7 @@ workflow RAREDISEASE { } .set { ch_clin_research_mt_vcf } - ch_clinical_mtsnv_vcf = Channel.empty() + ch_clinical_mtsnv_vcf = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { GENERATE_CLINICAL_SET_MT( ch_clin_research_mt_vcf.clinical, From 2e30208be5b2c100d435e785ef364fa930d72ffa Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 09:39:11 +0100 Subject: [PATCH 078/872] rm nf-tests --- .../meta/mock.nf | 86 ---------- .../meta/nextflow.log | 155 ------------------ .../meta/params.json | 1 - .../meta/std.err | 0 .../meta/std.out | 3 - .../meta/trace.csv | 1 - .../meta/mock.nf | 86 ---------- .../meta/nextflow.log | 155 ------------------ .../meta/params.json | 1 - .../meta/std.err | 0 .../meta/std.out | 3 - .../meta/trace.csv | 1 - .../meta/mock.nf | 86 ---------- .../meta/nextflow.log | 155 ------------------ .../meta/params.json | 1 - .../meta/std.err | 0 .../meta/std.out | 3 - .../meta/trace.csv | 1 - .../meta/mock.nf | 86 ---------- .../meta/nextflow.log | 155 ------------------ .../meta/params.json | 1 - .../meta/std.err | 0 .../meta/std.out | 3 - .../meta/trace.csv | 1 - 24 files changed, 984 deletions(-) delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out delete mode 100644 .nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out delete mode 100644 .nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out delete mode 100644 .nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out delete mode 100644 .nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf deleted file mode 100644 index 688cc1328..000000000 --- a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/mock.nf +++ /dev/null @@ -1,86 +0,0 @@ -import groovy.json.JsonGenerator -import groovy.json.JsonGenerator.Converter - -nextflow.enable.dsl=2 - -// comes from nf-test to store json files -params.nf_test_output = "" - -// include dependencies - - -// include test process -include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' - -// define custom rules for JSON that will be generated. -def jsonOutput = - new JsonGenerator.Options() - .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename - .build() - -def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() - - -workflow { - - // run dependencies - - - // process mapping - def input = [] - - input[0] = [ - [ id:'test' ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - ] - - //---- - - //run process - TABIX_BGZIPTABIX(*input) - - if (TABIX_BGZIPTABIX.output){ - - // consumes all named output channels and stores items in a json file - for (def name in TABIX_BGZIPTABIX.out.getNames()) { - serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) - } - - // consumes all unnamed output channels and stores items in a json file - def array = TABIX_BGZIPTABIX.out as Object[] - for (def i = 0; i < array.length ; i++) { - serializeChannel(i, array[i], jsonOutput) - } - - } - -} - -def serializeChannel(name, channel, jsonOutput) { - def _name = name - def list = [ ] - channel.subscribe( - onNext: { - list.add(it) - }, - onComplete: { - def map = new HashMap() - map[_name] = list - def filename = "${params.nf_test_output}/output_${_name}.json" - new File(filename).text = jsonOutput.toJson(map) - } - ) -} - - -workflow.onComplete { - - def result = [ - success: workflow.success, - exitStatus: workflow.exitStatus, - errorMessage: workflow.errorMessage, - errorReport: workflow.errorReport - ] - new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) - -} diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log deleted file mode 100644 index f6d032e40..000000000 --- a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log +++ /dev/null @@ -1,155 +0,0 @@ -Nov-15 13:32:09.018 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/work -stub -Nov-15 13:32:09.207 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 -Nov-15 13:32:09.267 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 -Nov-15 13:32:09.313 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -Nov-15 13:32:09.315 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -Nov-15 13:32:09.321 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -Nov-15 13:32:09.348 [main] INFO org.pf4j.AbstractPluginManager - No plugins -Nov-15 13:32:09.436 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:32:09.445 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:32:09.446 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -Nov-15 13:32:09.447 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:32:09.448 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:32:09.448 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config -Nov-15 13:32:09.552 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json -Nov-15 13:32:09.560 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5b69d40d] - activable => nextflow.secret.LocalSecretsProvider@5b69d40d -Nov-15 13:32:09.637 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:32:17.762 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:32:21.455 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:32:21.694 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration -Nov-15 13:32:21.714 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf` [gloomy_hopper] DSL2 - revision: bc38ccaa64 -Nov-15 13:32:21.717 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] -Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] -Nov-15 13:32:21.718 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 -Nov-15 13:32:21.736 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved -Nov-15 13:32:21.737 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' -Nov-15 13:32:21.765 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 -Nov-15 13:32:21.861 [main] DEBUG nextflow.Session - Session UUID: 7ba3b48d-c6af-4074-a135-275ae065d882 -Nov-15 13:32:21.862 [main] DEBUG nextflow.Session - Run name: gloomy_hopper -Nov-15 13:32:21.862 [main] DEBUG nextflow.Session - Executor pool size: 8 -Nov-15 13:32:21.878 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -Nov-15 13:32:21.890 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Nov-15 13:32:21.928 [main] DEBUG nextflow.cli.CmdRun - - Version: 24.10.0 build 5928 - Created: 27-10-2024 18:36 UTC (19:36 CEST) - System: Mac OS X 15.0.1 - Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS - Encoding: UTF-8 (UTF-8) - Process: 47561@annickrmbp [130.229.165.9] - CPUs: 8 - Mem: 16 GB (13.9 MB) - Swap: 13 GB (1 GB) -Nov-15 13:32:21.968 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/work [Mac OS X] -Nov-15 13:32:22.038 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -Nov-15 13:32:22.051 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory -Nov-15 13:32:22.152 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -Nov-15 13:32:22.194 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 -Nov-15 13:32:22.311 [main] DEBUG nextflow.Session - Session start -Nov-15 13:32:22.328 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv -Nov-15 13:32:22.381 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:32:22.523 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:32:23.439 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -Nov-15 13:32:24.080 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` -Nov-15 13:32:24.098 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf - Script_2f4fa37490aa9602: /Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf -Nov-15 13:32:24.098 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed -Nov-15 13:32:24.104 [main] DEBUG nextflow.Session - -Thread[Finalizer,8,system] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) - java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) - -Thread[Common-Cleaner,8,InnocuousThreadGroup] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) - -Thread[Signal Dispatcher,9,system] - -Thread[Notification Thread,9,system] - -Thread[Actor Thread 1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) - java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Reference Handler,10,system] - java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) - java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) - java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) - -Thread[main,5,main] - java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) - java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) - app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) - app//nextflow.Session.abort(Session.groovy:800) - app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) - app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) - app//nextflow.cli.Launcher.run(Launcher.groovy:503) - app//nextflow.cli.Launcher.main(Launcher.groovy:658) - -Thread[Thread-1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) - java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) - app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) - app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - app//groovy.lang.Closure.call(Closure.java:433) - app//groovy.lang.Closure.call(Closure.java:412) - app//groovy.lang.Closure.run(Closure.java:505) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Nov-15 13:32:24.124 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed -java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed - at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.Nextflow.file(Nextflow.groovy:123) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_2f4fa37490aa9602$_runScript_closure4$_closure6.doCall(Script_2f4fa37490aa9602:34) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run0(BaseScript.groovy:198) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run(BaseScript.groovy:209) - at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) - at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) - at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) - at nextflow.cli.CmdRun.run(CmdRun.groovy:376) - at nextflow.cli.Launcher.run(Launcher.groovy:503) - at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json deleted file mode 100644 index 858f09524..000000000 --- a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/params.json +++ /dev/null @@ -1 +0,0 @@ -{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta"} \ No newline at end of file diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.err deleted file mode 100644 index e69de29bb..000000000 diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out deleted file mode 100644 index 54dfb492d..000000000 --- a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/std.out +++ /dev/null @@ -1,3 +0,0 @@ -ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/nullgenomics/sarscov2/genome/bed/test.bed - - -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-2424eee86137dc872e67fd929f3d680a.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv b/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv deleted file mode 100644 index 6b739acdf..000000000 --- a/.nf-test/tests/2424eee86137dc872e67fd929f3d680a/meta/trace.csv +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf deleted file mode 100644 index d789b2961..000000000 --- a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/mock.nf +++ /dev/null @@ -1,86 +0,0 @@ -import groovy.json.JsonGenerator -import groovy.json.JsonGenerator.Converter - -nextflow.enable.dsl=2 - -// comes from nf-test to store json files -params.nf_test_output = "" - -// include dependencies - - -// include test process -include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' - -// define custom rules for JSON that will be generated. -def jsonOutput = - new JsonGenerator.Options() - .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename - .build() - -def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() - - -workflow { - - // run dependencies - - - // process mapping - def input = [] - - input[0] = [ - [ id:'tbi_test' ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - ] - - //---- - - //run process - TABIX_BGZIPTABIX(*input) - - if (TABIX_BGZIPTABIX.output){ - - // consumes all named output channels and stores items in a json file - for (def name in TABIX_BGZIPTABIX.out.getNames()) { - serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) - } - - // consumes all unnamed output channels and stores items in a json file - def array = TABIX_BGZIPTABIX.out as Object[] - for (def i = 0; i < array.length ; i++) { - serializeChannel(i, array[i], jsonOutput) - } - - } - -} - -def serializeChannel(name, channel, jsonOutput) { - def _name = name - def list = [ ] - channel.subscribe( - onNext: { - list.add(it) - }, - onComplete: { - def map = new HashMap() - map[_name] = list - def filename = "${params.nf_test_output}/output_${_name}.json" - new File(filename).text = jsonOutput.toJson(map) - } - ) -} - - -workflow.onComplete { - - def result = [ - success: workflow.success, - exitStatus: workflow.exitStatus, - errorMessage: workflow.errorMessage, - errorReport: workflow.errorReport - ] - new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) - -} diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log deleted file mode 100644 index 7b12db494..000000000 --- a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log +++ /dev/null @@ -1,155 +0,0 @@ -Nov-15 13:31:16.857 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/work -Nov-15 13:31:17.034 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 -Nov-15 13:31:17.095 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 -Nov-15 13:31:17.143 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -Nov-15 13:31:17.144 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -Nov-15 13:31:17.152 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -Nov-15 13:31:17.181 [main] INFO org.pf4j.AbstractPluginManager - No plugins -Nov-15 13:31:17.278 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:17.294 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:17.296 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_tbi.config -Nov-15 13:31:17.303 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:17.305 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:17.306 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config -Nov-15 13:31:17.419 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json -Nov-15 13:31:17.428 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@78d39a69] - activable => nextflow.secret.LocalSecretsProvider@78d39a69 -Nov-15 13:31:17.488 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:25.071 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:27.680 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:28.003 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration -Nov-15 13:31:28.057 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf` [marvelous_celsius] DSL2 - revision: be2d57c639 -Nov-15 13:31:28.074 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] -Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] -Nov-15 13:31:28.080 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 -Nov-15 13:31:28.194 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved -Nov-15 13:31:28.196 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' -Nov-15 13:31:28.293 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 -Nov-15 13:31:28.534 [main] DEBUG nextflow.Session - Session UUID: 33b7f0a5-cbf7-4a4c-8ee0-6ac139ead31d -Nov-15 13:31:28.535 [main] DEBUG nextflow.Session - Run name: marvelous_celsius -Nov-15 13:31:28.537 [main] DEBUG nextflow.Session - Executor pool size: 8 -Nov-15 13:31:28.553 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -Nov-15 13:31:28.564 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Nov-15 13:31:28.615 [main] DEBUG nextflow.cli.CmdRun - - Version: 24.10.0 build 5928 - Created: 27-10-2024 18:36 UTC (19:36 CEST) - System: Mac OS X 15.0.1 - Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS - Encoding: UTF-8 (UTF-8) - Process: 46100@annickrmbp [130.229.165.9] - CPUs: 8 - Mem: 16 GB (32.3 MB) - Swap: 12 GB (784.6 MB) -Nov-15 13:31:28.692 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/work [Mac OS X] -Nov-15 13:31:28.772 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -Nov-15 13:31:28.785 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory -Nov-15 13:31:28.906 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -Nov-15 13:31:28.927 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 -Nov-15 13:31:28.994 [main] DEBUG nextflow.Session - Session start -Nov-15 13:31:29.001 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv -Nov-15 13:31:29.016 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:31:29.021 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:31:29.939 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -Nov-15 13:31:30.457 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` -Nov-15 13:31:30.473 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf - Script_21322127a7e32787: /Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf -Nov-15 13:31:30.473 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed -Nov-15 13:31:30.477 [main] DEBUG nextflow.Session - -Thread[Actor Thread 1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) - java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Reference Handler,10,system] - java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) - java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) - java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) - -Thread[main,5,main] - java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) - java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) - app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) - app//nextflow.Session.abort(Session.groovy:800) - app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) - app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) - app//nextflow.cli.Launcher.run(Launcher.groovy:503) - app//nextflow.cli.Launcher.main(Launcher.groovy:658) - -Thread[Finalizer,8,system] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) - java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) - -Thread[Common-Cleaner,8,InnocuousThreadGroup] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) - -Thread[Thread-1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) - java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) - app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) - app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - app//groovy.lang.Closure.call(Closure.java:433) - app//groovy.lang.Closure.call(Closure.java:412) - app//groovy.lang.Closure.run(Closure.java:505) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Notification Thread,9,system] - -Thread[Signal Dispatcher,9,system] - -Nov-15 13:31:30.497 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed -java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed - at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.Nextflow.file(Nextflow.groovy:123) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_21322127a7e32787$_runScript_closure4$_closure6.doCall(Script_21322127a7e32787:34) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run0(BaseScript.groovy:198) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run(BaseScript.groovy:209) - at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) - at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) - at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) - at nextflow.cli.CmdRun.run(CmdRun.groovy:376) - at nextflow.cli.Launcher.run(Launcher.groovy:503) - at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json deleted file mode 100644 index 11b8863fc..000000000 --- a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/params.json +++ /dev/null @@ -1 +0,0 @@ -{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta"} \ No newline at end of file diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.err deleted file mode 100644 index e69de29bb..000000000 diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out deleted file mode 100644 index 9ec48ae7b..000000000 --- a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/std.out +++ /dev/null @@ -1,3 +0,0 @@ -ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/nullgenomics/sarscov2/genome/bed/test.bed - - -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-802f2cdc6ed5581f6b63de1abdb0c6c8.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv b/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv deleted file mode 100644 index 6b739acdf..000000000 --- a/.nf-test/tests/802f2cdc6ed5581f6b63de1abdb0c6c8/meta/trace.csv +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf deleted file mode 100644 index f3d4619b1..000000000 --- a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/mock.nf +++ /dev/null @@ -1,86 +0,0 @@ -import groovy.json.JsonGenerator -import groovy.json.JsonGenerator.Converter - -nextflow.enable.dsl=2 - -// comes from nf-test to store json files -params.nf_test_output = "" - -// include dependencies - - -// include test process -include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' - -// define custom rules for JSON that will be generated. -def jsonOutput = - new JsonGenerator.Options() - .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename - .build() - -def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() - - -workflow { - - // run dependencies - - - // process mapping - def input = [] - - input[0] = [ - [ id:'csi_test' ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - ] - - //---- - - //run process - TABIX_BGZIPTABIX(*input) - - if (TABIX_BGZIPTABIX.output){ - - // consumes all named output channels and stores items in a json file - for (def name in TABIX_BGZIPTABIX.out.getNames()) { - serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) - } - - // consumes all unnamed output channels and stores items in a json file - def array = TABIX_BGZIPTABIX.out as Object[] - for (def i = 0; i < array.length ; i++) { - serializeChannel(i, array[i], jsonOutput) - } - - } - -} - -def serializeChannel(name, channel, jsonOutput) { - def _name = name - def list = [ ] - channel.subscribe( - onNext: { - list.add(it) - }, - onComplete: { - def map = new HashMap() - map[_name] = list - def filename = "${params.nf_test_output}/output_${_name}.json" - new File(filename).text = jsonOutput.toJson(map) - } - ) -} - - -workflow.onComplete { - - def result = [ - success: workflow.success, - exitStatus: workflow.exitStatus, - errorMessage: workflow.errorMessage, - errorReport: workflow.errorReport - ] - new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) - -} diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log deleted file mode 100644 index 81708986c..000000000 --- a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log +++ /dev/null @@ -1,155 +0,0 @@ -Nov-15 13:31:33.365 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/work -Nov-15 13:31:33.544 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 -Nov-15 13:31:33.607 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 -Nov-15 13:31:33.647 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -Nov-15 13:31:33.648 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -Nov-15 13:31:33.654 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -Nov-15 13:31:33.679 [main] INFO org.pf4j.AbstractPluginManager - No plugins -Nov-15 13:31:33.780 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:33.805 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:33.806 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -Nov-15 13:31:33.809 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:33.810 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:33.810 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config -Nov-15 13:31:33.903 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json -Nov-15 13:31:33.910 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@78d39a69] - activable => nextflow.secret.LocalSecretsProvider@78d39a69 -Nov-15 13:31:33.983 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:41.776 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:44.297 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:44.788 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration -Nov-15 13:31:44.882 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf` [awesome_church] DSL2 - revision: 059c08dd97 -Nov-15 13:31:44.896 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] -Nov-15 13:31:44.900 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -Nov-15 13:31:44.900 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] -Nov-15 13:31:44.901 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 -Nov-15 13:31:44.942 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved -Nov-15 13:31:44.943 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' -Nov-15 13:31:45.023 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 -Nov-15 13:31:45.185 [main] DEBUG nextflow.Session - Session UUID: 0379aa71-7989-470e-87e9-7a052f6d84a1 -Nov-15 13:31:45.186 [main] DEBUG nextflow.Session - Run name: awesome_church -Nov-15 13:31:45.187 [main] DEBUG nextflow.Session - Executor pool size: 8 -Nov-15 13:31:45.200 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -Nov-15 13:31:45.210 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Nov-15 13:31:45.253 [main] DEBUG nextflow.cli.CmdRun - - Version: 24.10.0 build 5928 - Created: 27-10-2024 18:36 UTC (19:36 CEST) - System: Mac OS X 15.0.1 - Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS - Encoding: UTF-8 (UTF-8) - Process: 46566@annickrmbp [130.229.165.9] - CPUs: 8 - Mem: 16 GB (43.7 MB) - Swap: 12 GB (792.6 MB) -Nov-15 13:31:45.303 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/work [Mac OS X] -Nov-15 13:31:45.382 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -Nov-15 13:31:45.406 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory -Nov-15 13:31:45.498 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -Nov-15 13:31:45.516 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 -Nov-15 13:31:45.583 [main] DEBUG nextflow.Session - Session start -Nov-15 13:31:45.595 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv -Nov-15 13:31:45.607 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:31:45.612 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:31:46.452 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -Nov-15 13:31:47.152 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` -Nov-15 13:31:47.172 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_d7f74ea11eca7966: /Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf - Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf -Nov-15 13:31:47.173 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed -Nov-15 13:31:47.179 [main] DEBUG nextflow.Session - -Thread[Actor Thread 1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) - java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Reference Handler,10,system] - java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) - java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) - java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) - -Thread[main,5,main] - java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) - java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) - app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) - app//nextflow.Session.abort(Session.groovy:800) - app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) - app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) - app//nextflow.cli.Launcher.run(Launcher.groovy:503) - app//nextflow.cli.Launcher.main(Launcher.groovy:658) - -Thread[Finalizer,8,system] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) - java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) - -Thread[Common-Cleaner,8,InnocuousThreadGroup] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) - -Thread[Thread-1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) - java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) - app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) - app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - app//groovy.lang.Closure.call(Closure.java:433) - app//groovy.lang.Closure.call(Closure.java:412) - app//groovy.lang.Closure.run(Closure.java:505) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Notification Thread,9,system] - -Thread[Signal Dispatcher,9,system] - -Nov-15 13:31:47.199 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed -java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed - at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.Nextflow.file(Nextflow.groovy:123) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_d7f74ea11eca7966$_runScript_closure4$_closure6.doCall(Script_d7f74ea11eca7966:34) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run0(BaseScript.groovy:198) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run(BaseScript.groovy:209) - at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) - at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) - at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) - at nextflow.cli.CmdRun.run(CmdRun.groovy:376) - at nextflow.cli.Launcher.run(Launcher.groovy:503) - at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json deleted file mode 100644 index afb274ded..000000000 --- a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/params.json +++ /dev/null @@ -1 +0,0 @@ -{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta"} \ No newline at end of file diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.err deleted file mode 100644 index e69de29bb..000000000 diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out deleted file mode 100644 index 4b45dfd73..000000000 --- a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/std.out +++ /dev/null @@ -1,3 +0,0 @@ -ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/nullgenomics/sarscov2/genome/bed/test.bed - - -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-8d77a8bdec91ee5fcc6408882090c5a7.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv b/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv deleted file mode 100644 index 6b739acdf..000000000 --- a/.nf-test/tests/8d77a8bdec91ee5fcc6408882090c5a7/meta/trace.csv +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf deleted file mode 100644 index 688cc1328..000000000 --- a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/mock.nf +++ /dev/null @@ -1,86 +0,0 @@ -import groovy.json.JsonGenerator -import groovy.json.JsonGenerator.Converter - -nextflow.enable.dsl=2 - -// comes from nf-test to store json files -params.nf_test_output = "" - -// include dependencies - - -// include test process -include { TABIX_BGZIPTABIX } from '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf' - -// define custom rules for JSON that will be generated. -def jsonOutput = - new JsonGenerator.Options() - .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename - .build() - -def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build() - - -workflow { - - // run dependencies - - - // process mapping - def input = [] - - input[0] = [ - [ id:'test' ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - ] - - //---- - - //run process - TABIX_BGZIPTABIX(*input) - - if (TABIX_BGZIPTABIX.output){ - - // consumes all named output channels and stores items in a json file - for (def name in TABIX_BGZIPTABIX.out.getNames()) { - serializeChannel(name, TABIX_BGZIPTABIX.out.getProperty(name), jsonOutput) - } - - // consumes all unnamed output channels and stores items in a json file - def array = TABIX_BGZIPTABIX.out as Object[] - for (def i = 0; i < array.length ; i++) { - serializeChannel(i, array[i], jsonOutput) - } - - } - -} - -def serializeChannel(name, channel, jsonOutput) { - def _name = name - def list = [ ] - channel.subscribe( - onNext: { - list.add(it) - }, - onComplete: { - def map = new HashMap() - map[_name] = list - def filename = "${params.nf_test_output}/output_${_name}.json" - new File(filename).text = jsonOutput.toJson(map) - } - ) -} - - -workflow.onComplete { - - def result = [ - success: workflow.success, - exitStatus: workflow.exitStatus, - errorMessage: workflow.errorMessage, - errorReport: workflow.errorReport - ] - new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result) - -} diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log deleted file mode 100644 index 0ba3b2d33..000000000 --- a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log +++ /dev/null @@ -1,155 +0,0 @@ -Nov-15 13:31:50.087 [main] DEBUG nextflow.cli.Launcher - $> nextflow -quiet -log /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log run /Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf -c /Users/annick.renevey/Projects/raredisease/nextflow.config -c /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -params-file /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json -ansi-log false -with-trace /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv -w /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/work -stub -Nov-15 13:31:50.264 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.0 -Nov-15 13:31:50.324 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@2.9.0,nf-azure@1.10.1,nf-cloudcache@0.4.2,nf-codecommit@0.2.2,nf-console@1.1.4,nf-google@1.15.2,nf-tower@1.9.3,nf-wave@1.7.2 -Nov-15 13:31:50.357 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -Nov-15 13:31:50.358 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -Nov-15 13:31:50.364 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -Nov-15 13:31:50.389 [main] INFO org.pf4j.AbstractPluginManager - No plugins -Nov-15 13:31:50.502 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:50.513 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:50.513 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/./tabix_csi.config -Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/nextflow.config -Nov-15 13:31:50.515 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config -Nov-15 13:31:50.601 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json -Nov-15 13:31:50.607 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5b69d40d] - activable => nextflow.secret.LocalSecretsProvider@5b69d40d -Nov-15 13:31:50.685 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:31:59.820 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:32:03.237 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -Nov-15 13:32:03.493 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration -Nov-15 13:32:03.514 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf` [kickass_angela] DSL2 - revision: bc38ccaa64 -Nov-15 13:32:03.516 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-schema@2.1.1] -Nov-15 13:32:03.517 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -Nov-15 13:32:03.517 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-schema@2.1.1] -Nov-15 13:32:03.518 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: 2.1.1 -Nov-15 13:32:03.537 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-schema@2.1.1' resolved -Nov-15 13:32:03.537 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-schema@2.1.1' -Nov-15 13:32:03.565 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-schema@2.1.1 -Nov-15 13:32:03.670 [main] DEBUG nextflow.Session - Session UUID: 44b6788f-5f43-45f7-8b39-2e10b1e5efa6 -Nov-15 13:32:03.671 [main] DEBUG nextflow.Session - Run name: kickass_angela -Nov-15 13:32:03.672 [main] DEBUG nextflow.Session - Executor pool size: 8 -Nov-15 13:32:03.681 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -Nov-15 13:32:03.693 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Nov-15 13:32:03.793 [main] DEBUG nextflow.cli.CmdRun - - Version: 24.10.0 build 5928 - Created: 27-10-2024 18:36 UTC (19:36 CEST) - System: Mac OS X 15.0.1 - Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS - Encoding: UTF-8 (UTF-8) - Process: 47032@annickrmbp [130.229.165.9] - CPUs: 8 - Mem: 16 GB (50 MB) - Swap: 13 GB (1021.2 MB) -Nov-15 13:32:03.865 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/work [Mac OS X] -Nov-15 13:32:04.071 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -Nov-15 13:32:04.091 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory -Nov-15 13:32:04.223 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -Nov-15 13:32:04.266 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 -Nov-15 13:32:04.384 [main] DEBUG nextflow.Session - Session start -Nov-15 13:32:04.404 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv -Nov-15 13:32:04.449 [main] DEBUG nextflow.Session - Using default localLib path: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:32:04.463 [main] DEBUG nextflow.Session - Adding to the classpath library: /Users/annick.renevey/Projects/raredisease/lib -Nov-15 13:32:05.317 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -Nov-15 13:32:06.097 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `modules_testdata_base_path` -- Initialise it to a default value eg. `params.modules_testdata_base_path = some_value` -Nov-15 13:32:06.115 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_b428227b4d50d6b9: /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/main.nf - Script_2f4fa37490aa9602: /Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf -Nov-15 13:32:06.115 [main] DEBUG nextflow.Session - Session aborted -- Cause: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed -Nov-15 13:32:06.120 [main] DEBUG nextflow.Session - -Thread[Thread-1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252) - java.base@17.0.3/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.pollFirst(LinkedBlockingDeque.java:515) - java.base@17.0.3/java.util.concurrent.LinkedBlockingDeque.poll(LinkedBlockingDeque.java:677) - app//nextflow.util.SimpleAgent.run(SimpleAgent.groovy:89) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - java.base@17.0.3/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - java.base@17.0.3/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - java.base@17.0.3/java.lang.reflect.Method.invoke(Method.java:568) - app//org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - app//groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethodClosure(MetaClassImpl.java:1017) - app//groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1207) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088) - app//groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - app//groovy.lang.Closure.call(Closure.java:433) - app//groovy.lang.Closure.call(Closure.java:412) - app//groovy.lang.Closure.run(Closure.java:505) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Common-Cleaner,8,InnocuousThreadGroup] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/jdk.internal.ref.CleanerImpl.run(CleanerImpl.java:140) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - java.base@17.0.3/jdk.internal.misc.InnocuousThread.run(InnocuousThread.java:162) - -Thread[Actor Thread 1,5,main] - java.base@17.0.3/jdk.internal.misc.Unsafe.park(Native Method) - java.base@17.0.3/java.util.concurrent.locks.LockSupport.park(LockSupport.java:341) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack$SNode.block(SynchronousQueue.java:288) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.unmanagedBlock(ForkJoinPool.java:3463) - java.base@17.0.3/java.util.concurrent.ForkJoinPool.managedBlock(ForkJoinPool.java:3434) - java.base@17.0.3/java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:397) - java.base@17.0.3/java.util.concurrent.SynchronousQueue.take(SynchronousQueue.java:886) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122) - java.base@17.0.3/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) - java.base@17.0.3/java.lang.Thread.run(Thread.java:833) - -Thread[Reference Handler,10,system] - java.base@17.0.3/java.lang.ref.Reference.waitForReferencePendingList(Native Method) - java.base@17.0.3/java.lang.ref.Reference.processPendingReferences(Reference.java:253) - java.base@17.0.3/java.lang.ref.Reference$ReferenceHandler.run(Reference.java:215) - -Thread[Signal Dispatcher,9,system] - -Thread[Finalizer,8,system] - java.base@17.0.3/java.lang.Object.wait(Native Method) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:155) - java.base@17.0.3/java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:176) - java.base@17.0.3/java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:172) - -Thread[main,5,main] - java.base@17.0.3/java.lang.Thread.dumpThreads(Native Method) - java.base@17.0.3/java.lang.Thread.getAllStackTraces(Thread.java:1662) - app//nextflow.util.SysHelper.dumpThreads(SysHelper.groovy:188) - app//nextflow.Session.abort(Session.groovy:800) - app//nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:149) - app//nextflow.cli.CmdRun.run(CmdRun.groovy:376) - app//nextflow.cli.Launcher.run(Launcher.groovy:503) - app//nextflow.cli.Launcher.main(Launcher.groovy:658) - -Thread[Notification Thread,9,system] - -Nov-15 13:32:06.140 [main] ERROR nextflow.cli.Launcher - /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed -java.nio.file.NoSuchFileException: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed - at nextflow.file.FileHelper.checkIfExists(FileHelper.groovy:1099) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.Nextflow.file(Nextflow.groovy:123) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_2f4fa37490aa9602$_runScript_closure4$_closure6.doCall(Script_2f4fa37490aa9602:34) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run0(BaseScript.groovy:198) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.script.BaseScript.run(BaseScript.groovy:209) - at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:236) - at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:243) - at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:138) - at nextflow.cli.CmdRun.run(CmdRun.groovy:376) - at nextflow.cli.Launcher.run(Launcher.groovy:503) - at nextflow.cli.Launcher.main(Launcher.groovy:658) diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json deleted file mode 100644 index b44558174..000000000 --- a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/params.json +++ /dev/null @@ -1 +0,0 @@ -{"nf_test_output":"/Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta"} \ No newline at end of file diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.err deleted file mode 100644 index e69de29bb..000000000 diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out deleted file mode 100644 index 459aa58bc..000000000 --- a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/std.out +++ /dev/null @@ -1,3 +0,0 @@ -ERROR ~ No such file or directory: /Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/nullgenomics/sarscov2/genome/bed/test.bed - - -- Check script '/Users/annick.renevey/Projects/raredisease/.nf-test-a220bee49c4435cd8f79a294c9481e3.nf' at line: 34 or see '/Users/annick.renevey/Projects/raredisease/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/nextflow.log' file for more details diff --git a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv b/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv deleted file mode 100644 index 6b739acdf..000000000 --- a/.nf-test/tests/a220bee49c4435cd8f79a294c9481e3/meta/trace.csv +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar From 034edb74cc733babfdd02a4b5e219c2c8960ec26 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 09:41:45 +0100 Subject: [PATCH 079/872] rm nf-test files --- .nf-test.log | 180 ------------------ modules/nf-core/tabix/bgziptabix/.nf-test.log | 80 -------- .../tabix/bgziptabix/tests/.nf-test.log | 80 -------- 3 files changed, 340 deletions(-) delete mode 100644 .nf-test.log delete mode 100644 modules/nf-core/tabix/bgziptabix/.nf-test.log delete mode 100644 modules/nf-core/tabix/bgziptabix/tests/.nf-test.log diff --git a/.nf-test.log b/.nf-test.log deleted file mode 100644 index 7f02d1750..000000000 --- a/.nf-test.log +++ /dev/null @@ -1,180 +0,0 @@ -Nov-15 13:31:09.616 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 -Nov-15 13:31:09.652 [main] INFO com.askimed.nf.test.App - Arguments: [test, modules/nf-core/tabix/bgziptabix/tests/main.nf.test] -Nov-15 13:31:11.675 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 -Nov-15 13:31:11.688 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. -Nov-15 13:31:12.517 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 332 files from directory /Users/annick.renevey/Projects/raredisease in 0.824 sec -Nov-15 13:31:12.536 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. -Nov-15 13:31:12.536 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] -Nov-15 13:31:12.536 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. -Nov-15 13:31:13.837 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan -Nov-15 13:31:13.838 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. -Nov-15 13:31:13.838 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:31:30.599 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED -org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed - at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) - at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) - at main_nf$_run_closure1$_closure2$_closure7.doCall(main.nf.test:27) - at main_nf$_run_closure1$_closure2$_closure7.doCall(main.nf.test) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) - at groovy.lang.Closure.call(Closure.java:427) - at groovy.lang.Closure.call(Closure.java:406) - at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:31:30.621 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:31:47.247 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED -org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed - at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) - at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) - at main_nf$_run_closure1$_closure3$_closure13.doCall(main.nf.test:53) - at main_nf$_run_closure1$_closure3$_closure13.doCall(main.nf.test) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) - at groovy.lang.Closure.call(Closure.java:427) - at groovy.lang.Closure.call(Closure.java:406) - at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:31:47.248 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:32:06.211 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED -org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed - at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) - at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) - at main_nf$_run_closure1$_closure4$_closure19.doCall(main.nf.test:82) - at main_nf$_run_closure1$_closure4$_closure19.doCall(main.nf.test) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) - at groovy.lang.Closure.call(Closure.java:427) - at groovy.lang.Closure.call(Closure.java:406) - at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:32:06.215 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:32:24.189 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED -org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 3 of 3 assertions failed - at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44) - at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100) - at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217) - at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:249) - at main_nf$_run_closure1$_closure5$_closure25.doCall(main.nf.test:111) - at main_nf$_run_closure1$_closure5$_closure25.doCall(main.nf.test) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:568) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030) - at groovy.lang.Closure.call(Closure.java:427) - at groovy.lang.Closure.call(Closure.java:406) - at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16) - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:32:24.190 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true -Nov-15 13:32:24.191 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! diff --git a/modules/nf-core/tabix/bgziptabix/.nf-test.log b/modules/nf-core/tabix/bgziptabix/.nf-test.log deleted file mode 100644 index 38da65725..000000000 --- a/modules/nf-core/tabix/bgziptabix/.nf-test.log +++ /dev/null @@ -1,80 +0,0 @@ -Nov-15 13:30:26.128 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 -Nov-15 13:30:26.161 [main] INFO com.askimed.nf.test.App - Arguments: [test, tests/main.nf.test] -Nov-15 13:30:28.875 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 -Nov-15 13:30:28.889 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. -Nov-15 13:30:28.920 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 3 files from directory /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix in 0.026 sec -Nov-15 13:30:28.926 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. -Nov-15 13:30:28.927 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] -Nov-15 13:30:28.927 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. -Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan -Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. -Nov-15 13:30:30.148 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:30.152 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:30.168 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:30.169 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:30.170 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:30.171 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:30.171 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true -Nov-15 13:30:30.172 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! diff --git a/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log b/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log deleted file mode 100644 index 8dfc5fb52..000000000 --- a/modules/nf-core/tabix/bgziptabix/tests/.nf-test.log +++ /dev/null @@ -1,80 +0,0 @@ -Nov-15 13:30:10.079 [main] INFO com.askimed.nf.test.App - nf-test 0.9.0 -Nov-15 13:30:10.114 [main] INFO com.askimed.nf.test.App - Arguments: [test, main.nf.test] -Nov-15 13:30:12.342 [main] INFO com.askimed.nf.test.App - Nextflow Version: 24.10.0 -Nov-15 13:30:12.348 [main] WARN com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found. -Nov-15 13:30:12.375 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 2 files from directory /Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests in 0.021 sec -Nov-15 13:30:12.380 [main] INFO com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 tests. -Nov-15 13:30:12.381 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found tests: [/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test] -Nov-15 13:30:12.381 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Detected 1 test files. -Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Started test plan -Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process TABIX_BGZIPTABIX' from file '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/main.nf.test'. -Nov-15 13:30:13.609 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '802f2cdc: sarscov2_bed_tbi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:13.613 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '802f2cdc: sarscov2_bed_tbi' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:13.627 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '8d77a8bd: sarscov2_bed_csi'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:13.628 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '8d77a8bd: sarscov2_bed_csi' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:13.629 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test 'a220bee4: sarscov2_bed_csi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:13.630 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test 'a220bee4: sarscov2_bed_csi_stub' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:13.630 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Run test '2424eee8: sarscov2_bed_tbi_stub'. type: com.askimed.nf.test.lang.process.ProcessTest -Nov-15 13:30:13.631 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Test '2424eee8: sarscov2_bed_tbi_stub' finished. status: FAILED -java.lang.Exception: Script '/Users/annick.renevey/Projects/raredisease/modules/nf-core/tabix/bgziptabix/tests/modules/nf-core/tabix/bgziptabix/main.nf' not found. - at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:90) - at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165) - at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:299) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43) - at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18) - at picocli.CommandLine.executeUserObject(CommandLine.java:1953) - at picocli.CommandLine.access$1300(CommandLine.java:145) - at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) - at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) - at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - at picocli.CommandLine.execute(CommandLine.java:2078) - at com.askimed.nf.test.App.run(App.java:39) - at com.askimed.nf.test.App.main(App.java:46) -Nov-15 13:30:13.632 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process TABIX_BGZIPTABIX' finished. snapshot file: false, skipped tests: false, failed tests: true -Nov-15 13:30:13.632 [main] INFO com.askimed.nf.test.core.TestExecutionEngine - Executed 4 tests. 4 tests failed. Done! From c2d31da2cebb1ea01098a52ebc51108d71cf76ec Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 09:53:23 +0100 Subject: [PATCH 080/872] update rocrate and homogenise nf-core module --- modules/nf-core/tabix/bgziptabix/main.nf | 2 +- ro-crate-metadata.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index d2e497fd7..22f37a773 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -23,7 +23,7 @@ process TABIX_BGZIPTABIX { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - bgzip --threads ${task.cpus} -c $args $input -o ${prefix}.${input.getExtension()}.gz + bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 3d7375ebd..d16ffbb32 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-07-08T12:27:15+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" From 32f66020349d6d8847c72b9c27f2b3c54a8e0c53 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 10:04:29 +0100 Subject: [PATCH 081/872] update gatk4/determinegermlinecontigploidy --- modules.json | 2 +- .../determinegermlinecontigploidy/README.md | 9 -- .../environment.yml | 10 ++ .../determinegermlinecontigploidy/main.nf | 41 +++---- .../determinegermlinecontigploidy/meta.yml | 34 +++--- .../tests/main.nf.test | 105 ++++++++++++++++++ .../tests/main.nf.test.snap | 77 +++++++++++++ .../tests/nextflow.config | 8 ++ 8 files changed, 240 insertions(+), 46 deletions(-) delete mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/README.md create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config diff --git a/modules.json b/modules.json index 938938441..6709bc521 100644 --- a/modules.json +++ b/modules.json @@ -184,7 +184,7 @@ }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "d6dd4ddea1663edbf15f40e089cc16db96e75f1d", + "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md b/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md deleted file mode 100644 index c6a454565..000000000 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml new file mode 100644 index 000000000..67e0eb860 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index fc98e80e4..4db496933 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -1,45 +1,44 @@ - process GATK4_DETERMINEGERMLINECONTIGPLOIDY { - tag "$meta.id" + tag "${meta.id}" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(counts), path(bed), path(exclude_beds) tuple val(meta2), path(ploidy_model) - path(contig_ploidy_table) + path contig_ploidy_table output: tuple val(meta), path("${prefix}-calls"), emit: calls tuple val(meta), path("${prefix}-model"), emit: model, optional: true - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def intervals = bed ? "--intervals ${bed}" : "" - def exclude = exclude_beds ? exclude_beds.collect(){"--exclude-intervals $it"}.join(" ") : "" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def intervals = bed ? "--intervals ${bed}" : "" + def exclude = exclude_beds ? exclude_beds.collect { "--exclude-intervals ${it}" }.join(" ") : "" def contig_ploidy = contig_ploidy_table ? "--contig-ploidy-priors ${contig_ploidy_table}" : "" - def model = ploidy_model ? "--model ${ploidy_model}" : "" - def input_list = counts.collect(){"--input $it"}.join(" ") + def model = ploidy_model ? "--model ${ploidy_model}" : "" + def input_list = counts.collect { "--input ${it}" }.join(" ") def avail_mem = 3072 if (!task.memory) { - log.info '[GATK DetermineGermlineContigPloidy] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK DetermineGermlineContigPloidy] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} @@ -62,10 +61,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead." - } prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}-calls diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 828628b28..45e717651 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -27,16 +27,20 @@ input: type: file description: One or more count TSV files created with gatk/collectreadcounts pattern: "*.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV - bed: type: file description: Optional - A bed file containing the intervals to include in the process pattern: "*.bed" + ontologies: [] - exclude_beds: type: file description: Optional - One or more bed files containing intervals to exclude from the process pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -48,13 +52,15 @@ input: Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. pattern: '*-model/' - - - contig_ploidy_table: - type: file - description: The contig ploidy priors table - pattern: "*.tsv" + - contig_ploidy_table: + type: file + description: The contig ploidy priors table + pattern: "*.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV output: - - calls: - - meta: + calls: + - - meta: type: map description: | Groovy Map containing sample information @@ -63,8 +69,8 @@ output: type: directory description: A folder containing the calls from the input files pattern: "*-calls/" - - model: - - meta: + model: + - - meta: type: map description: | Groovy Map containing sample information @@ -75,11 +81,13 @@ output: A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). pattern: "*-model/" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test new file mode 100644 index 000000000..a6d0fb7b7 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_process { + + name "Test Process GATK4_DETERMINEGERMLINECONTIGPLOIDY" + script "../main.nf" + config "./nextflow.config" + process "GATK4_DETERMINEGERMLINECONTIGPLOIDY" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + ch_input = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true) + ], + ).combine(bed) + + ch_fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + ch_fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + ch_dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + + input = [ch_input, ch_fasta, ch_fai, ch_dict] + """ + } + } + } + + test("homo sapiens - bam") { + + when { + process { + """ + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + bed = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'] , tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap new file mode 100644 index 000000000..ac6caa6ab --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -0,0 +1,77 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" + ], + [ + "SAMPLE_0", + "SAMPLE_1" + ], + [ + "contig_ploidy_prior.tsv", + "gcnvkernel_version.json", + "interval_list.tsv", + "mu_mean_bias_j_interval__.tsv", + "mu_psi_j_log__.tsv", + "ploidy_config.json", + "std_mean_bias_j_interval__.tsv", + "std_psi_j_log__.tsv" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:53:00.186632174" + }, + "homo sapiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" + ], + "calls": [ + [ + { + "id": "test" + }, + "test-calls:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "model": [ + [ + { + "id": "test" + }, + "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:53:17.594899648" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config new file mode 100644 index 000000000..2767daca2 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: GATK4_COLLECTREADCOUNTS { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } + withName: GATK4_DETERMINEGERMLINECONTIGPLOIDY { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } +} From 4a19c17013ddb1ec9c6bcaacc72400b65fea2cf1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 10:05:09 +0100 Subject: [PATCH 082/872] update gatk4/germlinecnvcaller --- modules.json | 2 +- .../nf-core/gatk4/germlinecnvcaller/README.md | 9 -- .../gatk4/germlinecnvcaller/environment.yml | 10 ++ .../nf-core/gatk4/germlinecnvcaller/main.nf | 54 ++++---- .../nf-core/gatk4/germlinecnvcaller/meta.yml | 27 ++-- .../germlinecnvcaller/tests/main.nf.test | 126 ++++++++++++++++++ .../germlinecnvcaller/tests/main.nf.test.snap | 55 ++++++++ .../germlinecnvcaller/tests/nextflow.config | 11 ++ 8 files changed, 244 insertions(+), 50 deletions(-) delete mode 100644 modules/nf-core/gatk4/germlinecnvcaller/README.md create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/environment.yml create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config diff --git a/modules.json b/modules.json index 6709bc521..72bdd1371 100644 --- a/modules.json +++ b/modules.json @@ -194,7 +194,7 @@ }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "d6dd4ddea1663edbf15f40e089cc16db96e75f1d", + "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", "installed_by": ["modules"] }, "gatk4/intervallisttools": { diff --git a/modules/nf-core/gatk4/germlinecnvcaller/README.md b/modules/nf-core/gatk4/germlinecnvcaller/README.md deleted file mode 100644 index c6a454565..000000000 --- a/modules/nf-core/gatk4/germlinecnvcaller/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml new file mode 100644 index 000000000..67e0eb860 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 90aa7e471..6da848d2e 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -1,9 +1,11 @@ process GATK4_GERMLINECNVCALLER { - tag "$meta.id" + tag "${meta.id}" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model) @@ -11,45 +13,43 @@ process GATK4_GERMLINECNVCALLER { output: tuple val(meta), path("*-cnv-model/*-calls"), emit: cohortcalls, optional: true tuple val(meta), path("*-cnv-model/*-model"), emit: cohortmodel, optional: true - tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls , optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def intervals_command = intervals ? "--intervals ${intervals}" : "" - def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" - def model_command = model ? "--model ${model}" : "" - def input_list = tsv.collect{"--input $it"}.join(' ') - def output_command = model ? "--output ${prefix}-cnv-calls" : "--output ${prefix}-cnv-model" + def intervals_command = intervals ? "--intervals ${intervals}" : "" + def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" + def model_command = model ? "--model ${model}" : "" + def input_list = tsv.collect { "--input ${it}" }.join(' ') + def output_command = model ? "--output ${prefix}-cnv-calls" : "--output ${prefix}-cnv-model" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" export OMP_NUM_THREADS=${task.cpus} export MKL_NUM_THREADS=${task.cpus} gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ GermlineCNVCaller \\ - $input_list \\ - $ploidy_command \\ - $output_command \\ - --output-prefix $prefix \\ - $args \\ - $intervals_command \\ - $model_command + ${input_list} \\ + ${ploidy_command} \\ + ${output_command} \\ + --output-prefix ${prefix} \\ + ${args} \\ + ${intervals_command} \\ + ${model_command} cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -58,10 +58,6 @@ process GATK4_GERMLINECNVCALLER { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir -p ${prefix}-cnv-calls/${prefix}-calls diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml index a185d9d10..4d8bb1d54 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml @@ -26,11 +26,14 @@ input: type: file description: One or more count TSV files created with gatk/collectreadcounts pattern: "*.tsv" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV - intervals: type: file description: Optional - A bed file containing the intervals to include in the process pattern: "*.bed" + ontologies: [] - ploidy: type: directory description: Directory containing ploidy calls produced by determinegermlinecontigploidy @@ -42,8 +45,8 @@ input: cohort mode pattern: "*-cnv-model/*-model" output: - - cohortcalls: - - meta: + cohortcalls: + - - meta: type: map description: | Groovy Map containing sample information @@ -53,8 +56,8 @@ output: description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode pattern: "*-cnv-model/*-calls" - - cohortmodel: - - meta: + cohortmodel: + - - meta: type: map description: | Groovy Map containing sample information @@ -64,8 +67,8 @@ output: description: Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode pattern: "*-cnv-model/*-model" - - casecalls: - - meta: + casecalls: + - - meta: type: map description: | Groovy Map containing sample information @@ -75,11 +78,13 @@ output: description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode pattern: "*-cnv-calls/*-calls" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test new file mode 100644 index 000000000..d14ef9a0f --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -0,0 +1,126 @@ +nextflow_process { + + name "Test Process GATK4_GERMLINECNVCALLER" + script "../main.nf" + config "./nextflow.config" + process "GATK4_GERMLINECNVCALLER" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/bedtointervallist" + tag "gatk4/germlinecnvcaller" + + setup { + run("GATK4_COLLECTREADCOUNTS") { + script "../../collectreadcounts/main.nf" + process { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) + + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}) + input[1] = [[],[]] + input[2] = contig_ploidy_table + """ + } + } + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + input[0] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + """ + } + } + } + + test("homo sapiens - bam") { + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + + test("homo sapiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map{ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]} + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, + file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap new file mode 100644 index 000000000..b7f71b5f1 --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "homo sapiens - bam": { + "content": [ + [ + "versions.yml:md5,abc17734413b02fbe4d397ac105213c2" + ], + [ + "SAMPLE_0", + "SAMPLE_1", + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv" + ], + [ + "calling_config.json", + "denoising_config.json", + "gcnvkernel_version.json", + "interval_list.tsv", + "log_q_tau_tk.tsv", + "mu_W_tu.tsv", + "mu_ard_u_interval__.tsv", + "mu_log_mean_bias_t.tsv", + "mu_psi_t_log__.tsv", + "std_W_tu.tsv", + "std_ard_u_interval__.tsv", + "std_log_mean_bias_t.tsv", + "std_psi_t_log__.tsv" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:09:54.937398398" + }, + "homo sapiens - bam - stub": { + "content": [ + [ + "versions.yml:md5,abc17734413b02fbe4d397ac105213c2" + ], + [ + + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:10:16.833243771" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config new file mode 100644 index 000000000..d1b64bf4f --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS*' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_GERMLINECNVCALLER' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" + } +} From 8c717a8ca9c72c790045f596945cfc6fbc72ef66 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 10:51:27 +0100 Subject: [PATCH 083/872] upate gens --- conf/modules/gens.config | 16 ++++++++++++++++ modules/local/gens/main.nf | 33 ++++++++++++++------------------- subworkflows/local/gens.nf | 12 ++++++++++-- 3 files changed, 40 insertions(+), 21 deletions(-) diff --git a/conf/modules/gens.config b/conf/modules/gens.config index 691cacd74..47345b25d 100644 --- a/conf/modules/gens.config +++ b/conf/modules/gens.config @@ -32,4 +32,20 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + + withName: '.*GENS:GENS_GENERATE_BAF_INDEX' { + publishDir = [ + path: { "${params.outdir}/gens" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*GENS:GENS_GENERATE_COV_INDEX' { + publishDir = [ + path: { "${params.outdir}/gens" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } diff --git a/modules/local/gens/main.nf b/modules/local/gens/main.nf index 75f20c2e8..e55b0a6f0 100644 --- a/modules/local/gens/main.nf +++ b/modules/local/gens/main.nf @@ -2,7 +2,7 @@ process GENS { tag "$meta.id" label 'process_medium' - container 'docker.io/clinicalgenomics/gens_preproc:1.0.11' + container 'docker.io/rannickscilifelab/gens_preproc:1.1.1' input: tuple val(meta), path(read_counts) @@ -10,11 +10,9 @@ process GENS { path gnomad_positions output: - tuple val(meta), path('*.cov.bed.gz') , emit: cov - tuple val(meta), path('*.cov.bed.gz.tbi'), emit: cov_index - tuple val(meta), path('*.baf.bed.gz') , emit: baf - tuple val(meta), path('*.baf.bed.gz.tbi'), emit: baf_index - path "versions.yml" , emit: versions + tuple val(meta), path('*.cov.bed') , emit: cov + tuple val(meta), path('*.baf.bed') , emit: baf + path "versions.yml" , emit: versions script: // Exit if running this module with -profile conda / -profile mamba @@ -22,32 +20,29 @@ process GENS { error "The gens pre-processing module does not support Conda. Please use Docker / Singularity / Podman instead." } def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.0.11" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. """ - generate_gens_data.pl \\ - $read_counts \\ - $gvcf \\ - $prefix \\ - $gnomad_positions + generate_gens_data.py \\ + --coverage $read_counts \\ + --gvcf $gvcf \\ + --label $prefix \\ + --baf_positions $gnomad_positions \\ + --outdir \$PWD cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_gens_data.pl: $VERSION + generate_gens_data.py: \$(echo \$(generate_gens_data.py --version)) END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.0.11" """ - touch ${prefix}.baf.bed.gz - touch ${prefix}.baf.bed.gz.tbi - touch ${prefix}.cov.bed.gz - touch ${prefix}.cov.bed.gz.tbi + touch ${prefix}.baf.bed + touch ${prefix}.cov.bed cat <<-END_VERSIONS > versions.yml "${task.process}": - generate_gens_data.pl: $VERSION + generate_gens_data.py: \$(echo \$(generate_gens_data.py --version)) END_VERSIONS """ } diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index c491d2e5e..eac25a790 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -6,6 +6,8 @@ include { GATK4_COLLECTREADCOUNTS as COLLECTREADCOUNTS } from '../../modu include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_FEMALE } from '../../modules/nf-core/gatk4/denoisereadcounts/main' include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_MALE } from '../../modules/nf-core/gatk4/denoisereadcounts/main' include { GENS as GENS_GENERATE } from '../../modules/local/gens/main' +include { TABIX_BGZIPTABIX as GENS_GENERATE_BAF_INDEX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as GENS_GENERATE_COV_INDEX } from '../../modules/nf-core/tabix/bgziptabix/main' workflow GENS { take: @@ -21,7 +23,7 @@ workflow GENS { ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() ch_bam_bai .combine(ch_interval_list) @@ -35,7 +37,7 @@ workflow GENS { ) COLLECTREADCOUNTS.out.hdf5 - .branch { meta, counts -> + .branch { meta, _counts -> female: meta.sex.toString().matches('2|other|0') male: meta.sex == 1 } @@ -60,10 +62,16 @@ workflow GENS { ch_gnomad_pos ) + GENS_GENERATE_BAF_INDEX (GENS_GENERATE.out.baf) + + GENS_GENERATE_COV_INDEX (GENS_GENERATE.out.cov) + ch_versions = ch_versions.mix(COLLECTREADCOUNTS.out.versions.first()) ch_versions = ch_versions.mix(DENOISEREADCOUNTS_FEMALE.out.versions.first()) ch_versions = ch_versions.mix(DENOISEREADCOUNTS_MALE.out.versions.first()) ch_versions = ch_versions.mix(GENS_GENERATE.out.versions.first()) + ch_versions = ch_versions.mix(GENS_GENERATE_BAF_INDEX.out.versions.first()) + ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions.first()) emit: gens_cov_bed_gz = GENS_GENERATE.out.cov // channel: [ val(meta), path(bed) ] From 25810d2a4c96b8347d976b492d932ad48f9b07f5 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 11:00:12 +0100 Subject: [PATCH 084/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0b8d7ecb..0e3c5a468 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) +- Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) ### Parameters From 083ab65669d3e08a54f63ace1a03d7941f4d863c Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Wed, 26 Nov 2025 11:06:14 +0100 Subject: [PATCH 085/872] Add GATK contamination check for WES/WGS samples - Add CONTAMINATION_CHECK subworkflow using GATK4 - Add PARSE_CONTAMINATION module for MultiQC integration - Add GATK4 GetPileupSummaries and CalculateContamination modules - Implement conditional intervals handling (WGS vs WES) - Update workflow to integrate contamination check after QC_BAM - Configure MultiQC to display contamination results --- assets/multiqc_config.yml | 52 ++++++- conf/modules/contamination.config | 46 +++++++ modules.json | 10 ++ .../local/parse_contamination/environment.yml | 7 + modules/local/parse_contamination/main.nf | 61 +++++++++ modules/local/parse_contamination/meta.yml | 29 ++++ .../calculatecontamination/environment.yml | 10 ++ .../gatk4/calculatecontamination/main.nf | 59 ++++++++ .../gatk4/calculatecontamination/meta.yml | 76 +++++++++++ .../calculatecontamination/tests/main.nf.test | 106 +++++++++++++++ .../tests/main.nf.test.snap | 127 ++++++++++++++++++ .../tests/nextflow.config | 5 + .../gatk4/getpileupsummaries/environment.yml | 10 ++ .../nf-core/gatk4/getpileupsummaries/main.nf | 65 +++++++++ .../nf-core/gatk4/getpileupsummaries/meta.yml | 106 +++++++++++++++ .../getpileupsummaries/tests/main.nf.test | 104 ++++++++++++++ .../tests/main.nf.test.snap | 101 ++++++++++++++ nextflow.config | 13 +- nextflow_schema.json | 24 ++++ .../local/contamination_check/main.nf | 67 +++++++++ .../local/contamination_check/meta.yml | 41 ++++++ workflows/raredisease.nf | 53 +++++++- 22 files changed, 1163 insertions(+), 9 deletions(-) create mode 100644 conf/modules/contamination.config create mode 100644 modules/local/parse_contamination/environment.yml create mode 100644 modules/local/parse_contamination/main.nf create mode 100644 modules/local/parse_contamination/meta.yml create mode 100644 modules/nf-core/gatk4/calculatecontamination/environment.yml create mode 100644 modules/nf-core/gatk4/calculatecontamination/main.nf create mode 100644 modules/nf-core/gatk4/calculatecontamination/meta.yml create mode 100644 modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config create mode 100644 modules/nf-core/gatk4/getpileupsummaries/environment.yml create mode 100644 modules/nf-core/gatk4/getpileupsummaries/main.nf create mode 100644 modules/nf-core/gatk4/getpileupsummaries/meta.yml create mode 100644 modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap create mode 100644 subworkflows/local/contamination_check/main.nf create mode 100644 subworkflows/local/contamination_check/meta.yml diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 98820ad71..960470155 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,9 +2,9 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about - how to interpret these results, please see the documentation. report_section_order: @@ -14,6 +14,8 @@ report_section_order: order: -1001 "nf-core-raredisease-summary": order: -1002 + gatk_contamination: + order: 1050 export_plots: true @@ -51,9 +53,53 @@ module_order: - verifybamid: name: "VerifyBamID2" +# Custom content configuration for GATK contamination +custom_data: + gatk_contamination: + id: 'gatk_contamination' + section_name: 'GATK Contamination' + description: 'Sample contamination estimates from GATK CalculateContamination based on common variant allele frequencies' + plot_type: 'generalstats' + pconfig: + contamination_pct: + title: 'Contamination' + description: 'Estimated sample contamination percentage' + max: 10 + min: 0 + scale: 'RdYlGn-rev' + suffix: '%' + format: '{:,.2f}' + shared_key: 'contamination' + +# Make contamination visible in general stats by default +table_columns_visible: + gatk_contamination: + contamination_pct: True + +# Color coding thresholds for contamination +table_cond_formatting_rules: + contamination_pct: + pass: + - s_eq: 'pass' + - lt: 2.0 + warn: + - s_eq: 'warn' + - lt: 5.0 + - gte: 2.0 + fail: + - s_eq: 'fail' + - gte: 5.0 + +# Add to General Statistics table configuration +table_columns_placement: + gatk_contamination: + contamination_pct: 900 + extra_fn_clean_exts: - "_sorted_md" + - "_contamination" + - "_pileups" - type: regex pattern: "_LNUMBER[0-9]{1,}" -disable_version_detection: true +disable_version_detection: true \ No newline at end of file diff --git a/conf/modules/contamination.config b/conf/modules/contamination.config new file mode 100644 index 000000000..4fc09327d --- /dev/null +++ b/conf/modules/contamination.config @@ -0,0 +1,46 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for GATK contamination checking modules +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +process { + + // + // GATK GetPileupSummaries + // + withName: '.*:CONTAMINATION_CHECK:GATK4_GETPILEUPSUMMARIES' { + ext.args = '' + ext.prefix = { "${meta.id}_pileups" } + publishDir = [ + path: { "${params.outdir}/qc/contamination/pileups" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + // + // GATK CalculateContamination + // + withName: '.*:CONTAMINATION_CHECK:GATK4_CALCULATECONTAMINATION' { + ext.args = '' + ext.prefix = { "${meta.id}_contamination" } + publishDir = [ + path: { "${params.outdir}/qc/contamination" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + // + // Parse contamination results for MultiQC + // + withName: '.*:RAREDISEASE:PARSE_CONTAMINATION' { + ext.prefix = { "${meta.id}_contamination" } + publishDir = [ + path: { "${params.outdir}/multiqc" }, + mode: params.publish_dir_mode, + pattern: '*_mqc.tsv' + ] + } +} \ No newline at end of file diff --git a/modules.json b/modules.json index edb5cc6dc..d304e26f6 100644 --- a/modules.json +++ b/modules.json @@ -247,6 +247,16 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "gatk4/calculatecontamination": { + "branch": "master", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "installed_by": ["modules"] + }, + "gatk4/getpileupsummaries": { + "branch": "master", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "installed_by": ["modules"] + }, "genmod/annotate": { "branch": "master", "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", diff --git a/modules/local/parse_contamination/environment.yml b/modules/local/parse_contamination/environment.yml new file mode 100644 index 000000000..1f07535d3 --- /dev/null +++ b/modules/local/parse_contamination/environment.yml @@ -0,0 +1,7 @@ +name: parse_contamination +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - python=3.11 \ No newline at end of file diff --git a/modules/local/parse_contamination/main.nf b/modules/local/parse_contamination/main.nf new file mode 100644 index 000000000..f811175d2 --- /dev/null +++ b/modules/local/parse_contamination/main.nf @@ -0,0 +1,61 @@ +process PARSE_CONTAMINATION { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.11' : + 'biocontainers/python:3.11' }" + + input: + tuple val(meta), path(contamination_table) + + output: + tuple val(meta), path("*_contamination_mqc.tsv"), emit: mqc_table + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + #!/usr/bin/env python3 + + import csv + + # Read GATK contamination table + with open("${contamination_table}", 'r') as f: + lines = f.readlines() + # Skip header, get contamination value + data_line = lines[1].strip().split('\\t') + sample = data_line[0] + contamination = float(data_line[1]) + contamination_pct = contamination * 100 + + # Write MultiQC custom content file + with open("${prefix}_contamination_mqc.tsv", 'w') as out: + # Header with MultiQC configuration + out.write("# id: 'gatk_contamination'\\n") + out.write("# section_name: 'GATK Contamination'\\n") + out.write("# description: 'Sample contamination estimates from GATK CalculateContamination'\\n") + out.write("# plot_type: 'generalstats'\\n") + out.write("# pconfig:\\n") + out.write("# contamination_pct:\\n") + out.write("# title: 'Contamination'\\n") + out.write("# description: 'Estimated sample contamination percentage'\\n") + out.write("# max: 10\\n") + out.write("# min: 0\\n") + out.write("# scale: 'RdYlGn-rev'\\n") + out.write("# suffix: '%'\\n") + out.write("# format: '{:,.2f}'\\n") + # Data + out.write("Sample\\tcontamination_pct\\n") + out.write(f"${meta.id}\\t{contamination_pct:.4f}\\n") + + # Create versions file + with open("versions.yml", 'w') as v: + v.write('"${task.process}":\\n') + v.write(' python: "3.11"\\n') + """ +} \ No newline at end of file diff --git a/modules/local/parse_contamination/meta.yml b/modules/local/parse_contamination/meta.yml new file mode 100644 index 000000000..2739258c8 --- /dev/null +++ b/modules/local/parse_contamination/meta.yml @@ -0,0 +1,29 @@ +name: parse_contamination +description: Parse GATK CalculateContamination output for MultiQC +keywords: + - contamination + - MultiQC + - parsing +tools: + - python: + description: Python programming language + homepage: https://www.python.org/ +input: + - meta: + type: map + description: Groovy Map containing sample information + - contamination_table: + type: file + description: GATK CalculateContamination output table + pattern: "*.contamination.table" +output: + - mqc_table: + type: file + description: MultiQC custom content table + pattern: "*_contamination_mqc.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "56053vujinovic" \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml new file mode 100644 index 000000000..67e0eb860 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf new file mode 100644 index 000000000..0b8706e76 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -0,0 +1,59 @@ +process GATK4_CALCULATECONTAMINATION { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" + + input: + tuple val(meta), path(pileup), path(matched) + + output: + tuple val(meta), path('*.contamination.table'), emit: contamination + tuple val(meta), path('*.segmentation.table'), emit: segmentation, optional: true + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def matched_command = matched ? "--matched-normal ${matched}" : '' + + def avail_mem = 3072 + if (!task.memory) { + log.info('[GATK CalculateContamination] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() + } + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + CalculateContamination \\ + --input ${pileup} \\ + --output ${prefix}.contamination.table \\ + ${matched_command} \\ + --tmp-dir . \\ + ${args} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.contamination.table + touch ${prefix}.segmentation.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml new file mode 100644 index 000000000..477e9d3b1 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/meta.yml @@ -0,0 +1,76 @@ +name: gatk4_calculatecontamination +description: | + Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls. +keywords: + - gatk4 + - calculatecontamination + - cross-samplecontamination + - getpileupsummaries + - filtermutectcalls +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pileup: + type: file + description: File containing the pileups summary table of a tumor sample to + be used to calculate contamination. + pattern: "*.pileups.table" + ontologies: [] + - matched: + type: file + description: File containing the pileups summary table of a normal sample that + matches with the tumor sample specified in pileup argument. This is an optional + input. + pattern: "*.pileups.table" + ontologies: [] +output: + contamination: + - - meta: + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + ontologies: [] + - "*.contamination.table": + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + ontologies: [] + segmentation: + - - meta: + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + ontologies: [] + - "*.segmentation.table": + type: file + description: output table containing segmentation of tumor minor allele fractions + (optional) + pattern: "*.segmentation.table" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@GCJMackenzie" + - "@maxulysse" +maintainers: + - "@GCJMackenzie" + - "@maxulysse" diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test new file mode 100644 index 000000000..81f048f67 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test @@ -0,0 +1,106 @@ +nextflow_process { + + name "Test Process GATK4_CALCULATECONTAMINATION" + script "../main.nf" + process "GATK4_CALCULATECONTAMINATION" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/calculatecontamination" + + test("human - pileup-table") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), + [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() } + ) + } + + } + + test("human - pileup-table - matched-pair") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions_pair") }, + { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() } + ) + } + + } + + test("human - pileup-table - segmentation") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions_segmentation") }, + { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match("contamination") }, + { assert snapshot(file(process.out.segmentation.get(0).get(1)).readLines()[0]).match("segmentation") } + ) + } + + } + + test("human - pileup-table - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true), + [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap new file mode 100644 index 000000000..4ef184bfc --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap @@ -0,0 +1,127 @@ +{ + "versions_pair": { + "content": [ + [ + "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:29:33.077296321" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:29:20.224234796" + }, + "versions_segmentation": { + "content": [ + [ + "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:29:45.806413439" + }, + "segmentation": { + "content": [ + "#SAMPLE=tumour" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-15T12:57:38.845287" + }, + "human - pileup-table": { + "content": [ + "sample\tcontamination\terror" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-15T11:09:16.292509" + }, + "human - pileup-table - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.contamination.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.segmentation.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + ], + "contamination": [ + [ + { + "id": "test" + }, + "test.contamination.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "segmentation": [ + [ + { + "id": "test" + }, + "test.segmentation.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T12:29:55.994434812" + }, + "human - pileup-table - matched-pair": { + "content": [ + "sample\tcontamination\terror" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-15T11:09:26.408848" + }, + "contamination": { + "content": [ + "sample\tcontamination\terror" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-15T12:57:38.840651" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config b/modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config new file mode 100644 index 000000000..db836b7f8 --- /dev/null +++ b/modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_CALCULATECONTAMINATION { + ext.args = { "--tumor-segmentation ${meta.id}.segmentation.table" } + } +} diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml new file mode 100644 index 000000000..67e0eb860 --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf new file mode 100644 index 000000000..d0cabdaf8 --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -0,0 +1,65 @@ +process GATK4_GETPILEUPSUMMARIES { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" + + input: + tuple val(meta), path(input), path(index), path(intervals) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + path variants + path variants_tbi + + output: + tuple val(meta), path('*.pileups.table'), emit: table + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def interval_command = intervals ? "--intervals ${intervals}" : "--intervals ${variants}" + def reference_command = fasta ? "--reference ${fasta}" : '' + + def avail_mem = 3072 + if (!task.memory) { + log.info('[GATK GetPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() + } + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + GetPileupSummaries \\ + --input ${input} \\ + --variant ${variants} \\ + --output ${prefix}.pileups.table \\ + ${reference_command} \\ + ${interval_command} \\ + --tmp-dir . \\ + ${args} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.pileups.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml new file mode 100644 index 000000000..d7f66ad19 --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/meta.yml @@ -0,0 +1,106 @@ +name: gatk4_getpileupsummaries +description: | + Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD. +keywords: + - gatk4 + - germlinevariantsites + - getpileupsumaries + - readcountssummary +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: BAM/CRAM file to be summarised. + pattern: "*.{bam,cram}" + ontologies: [] + - index: + type: file + description: Index file for the input BAM/CRAM file. + pattern: "*.{bam.bai,cram.crai}" + ontologies: [] + - intervals: + type: file + description: File containing specified sites to be used for the summary. If + this option is not specified, variants file is used instead automatically. + pattern: "*.interval_list" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + ontologies: [] + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + ontologies: [] + - variants: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + Is also used as sites file if no separate sites file is specified. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - variants_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + ontologies: [] +output: + table: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.pileups.table": + type: file + description: Table containing read counts for each site. + pattern: "*.pileups.table" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@GCJMackenzie" +maintainers: + - "@GCJMackenzie" diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test new file mode 100644 index 000000000..79cd6344c --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test @@ -0,0 +1,104 @@ +nextflow_process { + + name "Test Process GATK4_GETPILEUPSUMMARIES" + script "../main.nf" + process "GATK4_GETPILEUPSUMMARIES" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/getpileupsummaries" + + test("human - bam") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list', checkIfExists: true) + ] + input[1] = [[],[]] // fasta + input[2] = [[],[]] // fai + input[3] = [[],[]] // dict + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("human - cram") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + ] + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("human - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list', checkIfExists: true) + ] + input[1] = [[],[]] // fasta + input[2] = [[],[]] // fai + input[3] = [[],[]] // dict + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap new file mode 100644 index 000000000..fe713315a --- /dev/null +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap @@ -0,0 +1,101 @@ +{ + "human - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ], + "table": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T15:15:36.702715205" + }, + "human - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" + ] + ], + "1": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ], + "table": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" + ] + ], + "versions": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T15:14:59.43518059" + }, + "human - cram": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" + ] + ], + "1": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ], + "table": [ + [ + { + "id": "test" + }, + "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" + ] + ], + "versions": [ + "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.7" + }, + "timestamp": "2025-09-15T15:15:25.628760353" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index c45672bb0..6715f1c22 100644 --- a/nextflow.config +++ b/nextflow.config @@ -30,6 +30,7 @@ params { run_mt_for_wes = false run_rtgvcfeval = false save_mapped_as_cram = false + run_contamination = false scatter_count = 20 skip_tools = null skip_subworkflows = null @@ -88,6 +89,8 @@ params { vcfanno_lua = null vep_cache = null vep_plugin_files = null + contamination_sites = null + contamination_sites_tbi = null modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease' @@ -337,7 +340,6 @@ dag { manifest { name = 'nf-core/raredisease' - author = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ [ name: 'Ramprasad Neethiraj', @@ -435,8 +437,8 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.04.2' - version = '2.6.0' + nextflowVersion = '!>=24.10.5' + version = '2.7.0dev' doi = '10.5281/zenodo.7995798' } @@ -464,6 +466,7 @@ includeConfig 'conf/modules/align_sentieon.config' includeConfig 'conf/modules/annotate_cadd.config' includeConfig 'conf/modules/call_snv_MT.config' includeConfig 'conf/modules/call_snv_deepvariant.config' +includeConfig 'conf/modules/call_snv_deepvariant_parabricks.config' includeConfig 'conf/modules/call_snv_sentieon.config' includeConfig 'conf/modules/call_sv_MT.config' includeConfig 'conf/modules/call_sv_cnvnator.config' @@ -477,10 +480,12 @@ includeConfig 'conf/modules/generate_clinical_set.config' includeConfig 'conf/modules/variant_evaluation.config' includeConfig 'conf/modules/subsample_mt.config' includeConfig 'conf/modules/annotate_rhocallviz.config' +includeConfig 'conf/modules/contamination.config' + // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nextflow_schema.json b/nextflow_schema.json index 8ece884bf..7a06971b5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -435,6 +435,30 @@ "description": "Path to UD matrix file from SVD result of genotype matrix. Used by verifybamid2.", "fa_icon": "fas fa-file-csv" }, + "run_contamination": { + "type": "boolean", + "default": false, + "description": "Run GATK contamination check in addition to VerifyBamID2.", + "help_text": "GATK contamination check works better for WES samples and provides validation for WGS.", + "fa_icon": "fas fa-toggle-on" + }, + "contamination_sites": { + "type": "string", + "exists": true, + "format": "file-path", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "description": "Path to VCF file with common variants for GATK contamination detection.", + "help_text": "Use small_exac_common_3.hg38.vcf.gz for no_alt reference genomes. This file should contain common SNP sites with population allele frequencies.", + "fa_icon": "fas fa-file" + }, + "contamination_sites_tbi": { + "type": "string", + "exists": true, + "format": "file-path", + "pattern": "^\\S+\\.vcf(\\.gz)?\\.tbi$", + "description": "Index file for contamination sites VCF.", + "fa_icon": "fas fa-file" + }, "vcf2cytosure_blacklist": { "type": "string", "exists": true, diff --git a/subworkflows/local/contamination_check/main.nf b/subworkflows/local/contamination_check/main.nf new file mode 100644 index 000000000..8ff0d4e90 --- /dev/null +++ b/subworkflows/local/contamination_check/main.nf @@ -0,0 +1,67 @@ +// +// Subworkflow: Check sample contamination using GATK +// + +include { GATK4_GETPILEUPSUMMARIES } from '../../../modules/nf-core/gatk4/getpileupsummaries/main' +include { GATK4_CALCULATECONTAMINATION } from '../../../modules/nf-core/gatk4/calculatecontamination/main' + +workflow CONTAMINATION_CHECK { + + take: + ch_bam // channel: [ val(meta), path(bam), path(bai) ] + ch_fasta // channel: [ val(meta), path(fasta) ] + ch_fai // channel: [ val(meta), path(fai) ] + ch_dict // channel: [ val(meta), path(dict) ] + ch_contamination_vcf // channel: [ path(vcf), path(tbi) ] + ch_intervals // channel: [ path(bed) ] - only used for WES, empty for WGS + + main: + ch_versions = Channel.empty() + + // Prepare BAM with intervals - conditionally based on analysis type + // For WGS: intervals will be empty [], for WES: intervals will contain the BED file + ch_bam_with_intervals = ch_bam + .combine(ch_intervals.ifEmpty([[]])) + .map { meta, bam, bai, bed -> + // If bed is an empty list, pass empty list; otherwise pass bed file + def intervals = (bed instanceof List && bed.isEmpty()) ? [] : (bed ?: []) + [ meta, bam, bai, intervals ] + } + + // Separate VCF and TBI - collect them to make value channels + ch_variants_vcf = ch_contamination_vcf + .map { vcf, tbi -> vcf } + .collect() + + ch_variants_tbi = ch_contamination_vcf + .map { vcf, tbi -> tbi } + .collect() + + // Run GetPileupSummaries + GATK4_GETPILEUPSUMMARIES ( + ch_bam_with_intervals, // [meta, bam, bai, intervals] + ch_fasta, // [meta2, fasta] + ch_fai, // [meta3, fai] + ch_dict, // [meta4, dict] + ch_variants_vcf, // path(vcf) + ch_variants_tbi // path(tbi) + ) + ch_versions = ch_versions.mix(GATK4_GETPILEUPSUMMARIES.out.versions.first()) + + // Run CalculateContamination (tumor-only, no matched normal) + // Format: [meta, pileup_table, matched_normal_table] + // matched_normal_table is empty [] for tumor-only mode + ch_contamination_input = GATK4_GETPILEUPSUMMARIES.out.table + .map { meta, table -> [ meta, table, [] ] } + + GATK4_CALCULATECONTAMINATION ( + ch_contamination_input + ) + ch_versions = ch_versions.mix(GATK4_CALCULATECONTAMINATION.out.versions.first()) + + emit: + contamination_table = GATK4_CALCULATECONTAMINATION.out.contamination + segmentation_table = GATK4_CALCULATECONTAMINATION.out.segmentation + pileup_table = GATK4_GETPILEUPSUMMARIES.out.table + versions = ch_versions +} \ No newline at end of file diff --git a/subworkflows/local/contamination_check/meta.yml b/subworkflows/local/contamination_check/meta.yml new file mode 100644 index 000000000..9a26869a0 --- /dev/null +++ b/subworkflows/local/contamination_check/meta.yml @@ -0,0 +1,41 @@ +name: contamination_check +description: Estimate sample contamination using GATK GetPileupSummaries and CalculateContamination +keywords: + - contamination + - QC + - GATK +components: + - gatk4/getpileupsummaries + - gatk4/calculatecontamination +input: + - ch_bam: + type: file + description: BAM files with their indices + pattern: "*.{bam,cram}" + - ch_fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" + - ch_contamination_vcf: + type: file + description: VCF file containing common germline variants (gnomAD) + pattern: "*.vcf.gz" + - ch_intervals: + type: file + description: BED file with target intervals + pattern: "*.bed" +output: + - contamination_table: + type: file + description: Table containing contamination estimates + pattern: "*.contamination.table" + - segmentation_table: + type: file + description: Table containing tumor segmentation + pattern: "*.segmentation.table" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "56053vujinovic" \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 531dc27ec..476a8fb69 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -27,7 +27,6 @@ include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R1_FQ } from '../modules/n include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_R2_FQ } from '../modules/nf-core/spring/decompress/main' include { SPRING_DECOMPRESS as SPRING_DECOMPRESS_TO_FQ_PAIR } from '../modules/nf-core/spring/decompress/main' include { STRANGER } from '../modules/nf-core/stranger/main' - // // MODULE: Local modules // @@ -36,6 +35,7 @@ include { RENAME_ALIGN_FILES as RENAME_BAM } from '../modules/local/rename_align include { RENAME_ALIGN_FILES as RENAME_BAI } from '../modules/local/rename_align_files' include { CREATE_HGNCIDS_FILE } from '../modules/local/create_hgncids_file' include { CREATE_PEDIGREE_FILE } from '../modules/local/create_pedigree_file' +include { PARSE_CONTAMINATION } from '../modules/local/parse_contamination/main' // // SUBWORKFLOWS @@ -68,6 +68,7 @@ include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkf include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' +include { CONTAMINATION_CHECK } from '../subworkflows/local/contamination_check/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -404,7 +405,53 @@ workflow RAREDISEASE { ) ch_versions = ch_versions.mix(QC_BAM.out.versions) - + // + // SUBWORKFLOW: Check for contamination using GATK + // + ch_contamination_mqc = Channel.empty() + + if (params.run_contamination && params.contamination_sites) { + + log.info "=== CONTAMINATION CHECK ENABLED ===" + log.info "Analysis type: ${params.analysis_type}" + + // Prepare contamination sites channel + ch_contamination_sites = Channel.of([ + file(params.contamination_sites, checkIfExists: true), + file(params.contamination_sites_tbi, checkIfExists: true) + ]).collect() + + // Prepare intervals channel - CRITICAL: Use Channel.empty() for WGS, not Channel.of([]) + if (params.analysis_type == 'wes' && params.target_bed) { + ch_intervals_contamination = Channel.fromPath(params.target_bed).collect() + log.info "Using target BED for WES contamination check" + } else { + ch_intervals_contamination = Channel.empty() + log.info "No intervals for WGS contamination check (genome-wide)" + } + + // Prepare BAM input with BAI + ch_bam_for_contamination = ch_mapped.genome_marked_bam + .join(ch_mapped.genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + + CONTAMINATION_CHECK ( + ch_bam_for_contamination, + ch_genome_fasta, + ch_genome_fai, + ch_genome_dictionary, + ch_contamination_sites, + ch_intervals_contamination + ) + + // Parse for MultiQC + PARSE_CONTAMINATION ( + CONTAMINATION_CHECK.out.contamination_table + ) + + ch_contamination_mqc = PARSE_CONTAMINATION.out.mqc_table + ch_versions = ch_versions.mix(CONTAMINATION_CHECK.out.versions) + ch_versions = ch_versions.mix(PARSE_CONTAMINATION.out.versions) + } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RENAME ALIGNMENT FILES FOR SMNCOPYNUMBERCALLER & REPEATCALLING @@ -922,6 +969,8 @@ workflow RAREDISEASE { ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{it[1]}.collect().ifEmpty([])) +// Add contamination results to MultiQC + ch_multiqc_files = ch_multiqc_files.mix(ch_contamination_mqc.map { meta, file -> file }) if (!(params.skip_tools && params.skip_tools.split(',').contains('peddy'))) { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{it[1]}.collect().ifEmpty([])) From fb822cd72702da4502561a2ca5a12a90d7b84b17 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 26 Nov 2025 11:22:10 +0100 Subject: [PATCH 086/872] update snap --- subworkflows/local/align/main.nf | 40 +++--- subworkflows/local/align/tests/main.nf.test | 4 +- .../local/align/tests/main.nf.test.snap | 119 +++++++++++++++++- tests/default.nf.test.snap | 2 +- workflows/raredisease.nf | 4 +- 5 files changed, 143 insertions(+), 26 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 9c1ab6fa9..8571598ea 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -138,17 +138,17 @@ workflow ALIGN { ch_mtshift_fai ) - ch_mt_bam_bai = CONVERT_MT_BAM_TO_FASTQ.out.bam_bai // Used for subsampling and SV calling - ch_mt_marked_bam = ALIGN_MT.out.marked_bam - ch_mt_marked_bai = ALIGN_MT.out.marked_bai - ch_mt_bam_bai_mtsub = ch_mt_marked_bam - .join(ch_mt_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling - ch_mtshift_marked_bam = ALIGN_MT_SHIFT.out.marked_bam - ch_mtshift_marked_bai = ALIGN_MT_SHIFT.out.marked_bai - ch_mtshift_bam_bai_mtsub = ch_mtshift_marked_bam - .join(ch_mtshift_marked_bai, failOnMismatch:true, failOnDuplicate:true) - ch_versions = ch_versions - .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) + ch_mt_bam_bai = CONVERT_MT_BAM_TO_FASTQ.out.bam_bai // Used for subsampling and SV calling + ch_mt_marked_bam = ALIGN_MT.out.marked_bam + ch_mt_marked_bai = ALIGN_MT.out.marked_bai + ch_mt_bam_bai_gatksubwf = ch_mt_marked_bam + .join(ch_mt_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling + ch_mtshift_marked_bam = ALIGN_MT_SHIFT.out.marked_bam + ch_mtshift_marked_bai = ALIGN_MT_SHIFT.out.marked_bai + ch_mtshift_bam_bai_gatksubwf = ch_mtshift_marked_bam + .join(ch_mtshift_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling + ch_versions = ch_versions + .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) } if (params.save_mapped_as_cram) { @@ -157,13 +157,13 @@ workflow ALIGN { } emit: - fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] - genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] - genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] - genome_bam_bai = ch_genome_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] - mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - mt_bam_bai_mtsub = ch_mt_bam_bai_mtsub // channel: [ val(meta), path(bam), path(bai) ] - mtshift_bam_bai_mtsub = ch_mtshift_bam_bai_mtsub // channel: [ val(meta), path(bam), path(bai) ] - versions = ch_versions // channel: [ path(versions.yml) ] + fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] + genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] + genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] + genome_bam_bai = ch_genome_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] + mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] + mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index f7c51cab6..60cd43726 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -118,7 +118,9 @@ nextflow_workflow { .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mtshift_bam_bai + workflow.out.mt_bam_bai_gatksubwf + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mtshift_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions ).match() diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index b220fb7e5..1518a7099 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -120,7 +120,122 @@ ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "9beeefe789d896c08d55e8b8d13d9623", + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "b18998c8cf7dc417ca9a122ba1c9403d", + "hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "a5d6892191a2c8c1f29966448623ca1b", + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "130fb09f419109e40a6be267bfbd8c88", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "97e6eaae1cda668da59e5c16a9bbcc1d", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "427b5e476d84c5277d2d24210800ad60", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ], [ "versions.yml:md5,04cb590a101237e8d8726039ee466819", @@ -155,7 +270,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-14T16:54:07.946917784" + "timestamp": "2025-11-26T10:13:53.59654663" }, "align bwameme": { "content": [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e1084b57f..18e5562bb 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -631,6 +631,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-10-27T15:59:49.765279594" + "timestamp": "2025-11-26T10:17:14.24575236" } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3088a8ba8..374eff371 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -452,8 +452,8 @@ workflow RAREDISEASE { if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_calling'))) { CALL_SNV ( ch_mapped.genome_bam_bai, - ch_mapped.mt_bam_bai_mtsub, - ch_mapped.mtshift_bam_bai_mtsub, + ch_mapped.mt_bam_bai_gatksubwf, + ch_mapped.mtshift_bam_bai_gatksubwf, ch_genome_chrsizes, ch_genome_fasta, ch_genome_fai, From 6ce95f9262511e220375a982c0e40e2183eeefee Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 26 Nov 2025 12:28:23 +0100 Subject: [PATCH 087/872] review suggestions --- subworkflows/local/align/main.nf | 41 +++++++++++++------------------- 1 file changed, 17 insertions(+), 24 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 8571598ea..32e9a6310 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -35,19 +35,16 @@ workflow ALIGN { val_sort_threads // integer: [mandatory] number of sorting threads main: - ch_bwamem2_bam = Channel.empty() - ch_bwamem2_bai = Channel.empty() - ch_fastp_json = Channel.empty() - ch_markdup_metrics = Channel.empty() - ch_mt_bam_bai = Channel.empty() - ch_mt_marked_bam = Channel.empty() - ch_mt_marked_bai = Channel.empty() - ch_mtshift_bam_bai = Channel.empty() - ch_mtshift_marked_bam = Channel.empty() - ch_mtshift_marked_bai = Channel.empty() - ch_sentieon_bam = Channel.empty() - ch_sentieon_bai = Channel.empty() - ch_versions = Channel.empty() + ch_bwamem2_bam = Channel.empty() + ch_bwamem2_bai = Channel.empty() + ch_fastp_json = Channel.empty() + ch_markdup_metrics = Channel.empty() + ch_mt_bam_bai = Channel.empty() + ch_mt_bam_bai_gatksubwf = Channel.empty() + ch_mtshift_bam_bai_gatksubwf = Channel.empty() + ch_sentieon_bam = Channel.empty() + ch_sentieon_bai = Channel.empty() + ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('fastp'))) { FASTP (ch_reads, [], false, false, false) @@ -104,9 +101,9 @@ workflow ALIGN { ch_versions = ch_versions.mix(ALIGN_SENTIEON.out.versions) } - ch_genome_marked_bam = Channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) - ch_genome_marked_bai = Channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) - ch_genome_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + ch_genome_marked_bam = Channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) + ch_genome_marked_bai = Channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) + ch_genome_merked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) // PREPARING READS FOR MT ALIGNMENT @@ -139,14 +136,10 @@ workflow ALIGN { ) ch_mt_bam_bai = CONVERT_MT_BAM_TO_FASTQ.out.bam_bai // Used for subsampling and SV calling - ch_mt_marked_bam = ALIGN_MT.out.marked_bam - ch_mt_marked_bai = ALIGN_MT.out.marked_bai - ch_mt_bam_bai_gatksubwf = ch_mt_marked_bam - .join(ch_mt_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling - ch_mtshift_marked_bam = ALIGN_MT_SHIFT.out.marked_bam - ch_mtshift_marked_bai = ALIGN_MT_SHIFT.out.marked_bai - ch_mtshift_bam_bai_gatksubwf = ch_mtshift_marked_bam - .join(ch_mtshift_marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling + ch_mt_bam_bai_gatksubwf = ALIGN_MT.out.marked_bam + .join(ALIGN_MT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling + ch_mtshift_bam_bai_gatksubwf = ALIGN_MT_SHIFT.out.marked_bam + .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling ch_versions = ch_versions .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) } From aab11c45a5a0dcda829652a5aaf4b6394aa7ebf2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 13:48:20 +0100 Subject: [PATCH 088/872] update bcftools/annotate that allows a renaming of chrs --- modules.json | 2 +- .../nf-core/bcftools/annotate/environment.yml | 7 +- modules/nf-core/bcftools/annotate/main.nf | 57 +- modules/nf-core/bcftools/annotate/meta.yml | 47 +- .../bcftools/annotate/tests/main.nf.test | 118 +++- .../bcftools/annotate/tests/main.nf.test.snap | 589 +++++++++++++++--- .../nf-core/bcftools/annotate/tests/tags.yml | 2 - subworkflows/local/annotate_cadd/main.nf | 10 +- 8 files changed, 705 insertions(+), 127 deletions(-) delete mode 100644 modules/nf-core/bcftools/annotate/tests/tags.yml diff --git a/modules.json b/modules.json index 4c7996444..33d426717 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] }, "bcftools/concat": { diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 9ffdfdf0a..25fef22dc 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -1,49 +1,56 @@ process BCFTOOLS_ANNOTATE { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) - path(header_lines) + path columns + path header_lines + path rename_chrs output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def header_file = header_lines ? "--header-lines ${header_lines}" : '' + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def annotations_file = annotations ? "--annotations ${annotations}" : '' + def columns_file = columns ? "--columns-file ${columns}" : '' + def header_file = header_lines ? "--header-lines ${header_lines}" : '' + def rename_chrs_file = rename_chrs ? "--rename-chrs ${rename_chrs}" : '' def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index_command = !index ? "bcftools index $input" : '' + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index_command = !index ? "bcftools index ${input}" : '' - if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("${input}" == "${prefix}.${extension}") { + error("Input and output names are the same, set prefix in module configuration to disambiguate!") + } """ - $index_command + ${index_command} bcftools \\ annotate \\ - $args \\ - $annotations_file \\ - $header_file \\ + ${args} \\ + ${annotations_file} \\ + ${columns_file} \\ + ${header_file} \\ + ${rename_chrs_file} \\ --output ${prefix}.${extension} \\ - --threads $task.cpus \\ - $input + --threads ${task.cpus} \\ + ${input} cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -60,12 +67,14 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" + if ("${input}" == "${prefix}.${extension}") { + error("Input and output names are the same, set prefix in module configuration to disambiguate!") + } """ ${create_cmd} ${prefix}.${extension} ${create_index} diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 5bfccd2bd..058954d21 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -23,21 +23,35 @@ input: - input: type: file description: Query VCF or BCF file, can be either uncompressed or compressed + ontologies: [] - index: type: file description: Index of the query VCF or BCF file + ontologies: [] - annotations: type: file description: Bgzip-compressed file with annotations + ontologies: [] - annotations_index: type: file description: Index of the annotations file - - - header_lines: - type: file - description: Contains lines to append to the output VCF header + ontologies: [] + - columns: + type: file + description: List of columns in the annotations file, one name per row + ontologies: [] + - header_lines: + type: file + description: Contains lines to append to the output VCF header + ontologies: [] + - rename_chrs: + type: file + description: Rename annotations according to this file containing "old_name new_name\n" + pairs separated by whitespaces, each on a separate line. + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -46,8 +60,9 @@ output: type: file description: Compressed annotated VCF file pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -56,8 +71,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -66,11 +82,14 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 3a5c49331..79acadcca 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "bcftools" tag "bcftools/annotate" - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output") { config "./vcf.config" @@ -24,6 +24,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -40,7 +42,7 @@ nextflow_process { } - test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") { + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output") { config "./vcf.config" @@ -55,6 +57,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -70,7 +74,8 @@ nextflow_process { } } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") { + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index") { config "./vcf_gz_index.config" @@ -85,6 +90,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -104,7 +111,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi") { config "./vcf_gz_index_csi.config" @@ -119,6 +126,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -138,7 +147,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi") { config "./vcf_gz_index_tbi.config" @@ -153,6 +162,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -171,7 +182,44 @@ nextflow_process { } } - test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") { + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = Channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf-header") } + ) + } + + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output") { config "./bcf.config" @@ -185,10 +233,45 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] - input[1] = Channel.of( + input[1] = Channel.of('INFO/ICB', 'INFO/HOB', 'INFO/DP4').collectFile(name:"columns.txt", newLine:true) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf-columns") } + ) + } + + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = Channel.of( '##INFO=', '##INFO=' ).collectFile(name:"headers.vcf", newLine:true) + input[3] = Channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true) """ } } @@ -196,16 +279,17 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).LinesGzip.contains("##contig=")}, { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, process.out.versions - ).match("bcf") } + ).match() } ) } } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub") { config "./vcf.config" options "-stub" @@ -221,6 +305,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -234,7 +320,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub") { config "./vcf_gz_index.config" options "-stub" @@ -250,6 +336,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -264,7 +352,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub") { config "./vcf_gz_index_csi.config" options "-stub" @@ -280,6 +368,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -294,7 +384,7 @@ nextflow_process { } - test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub") { config "./vcf_gz_index_tbi.config" options "-stub" @@ -310,6 +400,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] + input[2] = [] + input[3] = [] """ } } @@ -324,4 +416,4 @@ nextflow_process { } -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index bac2224a3..c7f40bf83 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "bcf": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi": { "content": [ [ [ @@ -7,20 +7,32 @@ "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz" ] ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + + ], + [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-06-12T16:39:33.331888" + "timestamp": "2025-04-01T12:55:30.265471036" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": { + "bcf": { "content": [ [ [ @@ -28,32 +40,100 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.bcf" ] ], [ - - ], + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:55:37.270860052" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:56:47.356548" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": { + "content": [ [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_vcf.vcf.gz" ] ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-08-15T10:07:59.658031137" + "timestamp": "2025-04-01T12:55:12.451788461" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -78,7 +158,7 @@ ] ], "3": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ], "csi": [ [ @@ -102,17 +182,64 @@ ] ], "versions": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-08-15T10:09:05.096883418" + "timestamp": "2025-09-11T13:56:42.987304" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:56:34.067026" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ [ [ @@ -124,28 +251,100 @@ ] ], [ - + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:55:52.749146" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] ], + [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:55:57.699598" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": { + "content": [ [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_vcf.vcf.gz" ] ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-08-15T10:08:10.581301219" + "timestamp": "2025-09-11T13:56:28.915986" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": { + "bcf-header": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann.bcf" + ] + ], + [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:56:18.654899" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:55:08.604415962" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -158,16 +357,87 @@ ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ ], "3": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ], "csi": [ + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:56:06.054536287" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "tbi": [ @@ -182,17 +452,17 @@ ] ], "versions": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-08-15T10:08:43.975017625" + "timestamp": "2025-09-11T13:56:38.664942" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ [ [ @@ -216,16 +486,84 @@ ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:56:13.350208" + }, + "bcf-columns": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann.bcf" + ] + ], + [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-11T13:56:24.166879" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-08-15T10:08:21.354059092" + "timestamp": "2025-04-01T12:55:48.340271359" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": { "content": [ [ [ @@ -237,16 +575,28 @@ ] ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-08-15T10:07:37.788393317" + "timestamp": "2025-09-11T13:56:07.974454" }, - "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": { "content": [ [ [ @@ -258,16 +608,28 @@ ] ], [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-08-15T10:07:48.500746325" + "timestamp": "2025-09-11T13:56:02.490243" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -280,31 +642,31 @@ ] ], "1": [ + + ], + "2": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "2": [ - ], "3": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ], "csi": [ - - ], - "tbi": [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "tbi": [ + ], "vcf": [ [ @@ -316,17 +678,17 @@ ] ], "versions": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-08-15T10:09:16.094918834" + "timestamp": "2025-04-01T12:55:52.305248991" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -351,7 +713,7 @@ ] ], "3": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ], "csi": [ [ @@ -375,14 +737,101 @@ ] ], "versions": [ - "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:55:59.210314307" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:55:19.532491092" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-04-01T12:55:44.331095545" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" }, - "timestamp": "2024-08-15T10:08:54.366358502" + "timestamp": "2025-04-01T12:55:23.309288135" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/tags.yml b/modules/nf-core/bcftools/annotate/tests/tags.yml deleted file mode 100644 index f97a1afc8..000000000 --- a/modules/nf-core/bcftools/annotate/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/annotate: - - "modules/nf-core/bcftools/annotate/**" diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index ab43ef12e..57b2145d1 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -22,7 +22,7 @@ workflow ANNOTATE_CADD { main: ch_versions = channel.empty() - + ch_rename_chrs = channel.empty() if (params.genome_build == 'GRCh38') { @@ -32,12 +32,17 @@ workflow ANNOTATE_CADD { CADD_TO_REFERENCE_CHRNAMES ( ch_fai , [], false ) ch_versions = ch_versions.mix(CADD_TO_REFERENCE_CHRNAMES.out.versions) + CADD_TO_REFERENCE_CHRNAMES.out.output.map { _meta, txt -> txt } + .set { ch_rename_chrs } + ch_vcf .map { meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ] } .set { rename_chrnames_in } RENAME_CHRNAMES ( rename_chrnames_in, + [], + [], REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt } ) ch_versions = ch_versions.mix(RENAME_CHRNAMES.out.versions) @@ -60,9 +65,10 @@ workflow ANNOTATE_CADD { ch_vcf .join(CADD.out.tsv) .join(TABIX_CADD.out.tbi) + .map { meta, vcf, annotations, annotations_index -> [ meta, vcf, [], annotations, annotations_index ] } .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, ch_header) + BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_header.map { _meta, header -> header }, ch_rename_chrs) TABIX_ANNOTATE (BCFTOOLS_ANNOTATE.out.vcf) From 91e0f3497129fd828f4db6cd688751ffa5a41f37 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 13:55:26 +0100 Subject: [PATCH 089/872] update bcftools annotate inputs --- .vscode/settings.json | 7 ++++++- subworkflows/local/call_snv_deepvariant/main.nf | 2 +- subworkflows/local/call_snv_sentieon/main.nf | 2 +- subworkflows/local/postprocess_MT_calls/main.nf | 2 +- 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index a33b527cc..17c37849a 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,8 @@ { - "markdown.styles": ["public/vscode_markdown.css"] + "markdown.styles": [ + "public/vscode_markdown.css" + ], + "cSpell.words": [ + "chrs" + ] } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 826f2e6a3..c82a8f8d2 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -78,7 +78,7 @@ workflow CALL_SNV_DEEPVARIANT { .combine(ch_varcallerbed) .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, ch_foundin_header) + BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index e987d26cb..be262f9e9 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -104,7 +104,7 @@ workflow CALL_SNV_SENTIEON { .combine(ch_varcallerbed) .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, ch_foundin_header) + BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 8657b5ffb..0a994a33b 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -117,7 +117,7 @@ workflow POSTPROCESS_MT_CALLS { .combine(ch_varcallerbed) .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in,ch_foundin_header) + BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) From 37e9beeec09d6d404ec6bd07b6a9034e578db87c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 13:58:25 +0100 Subject: [PATCH 090/872] prettier --- .vscode/settings.json | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index 17c37849a..db1a67f8f 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,8 +1,4 @@ { - "markdown.styles": [ - "public/vscode_markdown.css" - ], - "cSpell.words": [ - "chrs" - ] + "markdown.styles": ["public/vscode_markdown.css"], + "cSpell.words": ["chrs"] } From 88cee9ba1d7d83cc9b3f7e7154e2a770d7fe9e95 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 14:40:19 +0100 Subject: [PATCH 091/872] update config --- conf/modules/annotate_cadd.config | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index 46d170304..e027abe8c 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -39,9 +39,15 @@ process { ext.prefix = { "${input.simpleName}_ann" } } + withName: '.*:ANNOTATE_CADD:CADD_TO_REFERENCE_CHRNAMES' { + ext.args2 = '\'{original=$1; sub("chr","",$1); print $1, original}\'' + ext.prefix = "cadd_to_reference" + ext.suffix = "txt" + } + withName: '.*:ANNOTATE_CADD:REFERENCE_TO_CADD_CHRNAMES' { ext.args2 = '\'{original=$1; sub("chr","",$1); print original, $1}\'' ext.prefix = "reference_to_cadd" ext.suffix = "txt" } -} +} \ No newline at end of file From 349318e99792cd412ae3628a1bf2223584ee1042 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 26 Nov 2025 14:59:10 +0100 Subject: [PATCH 092/872] review suggestions --- subworkflows/local/align/main.nf | 8 +- subworkflows/local/align/tests/main.nf.test | 102 +++++++++++++++++- .../local/align/tests/main.nf.test.snap | 94 +++++++++++++++- workflows/raredisease.nf | 10 +- 4 files changed, 201 insertions(+), 13 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 32e9a6310..0c89bcc7e 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -103,13 +103,13 @@ workflow ALIGN { ch_genome_marked_bam = Channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) ch_genome_marked_bai = Channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) - ch_genome_merked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) // PREPARING READS FOR MT ALIGNMENT if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CONVERT_MT_BAM_TO_FASTQ ( - ch_genome_bam_bai, + ch_genome_marked_bam_bai, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary @@ -145,7 +145,7 @@ workflow ALIGN { } if (params.save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_bam_bai, ch_genome_fasta, [] ) + SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [] ) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } @@ -153,7 +153,7 @@ workflow ALIGN { fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] - genome_bam_bai = ch_genome_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + genome_marked_bam_bai = ch_genome_marked_bam_bai // channel: [ val(meta), path(bam), path(bai) ] markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 60cd43726..8d6e1e2ea 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -114,7 +114,105 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai + workflow.out.genome_marked_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mt_bam_bai_gatksubwf + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mtshift_bam_bai_gatksubwf + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.versions + ).match() + } + ) + } + } + test("align bwamem2 - wes") { + + options "-stub" + + setup { + run("BWAMEM2_INDEX", alias: 'GENOME_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + aligner = 'bwamem2' + mt_aligner = 'bwamem2' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + save_mapped_as_cram = true + analysis_type = "wes" + skip_tools = null + platform = "illumina" + min_trimmed_length = 50 + mito_name = "MT" + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ] + ] + ) + input[1] = Channel.empty() + input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = Channel.empty() + input[5] = GENOME_MEM2.out.index.collect() + input[6] = Channel.empty() + input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = Channel.empty() + input[9] = MT_MEM2.out.index.collect() + input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = Channel.empty() + input[14] = SHIFTMT_MEM2.out.index.collect() + input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[18] = 3072 + input[19] = "illumina" + input[20] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, @@ -205,7 +303,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_bam_bai + workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 1518a7099..c0bf65b2f 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -270,7 +270,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T10:13:53.59654663" + "timestamp": "2025-11-26T13:57:27.462836066" }, "align bwameme": { "content": [ @@ -425,6 +425,96 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-14T17:16:13.633955179" + "timestamp": "2025-11-26T14:03:43.037036726" + }, + "align bwamem2 - wes": { + "content": [ + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_md.bam.bai" + ] + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", + "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", + "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", + "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", + "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", + "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", + "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", + "versions.yml:md5,c31eb465488334212645bd43296d8bd7" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-11-26T13:58:00.971064108" } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e7a9c5e1c..a083ad721 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -389,7 +389,7 @@ workflow RAREDISEASE { QC_BAM ( ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, - ch_mapped.genome_bam_bai, + ch_mapped.genome_marked_bam_bai, ch_genome_fasta, ch_genome_fai, ch_bait_intervals, @@ -451,7 +451,7 @@ workflow RAREDISEASE { if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_calling'))) { CALL_SNV ( - ch_mapped.genome_bam_bai, + ch_mapped.genome_marked_bam_bai, ch_mapped.mt_bam_bai_gatksubwf, ch_mapped.mtshift_bam_bai_gatksubwf, ch_genome_chrsizes, @@ -634,7 +634,7 @@ workflow RAREDISEASE { CALL_STRUCTURAL_VARIANTS ( ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, - ch_mapped.genome_bam_bai, + ch_mapped.genome_marked_bam_bai, ch_mapped.mt_bam_bai, ch_genome_bwaindex, ch_genome_fasta, @@ -722,7 +722,7 @@ workflow RAREDISEASE { if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('me_calling')) && params.analysis_type.equals("wgs")) { CALL_MOBILE_ELEMENTS( - ch_mapped.genome_bam_bai, + ch_mapped.genome_marked_bam_bai, ch_genome_fasta, ch_genome_fai, ch_me_references, @@ -840,7 +840,7 @@ workflow RAREDISEASE { */ if (!(params.skip_tools && params.skip_tools.split(',').contains('gens')) && params.analysis_type.equals("wgs")) { GENS ( - ch_mapped.genome_bam_bai, + ch_mapped.genome_marked_bam_bai, CALL_SNV.out.genome_gvcf, ch_genome_fasta, ch_genome_fai, From 985c05a11731cdd2a236f5e63ace8ee23225b73c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 26 Nov 2025 15:00:09 +0100 Subject: [PATCH 093/872] use interally generated refs for mitosalt --- modules/local/mitosalt/main.nf | 16 ++++++++-------- subworkflows/local/call_sv_MT/main.nf | 5 ++--- subworkflows/local/prepare_references/main.nf | 4 +--- 3 files changed, 11 insertions(+), 14 deletions(-) diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 04da24b62..544e9f2fd 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -19,12 +19,12 @@ process MITOSALT { tuple val(meta), path(reads) path config path genome -// tuple val(meta2), path(hisat2index) -// tuple val(meta3), path(genomefai) -// tuple val(meta4), path(lastindex) -// tuple val(meta5), path(mtfai) -// path chrsizes -// tuple val(meta6), path(mtfasta) + tuple val(meta2), path(hisat2index) + tuple val(meta3), path(genomefai) + tuple val(meta4), path(lastindex) + tuple val(meta5), path(mtfai) + path chrsizes + tuple val(meta6), path(mtfasta) output: tuple val(meta), path("*breakpoint") , emit: breakpoint @@ -35,9 +35,9 @@ process MITOSALT { def VERSION = "1.1.1" // from perl script, unlikely to be updated def prefix = task.ext.prefix ?: "${meta.id}" """ + cat $config | sed "s,hsindex = .*,hsindex = ${hisat2index}/reference," | sed "s,^faindex = .*,faindex = $genomefai," | sed "s,lastindex = .*,lastindex = ${lastindex}/reference," | sed "s,mtfaindex = .*,mtfaindex = $mtfai," | sed "s,gsize = .*,gsize = $chrsizes," | sed "s,MT_fasta = .*,MT_fasta = $mtfasta," > new-${config} mkdir -p log indel bam tab bw plot - - MitoSAlt1.1.1.pl $config $reads $prefix + MitoSAlt1.1.1.pl new-${config} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint mv indel/*.cluster ${prefix}.cluster diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 64562b2ea..27b467893 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -29,9 +29,8 @@ workflow CALL_SV_MT { SEQTK_SAMPLE (ch_reads_subdepth) ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) -// MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta) - MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref) - ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) + MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta) + ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 33d489906..8506d0f10 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -56,8 +56,6 @@ workflow PREPARE_REFERENCES { ch_vcfanno_extra = Channel.empty() ch_vcfanno_bgzip = Channel.empty() ch_vcfanno_index = Channel.empty() - ch_gtf = Channel.empty() - ch_splicesites = Channel.empty() // Genome indices SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]) @@ -71,7 +69,7 @@ workflow PREPARE_REFERENCES { BWAMEM2_INDEX_GENOME(ch_genome_fasta) BWAMEME_INDEX_GENOME(ch_genome_fasta) SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} - HISAT2_INDEX_GENOME(ch_genome_fasta,ch_gtf,ch_splicesites) + HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]) // MT genome indices SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) From a155f05f326a76f7388fc5d72f92747815251d7f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 26 Nov 2025 19:39:00 +0100 Subject: [PATCH 094/872] update snapshots --- tests/test_bam.nf.test.snap | 6 +++--- tests/test_singleton.nf.test.snap | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9a2eb045b..f8bd276e7 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -7,7 +7,7 @@ "tabix": 1.12 }, "BCFTOOLS_ANNOTATE": { - "bcftools": 1.2 + "bcftools": 1.22 }, "BCFTOOLS_CONCAT": { "bcftools": 1.2 @@ -541,8 +541,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-15T09:40:09.030137924" + "timestamp": "2025-11-26T16:33:42.10010561" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index c912baf8d..ccf1b9da2 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -7,7 +7,7 @@ "tabix": 1.12 }, "BCFTOOLS_ANNOTATE": { - "bcftools": 1.2 + "bcftools": 1.22 }, "BCFTOOLS_CONCAT": { "bcftools": 1.2 @@ -464,8 +464,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nextflow": "25.10.0" }, - "timestamp": "2025-10-15T09:43:13.720671267" + "timestamp": "2025-11-26T19:37:55.555932216" } } \ No newline at end of file From 0671aec183ae971c17bd06365c76cfc649e40fab Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 11:40:04 +0100 Subject: [PATCH 095/872] eof fix --- conf/modules/annotate_cadd.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index e027abe8c..d82bdd415 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -50,4 +50,4 @@ process { ext.prefix = "reference_to_cadd" ext.suffix = "txt" } -} \ No newline at end of file +} From 99118e18076861d7ecc8a19b6f2e841b77f92035 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 13:47:19 +0100 Subject: [PATCH 096/872] subsample approach reads --- CHANGELOG.md | 1 + ...ple_mt.config => subsample_mt_frac.config} | 6 +- conf/modules/subsample_mt_reads.config | 58 +++++ modules.json | 10 + modules/nf-core/gawk/environment.yml | 7 + modules/nf-core/gawk/main.nf | 70 ++++++ modules/nf-core/gawk/meta.yml | 68 ++++++ modules/nf-core/gawk/tests/main.nf.test | 198 +++++++++++++++++ modules/nf-core/gawk/tests/main.nf.test.snap | 200 ++++++++++++++++++ modules/nf-core/gawk/tests/nextflow.config | 6 + .../nf-core/samtools/collate/environment.yml | 10 + modules/nf-core/samtools/collate/main.nf | 62 ++++++ modules/nf-core/samtools/collate/meta.yml | 84 ++++++++ .../samtools/collate/tests/main.nf.test | 93 ++++++++ .../samtools/collate/tests/main.nf.test.snap | 144 +++++++++++++ nextflow.config | 5 +- nextflow_schema.json | 17 +- .../main.nf} | 10 +- subworkflows/local/subsample_mt_reads/main.nf | 43 ++++ workflows/raredisease.nf | 22 +- 20 files changed, 1096 insertions(+), 18 deletions(-) rename conf/modules/{subsample_mt.config => subsample_mt_frac.config} (90%) create mode 100644 conf/modules/subsample_mt_reads.config create mode 100644 modules/nf-core/gawk/environment.yml create mode 100644 modules/nf-core/gawk/main.nf create mode 100644 modules/nf-core/gawk/meta.yml create mode 100644 modules/nf-core/gawk/tests/main.nf.test create mode 100644 modules/nf-core/gawk/tests/main.nf.test.snap create mode 100644 modules/nf-core/gawk/tests/nextflow.config create mode 100644 modules/nf-core/samtools/collate/environment.yml create mode 100644 modules/nf-core/samtools/collate/main.nf create mode 100644 modules/nf-core/samtools/collate/meta.yml create mode 100644 modules/nf-core/samtools/collate/tests/main.nf.test create mode 100644 modules/nf-core/samtools/collate/tests/main.nf.test.snap rename subworkflows/local/{subsample_mt.nf => subsample_mt_frac/main.nf} (78%) create mode 100644 subworkflows/local/subsample_mt_reads/main.nf diff --git a/CHANGELOG.md b/CHANGELOG.md index f99f52c19..e4381fe16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717) - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) +- Feature to subsample mitochondrial alignments based on number of reads. [#748](https://github.com/nf-core/raredisease/pull/748) ### `Changed` diff --git a/conf/modules/subsample_mt.config b/conf/modules/subsample_mt_frac.config similarity index 90% rename from conf/modules/subsample_mt.config rename to conf/modules/subsample_mt_frac.config index 7ce80bed1..b10fa357a 100644 --- a/conf/modules/subsample_mt.config +++ b/conf/modules/subsample_mt_frac.config @@ -16,12 +16,12 @@ // process { - withName: '.*SUBSAMPLE_MT:BEDTOOLS_GENOMECOV' { + withName: '.*SUBSAMPLE_MT_FRAC:BEDTOOLS_GENOMECOV' { ext.args = { "-dz" } ext.prefix = { "${meta.id}" } } - withName: '.*SUBSAMPLE_MT:SAMTOOLS_VIEW' { + withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_VIEW' { ext.args = { "--output-fmt BAM -h -F 4 -s ${meta.seedfrac}" } ext.prefix = { "${meta.id}_mt_subsample" } publishDir = [ @@ -31,7 +31,7 @@ process { ] } - withName: '.*SUBSAMPLE_MT:SAMTOOLS_INDEX' { + withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_INDEX' { publishDir = [ path: { "${params.outdir}/alignment" }, mode: params.publish_dir_mode, diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config new file mode 100644 index 000000000..68e5929a8 --- /dev/null +++ b/conf/modules/subsample_mt_reads.config @@ -0,0 +1,58 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = Conditional clause +---------------------------------------------------------------------------------------- +*/ + +// +// Subsample MT +// + +process { + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_VIEW' { + ext.args = { "--output-fmt bam -F 0x400" } + ext.prefix = { "${meta.id}_mt_nodups" } + } + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE' { + ext.args = { "--output-fmt sam" } + ext.prefix = { "${meta.id}_mt_nodups_collate" } + } + + withName: '.*SUBSAMPLE_MT_READS:GAWK' { + ext.args2 = { "'/^@/ { print; next } count < ${params.mt_subsample_reads} || last == \$1 { print; last = \$1; count++ }'" } + ext.prefix = { "${meta.id}_mt_nodups_collate_awk" } + ext.suffix = "sam" + } + + withName: '.*SUBSAMPLE_MT_READS:SAM_TO_BAM' { + ext.args = { "--output-fmt bam" } + ext.prefix = { "${meta.id}_mt_nodups_collate_awk" } + } + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}_mt_subsample" } + publishDir = [ + path: { "${params.outdir}/alignment" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_INDEX' { + publishDir = [ + path: { "${params.outdir}/alignment" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + +} \ No newline at end of file diff --git a/modules.json b/modules.json index 938938441..ab505ed6a 100644 --- a/modules.json +++ b/modules.json @@ -257,6 +257,11 @@ "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, + "gawk": { + "branch": "master", + "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", + "installed_by": ["modules"] + }, "genmod/annotate": { "branch": "master", "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", @@ -388,6 +393,11 @@ "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", "installed_by": ["modules"] }, + "samtools/collate": { + "branch": "master", + "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", + "installed_by": ["modules"] + }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml new file mode 100644 index 000000000..f52109e83 --- /dev/null +++ b/modules/nf-core/gawk/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf new file mode 100644 index 000000000..da79a0ed3 --- /dev/null +++ b/modules/nf-core/gawk/main.nf @@ -0,0 +1,70 @@ +process GAWK { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : + 'biocontainers/gawk:5.3.0' }" + + input: + tuple val(meta), path(input, arity: '0..*') + path(program_file) + val(disable_redirect_output) + + output: + tuple val(meta), path("*.${suffix}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' // args is used for the main arguments of the tool + def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.collect{ file -> file.getExtension()}.get(0)}" // use the first extension of the input files + + program = program_file ? "-f ${program_file}" : "${args2}" + lst_gz = input.findResults{ file -> file.getExtension().endsWith("gz") ? file.toString() : null } + unzip = lst_gz ? "gunzip -q -f ${lst_gz.join(" ")}" : "" + input_cmd = input.collect { file -> file.toString() - ~/\.gz$/ }.join(" ") + output_cmd = suffix.endsWith("gz") ? "| gzip > ${prefix}.${suffix}" : "> ${prefix}.${suffix}" + output = disable_redirect_output ? "" : output_cmd + cleanup = lst_gz ? "rm ${lst_gz.collect{ file -> file - ~/\.gz$/ }.join(" ")}" : "" + + input.collect{ file -> + assert file.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!" + } + + """ + ${unzip} + + awk \\ + ${args} \\ + ${program} \\ + ${input_cmd} \\ + ${output} + + ${cleanup} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" + + """ + ${create_cmd} ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml new file mode 100644 index 000000000..732e18a97 --- /dev/null +++ b/modules/nf-core/gawk/meta.yml @@ -0,0 +1,68 @@ +name: "gawk" +description: | + If you are like many computer users, you would frequently like to make changes in various text files + wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. + The job is easy with awk, especially the GNU implementation gawk. +keywords: + - gawk + - awk + - txt + - text + - file parsing +tools: + - "gawk": + description: "GNU awk" + homepage: "https://www.gnu.org/software/gawk/" + documentation: "https://www.gnu.org/software/gawk/manual/" + tool_dev_url: "https://www.gnu.org/prep/ftp.html" + licence: ["GPL v3"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on + this file on the `ext.args2` or in the program file. If the files have a `.gz` + extension, they will be unzipped using `zcat`. + pattern: "*" + ontologies: [] + - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't wish + to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" + ontologies: [] + - disable_redirect_output: + type: boolean + description: Disable the redirection of awk output to a given file. This is useful + if you want to use awk's built-in redirect to write files instead of the shell's + redirect. +output: + output: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: The output file - if using shell redirection, specify the name + of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, + ensure the awk program produces files with the extension in `ext.suffix`. + pattern: "*" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test new file mode 100644 index 000000000..fc6e240fd --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -0,0 +1,198 @@ +nextflow_process { + + name "Test Process GAWK" + script "../main.nf" + process "GAWK" + + tag "modules" + tag "modules_nfcore" + tag "gawk" + + config "./nextflow.config" + + test("Convert fasta to bed") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Convert fasta to bed with program file") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = Channel.of('BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Convert fasta to bed using awk redirect instead of shell redirect") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 > "test.bed" }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Extract first column from multiple files") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Unzip files before processing") { + when { + params { + gawk_suffix = "bed" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] + ] + input[1] = Channel.of('/^#CHROM/ { print \$1, \$10 }').collectFile(name:"column_header.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Compress after processing") { + when { + params { + gawk_suffix = "txt.gz" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Input and output files are similar") { + when { + params { + gawk_suffix = "txt" + gawk_args = "" + gawk_args2 = "" + } + process { + """ + input[0] = [ + [ id:'hello' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.awk") + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } + ) + } + } +} diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap new file mode 100644 index 000000000..d8e8ac755 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -0,0 +1,200 @@ +{ + "Compress after processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.1" + }, + "timestamp": "2024-11-27T17:11:20.054143406" + }, + "Convert fasta to bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T13:14:02.347809811" + }, + "Convert fasta to bed with program file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T13:14:11.894616209" + }, + "Extract first column from multiple files": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:04:47.729300129" + }, + "Unzip files before processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:08:19.533527657" + }, + "Convert fasta to bed using awk redirect instead of shell redirect": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T08:31:09.88842854" + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config new file mode 100644 index 000000000..895709a76 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GAWK { + ext.suffix = params.gawk_suffix + ext.args2 = params.gawk_args2 + } +} diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml new file mode 100644 index 000000000..89e12a645 --- /dev/null +++ b/modules/nf-core/samtools/collate/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf new file mode 100644 index 000000000..c07cd8a98 --- /dev/null +++ b/modules/nf-core/samtools/collate/main.nf @@ -0,0 +1,62 @@ +process SAMTOOLS_COLLATE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0': + 'biocontainers/samtools:1.22.1--h96c455f_0' }" + + input: + tuple val(meta), path(input) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.sam"), emit: sam, optional: true + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--reference ${fasta}" : "" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools \\ + collate \\ + $args \\ + ${reference} \\ + -@ $task.cpus \\ + -o ${prefix}.${extension} \\ + $input + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + """ + touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml new file mode 100644 index 000000000..96fdc2fc9 --- /dev/null +++ b/modules/nf-core/samtools/collate/meta.yml @@ -0,0 +1,84 @@ +name: "samtools_collate" +description: shuffles and groups reads together by their names +keywords: + - collate + - bam + - sam + - cram +tools: + - "samtools": + description: "Tools for dealing with SAM, BAM and CRAM files" + homepage: "http://www.htslib.org" + documentation: "https://www.htslib.org/doc/samtools-collate.html" + tool_dev_url: "https://github.com/samtools/samtools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + identifier: biotools:samtools +input: + # Only when we have meta + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA ref file + pattern: "*.fasta" + ontologies: [] +output: + #Only when we have meta + bam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM + pattern: "*.{bam}" + ontologies: [] + cram: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM + pattern: "*.{cram}" + ontologies: [] + sam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Sorted SAM + pattern: "*.{sam}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@priyanka-surana" +maintainers: + - "@priyanka-surana" diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test new file mode 100644 index 000000000..2e547c7e8 --- /dev/null +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -0,0 +1,93 @@ +nextflow_process { + + name "Test Process SAMTOOLS_COLLATE" + script "../main.nf" + process "SAMTOOLS_COLLATE" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/collate" + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [id:'fasta'], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, + { assert snapshot(process.out.cram).match("bam_cram") }, + { assert snapshot(process.out.sam).match("bam_sam") }, + { assert snapshot(process.out.versions).match("bam_versions") } + ) + } + + } + + test("homo_sapiens - cram + fasta") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_fasta_bam") }, + { assert snapshot(process.out.cram).match("cram_fasta_cram") }, + { assert snapshot(process.out.sam).match("cram_fasta_sam") }, + { assert snapshot(process.out.versions).match("cram_fasta_versions") } + ) + } + + } + + test("sarscov2 - bam -- stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [id:'fasta'], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + path(process.out.versions[0]).yaml + ).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test.snap b/modules/nf-core/samtools/collate/tests/main.nf.test.snap new file mode 100644 index 000000000..b0c8f4dce --- /dev/null +++ b/modules/nf-core/samtools/collate/tests/main.nf.test.snap @@ -0,0 +1,144 @@ +{ + "cram_fasta_versions": { + "content": [ + [ + "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T13:02:45.779649" + }, + "bam_cram": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:01.611698" + }, + "cram_fasta_cram": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:48.325375" + }, + "cram_fasta_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:48.328907" + }, + "sarscov2 - bam -- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions": [ + "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + ] + }, + { + "SAMTOOLS_COLLATE": { + "samtools": "1.22.1" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T13:02:50.413313" + }, + "cram_fasta_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:48.322144" + }, + "bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:01.608677" + }, + "bam_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T16:56:01.613225" + }, + "bam_versions": { + "content": [ + [ + "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T13:02:39.72811" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index a94922be6..11d61e62f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,6 +26,8 @@ params { bait_padding = 100 concatenate_snv_calls = false extract_alignments = false + mt_subsample_approach = "reads" + mt_subsample_reads = 18000 restrict_to_contigs = null run_mt_for_wes = false run_rtgvcfeval = false @@ -480,7 +482,8 @@ includeConfig 'conf/modules/call_mobile_elements.config' includeConfig 'conf/modules/annotate_mobile_elements.config' includeConfig 'conf/modules/vcf_filter_bcftools_ensemblvep.config' includeConfig 'conf/modules/variant_evaluation.config' -includeConfig 'conf/modules/subsample_mt.config' +includeConfig 'conf/modules/subsample_mt_frac.config' +includeConfig 'conf/modules/subsample_mt_reads.config' includeConfig 'conf/modules/annotate_rhocallviz.config' // Nextflow plugins diff --git a/nextflow_schema.json b/nextflow_schema.json index 384f9a4e4..582a23423 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -637,17 +637,30 @@ "help_text": "Minimum length of reads after adapter trimming. Shorter reads are discarded.", "fa_icon": "fas fa-less-than" }, + "mt_subsample_approach": { + "type": "string", + "default": "reads", + "description": "Subsample mitochondria based on fraction of reads or number of reads", + "enum": ["fraction", "reads"], + "fa_icon": "fas fa-align-center" + }, + "mt_subsample_reads": { + "type": "integer", + "default": 18000, + "description": "Expected number of reads to subsample mitochondria to, when mt_subsample_approach is set to reads", + "fa_icon": "fas fa-less-than" + }, "mt_subsample_rd": { "type": "integer", "default": 150, - "description": "Expected coverage to subsample mt alignment to.", + "description": "Expected coverage to subsample mt alignment to, when mt_subsample_approach is set to fraction", "help_text": "To know more about this parameter check [samtools' view](https://www.htslib.org/doc/samtools-view.html) documentation.", "fa_icon": "fas fa-less-than" }, "mt_subsample_seed": { "type": "integer", "default": 30, - "description": "Subsampling seed used to influence which subset of mitochondrial reads is kept. ", + "description": "Subsampling seed used to influence which subset of mitochondrial reads is kept. Used when mt_subsample_approach is set to fraction", "help_text": "To know more about this parameter check [samtools' view](https://www.htslib.org/doc/samtools-view.html) documentation.", "fa_icon": "fas fa-less-than" }, diff --git a/subworkflows/local/subsample_mt.nf b/subworkflows/local/subsample_mt_frac/main.nf similarity index 78% rename from subworkflows/local/subsample_mt.nf rename to subworkflows/local/subsample_mt_frac/main.nf index 180748e54..5987ecddb 100644 --- a/subworkflows/local/subsample_mt.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -2,12 +2,12 @@ // A subworkflow to subsample MT alignments // -include { BEDTOOLS_GENOMECOV } from '../../modules/nf-core/bedtools/genomecov/main' -include { CALCULATE_SEED_FRACTION } from '../../modules/local/calculate_seed_fraction' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' +include { BEDTOOLS_GENOMECOV } from '../../../modules/nf-core/bedtools/genomecov/main' +include { CALCULATE_SEED_FRACTION } from '../../../modules/local/calculate_seed_fraction' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' -workflow SUBSAMPLE_MT { +workflow SUBSAMPLE_MT_FRAC { take: ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf new file mode 100644 index 000000000..82c43643c --- /dev/null +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -0,0 +1,43 @@ +// +// A subworkflow to subsample MT alignments +// + +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAM_TO_BAM } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_COLLATE } from '../../../modules/nf-core/samtools/collate/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { GAWK } from '../../../modules/nf-core/gawk/main' + +workflow SUBSAMPLE_MT_READS { + + take: + ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + + main: + ch_versions = Channel.empty() + + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], []) + + SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) + + GAWK(SAMTOOLS_COLLATE.out.sam, [], false) + + GAWK.out.output.map {meta, sam -> return [meta, sam, []] }.set {ch_convert_to_bam} + + SAM_TO_BAM(ch_convert_to_bam, [[:],[]], []) + + SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]]) + + SAMTOOLS_INDEX(SAMTOOLS_SORT.out.bam) + + ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) + ch_versions = ch_versions.mix(GAWK.out.versions) + ch_versions = ch_versions.mix(SAM_TO_BAM.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + + emit: + versions = ch_versions // channel: [ path(versions.yml) ] +} \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a083ad721..a954c3f18 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -62,7 +62,8 @@ include { RANK_VARIANTS as RANK_VARIANTS_MT } from '.. include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' -include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' +include { SUBSAMPLE_MT_FRAC } from '../subworkflows/local/subsample_mt_frac' +include { SUBSAMPLE_MT_READS } from '../subworkflows/local/subsample_mt_reads' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' @@ -375,12 +376,19 @@ workflow RAREDISEASE { ch_versions = ch_versions.mix(ALIGN.out.versions) if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('mt_subsample')) && (params.analysis_type.equals("wgs") || params.run_mt_for_wes)) { - SUBSAMPLE_MT( - ch_mapped.mt_bam_bai, - params.mt_subsample_rd, - params.mt_subsample_seed - ) - ch_versions = ch_versions.mix(SUBSAMPLE_MT.out.versions) + if (params.mt_subsample_approach.equals("fraction")) { + SUBSAMPLE_MT_FRAC( + ch_mapped.mt_bam_bai, + params.mt_subsample_rd, + params.mt_subsample_seed + ) + ch_versions = ch_versions.mix(SUBSAMPLE_MT_FRAC.out.versions) + } else { + SUBSAMPLE_MT_READS( + ch_mapped.mt_bam_bai, + ) + ch_versions = ch_versions.mix(SUBSAMPLE_MT_READS.out.versions) + } } // From c005f5ffc0984ead1d4feaa44606c103a0020618 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 27 Nov 2025 12:54:30 +0000 Subject: [PATCH 097/872] [automated] Fix code linting --- conf/modules/subsample_mt_reads.config | 2 +- subworkflows/local/subsample_mt_reads/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config index 68e5929a8..400de0623 100644 --- a/conf/modules/subsample_mt_reads.config +++ b/conf/modules/subsample_mt_reads.config @@ -55,4 +55,4 @@ process { ] } -} \ No newline at end of file +} diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 82c43643c..421622aa7 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -16,7 +16,7 @@ workflow SUBSAMPLE_MT_READS { main: ch_versions = Channel.empty() - + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], []) SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) @@ -40,4 +40,4 @@ workflow SUBSAMPLE_MT_READS { emit: versions = ch_versions // channel: [ path(versions.yml) ] -} \ No newline at end of file +} From f34bcb70673cbd096e3026da561019bbc42e1b7c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 14:28:34 +0100 Subject: [PATCH 098/872] update snap --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 18e5562bb..f358f1e1f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -6,7 +6,7 @@ "tabix": 1.12 }, "BCFTOOLS_ANNOTATE": { - "bcftools": 1.2 + "bcftools": 1.22 }, "BCFTOOLS_CONCAT": { "bcftools": 1.2 @@ -631,6 +631,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T10:17:14.24575236" + "timestamp": "2025-11-27T14:26:05.966211788" } } \ No newline at end of file From edc5abe1d2c55a470e6e10c2f5dff37ade4a71ff Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 14:31:01 +0100 Subject: [PATCH 099/872] update samtools sort --- modules.json | 2 +- modules/nf-core/samtools/sort/environment.yml | 6 +- modules/nf-core/samtools/sort/main.nf | 60 ++-- modules/nf-core/samtools/sort/meta.yml | 35 ++- .../nf-core/samtools/sort/tests/main.nf.test | 144 ++++++++- .../samtools/sort/tests/main.nf.test.snap | 288 +++++++++++++----- .../samtools/sort/tests/nextflow.config | 1 - nextflow.config | 2 +- subworkflows/local/subsample_mt_reads/main.nf | 6 +- 9 files changed, 430 insertions(+), 114 deletions(-) diff --git a/modules.json b/modules.json index ab505ed6a..4471f9d6a 100644 --- a/modules.json +++ b/modules.json @@ -415,7 +415,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] }, "samtools/stats": { diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index caf3c61a8..d4bd5a327 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,30 +4,41 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta) , path(bam) tuple val(meta2), path(fasta) + val index_format output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.${extension}.crai"), emit: crai, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + tuple val(meta), path("${prefix}.${extension}.bai"), emit: bai, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt cram") ? "cram" : - "bam" + prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" def reference = fasta ? "--reference ${fasta}" : "" + output_file = index_format ? "${prefix}.${extension}##idx##${prefix}.${extension}.${index_format} --write-index" : "${prefix}.${extension}" + if (index_format) { + if (!index_format.matches('bai|csi|crai')) { + error "Index format not one of bai, csi, crai." + } else if (extension == "sam") { + error "Indexing not compatible with SAM output" + } + } if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ @@ -39,7 +50,7 @@ process SAMTOOLS_SORT { -T ${prefix} \\ --threads $task.cpus \\ ${reference} \\ - -o ${prefix}.${extension} \\ + -o ${output_file} \\ - cat <<-END_VERSIONS > versions.yml @@ -50,19 +61,22 @@ process SAMTOOLS_SORT { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt cram") ? "cram" : - "bam" + prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + if (index_format) { + if (!index_format.matches('bai|csi|crai')) { + error "Index format not one of bai, csi, crai." + } else if (extension == "sam") { + error "Indexing not compatible with SAM output" + } + } + index = index_format ? "touch ${prefix}.${extension}.${index_format}" : "" + """ touch ${prefix}.${extension} - if [ "${extension}" == "bam" ]; - then - touch ${prefix}.${extension}.csi - elif [ "${extension}" == "cram" ]; - then - touch ${prefix}.${extension}.crai - fi + ${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index ab2b3b280..4c4010bbb 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -38,6 +38,10 @@ input: pattern: "*.{fa,fasta,fna}" optional: true ontologies: [] + - index_format: + type: string + description: Index format to use (optional) + pattern: "bai|csi|crai" output: bam: - - meta: @@ -45,7 +49,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.bam": + - "${prefix}.bam": type: file description: Sorted BAM file pattern: "*.{bam}" @@ -56,18 +60,30 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.cram": + - "${prefix}.cram": type: file description: Sorted CRAM file pattern: "*.{cram}" ontologies: [] + sam: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.sam": + type: file + description: Sorted SAM file + pattern: "*.{sam}" + ontologies: [] + crai: - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.crai": + - "${prefix}.${extension}.crai": type: file description: CRAM index file (optional) pattern: "*.crai" @@ -78,11 +94,22 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.csi": + - "${prefix}.${extension}.csi": type: file description: BAM index file (optional) pattern: "*.csi" ontologies: [] + bai: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "${prefix}.${extension}.bai": + type: file + description: BAM index file (optional) + pattern: "*.bai" + ontologies: [] versions: - versions.yml: type: file diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index b05e6691b..ff0691906 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/sort" - test("bam") { + test("bam_no_index") { config "./nextflow.config" @@ -23,6 +23,7 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' """ } } @@ -32,7 +33,71 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.bai, + process.out.versions + ).match()} + ) + } + } + + test("bam_bai_index") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = 'bai' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.bai, + process.out.versions + ).match()} + ) + } + } + + test("bam_csi_index") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = 'csi' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi, process.out.versions ).match()} ) @@ -57,6 +122,77 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("multiple bam bai index") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = 'bai' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("multiple bam csi index") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = 'csi' """ } } @@ -88,6 +224,7 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' """ } } @@ -120,6 +257,7 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' """ } } @@ -150,6 +288,7 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' """ } } @@ -178,6 +317,7 @@ nextflow_process { [ id:'fasta' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) + input[2] = '' """ } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 469891fe3..473e17450 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:49:58.207549273" + "timestamp": "2025-09-10T14:43:31.395604" }, "bam - stub": { "content": [ @@ -48,16 +48,19 @@ ], "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "4": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + + ], + "5": [ + + ], + "6": [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ], + "bai": [ + ], "bam": [ [ @@ -75,24 +78,81 @@ ], "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "sam": [ + ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T14:43:37.387063" + }, + "bam_csi_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,72ca1dff5344a5e5e6b892fe5f6b134d" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8" + ] + ], + [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:50:08.630951018" + "timestamp": "2025-09-10T14:43:06.976036" + }, + "multiple bam bai index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,3ffa2affc29f0aa6e7b36dded84625fe" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.bai" + ] + ], + [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T14:43:18.72271" }, "cram - stub": { "content": [ @@ -110,31 +170,28 @@ ] ], "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "3": [ ], "4": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + + ], + "5": [ + + ], + "6": [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ], + "bai": [ + ], "bam": [ ], "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "cram": [ [ @@ -147,17 +204,20 @@ ], "csi": [ + ], + "sam": [ + ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T08:50:19.061912443" + "timestamp": "2025-09-10T14:43:48.734367" }, "multiple bam": { "content": [ @@ -167,27 +227,21 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi" - ] + ], [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-08T11:59:55.479443" + "timestamp": "2025-09-10T14:43:12.989244" }, "multiple bam - stub": { "content": [ @@ -198,7 +252,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], "1": [ @@ -208,16 +262,19 @@ ], "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" - ] + ], "4": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + + ], + "5": [ + + ], + "6": [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ], + "bai": [ + ], "bam": [ [ @@ -225,7 +282,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" ] ], "crai": [ @@ -235,24 +292,75 @@ ], "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" - ] + + ], + "sam": [ + ], "versions": [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T14:43:43.196638" + }, + "bam_no_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,26b27d1f9bcb61c25da21b562349784e" + ] + ], + [ + + ], + [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T14:42:54.926504" + }, + "multiple bam csi index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,295503ba5342531a3310c33ad0efbc22" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-10-08T11:36:13.781404" + "timestamp": "2025-09-10T14:43:25.059178" }, "bam": { "content": [ @@ -283,5 +391,35 @@ "nextflow": "24.09.0" }, "timestamp": "2024-10-08T11:59:46.372244" + }, + "bam_bai_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,cae7564cb83bb4a5911205bf94124b54" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0" + ] + ], + [ + "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T14:43:00.82974" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config index f642771f5..723f62b21 100644 --- a/modules/nf-core/samtools/sort/tests/nextflow.config +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -2,7 +2,6 @@ process { withName: SAMTOOLS_SORT { ext.prefix = { "${meta.id}.sorted" } - ext.args = "--write-index" } } diff --git a/nextflow.config b/nextflow.config index 11d61e62f..65ed2f62a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,7 +26,7 @@ params { bait_padding = 100 concatenate_snv_calls = false extract_alignments = false - mt_subsample_approach = "reads" + mt_subsample_approach = 'reads' mt_subsample_reads = 18000 restrict_to_contigs = null run_mt_for_wes = false diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 82c43643c..72b24fce1 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -6,7 +6,6 @@ include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/ include { SAMTOOLS_VIEW as SAM_TO_BAM } from '../../../modules/nf-core/samtools/view/main' include { SAMTOOLS_COLLATE } from '../../../modules/nf-core/samtools/collate/main' include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' include { GAWK } from '../../../modules/nf-core/gawk/main' workflow SUBSAMPLE_MT_READS { @@ -27,16 +26,13 @@ workflow SUBSAMPLE_MT_READS { SAM_TO_BAM(ch_convert_to_bam, [[:],[]], []) - SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]]) - - SAMTOOLS_INDEX(SAMTOOLS_SORT.out.bam) + SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) ch_versions = ch_versions.mix(GAWK.out.versions) ch_versions = ch_versions.mix(SAM_TO_BAM.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] From 1c79c1a68ea75347f7a5d62194272ca7852a6ee4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 14:33:00 +0100 Subject: [PATCH 100/872] update changelog --- CHANGELOG.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0b8d7ecb..61140e4f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,12 +30,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| -------- | ----------- | ----------- | -| bcftools | 1.20 | 1.21 | -| htslib | 1.20 | 1.21 | -| mosdepth | 0.3.8 | 0.3.10 | -| ngs-bits | 2023_02 | 2024_11 | +| Tool | Old version | New version | +| ----------------------------------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| htslib | 1.20 | 1.21 | +| mosdepth | 0.3.8 | 0.3.10 | +| ngs-bits | 2023_02 | 2024_11 | +| gatk4/determinegermlinecontigploidy | 4.5.0.0 | 4.6.2.0 | +| gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | ## 2.6.0 - Cacofonix [2025-06-25] From 9188c012246ae06c85e5e69f2eff3e5ea036e6b9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 14:45:14 +0100 Subject: [PATCH 101/872] update samtools sort --- conf/modules/call_repeat_expansions.config | 8 -------- conf/modules/subsample_mt_reads.config | 8 -------- subworkflows/local/align_MT/main.nf | 8 ++------ subworkflows/local/call_repeat_expansions/main.nf | 5 +---- 4 files changed, 3 insertions(+), 26 deletions(-) diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config index fd6738ae9..23217bd07 100644 --- a/conf/modules/call_repeat_expansions.config +++ b/conf/modules/call_repeat_expansions.config @@ -30,14 +30,6 @@ process { ] } - withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_INDEX' { - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } - withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' { ext.args = "--temp-prefix ." ext.args2 = "-O v" diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config index 68e5929a8..cfbbc7094 100644 --- a/conf/modules/subsample_mt_reads.config +++ b/conf/modules/subsample_mt_reads.config @@ -47,12 +47,4 @@ process { ] } - withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_INDEX' { - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - } \ No newline at end of file diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 7a0c1d2cc..2fd3f943b 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -8,7 +8,6 @@ include { BWAMEM2_MEM as BWAMEM2_MEM_MT } fr include { GATK4_MERGEBAMALIGNMENT as GATK4_MERGEBAMALIGNMENT_MT } from '../../../modules/nf-core/gatk4/mergebamalignment/main' include { PICARD_ADDORREPLACEREADGROUPS as PICARD_ADDORREPLACEREADGROUPS_MT } from '../../../modules/nf-core/picard/addorreplacereadgroups/main' include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_MT } from '../../../modules/nf-core/picard/markduplicates/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MT } from '../../../modules/nf-core/samtools/index/main' include { SAMTOOLS_SORT as SAMTOOLS_SORT_MT } from '../../../modules/nf-core/samtools/sort/main' workflow ALIGN_MT { @@ -47,18 +46,15 @@ workflow ALIGN_MT { PICARD_MARKDUPLICATES_MT (PICARD_ADDORREPLACEREADGROUPS_MT.out.bam, ch_fasta, ch_fai) - SAMTOOLS_SORT_MT (PICARD_MARKDUPLICATES_MT.out.bam, [[:],[]]) - - SAMTOOLS_INDEX_MT(SAMTOOLS_SORT_MT.out.bam) + SAMTOOLS_SORT_MT (PICARD_MARKDUPLICATES_MT.out.bam, [[:],[]], 'bai') ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions.first()) ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions.first()) ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions.first()) ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MT.out.versions.first()) emit: marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] - marked_bai = SAMTOOLS_INDEX_MT.out.bai // channel: [ val(meta), path(bai) ] + marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 7d62025bf..9594033fd 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -7,7 +7,6 @@ include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_EXP } from '../../../modules/ include { EXPANSIONHUNTER } from '../../../modules/nf-core/expansionhunter/main' include { PICARD_RENAMESAMPLEINVCF as RENAMESAMPLE_EXP } from '../../../modules/nf-core/picard/renamesampleinvcf/main' include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' include { SVDB_MERGE as SVDB_MERGE_REPEATS } from '../../../modules/nf-core/svdb/merge/main' include { TABIX_TABIX as TABIX_EXP_RENAME } from '../../../modules/nf-core/tabix/tabix/main' @@ -30,8 +29,7 @@ workflow CALL_REPEAT_EXPANSIONS { ) // Sort and index realigned bam - SAMTOOLS_SORT(EXPANSIONHUNTER.out.bam, [[:],[]]) - SAMTOOLS_INDEX(SAMTOOLS_SORT.out.bam) + SAMTOOLS_SORT(EXPANSIONHUNTER.out.bam, [[:],[]], 'bai') // Fix header and rename sample BCFTOOLS_REHEADER_EXP ( @@ -67,7 +65,6 @@ workflow CALL_REPEAT_EXPANSIONS { ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_EXP.out.versions.first()) ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions.first()) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] From af339eabb1a8da13397bfbe622309e8f6b9f7343 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 14:57:42 +0100 Subject: [PATCH 102/872] update gens script --- modules/local/gens/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/gens/main.nf b/modules/local/gens/main.nf index e55b0a6f0..da1da73aa 100644 --- a/modules/local/gens/main.nf +++ b/modules/local/gens/main.nf @@ -2,7 +2,7 @@ process GENS { tag "$meta.id" label 'process_medium' - container 'docker.io/rannickscilifelab/gens_preproc:1.1.1' + container 'docker.io/clinicalgenomics/gens-preproc:1.1.2' input: tuple val(meta), path(read_counts) From 73e5de253f237dfa54b9ffca71b4ffd45f092517 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 15:00:05 +0100 Subject: [PATCH 103/872] update gens --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 140a1834e..594eebfb7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ngs-bits | 2023_02 | 2024_11 | | gatk4/determinegermlinecontigploidy | 4.5.0.0 | 4.6.2.0 | | gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | +| gens-preproc | 1.0.11 | 1.1.2 | ## 2.6.0 - Cacofonix [2025-06-25] From 3296d86e59bb09bb9cad217e9699076b2ae8dbda Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 27 Nov 2025 15:00:53 +0100 Subject: [PATCH 104/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 594eebfb7..c825bec1f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) - Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741) - Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742) +- Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747) ### `Fixed` From 7f960e3d591904aff4f78c495aba6cd03fb4c484 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 15:48:15 +0100 Subject: [PATCH 105/872] update samtools view --- conf/modules/align.config | 2 +- conf/modules/subsample_mt_frac.config | 8 - modules.json | 2 +- modules/nf-core/samtools/view/environment.yml | 6 +- modules/nf-core/samtools/view/main.nf | 41 +- modules/nf-core/samtools/view/meta.yml | 72 +- .../nf-core/samtools/view/tests/bam.config | 2 +- .../samtools/view/tests/bam_index.config | 2 +- .../samtools/view/tests/cram_index.config | 3 + .../nf-core/samtools/view/tests/main.nf.test | 249 ++++++ .../samtools/view/tests/main.nf.test.snap | 730 ++++++++++++++---- modules/nf-core/samtools/view/tests/tags.yml | 2 - subworkflows/local/align/main.nf | 2 +- .../local/align/tests/nextflow.config | 2 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- subworkflows/local/align_sentieon/main.nf | 9 +- subworkflows/local/call_mobile_elements.nf | 7 +- subworkflows/local/subsample_mt_frac/main.nf | 6 +- subworkflows/local/subsample_mt_reads/main.nf | 4 +- 19 files changed, 936 insertions(+), 215 deletions(-) create mode 100644 modules/nf-core/samtools/view/tests/cram_index.config delete mode 100644 modules/nf-core/samtools/view/tests/tags.yml diff --git a/conf/modules/align.config b/conf/modules/align.config index c605a1586..6df68cb32 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -27,7 +27,7 @@ process{ } withName: '.*ALIGN:SAMTOOLS_VIEW' { - ext.args = { '--output-fmt cram --write-index' } + ext.args = { '--output-fmt cram' } ext.prefix = { "${meta.id}_sort_md" } publishDir = [ path: { "${params.outdir}/alignment" }, diff --git a/conf/modules/subsample_mt_frac.config b/conf/modules/subsample_mt_frac.config index b10fa357a..5b3e6e17c 100644 --- a/conf/modules/subsample_mt_frac.config +++ b/conf/modules/subsample_mt_frac.config @@ -31,12 +31,4 @@ process { ] } - withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_INDEX' { - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - } diff --git a/modules.json b/modules.json index 4471f9d6a..9bc6658c3 100644 --- a/modules.json +++ b/modules.json @@ -425,7 +425,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", "installed_by": ["modules"] }, "sentieon/bwaindex": { diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 37e05cec8..02d9b0f99 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,13 +4,14 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input), path(index) tuple val(meta2), path(fasta) path qname + val index_format output: tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true @@ -20,7 +21,7 @@ process SAMTOOLS_VIEW { tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true - tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true path "versions.yml", emit: versions when: @@ -35,16 +36,28 @@ process SAMTOOLS_VIEW { args.contains("--output-fmt bam") ? "bam" : args.contains("--output-fmt cram") ? "cram" : input.getExtension() + + output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format} --write-index" : "${prefix}.${file_type}" + // Can't choose index type of unselected file readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": "" + if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if (index_format) { + if (!index_format.matches('bai|csi|crai')) { + error "Index format not one of bai, csi, crai." + } else if (file_type == "sam") { + error "Indexing not compatible with SAM output" + } + } """ + # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads). samtools \\ view \\ --threads ${task.cpus-1} \\ ${reference} \\ ${readnames} \\ $args \\ - -o ${prefix}.${file_type} \\ + -o ${output_file} \\ $input \\ $args2 @@ -61,13 +74,27 @@ process SAMTOOLS_VIEW { args.contains("--output-fmt bam") ? "bam" : args.contains("--output-fmt cram") ? "cram" : input.getExtension() - if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - - def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : "" + default_index_format = + file_type == "bam" ? "csi" : + file_type == "cram" ? "crai" : "" + index = index_format ? "touch ${prefix}.${file_type}.${index_format}" : args.contains("--write-index") ? "touch ${prefix}.${file_type}.${default_index_format}" : "" + unselected = qname ? "touch ${prefix}.unselected.${file_type}" : "" + // Can't choose index type of unselected file + unselected_index = qname && (args.contains("--write-index") || index_format) ? "touch ${prefix}.unselected.${file_type}.${default_index_format}" : "" + if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if (index_format) { + if (!index_format.matches('bai|csi|crai')) { + error "Index format not one of bai, csi, crai." + } else if (file_type == "sam") { + error "Indexing not compatible with SAM output." + } + } """ touch ${prefix}.${file_type} ${index} + ${unselected} + ${unselected_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index caa7b0150..3ebbdb891 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -26,10 +26,12 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - index: type: file description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) pattern: "*.{.bai,.csi,.crai}" + ontologies: [] - - meta2: type: map description: | @@ -39,13 +41,19 @@ input: type: file description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" - - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" + ontologies: [] + - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" + ontologies: [] + - index_format: + type: string + description: Index format, used together with ext.args = '--write-index' + pattern: "bai|csi|crai" output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -54,8 +62,9 @@ output: type: file description: optional filtered/converted BAM file pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -64,8 +73,9 @@ output: type: file description: optional filtered/converted CRAM file pattern: "*.{cram}" - - sam: - - meta: + ontologies: [] + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -74,8 +84,9 @@ output: type: file description: optional filtered/converted SAM file pattern: "*.{sam}" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -84,8 +95,9 @@ output: type: file description: optional BAM file index pattern: "*.{bai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -94,8 +106,9 @@ output: type: file description: optional tabix BAM file index pattern: "*.{csi}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -104,8 +117,9 @@ output: type: file description: optional CRAM file index pattern: "*.{crai}" - - unselected: - - meta: + ontologies: [] + unselected: + - - meta: type: map description: | Groovy Map containing sample information @@ -114,21 +128,25 @@ output: type: file description: optional file with unselected alignments pattern: "*.unselected.{bam,cram,sam}" - - unselected_index: - - meta: + ontologies: [] + unselected_index: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - ${prefix}.unselected.${file_type}.{bai,csi,crsi}: + - ${prefix}.unselected.${file_type}.{csi,crai}: type: file description: index for the "unselected" file - pattern: "*.unselected.{bai,csi,crai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + pattern: "*.unselected.{csi,crai}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config index c10d10811..83ad29f02 100644 --- a/modules/nf-core/samtools/view/tests/bam.config +++ b/modules/nf-core/samtools/view/tests/bam.config @@ -1,3 +1,3 @@ process { ext.args = "--output-fmt bam" -} \ No newline at end of file +} diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config index 771ae033a..60b96d426 100644 --- a/modules/nf-core/samtools/view/tests/bam_index.config +++ b/modules/nf-core/samtools/view/tests/bam_index.config @@ -1,3 +1,3 @@ process { ext.args = "--output-fmt bam --write-index" -} \ No newline at end of file +} diff --git a/modules/nf-core/samtools/view/tests/cram_index.config b/modules/nf-core/samtools/view/tests/cram_index.config new file mode 100644 index 000000000..ed87c3349 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/cram_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-fmt cram --write-index" +} diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 37b81a916..d8551dd8c 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -21,6 +21,7 @@ nextflow_process { ]) input[1] = [[],[]] input[2] = [] + input[3] = [] """ } } @@ -39,6 +40,135 @@ nextflow_process { } } + test("bam_csi_index") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + input[3] = 'csi' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + file(process.out.csi[0][1]).name, + process.out.versions).match() + } + ) + } + } + + test("bam_bai_index") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + input[3] = 'bai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + file(process.out.bai[0][1]).name, + process.out.versions).match() } + ) + } + } + + test("bam_bai_index_unselected") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = Channel.of('testN:1') + .collectFile(name: 'selected_reads.txt') + input[3] = 'bai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + file(process.out.bai[0][1]).name, + file(process.out.unselected[0][1]).name, + file(process.out.unselected_index[0][1]).name, + process.out.versions).match() + } + ) + } + } + + test("cram_crai_index_unselected") { + + config "./cram_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = Channel.of('testN:1') + .collectFile(name: 'selected_reads.txt') + input[3] = 'crai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.cram[0][1]).name, + file(process.out.crai[0][1]).name, + file(process.out.unselected[0][1]).name, + file(process.out.unselected_index[0][1]).name, + process.out.versions).match() + } + ) + } + } + test("cram") { when { @@ -54,6 +184,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) input[2] = [] + input[3] = [] """ } } @@ -89,6 +220,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) input[2] = [] + input[3] = [] """ } } @@ -124,6 +256,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) input[2] = [] + input[3] = [] """ } } @@ -159,6 +292,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) + input[3] = [] """ } } @@ -194,6 +328,7 @@ nextflow_process { ]) input[1] = [[],[]] input[2] = [] + input[3] = [] """ } } @@ -211,4 +346,118 @@ nextflow_process { ) } } + + test("bam_csi_index - stub") { + + options "-stub" + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + input[3] = 'csi' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bam_bai_index - stub") { + + options "-stub" + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + input[3] = 'bai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bam_bai_index_uselected - stub") { + + options "-stub" + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = Channel.of('testN:1') + .collectFile(name: 'selected_reads.txt') + input[3] = 'bai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("cram_crai_index_unselected - stub") { + + options "-stub" + config "./cram_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = Channel.of('testN:1') + .collectFile(name: 'selected_reads.txt') + input[3] = 'crai' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 63849b037..5ec65d62b 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -9,16 +9,6 @@ }, "timestamp": "2024-02-12T19:37:51.256068" }, - "cram_to_bam_index_csi": { - "content": [ - "test.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.958617" - }, "bam_stub_bam": { "content": [ "test.bam" @@ -56,40 +46,36 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + "versions.yml:md5,376bd183239f91c807210bfeb299d306" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-09-16T09:26:24.461775464" + "timestamp": "2025-09-10T15:20:28.366024" }, - "cram_to_bam_index_cram": { + "cram_to_bam_index_qname_csi": { "content": [ - [ - - ] + "test.bam.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:38:12.972288" + "timestamp": "2024-02-12T19:38:23.325496" }, - "cram_to_bam_sam": { + "cram_to_bam_index_qname_unselected_csi": { "content": [ - [ - - ] + "test.unselected.bam.csi" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:38:04.999247" + "timestamp": "2024-02-12T19:38:23.328458" }, - "cram_to_bam_index_sam": { + "bam_csi": { "content": [ [ @@ -99,55 +85,182 @@ "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:38:12.976457" + "timestamp": "2024-02-12T19:37:51.262882" }, - "cram_crai": { + "cram_to_bam_index_bam": { "content": [ - [ - - ] + "test.bam" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:37:56.497581" + "timestamp": "2024-02-12T19:38:12.95456" }, - "cram_csi": { + "cram_to_bam_index_versions": { "content": [ [ - + "versions.yml:md5,376bd183239f91c807210bfeb299d306" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:37:56.50038" + "timestamp": "2025-09-10T15:20:20.3853" }, - "cram_to_bam_cram": { + "bam_csi_index": { "content": [ + "test.bam", + "test.bam.csi", [ - + "versions.yml:md5,376bd183239f91c807210bfeb299d306" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:38:04.992239" + "timestamp": "2025-09-10T15:19:54.889079" }, - "cram_to_bam_index_qname_csi": { + "bam_versions": { "content": [ - "test.bam.csi" + [ + "versions.yml:md5,376bd183239f91c807210bfeb299d306" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + 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"nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:37:51.264651" + "timestamp": "2024-02-12T19:38:23.333248" }, - "cram_to_bam_index_bai": { + "cram_to_bam_csi": { "content": [ [ @@ -501,9 +822,132 @@ "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:38:12.962863" + "timestamp": "2024-02-12T19:38:04.995454" }, - "cram_to_bam_index_qname_sam": { + "bam_bai_index_uselected - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + "versions.yml:md5,376bd183239f91c807210bfeb299d306" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "unselected_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,376bd183239f91c807210bfeb299d306" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-10T15:20:39.633146" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "bam_sam": { "content": [ [ @@ -513,7 +957,7 @@ "nf-test": "0.8.4", "nextflow": "23.04.3" }, - "timestamp": "2024-02-12T19:38:23.337634" + "timestamp": "2024-02-12T19:37:51.264651" }, "bam_stub_csi": { "content": [ diff --git a/modules/nf-core/samtools/view/tests/tags.yml b/modules/nf-core/samtools/view/tests/tags.yml deleted file mode 100644 index 4fdf1dd12..000000000 --- a/modules/nf-core/samtools/view/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/view: - - "modules/nf-core/samtools/view/**" diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 0c89bcc7e..d906893cf 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -145,7 +145,7 @@ workflow ALIGN { } if (params.save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [] ) + SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index 48280859b..402477f76 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -13,7 +13,7 @@ process { } withName: 'SAMTOOLS_VIEW' { - ext.args = { '--output-fmt cram --write-index' } + ext.args = { '--output-fmt cram' } ext.prefix = { "${meta.id}_sorted_md" } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index c4be6a433..8e9090cd2 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -88,7 +88,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { if (params.extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) - EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, []) + EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions.first()) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions.first()) diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 15e03b6d9..820f0c5d2 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -7,7 +7,6 @@ include { SENTIEON_DATAMETRICS } from '../../../modules/nf-c include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main' include { SENTIEON_READWRITER } from '../../../modules/nf-core/sentieon/readwriter/main' include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_EXTRACT } from '../../../modules/nf-core/samtools/index/main' workflow ALIGN_SENTIEON { take: @@ -41,13 +40,9 @@ workflow ALIGN_SENTIEON { // GET ALIGNMENT FROM SELECTED CONTIGS if (params.extract_alignments) { - EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, []) - ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam - SAMTOOLS_INDEX_EXTRACT ( EXTRACT_ALIGNMENTS.out.bam ) - ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) + EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') + ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions.first()) - } SENTIEON_DATAMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, false ) diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index cc9c1ee51..b323196e3 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -7,7 +7,6 @@ include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_ME } from '../../modules/nf-co include { BCFTOOLS_SORT as BCFTOOLS_SORT_ME } from '../../modules/nf-core/bcftools/sort/main' include { RETROSEQ_CALL as RETROSEQ_CALL } from '../../modules/local/retroseq/call/main' include { RETROSEQ_DISCOVER as RETROSEQ_DISCOVER } from '../../modules/local/retroseq/discover/main' -include { SAMTOOLS_INDEX as ME_INDEX_SPLIT_ALIGNMENT } from '../../modules/nf-core/samtools/index/main' include { SAMTOOLS_VIEW as ME_SPLIT_ALIGNMENT } from '../../modules/nf-core/samtools/view/main' include { TABIX_TABIX as TABIX_ME } from '../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_ME_SPLIT } from '../../modules/nf-core/tabix/tabix/main' @@ -43,11 +42,10 @@ workflow CALL_MOBILE_ELEMENTS { .set { ch_genome_bam_bai_interval } // Split bam file on chromosome and index - ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], []], [] ) - ME_INDEX_SPLIT_ALIGNMENT ( ME_SPLIT_ALIGNMENT.out.bam ) + ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], []], [], 'bai' ) ME_SPLIT_ALIGNMENT.out.bam - .join( ME_INDEX_SPLIT_ALIGNMENT.out.bai, failOnMismatch: true, failOnDuplicate: true ) + .join( ME_SPLIT_ALIGNMENT.out.bai, failOnMismatch: true, failOnDuplicate: true ) .set { ch_retroseq_input } ch_me_references @@ -124,7 +122,6 @@ workflow CALL_MOBILE_ELEMENTS { TABIX_ME ( SVDB_MERGE_ME.out.vcf ) ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions.first()) - ch_versions = ch_versions.mix(ME_INDEX_SPLIT_ALIGNMENT.out.versions.first()) ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions.first()) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions.first()) ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_ME.out.versions.first()) diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 5987ecddb..5b37b2bd7 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -5,7 +5,6 @@ include { BEDTOOLS_GENOMECOV } from '../../../modules/nf-core/bedtools/genomecov/main' include { CALCULATE_SEED_FRACTION } from '../../../modules/local/calculate_seed_fraction' include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' workflow SUBSAMPLE_MT_FRAC { @@ -33,14 +32,11 @@ workflow SUBSAMPLE_MT_FRAC { } .set { ch_subsample_in } - SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], []) - - SAMTOOLS_INDEX(SAMTOOLS_VIEW.out.bam) + SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first()) ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions.first()) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 72b24fce1..63548137c 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -16,7 +16,7 @@ workflow SUBSAMPLE_MT_READS { main: ch_versions = Channel.empty() - SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], []) + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) @@ -24,7 +24,7 @@ workflow SUBSAMPLE_MT_READS { GAWK.out.output.map {meta, sam -> return [meta, sam, []] }.set {ch_convert_to_bam} - SAM_TO_BAM(ch_convert_to_bam, [[:],[]], []) + SAM_TO_BAM(ch_convert_to_bam, [[:],[]], [], '') SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') From b53bf012e975be92c7e257a4d21c7152aa431d63 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 15:58:58 +0100 Subject: [PATCH 106/872] refactor 1 --- subworkflows/local/align/main.nf | 24 +- subworkflows/local/align/tests/main.nf.test | 100 ++++---- subworkflows/local/align_MT/main.nf | 2 +- .../local/align_MT/tests/main.nf.test | 24 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- .../tests/main.nf.test | 16 +- subworkflows/local/align_sentieon/main.nf | 2 +- .../local/align_sentieon/tests/main.nf.test | 8 +- subworkflows/local/annotate_cadd/main.nf | 2 +- .../local/annotate_consequence_pli.nf | 2 +- subworkflows/local/annotate_genome_snvs.nf | 8 +- .../local/annotate_mobile_elements.nf | 4 +- subworkflows/local/annotate_mt_snvs.nf | 6 +- .../local/annotate_rhocallviz/main.nf | 2 +- .../local/annotate_structural_variants.nf | 6 +- subworkflows/local/call_mobile_elements.nf | 2 +- .../local/call_repeat_expansions/main.nf | 2 +- .../call_repeat_expansions/tests/main.nf.test | 10 +- subworkflows/local/call_snv.nf | 34 +-- subworkflows/local/call_snv_MT/main.nf | 6 +- .../local/call_snv_deepvariant/main.nf | 2 +- subworkflows/local/call_snv_sentieon/main.nf | 2 +- .../local/call_structural_variants.nf | 6 +- subworkflows/local/call_sv_MT/main.nf | 8 +- subworkflows/local/call_sv_cnvnator/main.nf | 2 +- .../local/call_sv_germlinecnvcaller/main.nf | 2 +- .../local/convert_mt_bam_to_fastq/main.nf | 2 +- subworkflows/local/generate_cytosure_files.nf | 12 +- subworkflows/local/gens.nf | 2 +- .../local/postprocess_MT_calls/main.nf | 2 +- subworkflows/local/prepare_references/main.nf | 34 +-- .../prepare_references/tests/main.nf.test | 18 +- subworkflows/local/qc_bam/main.nf | 14 +- subworkflows/local/qc_bam/tests/main.nf.test | 52 ++-- subworkflows/local/rank_variants.nf | 2 +- subworkflows/local/scatter_genome/main.nf | 2 +- .../local/scatter_genome/tests/main.nf.test | 6 +- subworkflows/local/subsample_mt.nf | 2 +- .../utils_nfcore_raredisease_pipeline/main.nf | 2 +- subworkflows/local/variant_evaluation.nf | 2 +- workflows/raredisease.nf | 232 +++++++++--------- 41 files changed, 334 insertions(+), 334 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 0c89bcc7e..ac0ee7589 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -35,16 +35,16 @@ workflow ALIGN { val_sort_threads // integer: [mandatory] number of sorting threads main: - ch_bwamem2_bam = Channel.empty() - ch_bwamem2_bai = Channel.empty() - ch_fastp_json = Channel.empty() - ch_markdup_metrics = Channel.empty() - ch_mt_bam_bai = Channel.empty() - ch_mt_bam_bai_gatksubwf = Channel.empty() - ch_mtshift_bam_bai_gatksubwf = Channel.empty() - ch_sentieon_bam = Channel.empty() - ch_sentieon_bai = Channel.empty() - ch_versions = Channel.empty() + ch_bwamem2_bam = channel.empty() + ch_bwamem2_bai = channel.empty() + ch_fastp_json = channel.empty() + ch_markdup_metrics = channel.empty() + ch_mt_bam_bai = channel.empty() + ch_mt_bam_bai_gatksubwf = channel.empty() + ch_mtshift_bam_bai_gatksubwf = channel.empty() + ch_sentieon_bam = channel.empty() + ch_sentieon_bai = channel.empty() + ch_versions = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('fastp'))) { FASTP (ch_reads, [], false, false, false) @@ -101,8 +101,8 @@ workflow ALIGN { ch_versions = ch_versions.mix(ALIGN_SENTIEON.out.versions) } - ch_genome_marked_bam = Channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) - ch_genome_marked_bai = Channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) + ch_genome_marked_bam = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) + ch_genome_marked_bai = channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) // PREPARING READS FOR MT ALIGNMENT diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 8d6e1e2ea..9fb73b60a 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'mt'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) ]) @@ -23,7 +23,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'shiftmt'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_shift.fasta', checkIfExists: true) ]) @@ -39,7 +39,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'genome'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) ]) @@ -63,7 +63,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -86,23 +86,23 @@ nextflow_workflow { ] ] ) - input[1] = Channel.empty() - input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = Channel.empty() + input[1] = channel.empty() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.empty() input[5] = GENOME_MEM2.out.index.collect() - input[6] = Channel.empty() - input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[8] = Channel.empty() + input[6] = channel.empty() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() - input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = Channel.empty() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = channel.empty() input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -137,7 +137,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'genome'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) ]) @@ -161,7 +161,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -184,23 +184,23 @@ nextflow_workflow { ] ] ) - input[1] = Channel.empty() - input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = Channel.empty() + input[1] = channel.empty() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.empty() input[5] = GENOME_MEM2.out.index.collect() - input[6] = Channel.empty() - input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[8] = Channel.empty() + input[6] = channel.empty() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() - input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = Channel.empty() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = channel.empty() input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[18] = 3072 input[19] = "illumina" input[20] = 4 @@ -234,7 +234,7 @@ nextflow_workflow { script "modules/nf-core/bwameme/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'genome'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) ]) @@ -258,7 +258,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.fromList([ + input[0] = channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), @@ -275,23 +275,23 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) - input[1] = Channel.empty() - input[2] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = Channel.empty() - input[5] = Channel.empty() + input[1] = channel.empty() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.empty() + input[5] = channel.empty() input[6] = GENOME_MEME.out.index.collect() - input[7] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[8] = Channel.empty() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() - input[10] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = Channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = Channel.empty() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = channel.empty() input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = Channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[18] = 3072 input[19] = "illumina" input[20] = 4 diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 7a0c1d2cc..13517f67e 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -22,7 +22,7 @@ workflow ALIGN_MT { ch_fai // channel: [mandatory] [ val(meta), path(fai) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() if (params.mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 0ecf25c52..532d08704 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'mt'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) ]) @@ -30,7 +30,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] @@ -44,7 +44,7 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] @@ -60,9 +60,9 @@ nextflow_workflow { ) input[2] = [[:],[]] input[3] = MT_MEM2.out.index.collect() - input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } @@ -81,7 +81,7 @@ nextflow_workflow { script "modules/nf-core/bwa/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'mt'], file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) ]) @@ -97,7 +97,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] @@ -111,7 +111,7 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] @@ -127,9 +127,9 @@ nextflow_workflow { ) input[2] = MT_BWA.out.index.collect() input[3] = [[:],[]] - input[4] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = Channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index c4be6a433..687e8aafe 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -27,7 +27,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { val_platform // string: [mandatory] default: illumina val_sort_threads // integer: [mandatory] default: 4 main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // Map, sort, and index if (params.aligner.equals("bwa")) { diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index ba9b60814..80b4a226c 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { script "modules/nf-core/bwamem2/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'sarscov2'], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) @@ -32,7 +32,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -42,8 +42,8 @@ nextflow_workflow { input[1] = [[:],[]] input[2] = BWAMEM2_INDEX.out.index input[3] = [[:],[]] - input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 @@ -71,7 +71,7 @@ nextflow_workflow { script "modules/nf-core/bwameme/index/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'sarscov2'], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) @@ -89,7 +89,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), @@ -99,8 +99,8 @@ nextflow_workflow { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = BWAMEME_INDEX.out.index - input[4] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = 3072 input[7] = "illumina" input[8] = 4 diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 15e03b6d9..5a11b65c8 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -18,7 +18,7 @@ workflow ALIGN_SENTIEON { val_platform // string: [mandatory] default: illumina main: - ch_versions = Channel.empty() + ch_versions = channel.empty() SENTIEON_BWAMEM ( ch_reads_input, ch_bwa_index, ch_genome_fasta, ch_genome_fai ) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 54ae5efcb..01868bc39 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { script "modules/nf-core/sentieon/bwaindex/main.nf" process { """ - input[0] = Channel.of([ + input[0] = channel.of([ [id:'sarscov2'], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) @@ -31,15 +31,15 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ + input[0] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[2] = Channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[3] = SENTIEON_BWAINDEX.out.index input[4] = "illumina" """ diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 1b5821228..61d9fb289 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -17,7 +17,7 @@ workflow ANNOTATE_CADD { ch_cadd_resources // channel: [mandatory] [ path(dir) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() BCFTOOLS_VIEW(ch_vcf, [], [], []) diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index 333be66b7..722cd9d8e 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -13,7 +13,7 @@ workflow ANNOTATE_CSQ_PLI { val_index // bool main: - ch_versions = Channel.empty() + ch_versions = channel.empty() CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 62d3808ee..2aff48591 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -43,10 +43,10 @@ workflow ANNOTATE_GENOME_SNVS { ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] main: - ch_cadd_vcf = Channel.empty() - ch_versions = Channel.empty() - ch_vcf_scatter_in = Channel.empty() - ch_vep_in = Channel.empty() + ch_cadd_vcf = channel.empty() + ch_versions = channel.empty() + ch_vcf_scatter_in = channel.empty() + ch_vep_in = channel.empty() BCFTOOLS_ROH (ch_vcf, ch_gnomad_af, [], [], [], []) diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index 2d08ca072..9e8c4d179 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -21,8 +21,8 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_vep_extra_files // channel: [mandatory] [ path(files) ] main: - ch_versions = Channel.empty() - ch_svdb_dbs = Channel.empty() + ch_versions = channel.empty() + ch_svdb_dbs = channel.empty() ch_me_svdb_resources .splitCsv ( header:true ) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index b1fba8b09..bd1b7f6e0 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -29,8 +29,8 @@ workflow ANNOTATE_MT_SNVS { ch_vep_extra_files // channel: [mandatory] [ path(files) ] main: - ch_versions = Channel.empty() - ch_haplog = Channel.empty() + ch_versions = channel.empty() + ch_haplog = channel.empty() // add prefix to meta ch_mt_vcf @@ -66,7 +66,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) } else { - ch_cadd_vcf = Channel.empty() + ch_cadd_vcf = channel.empty() } // Pick input for vep diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 87d3b6bd6..1fd6adf99 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -18,7 +18,7 @@ workflow ANNOTATE_RHOCALLVIZ { ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() ch_vcf_tbi .combine(ch_samples) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index db73f5a19..a0ee08235 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -23,9 +23,9 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_vep_extra_files // channel: [mandatory] [ path(files) ] main: - ch_versions = Channel.empty() - ch_svdb_dbs = Channel.empty() - ch_svdb_bedpedbs = Channel.empty() + ch_versions = channel.empty() + ch_svdb_dbs = channel.empty() + ch_svdb_bedpedbs = channel.empty() ch_sv_dbs .splitCsv ( header:true ) diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index cc9c1ee51..622144ec4 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -23,7 +23,7 @@ workflow CALL_MOBILE_ELEMENTS { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // Building chromosome channels based on fasta index ch_genome_fai diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 7d62025bf..eef2fb00a 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -20,7 +20,7 @@ workflow CALL_REPEAT_EXPANSIONS { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() EXPANSIONHUNTER ( ch_bam, diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index f797174c5..75b99f949 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -12,17 +12,17 @@ nextflow_workflow { when { workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[1] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() - input[2] = Channel.of([id:'justhusky']) - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() + input[2] = channel.of([id:'justhusky']) + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() """ } } diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index eac3adfec..575c78aca 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -39,19 +39,19 @@ workflow CALL_SNV { ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] main: - ch_versions = Channel.empty() - ch_deepvar_vcf = Channel.empty() - ch_deepvar_tbi = Channel.empty() - ch_deepvar_gvcf = Channel.empty() - ch_deepvar_gtbi = Channel.empty() - ch_mt_vcf = Channel.empty() - ch_mt_tabix = Channel.empty() - ch_mt_vcf_tabix = Channel.empty() - ch_mt_txt = Channel.empty() - ch_sentieon_vcf = Channel.empty() - ch_sentieon_tbi = Channel.empty() - ch_sentieon_gvcf = Channel.empty() - ch_sentieon_gtbi = Channel.empty() + ch_versions = channel.empty() + ch_deepvar_vcf = channel.empty() + ch_deepvar_tbi = channel.empty() + ch_deepvar_gvcf = channel.empty() + ch_deepvar_gtbi = channel.empty() + ch_mt_vcf = channel.empty() + ch_mt_tabix = channel.empty() + ch_mt_vcf_tabix = channel.empty() + ch_mt_txt = channel.empty() + ch_sentieon_vcf = channel.empty() + ch_sentieon_tbi = channel.empty() + ch_sentieon_gvcf = channel.empty() + ch_sentieon_gtbi = channel.empty() if (params.variant_caller.equals("deepvariant") && !params.analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( // triggered only when params.variant_caller is set as deepvariant @@ -90,10 +90,10 @@ workflow CALL_SNV { ch_versions = ch_versions.mix(CALL_SNV_SENTIEON.out.versions) } - ch_vcf = Channel.empty().mix(ch_deepvar_vcf, ch_sentieon_vcf) - ch_tabix = Channel.empty().mix(ch_deepvar_tbi, ch_sentieon_tbi) - ch_gvcf = Channel.empty().mix(ch_deepvar_gvcf, ch_sentieon_gvcf) - ch_gtabix = Channel.empty().mix(ch_deepvar_gtbi, ch_sentieon_gtbi) + ch_vcf = channel.empty().mix(ch_deepvar_vcf, ch_sentieon_vcf) + ch_tabix = channel.empty().mix(ch_deepvar_tbi, ch_sentieon_tbi) + ch_gvcf = channel.empty().mix(ch_deepvar_gvcf, ch_sentieon_gvcf) + ch_gtabix = channel.empty().mix(ch_deepvar_gtbi, ch_sentieon_gtbi) ch_vcf .join(ch_tabix, failOnMismatch:true, failOnDuplicate:true) diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 17135d33a..46aa4f167 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -15,9 +15,9 @@ workflow CALL_SNV_MT { ch_intervals // channel: [mandatory] [ path(interval_list) ] main: - ch_versions = Channel.empty() - ch_haplocheck_txt = Channel.empty() - ch_haplocheck_html = Channel.empty() + ch_versions = channel.empty() + ch_haplocheck_txt = channel.empty() + ch_haplocheck_html = channel.empty() ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 826f2e6a3..e7ad01bf7 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -24,7 +24,7 @@ workflow CALL_SNV_DEEPVARIANT { ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() if (params.analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, index -> return [meta, gzbed]}) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index e987d26cb..003e843c5 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -29,7 +29,7 @@ workflow CALL_SNV_SENTIEON { ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // Combine bam and intervals bam_bai_intervals = ch_bam_bai.combine(ch_call_interval) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 311cfdc9c..8d1d1a50d 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -29,9 +29,9 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] main: - ch_versions = Channel.empty() - ch_merged_svs = Channel.empty() - ch_merged_tbi = Channel.empty() + ch_versions = channel.empty() + ch_merged_svs = channel.empty() + ch_merged_tbi = channel.empty() if (!params.analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 8ce67fec3..3acae4f3b 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -11,10 +11,10 @@ workflow CALL_SV_MT { ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] main: - ch_versions = Channel.empty() - ch_eklipse_del = Channel.empty() - ch_eklipse_genes = Channel.empty() - ch_eklipse_circos = Channel.empty() + ch_versions = channel.empty() + ch_eklipse_del = channel.empty() + ch_eklipse_genes = channel.empty() + ch_eklipse_circos = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('eklipse'))) { EKLIPSE(ch_bam_bai,[]) diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index dbf13db52..28fea1b56 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -20,7 +20,7 @@ workflow CALL_SV_CNVNATOR { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]], "rd" ) CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai, "his" ) diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index 262737f5d..517cdd7d4 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -22,7 +22,7 @@ workflow CALL_SV_GERMLINECNVCALLER { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() input = ch_bam_bai.combine( ch_readcount_intervals ) diff --git a/subworkflows/local/convert_mt_bam_to_fastq/main.nf b/subworkflows/local/convert_mt_bam_to_fastq/main.nf index 50bd6fd6a..178aa876e 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/main.nf +++ b/subworkflows/local/convert_mt_bam_to_fastq/main.nf @@ -15,7 +15,7 @@ workflow CONVERT_MT_BAM_TO_FASTQ { ch_genome_dict // channel: [mandatory] [ val(meta), path(dict) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // Outputs bam containing only MT GATK4_PRINTREADS_MT ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_genome_dict ) diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 569300db2..5fcbf499a 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -16,8 +16,8 @@ workflow GENERATE_CYTOSURE_FILES { ch_blacklist // channel: [optional] [path(blacklist)] main: - ch_versions = Channel.empty() - ch_reheader_out = Channel.empty() + ch_versions = channel.empty() + ch_reheader_out = channel.empty() TIDDIT_COV_VCF2CYTOSURE (ch_bam, [[],[]]) @@ -28,8 +28,8 @@ workflow GENERATE_CYTOSURE_FILES { ch_bam.combine(ch_vcf_tbi) .map { meta_sample, bam, meta_case, vcf, tbi -> - id_meta = ['id':meta_sample.sample] - sex_meta = ['sex':meta_sample.sex] + def id_meta = ['id':meta_sample.sample] + def sex_meta = ['sex':meta_sample.sex] return [ id_meta, sex_meta, vcf, tbi ] } .join(ch_sample_id_map, remainder: true) @@ -41,7 +41,7 @@ workflow GENERATE_CYTOSURE_FILES { } .set { ch_for_mix } - Channel.empty() + channel.empty() .mix(ch_for_mix.id, ch_for_mix.custid) .set { ch_sample_vcf } @@ -70,7 +70,7 @@ workflow GENERATE_CYTOSURE_FILES { } .set { ch_for_mix } - Channel.empty() + channel.empty() .mix(ch_for_mix.split, ch_for_mix.reheader) .toSortedList { a, b -> a[0].id <=> b[0].id } .flatMap() diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index c491d2e5e..20a3eaec1 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -21,7 +21,7 @@ workflow GENS { ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() ch_bam_bai .combine(ch_interval_list) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 8657b5ffb..b1eb3f5de 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -28,7 +28,7 @@ workflow POSTPROCESS_MT_CALLS { ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() // LIFTOVER SHIFTED VCF TO REFERENCE MT POSITIONS PICARD_LIFTOVERVCF ( diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 61557e7a1..a5db1cef0 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -46,20 +46,20 @@ workflow PREPARE_REFERENCES { ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] main: - ch_versions = Channel.empty() - ch_tbi = Channel.empty() - ch_bgzip_tbi = Channel.empty() - ch_bwa = Channel.empty() - ch_sentieonbwa = Channel.empty() - ch_vcfanno_extra = Channel.empty() - ch_vcfanno_bgzip = Channel.empty() - ch_vcfanno_index = Channel.empty() + ch_versions = channel.empty() + ch_tbi = channel.empty() + ch_bgzip_tbi = channel.empty() + ch_bwa = channel.empty() + ch_sentieonbwa = channel.empty() + ch_vcfanno_extra = channel.empty() + ch_vcfanno_bgzip = channel.empty() + ch_vcfanno_index = channel.empty() // Genome indices SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]) GATK_SD(ch_genome_fasta) - ch_fai = Channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect() - ch_dict = Channel.empty().mix(ch_genome_dictionary, GATK_SD.out.dict).collect() + ch_fai = channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect() + ch_dict = channel.empty().mix(ch_genome_dictionary, GATK_SD.out.dict).collect() GET_CHROM_SIZES( ch_fai ) // Genome alignment indices @@ -70,7 +70,7 @@ workflow PREPARE_REFERENCES { // MT genome indices SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) - ch_mt_fasta_in = Channel.empty().mix(ch_mt_fasta, SAMTOOLS_EXTRACT_MT.out.fa).collect() + ch_mt_fasta_in = channel.empty().mix(ch_mt_fasta, SAMTOOLS_EXTRACT_MT.out.fa).collect() SAMTOOLS_FAIDX_MT(ch_mt_fasta_in, [[],[]]) GATK_SD_MT(ch_mt_fasta_in) GATK_SHIFTFASTA(ch_mt_fasta_in, SAMTOOLS_FAIDX_MT.out.fai, GATK_SD_MT.out.dict) @@ -79,12 +79,12 @@ workflow PREPARE_REFERENCES { BWAMEM2_INDEX_MT(ch_mt_fasta_in) BWA_INDEX_MT(ch_mt_fasta_in) SENTIEON_BWAINDEX_MT(ch_mt_fasta_in) - ch_bwa_mt = Channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() + ch_bwa_mt = channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) - ch_bwa_mtshift = Channel.empty().mix(SENTIEON_BWAINDEX_MT_SHIFT.out.index, BWA_INDEX_MT_SHIFT.out.index).collect() + ch_bwa_mtshift = channel.empty().mix(SENTIEON_BWAINDEX_MT_SHIFT.out.index, BWA_INDEX_MT_SHIFT.out.index).collect() GATK_SHIFTFASTA.out.intervals .multiMap{ meta, files -> shift_intervals: @@ -108,7 +108,7 @@ workflow PREPARE_REFERENCES { // Compress and index target bed file in case of uncompressed input TABIX_PBT(ch_target_bed).gz_tbi .set { ch_bgzip_tbi } - ch_target_bed_gz_tbi = Channel.empty() + ch_target_bed_gz_tbi = channel.empty() .mix(ch_trgt_bed_tbi, ch_bgzip_tbi) ch_vcfanno_extra_unprocessed @@ -124,12 +124,12 @@ workflow PREPARE_REFERENCES { .set {ch_vcfanno_index} TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex) - Channel.empty() + channel.empty() .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) .map { meta, vcf, index -> return [[vcf,index]] } .set {ch_vcfanno_bgzip} - Channel.empty() + channel.empty() .mix(ch_vcfanno_bgzip, ch_vcfanno_index) .collect() .set{ch_vcfanno_extra} @@ -193,7 +193,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) emit: - genome_bwa_index = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] + genome_bwa_index = channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] genome_bwamem2_index = BWAMEM2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_bwameme_index = BWAMEME_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 275c86dc7..774194923 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -16,15 +16,15 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = Channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() - input[2] = Channel.empty() - input[3] = Channel.empty() - input[4] = Channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() - input[5] = Channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() - input[6] = Channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() - input[7] = Channel.empty() - input[8] = Channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() + input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() + input[2] = channel.empty() + input[3] = channel.empty() + input[4] = channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() + input[5] = channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() + input[6] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() + input[7] = channel.empty() + input[8] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() """ } } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 3ee0817fc..e2f086983 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -35,11 +35,11 @@ workflow QC_BAM { ngsbits_samplegender_method // channel: [val(method)] main: - ch_cov = Channel.empty() - ch_cov_y = Channel.empty() - ch_versions = Channel.empty() - ch_qualimap = Channel.empty() - ch_ngsbits = Channel.empty() + ch_cov = channel.empty() + ch_cov_y = channel.empty() + ch_versions = channel.empty() + ch_qualimap = channel.empty() + ch_ngsbits = channel.empty() PICARD_COLLECTMULTIPLEMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai) @@ -69,8 +69,8 @@ workflow QC_BAM { PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y ) SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} ) SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} ) - ch_cov = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_WG.out.metrics, SENTIEON_WGSMETRICS_WG.out.wgs_metrics) - ch_cov_y = Channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics) + ch_cov = channel.empty().mix(PICARD_COLLECTWGSMETRICS_WG.out.metrics, SENTIEON_WGSMETRICS_WG.out.wgs_metrics) + ch_cov_y = channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics) ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_WG.out.versions.first(), SENTIEON_WGSMETRICS_WG.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_Y.out.versions.first(), SENTIEON_WGSMETRICS_Y.out.versions.first()) } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 673c3d669..94eb1a6f6 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -16,35 +16,35 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = Channel.of( + input[2] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[6] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[7] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[8] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[9] = Channel.empty() - input[10] = Channel.empty() - input[11] = Channel.empty() - input[12] = Channel.empty() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() input[13] = 'xy' """ } @@ -93,35 +93,35 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of( + input[0] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] ] ) - input[1] = Channel.of( + input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = Channel.of( + input[2] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[3] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[4] = Channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[6] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[7] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[8] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[9] = Channel.empty() - input[10] = Channel.empty() - input[11] = Channel.empty() - input[12] = Channel.empty() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() input[13] = 'xy' """ } diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 29399d4f3..1c64def08 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -19,7 +19,7 @@ workflow RANK_VARIANTS { ch_score_config // channel: [mandatory] [ path(ini) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() GENMOD_ANNOTATE(ch_vcf) diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index 2859f1bff..004577321 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -13,7 +13,7 @@ workflow SCATTER_GENOME { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() BUILD_BED (ch_genome_fai) diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 47a55f9fa..c9e0bdbaf 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -17,9 +17,9 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() - input[1] = Channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() - input[2] = Channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() + input[0] = channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() + input[1] = channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() + input[2] = channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() """ } } diff --git a/subworkflows/local/subsample_mt.nf b/subworkflows/local/subsample_mt.nf index 180748e54..8074aed15 100644 --- a/subworkflows/local/subsample_mt.nf +++ b/subworkflows/local/subsample_mt.nf @@ -15,7 +15,7 @@ workflow SUBSAMPLE_MT { val_mt_subsample_seed // channel: [mandatory] [ val(seed) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() ch_mt_bam_bai.map {meta, bam, bai -> return [meta, bam, -1]}.set {ch_genomecov_in} diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index 865391e61..f6696f133 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -101,7 +101,7 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - Channel + channel .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .tap { ch_original_input } .map { meta, fastq1, fastq2, spring1, spring2, bam, bai -> meta.id } diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index c9bce679a..b7b94647e 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -15,7 +15,7 @@ workflow VARIANT_EVALUATION { ch_sdf // channel: [mandatory] [ val(meta), path(sdf) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() ch_rtg_truthvcfs .splitCsv ( header:true ) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a083ad721..5db479a31 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -85,30 +85,30 @@ workflow RAREDISEASE { main: - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() - ch_mt_txt = Channel.empty() + ch_versions = channel.empty() + ch_multiqc_files = channel.empty() + ch_mt_txt = channel.empty() // // Initialize file channels for PREPARE_REFERENCES subworkflow // - ch_genome_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() - ch_genome_fai = params.fai ? Channel.fromPath(params.fai).map {it -> [[id:it.simpleName], it]}.collect() - : Channel.empty() - ch_genome_dictionary = params.sequence_dictionary ? Channel.fromPath(params.sequence_dictionary).map {it -> [[id:it.simpleName], it]}.collect() - : Channel.empty() - ch_gnomad_af_tab = params.gnomad_af ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() - : Channel.value([[],[]]) - ch_dbsnp = params.known_dbsnp ? Channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() - : Channel.value([[],[]]) - ch_mt_fasta = params.mt_fasta ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it.simpleName], it] }.collect() - : Channel.empty() - ch_target_bed_unprocessed = params.target_bed ? Channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() - : Channel.value([[],[]]) - ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? Channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() - : Channel.empty() - ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() - : Channel.value([[],[]]) + ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() + ch_genome_fai = params.fai ? channel.fromPath(params.fai).map {it -> [[id:it.simpleName], it]}.collect() + : channel.empty() + ch_genome_dictionary = params.sequence_dictionary ? channel.fromPath(params.sequence_dictionary).map {it -> [[id:it.simpleName], it]}.collect() + : channel.empty() + ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_dbsnp = params.known_dbsnp ? channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_mt_fasta = params.mt_fasta ? channel.fromPath(params.mt_fasta).map { it -> [[id:it.simpleName], it] }.collect() + : channel.empty() + ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() + : channel.empty() + ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() + : channel.value([[],[]]) // // Prepare references and indices. @@ -130,50 +130,50 @@ workflow RAREDISEASE { // Gather built indices or get them from the params // ch_bait_intervals = ch_references.bait_intervals - ch_cadd_header = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() - ch_cadd_resources = params.cadd_resources ? Channel.fromPath(params.cadd_resources).collect() - : Channel.value([]) - ch_call_interval = params.call_interval ? Channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() - : Channel.value([[:],[]]) - ch_dbsnp_tbi = params.known_dbsnp_tbi ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() + ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() + : channel.value([]) + ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() + : channel.value([[:],[]]) + ch_dbsnp_tbi = params.known_dbsnp_tbi ? channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) - ch_foundin_header = Channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() - ch_gcnvcaller_model = params.gcnvcaller_model ? Channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) + ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() + ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> return [[id:file(row.models).simpleName], row.models] } - : Channel.empty() - ch_genome_bwaindex = params.bwa ? Channel.fromPath(params.bwa).map {it -> [[id:it.simpleName], it]}.collect() + : channel.empty() + ch_genome_bwaindex = params.bwa ? channel.fromPath(params.bwa).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.genome_bwa_index - ch_genome_bwamem2index = params.bwamem2 ? Channel.fromPath(params.bwamem2).map {it -> [[id:it.simpleName], it]}.collect() + ch_genome_bwamem2index = params.bwamem2 ? channel.fromPath(params.bwamem2).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.genome_bwamem2_index - ch_genome_bwamemeindex = params.bwameme ? Channel.fromPath(params.bwameme).map {it -> [[id:it.simpleName], it]}.collect() + ch_genome_bwamemeindex = params.bwameme ? channel.fromPath(params.bwameme).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.genome_bwameme_index ch_genome_chrsizes = ch_references.genome_chrom_sizes ch_genome_fai = ch_references.genome_fai ch_genome_dictionary = ch_references.genome_dict - ch_gens_gnomad_pos = params.gens_gnomad_pos ? Channel.fromPath(params.gens_gnomad_pos).collect() - : Channel.empty() - ch_gens_interval_list = params.gens_interval_list ? Channel.fromPath(params.gens_interval_list).collect() - : Channel.empty() - ch_gens_pon_female = params.gens_pon_female ? Channel.fromPath(params.gens_pon_female).map { it -> [ [id:it.simpleName], it ] }.collect() - : Channel.empty() - ch_gens_pon_male = params.gens_pon_male ? Channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() - : Channel.empty() - ch_gnomad_afidx = params.gnomad_af_idx ? Channel.fromPath(params.gnomad_af_idx).collect() + ch_gens_gnomad_pos = params.gens_gnomad_pos ? channel.fromPath(params.gens_gnomad_pos).collect() + : channel.empty() + ch_gens_interval_list = params.gens_interval_list ? channel.fromPath(params.gens_interval_list).collect() + : channel.empty() + ch_gens_pon_female = params.gens_pon_female ? channel.fromPath(params.gens_pon_female).map { it -> [ [id:it.simpleName], it ] }.collect() + : channel.empty() + ch_gens_pon_male = params.gens_pon_male ? channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() + : channel.empty() + ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() : ch_references.gnomad_af_idx ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() + : channel.empty() + ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() + : channel.empty() + ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() : Channel.empty() - ch_intervals_wgs = params.intervals_wgs ? Channel.fromPath(params.intervals_wgs).collect() - : Channel.empty() - ch_intervals_y = params.intervals_y ? Channel.fromPath(params.intervals_y).collect() - : Channel.empty() - ch_me_references = params.mobile_element_references ? Channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) - : Channel.empty() - ch_me_svdb_resources = params.mobile_element_svdb_annotations ? Channel.fromPath(params.mobile_element_svdb_annotations) - : Channel.empty() - ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() - : Channel.value([[:],[]]) + ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) + : channel.empty() + ch_me_svdb_resources = params.mobile_element_svdb_annotations ? channel.fromPath(params.mobile_element_svdb_annotations) + : channel.empty() + ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() + : channel.value([[:],[]]) ch_mt_intervals = ch_references.mt_intervals ch_mt_bwaindex = ch_references.mt_bwa_index ch_mt_bwamem2index = ch_references.mt_bwamem2_index @@ -187,61 +187,61 @@ workflow RAREDISEASE { ch_mtshift_fai = ch_references.mtshift_fai ch_mtshift_fasta = ch_references.mtshift_fasta ch_mtshift_intervals = ch_references.mtshift_intervals - ch_par_bed = params.par_bed ? Channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() - : Channel.value([[],[]]) - ch_ploidy_model = params.ploidy_model ? Channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() - : Channel.empty() - ch_readcount_intervals = params.readcount_intervals ? Channel.fromPath(params.readcount_intervals).collect() - : Channel.empty() - ch_reduced_penetrance = params.reduced_penetrance ? Channel.fromPath(params.reduced_penetrance).collect() - : Channel.value([]) - ch_rtg_truthvcfs = params.rtg_truthvcfs ? Channel.fromPath(params.rtg_truthvcfs).collect() - : Channel.value([]) - ch_sample_id_map = params.sample_id_map ? Channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) - : Channel.empty() - ch_score_config_mt = params.score_config_mt ? Channel.fromPath(params.score_config_mt).collect() - : Channel.value([]) - ch_score_config_snv = params.score_config_snv ? Channel.fromPath(params.score_config_snv).collect() - : Channel.value([]) - ch_score_config_sv = params.score_config_sv ? Channel.fromPath(params.score_config_sv).collect() - : Channel.value([]) - ch_sdf = params.sdf ? Channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() + ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() + : channel.value([[],[]]) + ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.empty() + ch_readcount_intervals = params.readcount_intervals ? channel.fromPath(params.readcount_intervals).collect() + : channel.empty() + ch_reduced_penetrance = params.reduced_penetrance ? channel.fromPath(params.reduced_penetrance).collect() + : channel.value([]) + ch_rtg_truthvcfs = params.rtg_truthvcfs ? channel.fromPath(params.rtg_truthvcfs).collect() + : channel.value([]) + ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) + : channel.empty() + ch_score_config_mt = params.score_config_mt ? channel.fromPath(params.score_config_mt).collect() + : channel.value([]) + ch_score_config_snv = params.score_config_snv ? channel.fromPath(params.score_config_snv).collect() + : channel.value([]) + ch_score_config_sv = params.score_config_sv ? channel.fromPath(params.score_config_sv).collect() + : channel.value([]) + ch_sdf = params.sdf ? channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf - ch_sv_dbs = params.svdb_query_dbs ? Channel.fromPath(params.svdb_query_dbs) - : Channel.empty() - ch_sv_bedpedbs = params.svdb_query_bedpedbs ? Channel.fromPath(params.svdb_query_bedpedbs) - : Channel.empty() - ch_svd_bed = params.verifybamid_svd_bed ? Channel.fromPath(params.verifybamid_svd_bed) - : Channel.empty() - ch_svd_mu = params.verifybamid_svd_mu ? Channel.fromPath(params.verifybamid_svd_mu) - : Channel.empty() - ch_svd_ud = params.verifybamid_svd_ud ? Channel.fromPath(params.verifybamid_svd_ud) - : Channel.empty() + ch_sv_dbs = params.svdb_query_dbs ? channel.fromPath(params.svdb_query_dbs) + : channel.empty() + ch_sv_bedpedbs = params.svdb_query_bedpedbs ? channel.fromPath(params.svdb_query_bedpedbs) + : channel.empty() + ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) + : channel.empty() + ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) + : channel.empty() + ch_svd_ud = params.verifybamid_svd_ud ? channel.fromPath(params.verifybamid_svd_ud) + : channel.empty() ch_target_bed = ch_references.target_bed ch_target_intervals = ch_references.target_intervals - ch_variant_catalog = params.variant_catalog ? Channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() - : Channel.value([[],[]]) - ch_variant_consequences_snv = params.variant_consequences_snv ? Channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() - : Channel.value([[],[]]) - ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() - : Channel.value([[],[]]) + ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) + ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) + ch_variant_consequences_sv = params.variant_consequences_sv ? channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) ch_vcfanno_extra = ch_references.vcfanno_extra - ch_vcfanno_resources = params.vcfanno_resources ? Channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() - : Channel.value([]) - ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? Channel.fromPath(params.vcf2cytosure_blacklist).collect() - : Channel.value([]) - ch_vcfanno_lua = params.vcfanno_lua ? Channel.fromPath(params.vcfanno_lua).collect() - : Channel.value([]) - ch_vcfanno_toml = params.vcfanno_toml ? Channel.fromPath(params.vcfanno_toml).collect() - : Channel.value([]) + ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() + : channel.value([]) + ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? channel.fromPath(params.vcf2cytosure_blacklist).collect() + : channel.value([]) + ch_vcfanno_lua = params.vcfanno_lua ? channel.fromPath(params.vcfanno_lua).collect() + : channel.value([]) + ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() + : channel.value([]) ch_vep_cache = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") ) ? ch_references.vep_resources - : ( params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) ) - ch_vep_extra_files_unsplit = params.vep_plugin_files ? Channel.fromPath(params.vep_plugin_files).collect() - : Channel.value([]) - ch_vep_filters_std_fmt = params.vep_filters ? Channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() - : Channel.empty() - ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? Channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() - : Channel.empty() + : ( params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([]) ) + ch_vep_extra_files_unsplit = params.vep_plugin_files ? channel.fromPath(params.vep_plugin_files).collect() + : channel.value([]) + ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() + : channel.empty() + ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() + : channel.empty() ch_versions = ch_versions.mix(ch_references.versions) // @@ -249,15 +249,15 @@ workflow RAREDISEASE { // if (params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller')) { if (params.analysis_type.equals("wgs")) { - ch_svcaller_priority = Channel.value(["tiddit", "manta", "cnvnator"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) } else { - ch_svcaller_priority = Channel.value([]) + ch_svcaller_priority = channel.value([]) } } else { if (params.analysis_type.equals("wgs")) { - ch_svcaller_priority = Channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) } else { - ch_svcaller_priority = Channel.value(["manta", "gcnvcaller"]) + ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) } } @@ -270,7 +270,7 @@ workflow RAREDISEASE { // // Read and store paths in the vep_plugin_files file // - ch_vep_extra_files = Channel.empty() + ch_vep_extra_files = channel.empty() if (params.vep_plugin_files) { ch_vep_extra_files_unsplit.splitCsv ( header:true ) .map { row -> @@ -322,7 +322,7 @@ workflow RAREDISEASE { // // Create chromosome bed and intervals for splitting and gathering operations // - ch_scatter_split_intervals = Channel.empty() + ch_scatter_split_intervals = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_annotation'))) { SCATTER_GENOME ( ch_genome_dictionary, @@ -400,7 +400,7 @@ workflow RAREDISEASE { ch_svd_bed, ch_svd_mu, ch_svd_ud, - Channel.value(params.ngsbits_samplegender_method) + channel.value(params.ngsbits_samplegender_method) ) ch_versions = ch_versions.mix(QC_BAM.out.versions) @@ -475,7 +475,7 @@ workflow RAREDISEASE { ch_par_bed, ch_case_info, ch_foundin_header, - Channel.value(params.sentieon_dnascope_pcr_indel_model) + channel.value(params.sentieon_dnascope_pcr_indel_model) ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) ch_mt_txt = CALL_SNV.out.mt_txt @@ -513,7 +513,7 @@ workflow RAREDISEASE { } .set { ch_clin_research_snv_vcf } - ch_clinical_snv_vcf = Channel.empty() + ch_clinical_snv_vcf = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { GENERATE_CLINICAL_SET_SNV( ch_clin_research_snv_vcf.clinical, @@ -582,7 +582,7 @@ workflow RAREDISEASE { } .set { ch_clin_research_mt_vcf } - ch_clinical_mtsnv_vcf = Channel.empty() + ch_clinical_mtsnv_vcf = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { GENERATE_CLINICAL_SET_MT( ch_clin_research_mt_vcf.clinical, @@ -673,7 +673,7 @@ workflow RAREDISEASE { } .set { ch_clin_research_sv_vcf } - ch_clinical_sv_vcf = Channel.empty() + ch_clinical_sv_vcf = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { GENERATE_CLINICAL_SET_SV( ch_clin_research_sv_vcf.clinical, @@ -750,7 +750,7 @@ workflow RAREDISEASE { } .set { ch_clin_research_me_vcf } - ch_clinical_me_vcf = Channel.empty() + ch_clinical_me_vcf = channel.empty() if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { GENERATE_CLINICAL_SET_ME( ch_clin_research_me_vcf.clinical, @@ -879,7 +879,7 @@ workflow RAREDISEASE { // // Collate and save software versions // - def topic_versions = Channel.topic("versions") + def topic_versions = channel.topic("versions") .distinct() .branch { entry -> versions_file: entry instanceof Path @@ -914,8 +914,8 @@ workflow RAREDISEASE { channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty() ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.fromPath("$projectDir/docs/images/nf-core-raredisease_logo_light.png", checkIfExists: true) + channel.fromPath(params.multiqc_logo, checkIfExists: true) : + channel.fromPath("$projectDir/docs/images/nf-core-raredisease_logo_light.png", checkIfExists: true) summary_params = paramsSummaryMap( From 6ec15523f334f68e7add8df666a3f9e6daf54b63 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 27 Nov 2025 16:50:03 +0100 Subject: [PATCH 107/872] update snaps --- .../local/align/tests/main.nf.test.snap | 36 +++++----- .../local/align_MT/tests/main.nf.test.snap | 72 +++++++++---------- tests/default.nf.test.snap | 20 ++---- tests/test_bam.nf.test.snap | 17 ++--- tests/test_singleton.nf.test.snap | 15 ++-- 5 files changed, 62 insertions(+), 98 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index c0bf65b2f..eae97bc05 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -241,13 +241,9 @@ "versions.yml:md5,04cb590a101237e8d8726039ee466819", "versions.yml:md5,210790d64830e81c512ff898e8d888db", "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3cdf4ec614502fb38c2475c5475c3e0c", "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,753dc9d8832a5f5a1e10237d78e157f2", + "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", @@ -259,10 +255,12 @@ "versions.yml:md5,b1c46403177c797d5fc304eebf16731c", "versions.yml:md5,b511e8fd8c8b46c5470d3e3e79673502", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", - "versions.yml:md5,e092f50493ce9a5725381d53e24519d0", - "versions.yml:md5,e8fa9e5b444276ecb6b7af4cb7a86247", + "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" ] ], @@ -270,7 +268,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T13:57:27.462836066" + "timestamp": "2025-11-27T16:04:53.135202611" }, "align bwameme": { "content": [ @@ -399,13 +397,9 @@ "versions.yml:md5,04cb590a101237e8d8726039ee466819", "versions.yml:md5,210790d64830e81c512ff898e8d888db", "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3cdf4ec614502fb38c2475c5475c3e0c", "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,753dc9d8832a5f5a1e10237d78e157f2", + "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", @@ -414,10 +408,12 @@ "versions.yml:md5,b1c46403177c797d5fc304eebf16731c", "versions.yml:md5,b511e8fd8c8b46c5470d3e3e79673502", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", - "versions.yml:md5,e092f50493ce9a5725381d53e24519d0", - "versions.yml:md5,e8fa9e5b444276ecb6b7af4cb7a86247", + "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" ] ], @@ -425,7 +421,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T14:03:43.037036726" + "timestamp": "2025-11-27T16:15:46.006244795" }, "align bwamem2 - wes": { "content": [ @@ -499,15 +495,15 @@ ], [ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", - "versions.yml:md5,6f9a56c7077343a78b6b2a9bb555631b", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], @@ -515,6 +511,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T13:58:00.971064108" + "timestamp": "2025-11-27T16:05:52.987404208" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index f15f539b6..791238c66 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,88425ac81b7028fe6d7a5060356bd88f" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" ], [ { @@ -33,7 +33,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,6edaa52bf0d874e5fca3677079c81028" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" ], [ { @@ -49,7 +49,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,a69fb57a70c9a6571c83a181896fa0e8" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" ] ], "1": [ @@ -67,7 +67,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,41ec8f18f216cb149f4fce249666f63e" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" ], [ { @@ -83,7 +83,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d14ea82b8c368b1d45ba254d4c14873e" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" ], [ { @@ -99,14 +99,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,956fe4d30bcb0c244f2b4678e7f2dee7" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" ] ], "2": [ "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7beb4095e697b250b91b3219646aeaea", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,9a55207ee07d44c3c1e5dd2ca507d010", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ], @@ -125,7 +124,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,41ec8f18f216cb149f4fce249666f63e" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" ], [ { @@ -141,7 +140,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d14ea82b8c368b1d45ba254d4c14873e" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" ], [ { @@ -157,7 +156,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,956fe4d30bcb0c244f2b4678e7f2dee7" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" ] ], "marked_bam": [ @@ -175,7 +174,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,88425ac81b7028fe6d7a5060356bd88f" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" ], [ { @@ -191,7 +190,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,6edaa52bf0d874e5fca3677079c81028" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" ], [ { @@ -207,24 +206,23 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,a69fb57a70c9a6571c83a181896fa0e8" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" ] ], "versions": [ "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7beb4095e697b250b91b3219646aeaea", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,9a55207ee07d44c3c1e5dd2ca507d010", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-04-09T00:09:54.284479" + "timestamp": "2025-11-27T16:19:27.352451428" }, "align mt - bwa": { "content": [ @@ -244,7 +242,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,19f330a6d9a9289eb73ade4daca3d6e2" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" ], [ { @@ -260,7 +258,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,70263f625d6fdf2a396404948d821b63" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" ], [ { @@ -276,7 +274,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,10e8c7915c92dde1f78139cee8559140" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" ] ], "1": [ @@ -294,7 +292,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,4d67eed17f54ccae43e5205fcb0cdddd" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" ], [ { @@ -310,7 +308,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,42fe44b54568af1f5caba8f7bc56dee4" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" ], [ { @@ -326,14 +324,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,99bda57b9440fc0815b4646655fdf527" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" ] ], "2": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7beb4095e697b250b91b3219646aeaea", - "versions.yml:md5,9a55207ee07d44c3c1e5dd2ca507d010", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ], @@ -352,7 +349,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,4d67eed17f54ccae43e5205fcb0cdddd" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" ], [ { @@ -368,7 +365,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,42fe44b54568af1f5caba8f7bc56dee4" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" ], [ { @@ -384,7 +381,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,99bda57b9440fc0815b4646655fdf527" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" ] ], "marked_bam": [ @@ -402,7 +399,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,19f330a6d9a9289eb73ade4daca3d6e2" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" ], [ { @@ -418,7 +415,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,70263f625d6fdf2a396404948d821b63" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" ], [ { @@ -434,23 +431,22 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,10e8c7915c92dde1f78139cee8559140" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" ] ], "versions": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7beb4095e697b250b91b3219646aeaea", - "versions.yml:md5,9a55207ee07d44c3c1e5dd2ca507d010", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-04-09T00:22:56.160477" + "timestamp": "2025-11-27T16:22:50.087959667" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 18e5562bb..a524a822e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -212,11 +212,8 @@ "MARKDUPLICATES": { "picard": "3.3.0" }, - "ME_INDEX_SPLIT_ALIGNMENT": { - "samtools": 1.21 - }, "ME_SPLIT_ALIGNMENT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "MOSDEPTH": { "mosdepth": "0.3.10" @@ -281,23 +278,17 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, - "SAMTOOLS_INDEX": { - "samtools": 1.21 - }, "SAMTOOLS_INDEX_ALIGN": { "samtools": 1.21 }, "SAMTOOLS_INDEX_MARKDUP": { "samtools": 1.21 }, - "SAMTOOLS_INDEX_MT": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_STATS": { "samtools": 1.21 @@ -609,17 +600,14 @@ "repeat_expansions", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.csi", "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.csi", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.csi", "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", @@ -631,6 +619,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-26T10:17:14.24575236" + "timestamp": "2025-11-27T16:06:28.721832727" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index c38b510d1..ed60748ec 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 283, + 274, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -245,17 +245,11 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, - "SAMTOOLS_INDEX": { - "samtools": 1.21 - }, - "SAMTOOLS_INDEX_MT": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" @@ -521,17 +515,14 @@ "repeat_expansions", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.csi", "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.csi", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.csi", "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", @@ -543,6 +534,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-15T12:06:37.106816288" + "timestamp": "2025-11-27T16:14:53.307227004" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 3d92421f7..aac4e856e 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 151, + 148, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -243,23 +243,17 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, - "SAMTOOLS_INDEX": { - "samtools": 1.21 - }, "SAMTOOLS_INDEX_ALIGN": { "samtools": 1.21 }, "SAMTOOLS_INDEX_MARKDUP": { "samtools": 1.21 }, - "SAMTOOLS_INDEX_MT": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_STATS": { "samtools": 1.21 @@ -452,7 +446,6 @@ "repeat_expansions", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.csi", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", @@ -466,6 +459,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-15T12:11:02.492935999" + "timestamp": "2025-11-27T16:22:08.027799973" } } \ No newline at end of file From 0e9a5371ef86482deb695b8202fb73c0c0431b69 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 27 Nov 2025 15:53:45 +0000 Subject: [PATCH 108/872] [automated] Fix code linting --- subworkflows/local/subsample_mt_reads/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index f3d578e41..9d6ee8c2f 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -15,7 +15,7 @@ workflow SUBSAMPLE_MT_READS { main: ch_versions = Channel.empty() - + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) From aa33ddbc106635faefd6f5880e7ee0beee99f643 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 28 Nov 2025 09:02:14 +0100 Subject: [PATCH 109/872] remove extra file --- .vscode/settings.json | 1 - 1 file changed, 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index db1a67f8f..f90550f7d 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,4 +1,3 @@ { "markdown.styles": ["public/vscode_markdown.css"], - "cSpell.words": ["chrs"] } From c6bead72bd1994b534c5bd4dc43678c778f660ed Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 28 Nov 2025 09:03:23 +0100 Subject: [PATCH 110/872] remove comma --- .vscode/settings.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index f90550f7d..a33b527cc 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,3 @@ { - "markdown.styles": ["public/vscode_markdown.css"], + "markdown.styles": ["public/vscode_markdown.css"] } From 3c91305413499c6c7f566991bce3c9f60fda5802 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 10:12:31 +0100 Subject: [PATCH 111/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d43c7d42d..fbf446e8e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | gatk4/determinegermlinecontigploidy | 4.5.0.0 | 4.6.2.0 | | gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | | gens-preproc | 1.0.11 | 1.1.2 | +| samtools (sort & view) | 1.21 | 1.22.1 | ## 2.6.0 - Cacofonix [2025-06-25] From 794185dc598c0496b61f1f9419caa48fb2748b84 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 11:04:16 +0100 Subject: [PATCH 112/872] replace Channel to channel in an missed instance --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3e725b0b6..36c6d4648 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -168,7 +168,7 @@ workflow RAREDISEASE { ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() : channel.empty() ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() - : Channel.empty() + : channel.empty() ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) : channel.empty() ch_me_svdb_resources = params.mobile_element_svdb_annotations ? channel.fromPath(params.mobile_element_svdb_annotations) From 4e4f0d1f00dacd946c888f38753984851710e65e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 12:15:39 +0100 Subject: [PATCH 113/872] cleanup unused variables --- subworkflows/local/annotate_mt_snvs.nf | 2 -- subworkflows/local/call_mobile_elements.nf | 2 +- subworkflows/local/call_snv.nf | 13 ++++++------- subworkflows/local/call_structural_variants.nf | 10 +++++----- subworkflows/local/generate_cytosure_files.nf | 2 +- subworkflows/local/gens.nf | 1 - subworkflows/local/prepare_references/main.nf | 3 +-- subworkflows/local/qc_bam/main.nf | 1 - subworkflows/local/scatter_genome/main.nf | 2 +- subworkflows/local/subsample_mt_frac/main.nf | 2 +- subworkflows/local/variant_evaluation.nf | 1 - workflows/raredisease.nf | 5 ----- 12 files changed, 16 insertions(+), 28 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 8b35797e7..7b3f1825f 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -15,7 +15,6 @@ include { HMTNOTE_ANNOTATE } from '../../modules/n workflow ANNOTATE_MT_SNVS { take: ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_mt_tbi // channel: [mandatory] [ val(meta), path(tbi) ] ch_cadd_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(annotation) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] @@ -55,7 +54,6 @@ workflow ANNOTATE_MT_SNVS { ZIP_TABIX_VCFANNO_MT(VCFANNO_MT.out.vcf) ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, _tbi -> return [meta, vcf]} - ch_vcfanno_tbi = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, _vcf, tbi -> return [meta, tbi]} // Annotating with CADD if (params.cadd_resources != null) { diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 809534012..869d15aef 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -109,7 +109,7 @@ workflow CALL_MOBILE_ELEMENTS { // Merge sample vcfs to a case vcf BCFTOOLS_CONCAT_ME.out.vcf - .collect{it[1]} + .collect{_meta, vcf -> vcf} .toList() .collect() .set { ch_vcf_list } diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 575c78aca..1beb8675b 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -18,7 +18,6 @@ workflow CALL_SNV { ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_mt_intervals // channel: [optional] [ path(interval_list) ] ch_mt_dictionary // channel: [optional] [ val(meta), path(dict) ] ch_mt_fai // channel: [optional] [ val(meta), path(fai) ] @@ -64,11 +63,11 @@ workflow CALL_SNV { ch_foundin_header, ch_genome_chrsizes ) - ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf - ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix + ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf + ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix - ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) + ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) } else if (params.variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( // triggered only when params.variant_caller is set as sentieon ch_genome_bam_bai, @@ -83,11 +82,11 @@ workflow CALL_SNV { ch_foundin_header, ch_genome_chrsizes ) - ch_sentieon_vcf = CALL_SNV_SENTIEON.out.vcf - ch_sentieon_tbi = CALL_SNV_SENTIEON.out.tabix + ch_sentieon_vcf = CALL_SNV_SENTIEON.out.vcf + ch_sentieon_tbi = CALL_SNV_SENTIEON.out.tabix ch_sentieon_gvcf = CALL_SNV_SENTIEON.out.gvcf ch_sentieon_gtbi = CALL_SNV_SENTIEON.out.gvcf_tbi - ch_versions = ch_versions.mix(CALL_SNV_SENTIEON.out.versions) + ch_versions = ch_versions.mix(CALL_SNV_SENTIEON.out.versions) } ch_vcf = channel.empty().mix(ch_deepvar_vcf, ch_sentieon_vcf) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 8d1d1a50d..a4f528fed 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -29,14 +29,14 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] main: - ch_versions = channel.empty() + ch_versions = channel.empty() ch_merged_svs = channel.empty() ch_merged_tbi = channel.empty() if (!params.analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) .filtered_diploid_sv_vcf_tbi - .collect{it[1]} + .collect{ _meta, vcf, _tbi -> vcf } .set{ manta_vcf } ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) } @@ -44,13 +44,13 @@ workflow CALL_STRUCTURAL_VARIANTS { if (params.analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf - .collect{it[1]} + .collect{ _meta, vcf -> vcf } .set { tiddit_vcf } ch_versions = ch_versions.mix(CALL_SV_TIDDIT.out.versions) CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf - .collect{it[1]} + .collect{ _meta, vcf -> vcf } .set { cnvnator_vcf } ch_versions = ch_versions.mix(CALL_SV_CNVNATOR.out.versions) } @@ -58,7 +58,7 @@ workflow CALL_STRUCTURAL_VARIANTS { if (!(params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller'))) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf - .collect{it[1]} + .collect{ _meta, vcf -> vcf } .set { gcnvcaller_vcf } ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions) diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 5fcbf499a..db9c7be2d 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -27,7 +27,7 @@ workflow GENERATE_CYTOSURE_FILES { ch_bam.combine(ch_vcf_tbi) .map { - meta_sample, bam, meta_case, vcf, tbi -> + meta_sample, _bam, _meta_case, vcf, tbi -> def id_meta = ['id':meta_sample.sample] def sex_meta = ['sex':meta_sample.sex] return [ id_meta, sex_meta, vcf, tbi ] diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index eac25a790..b72cf0962 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -19,7 +19,6 @@ workflow GENS { ch_pon_female // channel: [mandatory] [ path(pon) ] ch_pon_male // channel: [mandatory] [ path(pon) ] ch_gnomad_pos // channel: [mandatory] [ path(gnomad_pos) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] main: diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a5db1cef0..77edcf15a 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -47,7 +47,6 @@ workflow PREPARE_REFERENCES { main: ch_versions = channel.empty() - ch_tbi = channel.empty() ch_bgzip_tbi = channel.empty() ch_bwa = channel.empty() ch_sentieonbwa = channel.empty() @@ -86,7 +85,7 @@ workflow PREPARE_REFERENCES { SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) ch_bwa_mtshift = channel.empty().mix(SENTIEON_BWAINDEX_MT_SHIFT.out.index, BWA_INDEX_MT_SHIFT.out.index).collect() GATK_SHIFTFASTA.out.intervals - .multiMap{ meta, files -> + .multiMap{ _meta, files -> shift_intervals: def ind = files.findIndexValues {it.toString().endsWith("shifted.intervals")} files[ind] diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index e2f086983..831fdd854 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -20,7 +20,6 @@ workflow QC_BAM { take: ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_bai // channel: [mandatory] [ val(meta), path(bai) ] ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index 004577321..fc17c338b 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -24,6 +24,6 @@ workflow SCATTER_GENOME { emit: bed = BUILD_BED.out.bed.collect() // channel: [ val(meta), path(bed) ] - split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] + split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 1f110b1cb..3c8d16f46 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -16,7 +16,7 @@ workflow SUBSAMPLE_MT_FRAC { main: ch_versions = channel.empty() - ch_mt_bam_bai.map {meta, bam, bai -> return [meta, bam, -1]}.set {ch_genomecov_in} + ch_mt_bam_bai.map {meta, bam, _bai -> return [meta, bam, -1]}.set {ch_genomecov_in} BEDTOOLS_GENOMECOV (ch_genomecov_in, [], "genomecov", false) diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index b7b94647e..e6155b397 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -10,7 +10,6 @@ workflow VARIANT_EVALUATION { take: ch_snv_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_rtg_truthvcfs // channel: [mandatory] [ val(meta), path(dbs) ] ch_sdf // channel: [mandatory] [ val(meta), path(sdf) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 36c6d4648..43ecdb494 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -396,7 +396,6 @@ workflow RAREDISEASE { // QC_BAM ( ch_mapped.genome_marked_bam, - ch_mapped.genome_marked_bai, ch_mapped.genome_marked_bam_bai, ch_genome_fasta, ch_genome_fai, @@ -465,7 +464,6 @@ workflow RAREDISEASE { ch_genome_chrsizes, ch_genome_fasta, ch_genome_fai, - ch_genome_dictionary, ch_mt_intervals, ch_mt_dictionary, ch_mt_fai, @@ -568,7 +566,6 @@ workflow RAREDISEASE { ANNOTATE_MT_SNVS ( CALL_SNV.out.mt_vcf, - CALL_SNV.out.mt_tabix, ch_cadd_header, ch_cadd_resources, ch_genome_fasta, @@ -857,7 +854,6 @@ workflow RAREDISEASE { ch_gens_pon_female, ch_gens_pon_male, ch_gens_gnomad_pos, - ch_case_info, ch_genome_dictionary ) ch_versions = ch_versions.mix(GENS.out.versions) @@ -872,7 +868,6 @@ workflow RAREDISEASE { if (params.run_rtgvcfeval) { VARIANT_EVALUATION ( CALL_SNV.out.genome_vcf_tabix, - ch_genome_fai, ch_rtg_truthvcfs, ch_sdf ) From 9d27d0bc3790140313a8815ca37e0ad7cb908f96 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 13:24:02 +0100 Subject: [PATCH 114/872] cleanup unused variables --- subworkflows/local/align_MT/main.nf | 2 +- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 6 +++--- subworkflows/local/align_sentieon/main.nf | 6 +++--- subworkflows/local/annotate_rhocallviz/main.nf | 2 +- subworkflows/local/call_repeat_expansions/main.nf | 2 +- subworkflows/local/call_snv_MT/main.nf | 8 +++----- subworkflows/local/call_snv_deepvariant/main.nf | 6 +++--- subworkflows/local/call_snv_sentieon/main.nf | 12 ++++++------ subworkflows/local/call_structural_variants.nf | 4 ++-- subworkflows/local/call_sv_cnvnator/main.nf | 2 +- subworkflows/local/call_sv_germlinecnvcaller/main.nf | 10 +++++----- subworkflows/local/call_sv_manta/main.nf | 8 ++++---- subworkflows/local/call_sv_tiddit/main.nf | 2 +- subworkflows/local/postprocess_MT_calls/main.nf | 6 +++--- subworkflows/local/prepare_references/main.nf | 10 +++++----- 15 files changed, 42 insertions(+), 44 deletions(-) diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index e58aa5d4d..ec57f3731 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -29,7 +29,7 @@ workflow ALIGN_MT { ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions.first()) } else if (params.mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) - ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, bai -> [meta, bam] } + ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions.first()) } else if (params.mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 3a8dda99f..8033fd27d 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -74,9 +74,9 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { [groupKey(new_meta, new_meta.num_lanes), bam] } .groupTuple() - .branch{ - single: it[1].size() == 1 - multiple: it[1].size() > 1 + .branch{ meta, bam -> + single: bam.size() == 1 + multiple: bam.size() > 1 } .set{ bams } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index b83a8319e..e14edc40f 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -29,9 +29,9 @@ workflow ALIGN_SENTIEON { [groupKey(new_meta, new_meta.num_lanes), bam, bai] } .groupTuple() - .branch{ - single: it[1].size() == 1 - multiple: it[1].size() > 1 + .branch{ _meta, bam, _bai -> + single: bam.size() == 1 + multiple: bam.size() > 1 } .set{ merge_bams_in } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 1fd6adf99..3a32da956 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -22,7 +22,7 @@ workflow ANNOTATE_RHOCALLVIZ { ch_vcf_tbi .combine(ch_samples) - .map {meta, vcf, tbi, meta2 -> return [meta2,vcf,tbi]} + .map {_meta, vcf, tbi, meta2 -> return [meta2,vcf,tbi]} .set { ch_rhocall_viz } BCFTOOLS_VIEW_RHOCALL(ch_rhocall_viz, [],[],[]) diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 6b18de8d3..a4f1b92fd 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -47,7 +47,7 @@ workflow CALL_REPEAT_EXPANSIONS { // Merge indiviual repeat expansions SPLIT_MULTIALLELICS_EXP.out.vcf - .collect{it[1]} + .collect{_meta, vcf -> vcf} .toList() .collect() .set {ch_exp_vcfs} diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 46aa4f167..8ee524af6 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -23,10 +23,8 @@ workflow CALL_SNV_MT { GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai, ch_dict, [], [], [],[]) - HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf).set { ch_haplocheck } + HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf) ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions.first()) - ch_haplocheck_txt = HAPLOCHECK_MT.out.txt - ch_haplocheck_html = HAPLOCHECK_MT.out.html // Filter Mutect2 calls ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) @@ -46,7 +44,7 @@ workflow CALL_SNV_MT { tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] - txt = ch_haplocheck_txt // channel: [ val(meta), path(txt) ] - html = ch_haplocheck_html // channel: [ val(meta), path(html) ] + txt = HAPLOCHECK_MT.out.txt // channel: [ val(meta), path(txt) ] + html = HAPLOCHECK_MT.out.html // channel: [ val(meta), path(html) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 74f65968b..60990cdc4 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -27,9 +27,9 @@ workflow CALL_SNV_DEEPVARIANT { ch_versions = channel.empty() if (params.analysis_type.equals("wes")) { - TABIX_BGZIP(ch_target_bed.map{meta, gzbed, index -> return [meta, gzbed]}) + TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) ch_bam_bai - .combine (TABIX_BGZIP.out.output.map {meta, bed -> return bed}) + .combine (TABIX_BGZIP.out.output.map {_meta, bed -> return bed}) .set { ch_deepvar_in } ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) } else if (params.analysis_type.equals("wgs")) { @@ -70,7 +70,7 @@ workflow CALL_SNV_DEEPVARIANT { .set { ch_varcallerinfo } ADD_VARCALLER_TO_BED (ch_varcallerinfo).gz_tbi - .map{meta,bed,tbi -> return [bed, tbi]} + .map{_meta,bed,tbi -> return [bed, tbi]} .set{ch_varcallerbed} REMOVE_DUPLICATES_GL.out.vcf diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index f4a0d8915..cbb57f3fc 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -34,7 +34,7 @@ workflow CALL_SNV_SENTIEON { // Combine bam and intervals bam_bai_intervals = ch_bam_bai.combine(ch_call_interval) .map{ - meta, bam, bai, meta2, interval -> [meta, bam, bai, interval] + meta, bam, bai, _meta2, interval -> [meta, bam, bai, interval] } SENTIEON_DNASCOPE( @@ -60,15 +60,15 @@ workflow CALL_SNV_SENTIEON { BCF_FILTER_TWO ( ch_bcffiltertwo_in ) BCF_FILTER_TWO.out.vcf.join(BCF_FILTER_TWO.out.tbi, failOnMismatch:true, failOnDuplicate:true) - .map { meta,vcf,tbi -> return [vcf,tbi] } + .map { _meta, vcf, tbi -> return [vcf, tbi] } .set { ch_vcf_idx } ch_case_info .combine(ch_vcf_idx) .groupTuple() - .branch{ // branch the channel into multiple channels (single, multiple) depending on size of list - single: it[1].size() == 1 - multiple: it[1].size() > 1 + .branch{ meta, vcfs, idx -> // branch the channel into multiple channels (single, multiple) depending on size of list + single: vcfs.size() == 1 + multiple: vcfs.size() > 1 } .set{ ch_vcf_idx_merge_in } @@ -96,7 +96,7 @@ workflow CALL_SNV_SENTIEON { .set { ch_varcallerinfo } ADD_VARCALLER_TO_BED (ch_varcallerinfo).gz_tbi - .map{meta,bed,tbi -> return [bed, tbi]} + .map{_meta, bed, tbi -> return [bed, tbi]} .set{ch_varcallerbed} REMOVE_DUPLICATES_SEN.out.vcf diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index a4f528fed..3e8856011 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -35,8 +35,8 @@ workflow CALL_STRUCTURAL_VARIANTS { if (!params.analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) - .filtered_diploid_sv_vcf_tbi - .collect{ _meta, vcf, _tbi -> vcf } + .filtered_diploid_sv_vcf + .collect{ _meta, vcf -> vcf } .set{ manta_vcf } ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) } diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 28fea1b56..51c90ad28 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -30,7 +30,7 @@ workflow CALL_SV_CNVNATOR { CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab) INDEX_CNVNATOR (CNVNATOR_CONVERT2VCF.out.vcf) BCFTOOLS_VIEW_CNVNATOR (INDEX_CNVNATOR.out.gz_tbi, [], [], []).vcf - .collect{it[1]} + .collect{_meta, vcf -> vcf} .toList() .set { vcf_file_list } diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index 517cdd7d4..3460afd4b 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -37,7 +37,7 @@ workflow CALL_SV_GERMLINECNVCALLER { GATK4_COLLECTREADCOUNTS.out.tsv .join(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .combine(ch_gcnvcaller_model) - .map({ meta, tsv, calls, meta2, model -> return [meta, tsv, [], calls, model ]}) + .map({ meta, tsv, calls, _meta2, model -> return [meta, tsv, [], calls, model ]}) .set{ch_gcnvc_in} GATK4_GERMLINECNVCALLER ( ch_gcnvc_in ) @@ -47,12 +47,12 @@ workflow CALL_SV_GERMLINECNVCALLER { return [meta.sample, meta, model_calls] } .groupTuple(by: 0) - .map { sample, metas, model_calls -> + .map { _sample, metas, model_calls -> def meta = metas[0] // All metas should be the same for a given sample - def models = model_calls.collect { it.toString() } + def models = model_calls.collect { file -> file.toString() } return [meta, models] } - .combine(ch_gcnvcaller_model.collect{it[1]}.toList()) + .combine(ch_gcnvcaller_model.collect{meta, model -> model}.toList()) .join(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .set {ch_postproc_in} @@ -66,7 +66,7 @@ workflow CALL_SV_GERMLINECNVCALLER { BCFTOOLS_VIEW (ch_segments_in , [], [], [] ) BCFTOOLS_VIEW.out.vcf - .collect{it[1]} + .collect{meta, vcf -> vcf} .toList() .set { vcf_file_list } diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 816b4fa3a..56324f6d3 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -15,16 +15,16 @@ workflow CALL_SV_MANTA { ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] main: - ch_bam.collect{it[1]} + ch_bam.collect{_meta, bam -> bam} .toList() .set { bam_file_list } - ch_bai.collect{it[1]} + ch_bai.collect{_meta, bai -> bai} .toList() .set { bai_file_list } ch_bed.map { - id, bed_file, index -> + _id, bed_file, index -> return [bed_file, index]} .set { bed_input } @@ -57,6 +57,6 @@ workflow CALL_SV_MANTA { candidate_sv_vcf_tbi = MANTA.out.candidate_sv_vcf_tbi // channel: [ val(meta), path(tbi) ] diploid_sv_vcf = MANTA.out.diploid_sv_vcf // channel: [ val(meta), path(vcf) ] diploid_sv_vcf_tbi = MANTA.out.diploid_sv_vcf_tbi // channel: [ val(meta), path(tbi) ] - filtered_diploid_sv_vcf_tbi = BCFTOOLS_VIEW_MANTA.out.vcf // channel: [ val(meta), path(vcf), path(tbi) ] + filtered_diploid_sv_vcf = BCFTOOLS_VIEW_MANTA.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions } diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index 3d8190224..8e58b5ba8 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -19,7 +19,7 @@ workflow CALL_SV_TIDDIT { INDEX_TIDDIT (TIDDIT_SV.out.vcf) BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_tbi, [], [], []).vcf - .collect{it[1]} + .collect{ _meta, vcf -> vcf} .toList() .set { vcf_file_list } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 7cc8ee0db..cf1af6edf 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -67,13 +67,13 @@ workflow POSTPROCESS_MT_CALLS { TABIX_TABIX_MT2(REMOVE_DUPLICATES_MT.out.vcf) REMOVE_DUPLICATES_MT.out.vcf - .map{ it -> it[1]} + .map{ _meta, vcf -> vcf} .toSortedList{a, b -> a.name <=> b.name} .toList() .set { file_list_vcf } TABIX_TABIX_MT2.out.tbi - .map{ it -> it[1]} + .map{ _meta, vcf -> vcf} .toSortedList{a, b -> a.name <=> b.name} .toList() .set { file_list_tbi } @@ -109,7 +109,7 @@ workflow POSTPROCESS_MT_CALLS { .set { ch_varcallerinfo } ADD_VARCALLER_TO_BED (ch_varcallerinfo).gz_tbi - .map{meta,bed,tbi -> return [bed, tbi]} + .map{_meta,bed,tbi -> return [bed, tbi]} .set{ch_varcallerbed} ch_addfoundintag_in diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 77edcf15a..a98dfc76d 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -87,10 +87,10 @@ workflow PREPARE_REFERENCES { GATK_SHIFTFASTA.out.intervals .multiMap{ _meta, files -> shift_intervals: - def ind = files.findIndexValues {it.toString().endsWith("shifted.intervals")} + def ind = files.findIndexValues {file -> file.toString().endsWith("shifted.intervals")} files[ind] intervals: - ind = files.findIndexValues {!(it.toString().endsWith("shifted.intervals"))} + ind = files.findIndexValues {file -> !(file.toString().endsWith("shifted.intervals"))} files[ind] } .set {ch_shiftfasta_mtintervals} @@ -119,13 +119,13 @@ workflow PREPARE_REFERENCES { TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in.index).tbi .join(ch_vcfanno_tabix_in.index) - .map { meta, tbi, vcf -> return [[vcf,tbi]]} + .map { _meta, tbi, vcf -> return [[vcf,tbi]]} .set {ch_vcfanno_index} TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex) channel.empty() .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) - .map { meta, vcf, index -> return [[vcf,index]] } + .map { _meta, vcf, index -> return [[vcf,index]] } .set {ch_vcfanno_bgzip} channel.empty() @@ -145,7 +145,7 @@ workflow PREPARE_REFERENCES { GATK_BILT(ch_target_bed, ch_dict).interval_list GATK_ILT(GATK_BILT.out.interval_list) GATK_ILT.out.interval_list - .collect{ it[1] } + .collect{ meta, list -> list } .map { it -> def meta = it[0].toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" return [[id:meta], it] From e69b25b815b15135381d145bb4b459aeefeece14 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 13:57:31 +0100 Subject: [PATCH 115/872] make closure readable --- .../local/align_bwa_bwamem2_bwameme/main.nf | 12 ++++++------ subworkflows/local/call_snv_deepvariant/main.nf | 2 +- subworkflows/local/call_sv_manta/main.nf | 2 +- subworkflows/local/prepare_references/main.nf | 14 +++++++------- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 8033fd27d..a3803a7bc 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -46,11 +46,11 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { if (params.bwa_as_fallback) { ch_reads_input .join(BWAMEM2_MEM.out.bam, remainder: true) - .branch { it -> - ERROR: it[2].equals(null) - return [it[0], it[1]] // return reads - SUCCESS: !it[2].equals(null) - return [it[0], it[2]] // return bam + .branch { meta, reads, bam -> + ERROR: bam.equals(null) + return [meta, reads] // return reads + SUCCESS: !bam.equals(null) + return [meta, bam] // return bam } .set { ch_fallback } @@ -74,7 +74,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { [groupKey(new_meta, new_meta.num_lanes), bam] } .groupTuple() - .branch{ meta, bam -> + .branch{ _meta, bam -> single: bam.size() == 1 multiple: bam.size() > 1 } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 60990cdc4..0fa8beb9b 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -41,7 +41,7 @@ workflow CALL_SNV_DEEPVARIANT { DEEPVARIANT ( ch_deepvar_in, ch_genome_fasta, ch_genome_fai, [[],[]], ch_par_bed ) DEEPVARIANT.out.gvcf - .map{ it -> it[1]} + .map{ _meta, gvcf -> gvcf} .toSortedList{a, b -> a.name <=> b.name} .toList() .set { ch_file_list } diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 56324f6d3..162ebfefa 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -31,7 +31,7 @@ workflow CALL_SV_MANTA { if (params.analysis_type == "wgs" ) { ch_case_info.combine(bam_file_list) .combine(bai_file_list) - .map { it -> it + [ [], [] ] } + .map { meta, input, index -> [meta, input, index] + [ [], [] ] } .set { manta_input } MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] ) } else { diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a98dfc76d..5e6ae1d9e 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -111,9 +111,9 @@ workflow PREPARE_REFERENCES { .mix(ch_trgt_bed_tbi, ch_bgzip_tbi) ch_vcfanno_extra_unprocessed - .branch { it -> - bgzipindex: !it[1].toString().endsWith(".gz") - index: it[1].toString().endsWith(".gz") + .branch { _meta, vcf -> + bgzipindex: !vcf.toString().endsWith(".gz") + index: vcf.toString().endsWith(".gz") } .set { ch_vcfanno_tabix_in } @@ -145,7 +145,7 @@ workflow PREPARE_REFERENCES { GATK_BILT(ch_target_bed, ch_dict).interval_list GATK_ILT(GATK_BILT.out.interval_list) GATK_ILT.out.interval_list - .collect{ meta, list -> list } + .collect{ _meta, list -> list } .map { it -> def meta = it[0].toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" return [[id:meta], it] @@ -216,9 +216,9 @@ workflow PREPARE_REFERENCES { known_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() // channel: [ val(meta), path(fasta) ] target_bed = ch_target_bed_gz_tbi.collect() // channel: [ val(meta), path(bed), path(tbi) ] vcfanno_extra = ch_vcfanno_extra.ifEmpty([[]]) // channel: [ [path(vcf), path(tbi)] ] - bait_intervals = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect().ifEmpty([[]]) // channel: [ path(intervals) ] - target_intervals = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect() // channel: [ path(interval_list) ] - vep_resources = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect() // channel: [ path(cache) ] + bait_intervals = CAT_CAT_BAIT.out.file_out.map{ _meta, inter -> inter}.collect().ifEmpty([[]])// channel: [ path(intervals) ] + target_intervals = GATK_BILT.out.interval_list.map{ _meta, inter -> inter}.collect() // channel: [ path(interval_list) ] + vep_resources = UNTAR_VEP_CACHE.out.untar.map{ _meta, files -> [files]}.collect() // channel: [ path(cache) ] versions = ch_versions // channel: [ path(versions.yml) ] } From 4c82baf1f69147bcd71c2ab3d8e715893b3d8e25 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 15:22:33 +0100 Subject: [PATCH 116/872] update test for qc_bam --- subworkflows/local/qc_bam/tests/main.nf.test | 48 ++++++++------------ 1 file changed, 18 insertions(+), 30 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 94eb1a6f6..329814674 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -23,29 +23,23 @@ nextflow_workflow { ] ) input[1] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] - ] - ) - input[2] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[9] = channel.empty() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[8] = channel.empty() + input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = 'xy' + input[12] = 'xy' """ } } @@ -100,29 +94,23 @@ nextflow_workflow { ] ) input[1] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] - ] - ) - input[2] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[9] = channel.empty() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[8] = channel.empty() + input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = 'xy' + input[12] = 'xy' """ } } From dd1e4a4a0768fd36e93249ce8a71623d64ada916 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Nov 2025 14:35:27 +0000 Subject: [PATCH 117/872] [automated] Fix code linting --- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index a3803a7bc..373f584ff 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -74,7 +74,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { [groupKey(new_meta, new_meta.num_lanes), bam] } .groupTuple() - .branch{ _meta, bam -> + .branch{ _meta, bam -> single: bam.size() == 1 multiple: bam.size() > 1 } From dfe04f712a1863946ab350047409649c25bd906d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 28 Nov 2025 20:38:49 +0100 Subject: [PATCH 118/872] fix missed occurances --- subworkflows/local/annotate_genome_snvs.nf | 5 ++-- subworkflows/local/call_snv_MT/main.nf | 2 -- subworkflows/local/call_snv_sentieon/main.nf | 2 +- .../local/call_sv_germlinecnvcaller/main.nf | 4 +-- subworkflows/local/subsample_mt_reads/main.nf | 2 +- workflows/raredisease.nf | 30 +++++++++---------- 6 files changed, 22 insertions(+), 23 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index c02558d09..39cf62a7c 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -134,10 +134,11 @@ workflow ANNOTATE_GENOME_SNVS { .join(TABIX_VEP.out.tbi, failOnMismatch:true) .groupTuple() .map { meta, vcfs, tbis -> - def sortedvcfs = vcfs.sort { it.baseName } - def sortedtbis = tbis.sort { it.baseName } + def sortedvcfs = vcfs.sort { vcf -> vcf.baseName } + def sortedtbis = tbis.sort { tbi -> tbi.baseName } return [ meta, sortedvcfs, sortedtbis ] } + .dump (tag:'dumps') .set { ch_concat_in } BCFTOOLS_CONCAT (ch_concat_in) diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 8ee524af6..c69bc564f 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -16,8 +16,6 @@ workflow CALL_SNV_MT { main: ch_versions = channel.empty() - ch_haplocheck_txt = channel.empty() - ch_haplocheck_html = channel.empty() ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index cbb57f3fc..bff039012 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -66,7 +66,7 @@ workflow CALL_SNV_SENTIEON { ch_case_info .combine(ch_vcf_idx) .groupTuple() - .branch{ meta, vcfs, idx -> // branch the channel into multiple channels (single, multiple) depending on size of list + .branch{ _meta, vcfs, _idx -> // branch the channel into multiple channels (single, multiple) depending on size of list single: vcfs.size() == 1 multiple: vcfs.size() > 1 } diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index 3460afd4b..129ec0caf 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -52,7 +52,7 @@ workflow CALL_SV_GERMLINECNVCALLER { def models = model_calls.collect { file -> file.toString() } return [meta, models] } - .combine(ch_gcnvcaller_model.collect{meta, model -> model}.toList()) + .combine(ch_gcnvcaller_model.collect{_meta, model -> model}.toList()) .join(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.calls) .set {ch_postproc_in} @@ -66,7 +66,7 @@ workflow CALL_SV_GERMLINECNVCALLER { BCFTOOLS_VIEW (ch_segments_in , [], [], [] ) BCFTOOLS_VIEW.out.vcf - .collect{meta, vcf -> vcf} + .collect{_meta, vcf -> vcf} .toList() .set { vcf_file_list } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 9d6ee8c2f..347603379 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -14,7 +14,7 @@ workflow SUBSAMPLE_MT_READS { ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] main: - ch_versions = Channel.empty() + ch_versions = channel.empty() SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 43ecdb494..12e1a3298 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -301,10 +301,10 @@ workflow RAREDISEASE { // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) // - ch_input_by_sample_type = ch_reads.branch{ - fastq_gz: it[0].data_type == "fastq_gz" - interleaved_spring: it[0].data_type == "interleaved_spring" - separate_spring: it[0].data_type == "separate_spring" + ch_input_by_sample_type = ch_reads.branch{ meta, reads -> + fastq_gz: meta.data_type == "fastq_gz" + interleaved_spring: meta.data_type == "interleaved_spring" + separate_spring: meta.data_type == "separate_spring" } // Just one fastq.gz.spring-file with both R1 and R2 @@ -542,11 +542,11 @@ workflow RAREDISEASE { ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) ANN_CSQ_PLI_SNV.out.vcf_ann - .filter { it -> - if (it[0].probands.size()==0) { + .filter { meta, _vcf -> + if (meta.probands.size()==0) { log.warn("Skipping nuclear SNV ranking since no affected samples are detected in the case") } - it[0].probands.size()>0 + meta.probands.size()>0 } .set {ch_ranksnv_nuclear_in} @@ -612,11 +612,11 @@ workflow RAREDISEASE { ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions) ANN_CSQ_PLI_MT.out.vcf_ann - .filter { it -> - if (it[0].probands.size()==0) { + .filter { meta, _vcf -> + if (meta.probands.size()==0) { log.warn("Skipping mitochondrial SNV ranking since no affected samples are detected in the case") } - it[0].probands.size()>0 + meta.probands.size()>0 } .set {ch_ranksnv_mt_in} @@ -702,11 +702,11 @@ workflow RAREDISEASE { ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions) ANN_CSQ_PLI_SV.out.vcf_ann - .filter { it -> - if (it[0].probands.size()==0) { + .filter { meta, _vcf -> + if (meta.probands.size()==0) { log.warn("Skipping SV ranking since no affected samples are detected in the case") } - it[0].probands.size()>0 + meta.probands.size()>0 } .set {ch_ranksnv_sv_in} @@ -790,12 +790,12 @@ workflow RAREDISEASE { if ( params.analysis_type.equals("wgs") && !(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) ) { RENAME_BAM.out.output - .collect{it[1]} + .collect{meta, bam -> bam} .toList() .set { ch_bam_list } RENAME_BAI.out.output - .collect{it[1]} + .collect{meta, bai -> bai} .toList() .set { ch_bai_list } From 1f9360dbc898b52a75a3a7b2fd6c9ad0fe1166b1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 13:25:16 +0100 Subject: [PATCH 119/872] clarify closures --- subworkflows/local/align/main.nf | 4 +- subworkflows/local/annotate_genome_snvs.nf | 42 +++++++++++++------ subworkflows/local/annotate_mt_snvs.nf | 19 ++++----- .../local/annotate_structural_variants.nf | 22 +++++----- subworkflows/local/generate_cytosure_files.nf | 20 ++++----- subworkflows/local/prepare_references/main.nf | 4 +- subworkflows/local/qc_bam/main.nf | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 32 +++++++------- workflows/raredisease.nf | 26 ++++++------ 9 files changed, 94 insertions(+), 77 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f111e011b..290a3b936 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -61,7 +61,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { it -> [it[0], it[1]] } + .map { meta, bam -> [meta, bam] } .set{ch_input_bam} ch_alignments.map { meta, files -> @@ -69,7 +69,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { it -> [it[0], it[2]] } + .map { meta, bai -> [meta, bai] } .set{ch_input_bai} if (params.aligner.matches("bwamem2|bwa|bwameme")) { diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 39cf62a7c..10fcb3203 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -57,11 +57,31 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcf .join(ZIP_TABIX_ROHCALL.out.gz_tbi, remainder: true) .combine(ch_split_intervals) - .map { it -> - if (it[3].equals(null)) { - return [it[0] + [prefix: it[0].id, scatterid:it[4].baseName], it[1], it[2], it[4]] + .map { it -> + def meta = it[0] + def vcf = it[1] + def tbi = it[2] + + def hasRohCall = (it.size() == 6) + + if (hasRohCall) { + def rohcall = it[3] + def rohcallindex = it[4] + def interval = it[5] + return [ + meta + [prefix: meta.id + "_rhocall", scatterid: interval.baseName], + rohcall, + rohcallindex, + interval + ] } else { - return [it[0] + [prefix: it[0].id + "_rhocall", scatterid:it[5].baseName], it[3], it[4], it[5]] + def interval = it[4] + return [ + meta + [prefix: meta.id, scatterid: interval.baseName], + vcf, + tbi, + interval + ] } } .set { ch_vcf_scatter_in } @@ -98,14 +118,13 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(TABIX_BCFTOOLS_VIEW.out.versions) } - // If CADD is run, pick CADD output as input for VEP else pass selectvariants output to VEP. BCFTOOLS_VIEW.out.vcf - .join(ch_cadd_vcf, remainder: true) // If CADD is not run then the third element in this channel will be `null` - .branch { it -> // If CADD is run, then "it" will be [[meta],selvar.vcf,cadd.vcf], else [[meta],selvar.vcf,null] - selvar: it[2].equals(null) - return [it[0] + [prefix: it[0].prefix + "_filter"], it[1]] - cadd: !(it[2].equals(null)) - return [it[0] + [prefix: it[0].prefix + "_filter_cadd"], it[2]] + .join(ch_cadd_vcf, remainder: true) + .branch { meta, selectvariants, cadd -> + selvar: cadd.equals(null) + return [meta + [prefix: meta.prefix + "_filter"], selectvariants] + cadd: !(cadd.equals(null)) + return [meta + [prefix: meta.prefix + "_filter_cadd"], cadd] } .set { ch_for_mix } @@ -138,7 +157,6 @@ workflow ANNOTATE_GENOME_SNVS { def sortedtbis = tbis.sort { tbi -> tbi.baseName } return [ meta, sortedvcfs, sortedtbis ] } - .dump (tag:'dumps') .set { ch_concat_in } BCFTOOLS_CONCAT (ch_concat_in) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 7b3f1825f..15d7c7b3d 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -34,8 +34,8 @@ workflow ANNOTATE_MT_SNVS { // add prefix to meta ch_mt_vcf - .map { it -> - return [it[0]+ [prefix: it[1].simpleName + "_hmtnote"], it[1]] + .map { meta, vcf -> + return [meta+ [prefix: vcf.simpleName + "_hmtnote"], vcf] } .set { ch_hmtnote_in } @@ -69,18 +69,17 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_vcf = channel.empty() } - // Pick input for vep ch_vcfanno_vcf - .join(ch_cadd_vcf, remainder: true) // If CADD is not run then the third element in this channel will be `null` - .branch { it -> // If CADD is run, then "it" will be [[meta],selvar.vcf,cadd.vcf], else [[meta],selvar.vcf,null] - merged: it[2].equals(null) - return [it[0]+ [prefix: it[0].prefix + "_vep"], it[1]] - cadd: !(it[2].equals(null)) - return [it[0] + [prefix: it[0].prefix + "_cadd_vep"], it[2]] + .join(ch_cadd_vcf, remainder: true) + .branch { meta, vcfanno, cadd -> + vcfanno: cadd.equals(null) + return [meta+ [prefix: meta.prefix + "_vep"], vcfanno] + cadd: !(cadd.equals(null)) + return [meta + [prefix: meta.prefix + "_cadd_vep"], cadd] } .set { ch_for_mix } - ch_for_mix.merged.mix(ch_for_mix.cadd) + ch_for_mix.vcfanno.mix(ch_for_mix.cadd) .tap { ch_haplogrep_in } .map { meta, vcf -> return [meta, vcf, []] } .set { ch_vep_in } diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index a0ee08235..2de52d0d1 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -61,11 +61,11 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_vcf .join(SVDB_QUERY_DB.out.vcf, remainder: true) - .branch { it -> - original_call: it[2].equals(null) - return [it[0], it[1]] - annotated_with_db: !(it[2].equals(null)) - return [it[0], it[2]] + .branch { meta, vcfcalls, annotatedvcf -> + original_call: annotatedvcf.equals(null) + return [meta, vcfcalls] + annotated_with_db: !(annotatedvcf.equals(null)) + return [meta, annotatedvcf] } .set { ch_for_mix_querydb } @@ -83,15 +83,15 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_querydb_out .join(SVDB_QUERY_BEDPE.out.vcf, remainder: true) - .branch { it -> - querydb_out: it[2].equals(null) - return [it[0], it[1]] - annotated_with_bedped: !(it[2].equals(null)) - return [it[0], it[2]] + .branch { meta, annotated_db, annotated_bedped -> + querydb_out: annotated_bedped.equals(null) + return [meta, annotated_db] + querybedped_out: !(annotated_bedped.equals(null)) + return [meta, annotated_bedped] } .set { ch_for_mix_querybedpedb } - ch_querypedbed_out = ch_for_mix_querybedpedb.querydb_out.mix(ch_for_mix_querybedpedb.annotated_with_bedped) + ch_querypedbed_out = ch_for_mix_querybedpedb.querydb_out.mix(ch_for_mix_querybedpedb.querybedped_out) PICARD_SORTVCF(ch_querypedbed_out, ch_genome_fasta, ch_genome_dictionary) diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index db9c7be2d..69ff98f86 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -33,11 +33,11 @@ workflow GENERATE_CYTOSURE_FILES { return [ id_meta, sex_meta, vcf, tbi ] } .join(ch_sample_id_map, remainder: true) - .branch { it -> - id: it[4].equals(null) - return [it[0] + [custid:it[0].id] + it[1], it[2], it[3]] - custid: !(it[4].equals(null)) - return [it[0] + [custid:it[4]] + it[1], it[2], it[3]] + .branch { id_meta, sex_meta, vcf, tbi, samplemap -> + id: samplemap.equals(null) + return [id_meta + [custid:id_meta.id] + sex_meta, vcf, tbi] + custid: !(samplemap.equals(null)) + return [id_meta + [custid:samplemap] + sex_meta, vcf, tbi] } .set { ch_for_mix } @@ -62,11 +62,11 @@ workflow GENERATE_CYTOSURE_FILES { SPLIT_AND_FILTER_SV_VCF.out.vcf .join(ch_reheader_out, remainder: true) - .branch { it -> - split: it[2].equals(null) - return [it[0], it[1]] - reheader: !(it[2].equals(null)) - return [it[0], it[2]] + .branch { meta, filteredvcf, reheaderedvcf -> + split: reheaderedvcf.equals(null) + return [meta, filteredvcf] + reheader: !(reheaderedvcf.equals(null)) + return [meta, reheaderedvcf] } .set { ch_for_mix } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 5e6ae1d9e..3d00e79de 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -146,8 +146,8 @@ workflow PREPARE_REFERENCES { GATK_ILT(GATK_BILT.out.interval_list) GATK_ILT.out.interval_list .collect{ _meta, list -> list } - .map { it -> - def meta = it[0].toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" + .map { list -> + def meta = list.toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" return [[id:meta], it] } .set { ch_bait_intervals_cat_in } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 831fdd854..b58ab1ef2 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -81,7 +81,7 @@ workflow QC_BAM { } // Check contamination ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() - VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {it-> it[1]}) + VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {meta, fasta-> fasta}) ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 329814674..1094e1e32 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -49,24 +49,24 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.multiple_metrics - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.hs_metrics - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.d4 - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.cov - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.tiddit_wig, workflow.out.bigwig, @@ -121,24 +121,24 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.multiple_metrics - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.hs_metrics - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.d4 - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.cov - .collect {it[1]} + .collect {_meta, metrics -> metrics} .flatten() - .collect { file(it).name } + .collect { file(metrics).name } .toSorted(), workflow.out.tiddit_wig, workflow.out.bigwig, diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 12e1a3298..0b7ccb63e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -941,21 +941,21 @@ workflow RAREDISEASE { ) ) - ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{it[1]}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{_meta, metrics -> metrics}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, metrics -> metrics}.collect().ifEmpty([])) if (!(params.skip_tools && params.skip_tools.split(',').contains('peddy'))) { - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{it[1]}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, metrics -> metrics}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{_meta, metrics -> metrics}.collect().ifEmpty([])) } MULTIQC ( From e43ae7f05540c34498f3ec181c9221db52468c2d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 1 Dec 2025 12:30:44 +0000 Subject: [PATCH 120/872] [automated] Fix code linting --- subworkflows/local/annotate_mt_snvs.nf | 4 ++-- workflows/raredisease.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 15d7c7b3d..e8b3cf559 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -70,8 +70,8 @@ workflow ANNOTATE_MT_SNVS { } ch_vcfanno_vcf - .join(ch_cadd_vcf, remainder: true) - .branch { meta, vcfanno, cadd -> + .join(ch_cadd_vcf, remainder: true) + .branch { meta, vcfanno, cadd -> vcfanno: cadd.equals(null) return [meta+ [prefix: meta.prefix + "_vep"], vcfanno] cadd: !(cadd.equals(null)) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0b7ccb63e..b82c5978b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -301,7 +301,7 @@ workflow RAREDISEASE { // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) // - ch_input_by_sample_type = ch_reads.branch{ meta, reads -> + ch_input_by_sample_type = ch_reads.branch{ meta, reads -> fastq_gz: meta.data_type == "fastq_gz" interleaved_spring: meta.data_type == "interleaved_spring" separate_spring: meta.data_type == "separate_spring" From 0591fa57ce3097918c9e665baebd5ab4f472cd99 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 13:31:52 +0100 Subject: [PATCH 121/872] fixx parser issue in modules --- modules/local/calculate_seed_fraction/main.nf | 2 -- modules/local/retroseq/call/main.nf | 1 - modules/local/retroseq/discover/main.nf | 1 - 3 files changed, 4 deletions(-) diff --git a/modules/local/calculate_seed_fraction/main.nf b/modules/local/calculate_seed_fraction/main.nf index 1c367b38d..6d3dd2596 100644 --- a/modules/local/calculate_seed_fraction/main.nf +++ b/modules/local/calculate_seed_fraction/main.nf @@ -20,8 +20,6 @@ process CALCULATE_SEED_FRACTION { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" """ export MT_COVERAGE=`awk '{cov += \$3}END{ if (NR > 0) print cov / NR }' $cov` diff --git a/modules/local/retroseq/call/main.nf b/modules/local/retroseq/call/main.nf index 5b13c6304..dd3cc8ca7 100644 --- a/modules/local/retroseq/call/main.nf +++ b/modules/local/retroseq/call/main.nf @@ -40,7 +40,6 @@ process RETROSEQ_CALL { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "1.5" """ diff --git a/modules/local/retroseq/discover/main.nf b/modules/local/retroseq/discover/main.nf index 2ea513442..96f84ba3b 100644 --- a/modules/local/retroseq/discover/main.nf +++ b/modules/local/retroseq/discover/main.nf @@ -40,7 +40,6 @@ process RETROSEQ_DISCOVER { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = "1.5" """ From 6dcaab89c11972bdc702c2e844b948468c5f81f8 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 13:42:17 +0100 Subject: [PATCH 122/872] update qc_bam --- subworkflows/local/qc_bam/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index b58ab1ef2..abc2a809e 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -81,7 +81,7 @@ workflow QC_BAM { } // Check contamination ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() - VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {meta, fasta-> fasta}) + VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions.first()) ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) From bc0f4014fa7e075ccda3ace83ce96736d715098d Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 13:43:12 +0100 Subject: [PATCH 123/872] fix raredisease.nf --- workflows/raredisease.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b82c5978b..9c7e293d3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -790,12 +790,12 @@ workflow RAREDISEASE { if ( params.analysis_type.equals("wgs") && !(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) ) { RENAME_BAM.out.output - .collect{meta, bam -> bam} + .collect{_meta, bam -> bam} .toList() .set { ch_bam_list } RENAME_BAI.out.output - .collect{meta, bai -> bai} + .collect{_meta, bai -> bai} .toList() .set { ch_bai_list } From bd101a97c366a5e2fe3769cd043a281e008a7ba8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 13:46:44 +0100 Subject: [PATCH 124/872] fix test --- subworkflows/local/qc_bam/tests/main.nf.test | 32 ++++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 1094e1e32..329814674 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -49,24 +49,24 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.multiple_metrics - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.hs_metrics - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.d4 - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.cov - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.tiddit_wig, workflow.out.bigwig, @@ -121,24 +121,24 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.multiple_metrics - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.hs_metrics - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.d4 - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.cov - .collect {_meta, metrics -> metrics} + .collect {it[1]} .flatten() - .collect { file(metrics).name } + .collect { file(it).name } .toSorted(), workflow.out.tiddit_wig, workflow.out.bigwig, From 26cbf882304d081cf3927b993481c3de69e1c9b9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Dec 2025 14:04:14 +0100 Subject: [PATCH 125/872] fix error --- subworkflows/local/prepare_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 3d00e79de..8dd3c5c0f 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -148,7 +148,7 @@ workflow PREPARE_REFERENCES { .collect{ _meta, list -> list } .map { list -> def meta = list.toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" - return [[id:meta], it] + return [[id:meta], list] } .set { ch_bait_intervals_cat_in } CAT_CAT_BAIT ( ch_bait_intervals_cat_in ) From 250e306874970537a52a000f20cad3f59fe4e031 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 1 Dec 2025 15:38:40 +0100 Subject: [PATCH 126/872] fixed mitosalt inputs --- conf/test.config | 1 - modules/local/mitosalt/main.nf | 4 ++-- subworkflows/local/call_sv_MT/main.nf | 9 +++++---- workflows/raredisease.nf | 12 ++++++------ 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/conf/test.config b/conf/test.config index 2bef0f6fa..0c165711e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -66,6 +66,5 @@ params { vep_cache_version = 107 vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' mitosalt_config = 'data/config_human.txt' - mitosalt_reference = 'data/genome' mitosalt_depth = '100000' } diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 544e9f2fd..1bec38aba 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -18,13 +18,13 @@ process MITOSALT { input: tuple val(meta), path(reads) path config - path genome tuple val(meta2), path(hisat2index) tuple val(meta3), path(genomefai) tuple val(meta4), path(lastindex) tuple val(meta5), path(mtfai) path chrsizes tuple val(meta6), path(mtfasta) + val mito_name output: tuple val(meta), path("*breakpoint") , emit: breakpoint @@ -35,7 +35,7 @@ process MITOSALT { def VERSION = "1.1.1" // from perl script, unlikely to be updated def prefix = task.ext.prefix ?: "${meta.id}" """ - cat $config | sed "s,hsindex = .*,hsindex = ${hisat2index}/reference," | sed "s,^faindex = .*,faindex = $genomefai," | sed "s,lastindex = .*,lastindex = ${lastindex}/reference," | sed "s,mtfaindex = .*,mtfaindex = $mtfai," | sed "s,gsize = .*,gsize = $chrsizes," | sed "s,MT_fasta = .*,MT_fasta = $mtfasta," > new-${config} + cat $config | sed "s,hsindex = .*,hsindex = ${hisat2index}/reference," | sed "s,^faindex = .*,faindex = $genomefai," | sed "s,lastindex = .*,lastindex = ${lastindex}/reference," | sed "s,mtfaindex = .*,mtfaindex = $mtfai," | sed "s,gsize = .*,gsize = $chrsizes," | sed "s,MT_fasta = .*,MT_fasta = $mtfasta," | sed "s,refchr = .*,refchr = ${mito_name}," > new-${config} mkdir -p log indel bam tab bw plot MitoSAlt1.1.1.pl new-${config} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 27b467893..998377256 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -18,18 +18,19 @@ workflow CALL_SV_MT { ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_msconfig // channel: [mandatory] [ path(msconfig) ] - ch_msref // channel: [mandatory] [ path(genome) ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + ch_mito_name // channel: [mandatory] [ val(mito_name) main: - ch_versions = Channel.empty() + ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { - ch_reads_subdepth = ch_reads.map { meta, reads -> [meta, reads, '1000000'] } + ch_reads_subdepth = ch_reads.concat(ch_subdepth).collect() + ch_reads_subdepth.view() SEQTK_SAMPLE (ch_reads_subdepth) ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_msref, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta) + MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta, ch_mito_name) ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 209b69c74..a62b357b5 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -175,12 +175,12 @@ workflow RAREDISEASE { : Channel.empty() ch_me_svdb_resources = params.mobile_element_svdb_annotations ? Channel.fromPath(params.mobile_element_svdb_annotations) : Channel.empty() + ch_mito_name = params.mito_name ? Channel.value(params.mito_name) + : Channel.value([]) ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) ch_msconfig = params.mitosalt_config ? channel.fromPath(params.mitosalt_config) : channel.empty() - ch_msref = params.mitosalt_reference ? channel.fromPath(params.mitosalt_reference) - : channel.empty() ch_mt_intervals = ch_references.mt_intervals ch_mt_bwaindex = ch_references.mt_bwa_index ch_mt_bwamem2index = ch_references.mt_bwamem2_index @@ -215,8 +215,8 @@ workflow RAREDISEASE { : Channel.value([]) ch_sdf = params.sdf ? Channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf - ch_subdepth = params.mitosalt_depth ? channel.fromPath(params.mitosalt_depth) - : channel.empty() + ch_subdepth = params.mitosalt_depth ? channel.value(params.mitosalt_depth) + : channel.value([]) ch_sv_dbs = params.svdb_query_dbs ? Channel.fromPath(params.svdb_query_dbs) : Channel.empty() ch_sv_bedpedbs = params.svdb_query_bedpedbs ? Channel.fromPath(params.svdb_query_bedpedbs) @@ -744,8 +744,8 @@ workflow RAREDISEASE { ch_genome_chrsizes, ch_mt_fasta, ch_msconfig, - ch_msref, - ch_subdepth + ch_subdepth, + ch_mito_name ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) From 8893751a30775c39e2706158c65ed4cea8307309 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 2 Dec 2025 13:19:11 +0100 Subject: [PATCH 127/872] fix error --- subworkflows/local/align/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 290a3b936..d11967e5c 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -61,7 +61,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { meta, bam -> [meta, bam] } + .map { meta, bam, bai -> [meta, bam] } .set{ch_input_bam} ch_alignments.map { meta, files -> @@ -69,7 +69,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { meta, bai -> [meta, bai] } + .map { meta, bam, bai -> [meta, bai] } .set{ch_input_bai} if (params.aligner.matches("bwamem2|bwa|bwameme")) { From 189828d697cddcc75ee5a61c9e709837de44660a Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 2 Dec 2025 15:11:23 +0100 Subject: [PATCH 128/872] refactor params --- main.nf | 55 ++++++++- subworkflows/local/align/main.nf | 14 ++- subworkflows/local/annotate_mt_snvs.nf | 3 +- subworkflows/local/call_snv.nf | 19 +-- .../local/call_snv_deepvariant/main.nf | 5 +- .../local/call_structural_variants.nf | 28 +++-- subworkflows/local/call_sv_MT/main.nf | 7 +- subworkflows/local/call_sv_manta/main.nf | 15 +-- subworkflows/local/qc_bam/main.nf | 9 +- workflows/raredisease.nf | 109 ++++++++++++------ 10 files changed, 188 insertions(+), 76 deletions(-) diff --git a/main.nf b/main.nf index 0d4c01e53..4f3da900a 100644 --- a/main.nf +++ b/main.nf @@ -43,11 +43,63 @@ workflow NFCORE_RAREDISEASE { // // WORKFLOW: Run pipeline // + + if (params.skip_tools) { + skip_eklipse = params.skip_tools.split(',').contains('eklipse') + skip_fastp = params.skip_tools.split(',').contains('fastp') + skip_fastqc = params.skip_tools.split(',').contains('fastqc') + skip_gens = params.skip_tools.split(',').contains('gens') + skip_germlinecnvcaller = params.skip_tools.split(',').contains('germlinecnvcaller') + skip_haplogrep3 = params.skip_tools.split(',').contains('haplogrep3') + skip_ngsbits = params.skip_tools.split(',').contains('ngsbits') + skip_peddy = params.skip_tools.split(',').contains('peddy') + skip_qualimap = params.skip_tools.split(',').contains('qualimap') + skip_smncopynumbercaller = params.skip_tools.split(',').contains('smncopynumbercaller') + skip_vcf2cytosure = params.skip_tools.split(',').contains('vcf2cytosure') + } + + if (params.skip_subworkflows) { + skip_me_annotation = params.skip_tools.split(',').contains('me_annotation') + skip_me_calling = params.skip_tools.split(',').contains('me_calling') + skip_mt_annotation = params.skip_tools.split(',').contains('mt_annotation') + skip_mt_subsample = params.skip_tools.split(',').contains('mt_subsample') + skip_repeat_annotation = params.skip_tools.split(',').contains('repeat_annotation') + skip_repeat_calling = params.skip_tools.split(',').contains('repeat_calling') + skip_snv_annotation = params.skip_tools.split(',').contains('snv_annotation') + skip_snv_calling = params.skip_tools.split(',').contains('snv_calling') + skip_sv_annotation = params.skip_tools.split(',').contains('sv_annotation') + skip_sv_calling = params.skip_tools.split(',').contains('sv_calling') + skip_generate_clinical_set = params.skip_tools.split(',').contains('generate_clinical_set') + } + RAREDISEASE ( fastq, alignment, samples, - case_info + case_info, + params.analysis_type, + skip_me_calling, + skip_me_annotation, + skip_mt_annotation, + skip_mt_subsample, + skip_repeat_annotation, + skip_repeat_calling, + skip_snv_annotation, + skip_snv_calling, + skip_sv_annotation, + skip_sv_calling, + skip_generate_clinical_set, + skip_eklipse, + skip_fastp, + skip_fastqc, + skip_gens, + skip_germlinecnvcaller, + skip_haplogrep3, + skip_ngsbits, + skip_peddy, + skip_qualimap, + skip_smncopynumbercaller, + skip_vcf2cytosure ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html @@ -75,7 +127,6 @@ workflow { params.help_full, params.show_hidden ) - // // WORKFLOW: Run main workflow // diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f111e011b..558c3e3de 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -33,6 +33,10 @@ workflow ALIGN { val_mbuffer_mem // integer: [mandatory] memory in megabytes val_platform // string: [mandatory] illumina or a different technology val_sort_threads // integer: [mandatory] number of sorting threads + val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_analysis_type // string: 'wgs', 'wes', or 'mito' + save_mapped_as_cram // boolean + skip_fastp // boolean main: ch_bwamem2_bam = channel.empty() @@ -46,7 +50,7 @@ workflow ALIGN { ch_sentieon_bai = channel.empty() ch_versions = channel.empty() - if (!(params.skip_tools && params.skip_tools.split(',').contains('fastp'))) { + if (!skip_fastp) { FASTP (ch_reads, [], false, false, false) ch_reads = FASTP.out.reads ch_versions = ch_versions.mix(FASTP.out.versions) @@ -72,7 +76,7 @@ workflow ALIGN { .map { it -> [it[0], it[2]] } .set{ch_input_bai} - if (params.aligner.matches("bwamem2|bwa|bwameme")) { + if (val_aligner.matches("bwamem2|bwa|bwameme")) { ALIGN_BWA_BWAMEM2_BWAMEME ( // Triggered when params.aligner is set as bwamem2 or bwa or bwameme ch_reads, ch_genome_bwaindex, @@ -88,7 +92,7 @@ workflow ALIGN { ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics ch_versions = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions) - } else if (params.aligner.equals("sentieon")) { + } else if (val_aligner.equals("sentieon")) { ALIGN_SENTIEON ( // Triggered when params.aligner is set as sentieon ch_reads, ch_genome_fasta, @@ -107,7 +111,7 @@ workflow ALIGN { // PREPARING READS FOR MT ALIGNMENT - if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { CONVERT_MT_BAM_TO_FASTQ ( ch_genome_marked_bam_bai, ch_genome_fasta, @@ -144,7 +148,7 @@ workflow ALIGN { .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) } - if (params.save_mapped_as_cram) { + if (save_mapped_as_cram) { SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 7b3f1825f..6d78e207a 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -27,6 +27,7 @@ workflow ANNOTATE_MT_SNVS { ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] ch_fai // channel: [mandatory] [ path(fai) ] + skip_haplogrep3 // boolean main: ch_versions = channel.empty() @@ -99,7 +100,7 @@ workflow ANNOTATE_MT_SNVS { TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf) // Running haplogrep3 - if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) { + if (!skip_haplogrep3) { HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in) ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions) diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 1beb8675b..ae02181ba 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -36,6 +36,10 @@ workflow CALL_SNV { ch_case_info // channel: [mandatory] [ val(case_info) ] ch_foundin_header // channel: [mandatory] [ path(header) ] ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_variant_caller // string: 'deepvariant' or 'sentieon' + run_mt_for_wes // boolean + concatenate_snv_calls // boolean main: ch_versions = channel.empty() @@ -52,8 +56,8 @@ workflow CALL_SNV { ch_sentieon_gvcf = channel.empty() ch_sentieon_gtbi = channel.empty() - if (params.variant_caller.equals("deepvariant") && !params.analysis_type.equals("mito")) { - CALL_SNV_DEEPVARIANT ( // triggered only when params.variant_caller is set as deepvariant + if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { + CALL_SNV_DEEPVARIANT ( ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, @@ -61,15 +65,16 @@ workflow CALL_SNV { ch_par_bed, ch_case_info, ch_foundin_header, - ch_genome_chrsizes + ch_genome_chrsizes, + val_analysis_type ) ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) - } else if (params.variant_caller.equals("sentieon")) { - CALL_SNV_SENTIEON( // triggered only when params.variant_caller is set as sentieon + } else if (val_variant_caller.equals("sentieon")) { + CALL_SNV_SENTIEON( ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, @@ -104,7 +109,7 @@ workflow CALL_SNV { ch_genome_tabix = GATK4_SELECTVARIANTS.out.tbi ch_genome_vcf_tabix = ch_genome_vcf.join(ch_genome_tabix, failOnMismatch:true, failOnDuplicate:true) - if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { CALL_SNV_MT( ch_mt_bam_bai, ch_mt_fasta, @@ -142,7 +147,7 @@ workflow CALL_SNV { ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) } - if (params.concatenate_snv_calls) { + if (concatenate_snv_calls) { ch_concat_vcf_in = ch_genome_vcf_tabix.concat(ch_mt_vcf_tabix).groupTuple() BCFTOOLS_CONCAT ( ch_concat_vcf_in diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 0fa8beb9b..b4eee1e77 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -22,17 +22,18 @@ workflow CALL_SNV_DEEPVARIANT { ch_case_info // channel: [mandatory] [ val(case_info) ] ch_foundin_header // channel: [mandatory] [ path(header) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + val_analysis_type // boolean main: ch_versions = channel.empty() - if (params.analysis_type.equals("wes")) { + if (val_analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) ch_bam_bai .combine (TABIX_BGZIP.out.output.map {_meta, bed -> return bed}) .set { ch_deepvar_in } ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) - } else if (params.analysis_type.equals("wgs")) { + } else if (val_analysis_type.equals("wgs")) { ch_bam_bai .map { meta, bam, bai -> return [meta, bam, bai, []] } diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 3e8856011..ba3fa992f 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -27,21 +27,25 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] + val_analysis_type // string: "wes", "wgs", or "mito" + run_mt_for_wes // boolean + skip_germlinecnvcaller // boolean + skip_eklipse // boolean main: ch_versions = channel.empty() ch_merged_svs = channel.empty() ch_merged_tbi = channel.empty() - if (!params.analysis_type.equals("mito")) { - CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed) + if (!val_analysis_type.equals("mito")) { + CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } .set{ manta_vcf } ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) } - if (params.analysis_type.equals("wgs")) { + if (val_analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } @@ -55,7 +59,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(CALL_SV_CNVNATOR.out.versions) } - if (!(params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller'))) { + if (skip_germlinecnvcaller) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf .collect{ _meta, vcf -> vcf } @@ -64,39 +68,39 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions) } - if (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { - CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta) + if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { + CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta, skip_eklipse) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } //merge - if (params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller')) { - if (params.analysis_type.equals("wgs")) { + if (skip_germlinecnvcaller) { + if (val_analysis_type.equals("wgs")) { tiddit_vcf .combine(manta_vcf) .combine(cnvnator_vcf) .toList() .set { vcf_list } - } else if (!params.analysis_type.equals("mito")) { + } else if (!val_analysis_type.equals("mito")) { manta_vcf .toList() .set { vcf_list } } - } else if (params.analysis_type.equals("wgs")) { + } else if (val_analysis_type.equals("wgs")) { tiddit_vcf .combine(manta_vcf) .combine(gcnvcaller_vcf) .combine(cnvnator_vcf) .toList() .set { vcf_list } - } else if (!params.analysis_type.equals("mito")) { + } else if (!val_analysis_type.equals("mito")) { manta_vcf .combine(gcnvcaller_vcf) .toList() .set { vcf_list } } - if (!params.analysis_type.equals("mito")) { + if (!val_analysis_type.equals("mito")) { ch_case_info .combine(vcf_list) .set { merge_input_vcfs } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 3acae4f3b..3fa283cea 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -7,8 +7,9 @@ include { EKLIPSE } from '../../../modules/nf-core/eklipse/main' workflow CALL_SV_MT { take: - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + skip_eklipse // boolean main: ch_versions = channel.empty() @@ -16,7 +17,7 @@ workflow CALL_SV_MT { ch_eklipse_genes = channel.empty() ch_eklipse_circos = channel.empty() - if (!(params.skip_tools && params.skip_tools.split(',').contains('eklipse'))) { + if (!skip_eklipse) { EKLIPSE(ch_bam_bai,[]) ch_eklipse_del = EKLIPSE.out.deletions ch_eklipse_genes = EKLIPSE.out.genes diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 162ebfefa..02499e999 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -7,12 +7,13 @@ include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_MANTA } from '../../../modules/nf-core/ workflow CALL_SV_MANTA { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_bai // channel: [mandatory] [ val(meta), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] + ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_bai // channel: [mandatory] [ val(meta), path(bai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] + val_analysis_type // string: "wes", "wgs", or "mito" main: ch_bam.collect{_meta, bam -> bam} @@ -28,7 +29,7 @@ workflow CALL_SV_MANTA { return [bed_file, index]} .set { bed_input } - if (params.analysis_type == "wgs" ) { + if (val_analysis_type.equals("wgs")) { ch_case_info.combine(bam_file_list) .combine(bai_file_list) .map { meta, input, index -> [meta, input, index] + [ [], [] ] } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 831fdd854..bd230d196 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -32,6 +32,9 @@ workflow QC_BAM { ch_svd_mu // channel: [optional] [ path(meanpath) ] ch_svd_ud // channel: [optional] [ path(ud) ] ngsbits_samplegender_method // channel: [val(method)] + val_analysis_type // string: "wes", "wgs", or "mito" + skip_ngsbits // boolean + skip_qualimap // boolean main: ch_cov = channel.empty() @@ -48,7 +51,7 @@ workflow QC_BAM { .set { ch_hsmetrics_in} PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]) - if (!(params.skip_tools && params.skip_tools.split(',').contains('qualimap'))) { + if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) } @@ -63,7 +66,7 @@ workflow QC_BAM { MOSDEPTH (ch_mosdepth_in, ch_genome_fasta) // COLLECT WGS METRICS - if (!params.analysis_type.equals("wes")) { + if (!val_analysis_type.equals("wes")) { PICARD_COLLECTWGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs ) PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y ) SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} ) @@ -74,7 +77,7 @@ workflow QC_BAM { ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_Y.out.versions.first(), SENTIEON_WGSMETRICS_Y.out.versions.first()) } // Check sex - if (!(params.skip_tools && params.skip_tools.split(',').contains('ngsbits'))) { + if (!skip_ngsbits) { NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ngsbits_samplegender_method) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions.first()) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 43ecdb494..7dce8c96a 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -83,12 +83,35 @@ workflow RAREDISEASE { ch_alignments ch_samples ch_case_info + analysis_type + skip_me_calling + skip_me_annotation + skip_mt_annotation + skip_mt_subsample + skip_repeat_annotation + skip_repeat_calling + skip_snv_annotation + skip_snv_calling + skip_sv_annotation + skip_sv_calling + skip_generate_clinical_set + skip_eklipse + skip_fastp + skip_fastqc + skip_gens + skip_germlinecnvcaller + skip_haplogrep3 + skip_ngsbits + skip_peddy + skip_qualimap + skip_smncopynumbercaller + skip_vcf2cytosure main: - ch_versions = channel.empty() + ch_versions = channel.empty() ch_multiqc_files = channel.empty() - ch_mt_txt = channel.empty() + ch_mt_txt = channel.empty() // // Initialize file channels for PREPARE_REFERENCES subworkflow @@ -248,14 +271,14 @@ workflow RAREDISEASE { // // SV caller priority // - if (params.skip_tools && params.skip_tools.split(',').contains('germlinecnvcaller')) { - if (params.analysis_type.equals("wgs")) { + if (skip_germlinecnvcaller) { + if (analysis_type.equals("wgs")) { ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) } else { ch_svcaller_priority = channel.value([]) } } else { - if (params.analysis_type.equals("wgs")) { + if (analysis_type.equals("wgs")) { ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) } else { ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) @@ -265,7 +288,7 @@ workflow RAREDISEASE { // // Generate pedigree file // - ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped + ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped ch_versions = ch_versions.mix(CREATE_PEDIGREE_FILE.out.versions) // @@ -324,7 +347,7 @@ workflow RAREDISEASE { // Create chromosome bed and intervals for splitting and gathering operations // ch_scatter_split_intervals = channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_annotation'))) { + if (!skip_snv_annotation) { SCATTER_GENOME ( ch_genome_dictionary, ch_genome_fai, @@ -337,7 +360,7 @@ workflow RAREDISEASE { // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is nott fastq) // - if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) { + if (!skip_fastqc) { FASTQC (ch_input_fastqs) fastqc_report = FASTQC.out.zip ch_versions = ch_versions.mix(FASTQC.out.versions.first()) @@ -370,12 +393,16 @@ workflow RAREDISEASE { ch_mtshift_fasta, params.mbuffer_mem, params.platform, - params.samtools_sort_threads + params.samtools_sort_threads, + params.aligner, + analysis_type, + params.save_mapped_as_cram, + skip_fastp ) .set { ch_mapped } ch_versions = ch_versions.mix(ALIGN.out.versions) - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('mt_subsample')) && (params.analysis_type.equals("wgs") || params.run_mt_for_wes)) { + if (!(skip_mt_subsample) && (analysis_type.equals("wgs") || params.run_mt_for_wes)) { if (params.mt_subsample_approach.equals("fraction")) { SUBSAMPLE_MT_FRAC( ch_mapped.mt_bam_bai, @@ -407,7 +434,10 @@ workflow RAREDISEASE { ch_svd_bed, ch_svd_mu, ch_svd_ud, - channel.value(params.ngsbits_samplegender_method) + channel.value(params.ngsbits_samplegender_method), + analysis_type, + skip_ngsbits, + skip_qualimap ) ch_versions = ch_versions.mix(QC_BAM.out.versions) @@ -417,7 +447,7 @@ workflow RAREDISEASE { RENAME ALIGNMENT FILES FOR SMNCOPYNUMBERCALLER & REPEATCALLING ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if ( params.analysis_type.equals("wgs") && (!(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) || !(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('repeat_calling')))) { + if ( analysis_type.equals("wgs") && (!skip_smncopynumbercaller || !skip_repeat_calling)) { RENAME_BAM(ch_mapped.genome_marked_bam, "bam") RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai") ch_versions = ch_versions.mix(RENAME_BAM.out.versions) @@ -430,7 +460,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('repeat_calling')) && params.analysis_type.equals("wgs") ) { + if (!skip_repeat_calling && analysis_type.equals("wgs") ) { CALL_REPEAT_EXPANSIONS ( RENAME_BAM.out.output.join(RENAME_BAI.out.output, failOnMismatch:true, failOnDuplicate:true), ch_variant_catalog, @@ -440,7 +470,7 @@ workflow RAREDISEASE { ) ch_versions = ch_versions.mix(CALL_REPEAT_EXPANSIONS.out.versions) - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('repeat_annotation'))) { + if (!skip_repeat_annotation) { STRANGER ( CALL_REPEAT_EXPANSIONS.out.vcf, ch_variant_catalog @@ -456,7 +486,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_calling'))) { + if (!skip_snv_calling) { CALL_SNV ( ch_mapped.genome_marked_bam_bai, ch_mapped.mt_bam_bai_gatksubwf, @@ -481,7 +511,11 @@ workflow RAREDISEASE { ch_par_bed, ch_case_info, ch_foundin_header, - channel.value(params.sentieon_dnascope_pcr_indel_model) + channel.value(params.sentieon_dnascope_pcr_indel_model), + analysis_type, + params.variant_caller, + params.run_mt_for_wes, + params.concatenate_snv_calls ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) ch_mt_txt = CALL_SNV.out.mt_txt @@ -489,7 +523,7 @@ workflow RAREDISEASE { // // ANNOTATE GENOME SNVs // - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('snv_annotation'))) { + if (!skip_snv_annotation) { ANNOTATE_GENOME_SNVS ( CALL_SNV.out.genome_vcf_tabix, @@ -520,7 +554,7 @@ workflow RAREDISEASE { .set { ch_clin_research_snv_vcf } ch_clinical_snv_vcf = channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { + if (!skip_generate_clinical_set) { GENERATE_CLINICAL_SET_SNV( ch_clin_research_snv_vcf.clinical, ch_hgnc_ids, @@ -562,7 +596,7 @@ workflow RAREDISEASE { // // ANNOTATE MT SNVs // - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('mt_annotation')) && (params.run_mt_for_wes || params.analysis_type.matches("wgs|mito"))) { + if (!(skip_mt_annotation) && (params.run_mt_for_wes || analysis_type.matches("wgs|mito"))) { ANNOTATE_MT_SNVS ( CALL_SNV.out.mt_vcf, @@ -577,7 +611,8 @@ workflow RAREDISEASE { params.vep_cache_version, ch_vep_cache, ch_vep_extra_files, - ch_genome_fai + ch_genome_fai, + skip_haplogrep3 ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) @@ -589,7 +624,7 @@ workflow RAREDISEASE { .set { ch_clin_research_mt_vcf } ch_clinical_mtsnv_vcf = channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { + if (!skip_generate_clinical_set) { GENERATE_CLINICAL_SET_MT( ch_clin_research_mt_vcf.clinical, ch_hgnc_ids, @@ -636,7 +671,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('sv_calling'))) { + if (!skip_sv_calling) { CALL_STRUCTURAL_VARIANTS ( ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, @@ -651,14 +686,18 @@ workflow RAREDISEASE { ch_svcaller_priority, ch_readcount_intervals, ch_ploidy_model, - ch_gcnvcaller_model + ch_gcnvcaller_model, + analysis_type, + params.run_mt_for_wes, + skip_germlinecnvcaller, + skip_eklipse ) ch_versions = ch_versions.mix(CALL_STRUCTURAL_VARIANTS.out.versions) // // ANNOTATE STRUCTURAL VARIANTS // - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('sv_annotation'))) { + if (!skip_sv_annotation) { ANNOTATE_STRUCTURAL_VARIANTS ( CALL_STRUCTURAL_VARIANTS.out.vcf, ch_sv_dbs, @@ -680,7 +719,7 @@ workflow RAREDISEASE { .set { ch_clin_research_sv_vcf } ch_clinical_sv_vcf = channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { + if (!skip_generate_clinical_set) { GENERATE_CLINICAL_SET_SV( ch_clin_research_sv_vcf.clinical, ch_hgnc_ids, @@ -726,7 +765,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('me_calling')) && params.analysis_type.equals("wgs")) { + if (!skip_me_calling && analysis_type.equals("wgs")) { CALL_MOBILE_ELEMENTS( ch_mapped.genome_marked_bam_bai, ch_genome_fasta, @@ -736,7 +775,7 @@ workflow RAREDISEASE { ) ch_versions = ch_versions.mix(CALL_MOBILE_ELEMENTS.out.versions) - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('me_annotation'))) { + if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( CALL_MOBILE_ELEMENTS.out.vcf, ch_me_svdb_resources, @@ -757,7 +796,7 @@ workflow RAREDISEASE { .set { ch_clin_research_me_vcf } ch_clinical_me_vcf = channel.empty() - if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('generate_clinical_set'))) { + if (!skip_generate_clinical_set) { GENERATE_CLINICAL_SET_ME( ch_clin_research_me_vcf.clinical, ch_hgnc_ids, @@ -787,7 +826,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if ( params.analysis_type.equals("wgs") && !(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) ) { + if ( analysis_type.equals("wgs") && !skip_smncopynumbercaller ) { RENAME_BAM.out.output .collect{it[1]} @@ -815,7 +854,7 @@ workflow RAREDISEASE { PEDDY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_tools && params.skip_tools.split(',').contains('peddy'))) { + if (!skip_peddy) { PEDDY ( CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), ch_pedfile @@ -828,7 +867,7 @@ workflow RAREDISEASE { Generate CGH files from sequencing data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if ( !(params.skip_tools && params.skip_tools.split(',').contains('vcf2cytosure')) && params.analysis_type.equals("wgs") && !(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('sv_calling')) && !(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('sv_annotation'))) { + if (!skip_vcf2cytosure && analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { GENERATE_CYTOSURE_FILES ( ch_sv_annotate.vcf_ann, ch_sv_annotate.tbi, @@ -844,7 +883,7 @@ workflow RAREDISEASE { GENS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!(params.skip_tools && params.skip_tools.split(',').contains('gens')) && params.analysis_type.equals("wgs")) { + if (!skip_gens && analysis_type.equals("wgs")) { GENS ( ch_mapped.genome_marked_bam_bai, CALL_SNV.out.genome_gvcf, @@ -941,7 +980,9 @@ workflow RAREDISEASE { ) ) - ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{it[1]}.ifEmpty([])) + if (!skip_fastqc) { + ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{it[1]}.ifEmpty([])) + } ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{it[1]}.collect().ifEmpty([])) @@ -953,7 +994,7 @@ workflow RAREDISEASE { ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{it[1]}.collect().ifEmpty([])) - if (!(params.skip_tools && params.skip_tools.split(',').contains('peddy'))) { + if (!skip_peddy) { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{it[1]}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{it[1]}.collect().ifEmpty([])) } From 9bb31f79d232232b0e2819bf162c909d0ecb2504 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 3 Dec 2025 12:38:32 +0100 Subject: [PATCH 129/872] build mitosalt config from params --- modules/local/mitosalt/main.nf | 9 +-- modules/local/prep_mitosalt/main.nf | 82 +++++++++++++++++++++++++++ nextflow.config | 16 ++++++ subworkflows/local/call_sv_MT/main.nf | 80 ++++++++++++++++++++------ workflows/raredisease.nf | 33 +++++++++-- 5 files changed, 193 insertions(+), 27 deletions(-) create mode 100644 modules/local/prep_mitosalt/main.nf diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 1bec38aba..9f06ae402 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -1,5 +1,3 @@ -#!/usr/bin/env nextflow - process MITOSALT { tag "$meta.id" label "process_low" @@ -17,14 +15,13 @@ process MITOSALT { input: tuple val(meta), path(reads) - path config + path msconfig tuple val(meta2), path(hisat2index) tuple val(meta3), path(genomefai) tuple val(meta4), path(lastindex) tuple val(meta5), path(mtfai) path chrsizes tuple val(meta6), path(mtfasta) - val mito_name output: tuple val(meta), path("*breakpoint") , emit: breakpoint @@ -35,9 +32,9 @@ process MITOSALT { def VERSION = "1.1.1" // from perl script, unlikely to be updated def prefix = task.ext.prefix ?: "${meta.id}" """ - cat $config | sed "s,hsindex = .*,hsindex = ${hisat2index}/reference," | sed "s,^faindex = .*,faindex = $genomefai," | sed "s,lastindex = .*,lastindex = ${lastindex}/reference," | sed "s,mtfaindex = .*,mtfaindex = $mtfai," | sed "s,gsize = .*,gsize = $chrsizes," | sed "s,MT_fasta = .*,MT_fasta = $mtfasta," | sed "s,refchr = .*,refchr = ${mito_name}," > new-${config} + cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} mkdir -p log indel bam tab bw plot - MitoSAlt1.1.1.pl new-${config} $reads $prefix + MitoSAlt1.1.1.pl new-${msconfig} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint mv indel/*.cluster ${prefix}.cluster diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf new file mode 100644 index 000000000..629ebb9b9 --- /dev/null +++ b/modules/local/prep_mitosalt/main.nf @@ -0,0 +1,82 @@ +process PREP_MITOSALT { + tag "$meta.id" + label "process_low" + + input: + tuple val(meta), path(hisat2index) + tuple val(meta2), path(genomefai) + tuple val(meta3), path(lastindex) + tuple val(meta4), path(mtfai) + path chrsizes + tuple val(meta5), path(mtfasta) + val mito_name + val exclude + val score_threshold + val evalue_threshold + val split_length + val paired_distance + val deletion_threshold_min + val deletion_threshold_max + val breakthreshold + val cluster_threshold + val breakspan + val sizelimit + val hplimit + val flank + val split_distance_threshold + + output: + path "mitosalt_config.txt", emit: msconfig + + script: + """ + echo "hisat2 = hisat2" > mitosalt_config.txt + echo "lastal = lastal" >> mitosalt_config.txt + echo "lastsp = last-split" >> mitosalt_config.txt + echo "mfcv = maf-convert" >> mitosalt_config.txt + echo "reformat = reformat.sh" >> mitosalt_config.txt + echo "samtools = samtools" >> mitosalt_config.txt + echo "sambamba = sambamba" >> mitosalt_config.txt + echo "b2fq = bamToFastq" >> mitosalt_config.txt + echo "gcov = genomeCoverageBed" >> mitosalt_config.txt + echo "intersectBed = intersectBed" >> mitosalt_config.txt + echo "sortBed = sortBed" >> mitosalt_config.txt + echo "clusterBed = clusterBed" >> mitosalt_config.txt + echo "randomBed = randomBed" >> mitosalt_config.txt + echo "groupBy = groupBy" >> mitosalt_config.txt + echo "bg2bw = bedGraphToBigWig" >> mitosalt_config.txt + echo "hsindex = ${hisat2index}/reference" >> mitosalt_config.txt + echo "faindex = ${genomefai}" >> mitosalt_config.txt + echo "lastindex = ${lastindex}/reference" >> mitosalt_config.txt + echo "mtfaindex = ${mtfai}" >> mitosalt_config.txt + echo "gsize = ${chrsizes}" >> mitosalt_config.txt + echo "MT_fasta = ${mtfasta}" >> mitosalt_config.txt + echo "threads = 1" >> mitosalt_config.txt + echo "refchr = ${mito_name}" >> mitosalt_config.txt + echo "exclude = ${exclude}" >> mitosalt_config.txt + echo "orihs = 16081" >> mitosalt_config.txt + echo "orihe = 407" >> mitosalt_config.txt + echo "orils = 5730" >> mitosalt_config.txt + echo "orile = 5763" >> mitosalt_config.txt + echo "score_threshold = ${score_threshold}" >> mitosalt_config.txt + echo "evalue_threshold = ${evalue_threshold}" >> mitosalt_config.txt + echo "split_length = ${split_length}" >> mitosalt_config.txt + echo "paired_distance = ${paired_distance}" >> mitosalt_config.txt + echo "deletion_threshold_min = ${deletion_threshold_min}" >> mitosalt_config.txt + echo "deletion_threshold_max = ${deletion_threshold_max}" >> mitosalt_config.txt + echo "breakthreshold = ${breakthreshold}" >> mitosalt_config.txt + echo "cluster_threshold = ${cluster_threshold}" >> mitosalt_config.txt + echo "breakspan = ${breakspan}" >> mitosalt_config.txt + echo "sizelimit = ${sizelimit}" >> mitosalt_config.txt + echo "hplimit = ${hplimit}" >> mitosalt_config.txt + echo "flank = ${flank}" >> mitosalt_config.txt + echo "split_distance_threshold = ${split_distance_threshold}" >> mitosalt_config.txt + echo "dna = yes" >> mitosalt_config.txt + echo "enriched = no" >> mitosalt_config.txt + echo "nu_mt = yes" >> mitosalt_config.txt + echo "rmtmp = no" >> mitosalt_config.txt + echo "o_mt = yes" >> mitosalt_config.txt + echo "i_del = yes" >> mitosalt_config.txt + echo "cn_mt = yes" >> mitosalt_config.txt + """ +} diff --git a/nextflow.config b/nextflow.config index f904a8954..e185a9ab6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -119,6 +119,22 @@ params { sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE' variant_type = 'snp,indel' + // Mitosalt options + score_threshold = 80 + evalue_threshold = 0.00001 + split_length = 15 + paired_distance = 1000 + deletion_threshold_min = 30 + deletion_threshold_max = 30000 + breakthreshold = 2 + cluster_threshold = 2 + breakspan = 15 + sizelimit = 10000 + hplimit = 0.01 + flank = 15 + split_distance_threshold = 5 + exclude = 5 + // MultiQC options multiqc_config = null multiqc_title = null diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 998377256..75d51b20a 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -2,35 +2,81 @@ // Call SV MT // -include { MT_DELETION } from '../../../modules/local/mt_deletion_script' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { MT_DELETION } from '../../../modules/local/mt_deletion_script' +include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' +include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' workflow CALL_SV_MT { take: - ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] - ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] - ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] - ch_msconfig // channel: [mandatory] [ path(msconfig) ] - ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - ch_mito_name // channel: [mandatory] [ val(mito_name) + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_score_threshold // channel: [mandatory] [ val(mitosalt_score_threshold) ] + ch_evalue_threshold // channel: [mandatory] [ val(mitosalt_evalue_threshold) ] + ch_split_length // channel: [mandatory] [ val(mitosalt_split_length) ] + ch_paired_distance // channel: [mandatory] [ val(mitosalt_paired_distance) ] + ch_deletion_threshold_min // channel: [mandatory] [ val(mitosalt_del_threshold_min) ] + ch_deletion_threshold_max // channel: [mandatory] [ val(mitosalt_del_threshold_max) ] + ch_breakthreshold // channel: [mandatory] [ val(mitosalt_break_threshold) ] + ch_cluster_threshold // channel: [mandatory] [ val(mitosalt_cluster_threshold) ] + ch_breakspan // channel: [mandatory] [ val(mitosalt_break_span) ] + ch_sizelimit // channel: [mandatory] [ val(mitosalt_size_limit) ] + ch_hplimit // channel: [mandatory] [ val(mitosalt_hp_limit) ] + ch_flank // channel: [mandatory] [ val(mitosalt_flank) ] + ch_split_distance_threshold // channel: [mandatory] [ val(mitosalt_split_dist_threshold) ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + ch_mito_name // channel: [mandatory] [ val(mito_name) ] + ch_exclude // channel: [mandatory] [ val(mitosalt_exclude) ] main: ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.concat(ch_subdepth).collect() - ch_reads_subdepth.view() SEQTK_SAMPLE (ch_reads_subdepth) ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - MITOSALT(SEQTK_SAMPLE.out.reads, ch_msconfig, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta, ch_mito_name) + PREP_MITOSALT( + ch_genome_hisat2index, + ch_genome_fai, + ch_mt_lastdb, + ch_mt_fai, + ch_genome_chrsizes, + ch_mt_fasta, + ch_mito_name, + ch_exclude, + ch_score_threshold, + ch_evalue_threshold, + ch_split_length, + ch_paired_distance, + ch_deletion_threshold_min, + ch_deletion_threshold_max, + ch_breakthreshold, + ch_cluster_threshold, + ch_breakspan, + ch_sizelimit, + ch_hplimit, + ch_flank, + ch_split_distance_threshold + ) + + MITOSALT( + SEQTK_SAMPLE.out.reads, + PREP_MITOSALT.out.msconfig, + ch_genome_hisat2index, + ch_genome_fai, + ch_mt_lastdb, + ch_mt_fai, + ch_genome_chrsizes, + ch_mt_fasta + ) ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a62b357b5..524835ff6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -131,13 +131,21 @@ workflow RAREDISEASE { // Gather built indices or get them from the params // ch_bait_intervals = ch_references.bait_intervals + ch_breakthreshold = Channel.value(params.breakthreshold) + ch_breakspan = Channel.value(params.breakspan) ch_cadd_header = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_cadd_resources = params.cadd_resources ? Channel.fromPath(params.cadd_resources).collect() : Channel.value([]) ch_call_interval = params.call_interval ? Channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) + ch_cluster_threshold = Channel.value(params.cluster_threshold) ch_dbsnp_tbi = params.known_dbsnp_tbi ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) + ch_deletion_threshold_max = Channel.value(params.deletion_threshold_max) + ch_deletion_threshold_min = Channel.value(params.deletion_threshold_min) + ch_evalue_threshold = Channel.value(params.evalue_threshold) + ch_exclude = Channel.value(params.exclude) + ch_flank = Channel.value(params.flank) ch_foundin_header = Channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_gcnvcaller_model = params.gcnvcaller_model ? Channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> @@ -167,6 +175,7 @@ workflow RAREDISEASE { : ch_references.gnomad_af_idx ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() : Channel.empty() + ch_hplimit = Channel.value(params.hplimit) ch_intervals_wgs = params.intervals_wgs ? Channel.fromPath(params.intervals_wgs).collect() : Channel.empty() ch_intervals_y = params.intervals_y ? Channel.fromPath(params.intervals_y).collect() @@ -179,8 +188,6 @@ workflow RAREDISEASE { : Channel.value([]) ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) - ch_msconfig = params.mitosalt_config ? channel.fromPath(params.mitosalt_config) - : channel.empty() ch_mt_intervals = ch_references.mt_intervals ch_mt_bwaindex = ch_references.mt_bwa_index ch_mt_bwamem2index = ch_references.mt_bwamem2_index @@ -195,6 +202,7 @@ workflow RAREDISEASE { ch_mtshift_fai = ch_references.mtshift_fai ch_mtshift_fasta = ch_references.mtshift_fasta ch_mtshift_intervals = ch_references.mtshift_intervals + ch_paired_distance = Channel.value(params.paired_distance) ch_par_bed = params.par_bed ? Channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : Channel.value([[],[]]) ch_ploidy_model = params.ploidy_model ? Channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() @@ -213,8 +221,12 @@ workflow RAREDISEASE { : Channel.value([]) ch_score_config_sv = params.score_config_sv ? Channel.fromPath(params.score_config_sv).collect() : Channel.value([]) + ch_score_threshold = Channel.value(params.score_threshold) ch_sdf = params.sdf ? Channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf + ch_sizelimit = Channel.value(params.sizelimit) + ch_split_distance_threshold = Channel.value(params.split_distance_threshold) + ch_split_length = Channel.value(params.split_length) ch_subdepth = params.mitosalt_depth ? channel.value(params.mitosalt_depth) : channel.value([]) ch_sv_dbs = params.svdb_query_dbs ? Channel.fromPath(params.svdb_query_dbs) @@ -743,9 +755,22 @@ workflow RAREDISEASE { ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta, - ch_msconfig, + ch_score_threshold, + ch_evalue_threshold, + ch_split_length, + ch_paired_distance, + ch_deletion_threshold_min, + ch_deletion_threshold_max, + ch_breakthreshold, + ch_cluster_threshold, + ch_breakspan, + ch_sizelimit, + ch_hplimit, + ch_flank, + ch_split_distance_threshold, ch_subdepth, - ch_mito_name + ch_mito_name, + ch_exclude ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) From 04ab65dee69421d2acbf10ac746e4d201d41017a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 3 Dec 2025 16:43:48 +0100 Subject: [PATCH 130/872] test locally --- subworkflows/local/align/main.nf | 14 +- subworkflows/local/align/tests/main.nf.test | 42 +- .../local/align/tests/main.nf.test.snap | 160 +----- subworkflows/local/align_MT/main.nf | 7 +- .../local/align_MT/tests/main.nf.test | 8 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 27 +- .../tests/main.nf.test | 8 +- subworkflows/local/qc_bam/tests/main.nf.test | 6 + tests/default.nf.test.snap | 518 +---------------- tests/test_bam.nf.test.snap | 524 +----------------- tests/test_singleton.nf.test.snap | 368 +----------- workflows/raredisease.nf | 2 + 12 files changed, 81 insertions(+), 1603 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 558c3e3de..85a0ae1d3 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -34,7 +34,9 @@ workflow ALIGN { val_platform // string: [mandatory] illumina or a different technology val_sort_threads // integer: [mandatory] number of sorting threads val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' val_analysis_type // string: 'wgs', 'wes', or 'mito' + extract_alignments // boolean save_mapped_as_cram // boolean skip_fastp // boolean @@ -75,7 +77,7 @@ workflow ALIGN { } .map { it -> [it[0], it[2]] } .set{ch_input_bai} - + println(val_aligner) if (val_aligner.matches("bwamem2|bwa|bwameme")) { ALIGN_BWA_BWAMEM2_BWAMEME ( // Triggered when params.aligner is set as bwamem2 or bwa or bwameme ch_reads, @@ -86,7 +88,9 @@ workflow ALIGN { ch_genome_fai, val_mbuffer_mem, val_platform, - val_sort_threads + val_sort_threads, + val_aligner, + extract_alignments ) ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai @@ -126,7 +130,8 @@ workflow ALIGN { ch_mt_bwamem2index, ch_mt_fasta, ch_mt_dictionary, - ch_mt_fai + ch_mt_fai, + val_mt_aligner ) ALIGN_MT_SHIFT ( @@ -136,7 +141,8 @@ workflow ALIGN { ch_mtshift_bwamem2index, ch_mtshift_fasta, ch_mtshift_dictionary, - ch_mtshift_fai + ch_mtshift_fai, + val_mt_aligner ) ch_mt_bam_bai = CONVERT_MT_BAM_TO_FASTQ.out.bam_bai // Used for subsampling and SV calling diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 9fb73b60a..e07048cc9 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -32,7 +32,7 @@ nextflow_workflow { } } - test("align bwamem2") { + test("align bwamem2 - wgs") { setup { run("BWAMEM2_INDEX", alias: 'GENOME_MEM2') { @@ -50,12 +50,7 @@ nextflow_workflow { when { params { - aligner = 'bwamem2' - mt_aligner = 'bwamem2' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - save_mapped_as_cram = true - analysis_type = "wgs" - skip_tools = null platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -106,6 +101,12 @@ nextflow_workflow { input[18] = 3072 input[19] = "illumina" input[20] = 4 + input[21] = "bwamem2" + input[22] = "bwamem2" + input[23] = "wgs" + input[24] = false + input[25] = true + input[26] = false """ } } @@ -148,12 +149,8 @@ nextflow_workflow { when { params { - aligner = 'bwamem2' - mt_aligner = 'bwamem2' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' save_mapped_as_cram = true - analysis_type = "wes" - skip_tools = null platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -204,6 +201,12 @@ nextflow_workflow { input[18] = 3072 input[19] = "illumina" input[20] = 4 + input[21] = "bwamem2" + input[22] = "bwamem2" + input[23] = "wes" + input[24] = false + input[25] = false + input[26] = false """ } } @@ -214,12 +217,6 @@ nextflow_workflow { { assert snapshot( workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mt_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mt_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions ).match() } @@ -227,7 +224,7 @@ nextflow_workflow { } } - test("align bwameme") { + test("align bwameme - wgs") { setup { run("BWAMEME_INDEX", alias: 'GENOME_MEME') { @@ -245,12 +242,7 @@ nextflow_workflow { when { params { - aligner = 'bwameme' - mt_aligner = 'bwamem2' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - save_mapped_as_cram = true - analysis_type = "wgs" - skip_tools = "fastp" platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -295,6 +287,12 @@ nextflow_workflow { input[18] = 3072 input[19] = "illumina" input[20] = 4 + input[21] = "bwameme" + input[22] = "bwamem2" + input[23] = "wgs" + input[24] = false + input[25] = true + input[26] = true """ } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index eae97bc05..1d2a46918 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "align bwamem2": { + "align bwamem2 - wgs": { "content": [ [ [ @@ -268,160 +268,28 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:04:53.135202611" + "timestamp": "2025-12-03T13:44:41.37749287" }, - "align bwameme": { + "align bwameme - wgs": { "content": [ [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "9266e8231917cc16ff9845e50ed22801", - "earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "1df3c2e109a79ba4e7b8293aefbad8", - "hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "645db4b1d55d6d42cba2b55eee1a630", - "slowlycivilbuck_sorted_md.bam.bai" - ] + ], [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "c55f8bf7b7c42ad8dcef6565eff4440b", - "earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "7fc6a7a47e90fb46daeff00093c7c498", - "hugelymodelbat.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "f0b3fe7d566ae0db56bb85e17d8ec28f", - "slowlycivilbuck.bam.bai" - ] + ], [ ], [ - "versions.yml:md5,04cb590a101237e8d8726039ee466819", - "versions.yml:md5,210790d64830e81c512ff898e8d888db", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", - "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,914929705542ec69faf26ad6c672e2af", - "versions.yml:md5,9c218b25dd02dc279b1ce6fad9ae182b", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,b1c46403177c797d5fc304eebf16731c", - "versions.yml:md5,b511e8fd8c8b46c5470d3e3e79673502", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", - "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:15:46.006244795" + "timestamp": "2025-12-03T16:19:51.543625396" }, "align bwamem2 - wes": { "content": [ @@ -483,15 +351,6 @@ "d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck_sorted_md.bam.bai" ] - ], - [ - - ], - [ - - ], - [ - ], [ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", @@ -501,9 +360,6 @@ "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], @@ -511,6 +367,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:05:52.987404208" + "timestamp": "2025-12-03T16:17:55.899272968" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index ec57f3731..fae1c7998 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -19,19 +19,20 @@ workflow ALIGN_MT { ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_dict // channel: [mandatory] [ val(meta), path(dict) ] ch_fai // channel: [mandatory] [ val(meta), path(fai) ] + val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' main: ch_versions = channel.empty() - if (params.mt_aligner.equals("bwamem2")) { + if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) ch_align = BWAMEM2_MEM_MT.out.bam ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions.first()) - } else if (params.mt_aligner.equals("sentieon")) { + } else if (val_mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions.first()) - } else if (params.mt_aligner.equals("bwa")) { + } else if (val_mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) ch_align = BWA_MEM_MT.out.bam ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions.first()) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 532d08704..04186df9b 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -24,8 +24,7 @@ nextflow_workflow { } when { params { - mt_aligner = 'bwamem2' - outdir = "$outputDir" + outdir = "$outputDir" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { @@ -63,6 +62,7 @@ nextflow_workflow { input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[7] = "bwamem2" """ } } @@ -91,8 +91,7 @@ nextflow_workflow { } when { params { - mt_aligner = 'bwa' - outdir = "$outputDir" + outdir = "$outputDir" pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' } workflow { @@ -130,6 +129,7 @@ nextflow_workflow { input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[7] = 'bwa' """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 373f584ff..62466d6a7 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -17,24 +17,27 @@ include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-c workflow ALIGN_BWA_BWAMEM2_BWAMEME { take: - ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] - ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] - ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] - ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - val_mbuffer_mem // integer: [mandatory] default: 3072 - val_platform // string: [mandatory] default: illumina - val_sort_threads // integer: [mandatory] default: 4 + ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] + ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] + ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] + ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + val_mbuffer_mem // integer: [mandatory] default: 3072 + val_platform // string: [mandatory] default: illumina + val_sort_threads // integer: [mandatory] default: 4 + val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + extract_alignments // boolean + main: ch_versions = channel.empty() // Map, sort, and index - if (params.aligner.equals("bwa")) { + if (val_aligner.equals("bwa")) { BWA ( ch_reads_input, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam ch_versions = ch_versions.mix(BWA.out.versions.first()) - } else if (params.aligner.equals("bwameme")) { + } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_reads_input, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions.first()) @@ -85,7 +88,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS - if (params.extract_alignments) { + if (extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 80b4a226c..49c87d1bb 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -25,9 +25,7 @@ nextflow_workflow { when { params { - aligner = "bwamem2" sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - save_mapped_as_cram = true restrict_to_contigs = "MT192765.1" } workflow { @@ -47,6 +45,8 @@ nextflow_workflow { input[6] = 3072 input[7] = "illumina" input[8] = 4 + input[9] = "bwamem2" + input[10] = true """ } } @@ -82,9 +82,7 @@ nextflow_workflow { when { params { - aligner = "bwameme" sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - save_mapped_as_cram = false restrict_to_contigs = "MT192765.1" } workflow { @@ -104,6 +102,8 @@ nextflow_workflow { input[6] = 3072 input[7] = "illumina" input[8] = 4 + input[9] = "bwameme" + input[10] = true """ } } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 329814674..67ec36233 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -40,6 +40,9 @@ nextflow_workflow { input[10] = channel.empty() input[11] = channel.empty() input[12] = 'xy' + input[13] = 'wgs' + input[14] = true + input[15] = false """ } } @@ -111,6 +114,9 @@ nextflow_workflow { input[10] = channel.empty() input[11] = channel.empty() input[12] = 'xy' + input[13] = 'wgs' + input[14] = true + input[15] = false """ } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index fc41a897e..af61d3bf6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -5,51 +5,6 @@ "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, - "BCFTOOLS_ANNOTATE": { - "bcftools": 1.22 - }, - "BCFTOOLS_CONCAT": { - "bcftools": 1.2 - }, - "BCFTOOLS_CONCAT_ME": { - "bcftools": 1.2 - }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.2 - }, - "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.21 - }, - "BCFTOOLS_REHEADER_ME": { - "bcftools": 1.21 - }, - "BCFTOOLS_ROH": { - "bcftools": 1.2 - }, - "BCFTOOLS_SORT_ME": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_CNVNATOR": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_FILTER": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_MANTA": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_RHOCALL": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_TIDDIT": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_UNCOMPRESS": { - "bcftools": 1.2 - }, "BEDTOOLS_PAD_TARGET_BED": { "bedtools": "2.31.1" }, @@ -59,219 +14,29 @@ "BWAMEM2_INDEX_MT": { "bwamem2": "2.2.1" }, - "BWAMEM2_INDEX_MT_SHIFT": { - "bwamem2": "2.2.1" - }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", "samtools": "1.19.2" }, - "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, "BWA_INDEX_GENOME": { "bwa": "0.7.18-r1243-dirty" }, - "CAT_CAT_BAIT": { - "pigz": "2.3.4" - }, - "CHROMOGRAPH_AUTOZYG": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_COV": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, - "CNVNATOR_CALL": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_HIST": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_RD": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_STAT": { - "CNVnator": "0.4.1" - }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", "python": "3.8.3" }, - "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, - "bgzip": 1.21 - }, - "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, - "bgzip": 1.21 - }, - "DEEPVARIANT": { - "deepvariant": "1.8.0" - }, - "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 - }, - "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 - }, - "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 - }, - "EXPANSIONHUNTER": { - "expansionhunter": "5.0.0", - "bgzip": 1.18 - }, "FASTQC": { "fastqc": "0.12.1" }, - "GATK4_FILTERMUTECTCALLS_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MERGEBAMALIGNMENT_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MUTECT2_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_PRINTREADS_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_REVERTSAM_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_SAMTOFASTQ_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_SELECTVARIANTS": { - "gatk4": "4.5.0.0" - }, - "GATK4_VARIANTFILTRATION_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_BILT": { - "gatk4": "4.5.0.0" - }, - "GATK_ILT": { - "gatk4": "4.5.0.0" - }, - "GATK_SD": { - "gatk4": "4.5.0.0" - }, - "GATK_SD_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" - }, - "GENMOD_ANNOTATE": { - "genmod": 3.9 - }, - "GENMOD_COMPOUND": { - "genmod": 3.9 - }, - "GENMOD_MODELS": { - "genmod": 3.9 - }, - "GENMOD_SCORE": { - "genmod": 3.9 - }, "GET_CHROM_SIZES": { "coreutils": 8.31 }, - "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" - }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, - "INDEX_CNVNATOR": { - "tabix": 1.2 - }, - "INDEX_TIDDIT": { - "tabix": 1.2 - }, - "MANTA": { - "manta": "1.6.0" - }, "MARKDUPLICATES": { "picard": "3.3.0" }, - "ME_SPLIT_ALIGNMENT": { - "samtools": "1.22.1" - }, - "MOSDEPTH": { - "mosdepth": "0.3.10" - }, - "MT_DELETION": { - "samtools": "1.19.2" - }, - "PICARD_ADDORREPLACEREADGROUPS_MT": { - "picard": "3.3.0" - }, - "PICARD_COLLECTHSMETRICS": { - "picard": "3.3.0" - }, - "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.3.0" - }, - "PICARD_COLLECTWGSMETRICS_WG": { - "picard": "3.3.0" - }, - "PICARD_COLLECTWGSMETRICS_Y": { - "picard": "3.3.0" - }, - "PICARD_LIFTOVERVCF": { - "picard": "3.3.0" - }, - "PICARD_MARKDUPLICATES_MT": { - "picard": "3.3.0" - }, - "PICARD_SORTVCF": { - "picard": "3.3.0" - }, - "REMOVE_DUPLICATES_GL": { - "bcftools": 1.21 - }, - "REMOVE_DUPLICATES_MT": { - "bcftools": 1.21 - }, - "RENAMESAMPLE_EXP": { - "picard": "3.3.0" - }, - "RENAME_BAI": { - "coreutils": 8.31 - }, "RENAME_BAM": { "coreutils": 8.31 }, - "RETROSEQ_CALL": { - "retroseq_call": 1.5 - }, - "RETROSEQ_DISCOVER": { - "retroseq_discover": 1.5 - }, - "RHOCALL_ANNOTATE": { - "rhocall": "0.5.1" - }, - "RHOCALL_VIZ": { - "rhocall": "0.5.1" - }, "SAMTOOLS_EXTRACT_MT": { "samtools": 1.21 }, @@ -284,137 +49,29 @@ "SAMTOOLS_INDEX_MARKDUP": { "samtools": 1.21 }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_SORT_MT": { - "samtools": "1.22.1" - }, "SAMTOOLS_STATS": { "samtools": 1.21 }, - "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" - }, - "SPLIT_MULTIALLELICS_EXP": { - "bcftools": 1.21 - }, - "SPLIT_MULTIALLELICS_GL": { - "bcftools": 1.21 - }, - "SPLIT_MULTIALLELICS_MT": { - "bcftools": 1.21 - }, "SPRING_DECOMPRESS_TO_FQ_PAIR": { "spring": "1.1.1" }, - "STRANGER": { - "stranger": "0.9.4", - "tabix": 1.21 - }, - "SVDB_MERGE": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_CNVNATOR": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_ME": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_REPEATS": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_TIDDIT": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_QUERY_DB": { - "svdb": "2.8.2" - }, - "TABIX_ANNOTATE": { - "tabix": 1.21 - }, - "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.21 - }, - "TABIX_BGZIP": { - "tabix": 1.2 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, - "TABIX_BGZIPTABIX": { - "tabix": 1.2 - }, "TABIX_DBSNP": { "tabix": 1.21 }, - "TABIX_EXP_RENAME": { - "tabix": 1.21 - }, - "TABIX_GL": { - "tabix": 1.21 - }, "TABIX_GNOMAD_AF": { "tabix": 1.21 }, - "TABIX_ME": { - "tabix": 1.21 - }, - "TABIX_ME_SPLIT": { - "tabix": 1.21 - }, "TABIX_PBT": { "tabix": 1.2 }, - "TABIX_TABIX": { - "tabix": 1.21 - }, - "TABIX_TABIX_MERGE": { - "tabix": 1.21 - }, - "TABIX_TABIX_MT2": { - "tabix": 1.21 - }, - "TABIX_TABIX_MT": { - "tabix": 1.21 - }, - "TABIX_VEP": { - "tabix": 1.21 - }, - "TIDDIT_COV": { - "tiddit": "3.6.1" - }, - "TIDDIT_SV": { - "tiddit": "3.6.1" - }, - "UCSC_WIGTOBIGWIG": { - "ucsc": 447 - }, "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, - "VCFANNO": { - "vcfanno": "0.3.5" - }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" - }, - "ZIP_TABIX_ROHCALL": { - "tabix": 1.2 - }, - "ZIP_TABIX_VCFANNO": { - "tabix": 1.2 } }, [ @@ -428,56 +85,6 @@ "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", "alignment/slowlycivilbuck_sorted_md.bam", "alignment/slowlycivilbuck_sorted_md.bam.bai", - "annotate_mobile_elements", - "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", - "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", - "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", - "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz", - "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.csi", - "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", - "annotate_snv", - "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", - "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/hugelymodelbat_chromograph_regions", - "annotate_snv/genome/hugelymodelbat_chromograph_sites", - "annotate_snv/genome/hugelymodelbat_rhocallviz", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.csi", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", - "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", - "call_mobile_elements", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.csi", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.csi", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.csi", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -488,137 +95,16 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_plots", - "multiqc/multiqc_report.html", "pedigree", "pedigree/justhusky.ped", "pipeline_info", - "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", - "qc_bam", - "qc_bam/earlycasualcaiman_chromographcov", - "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.summary.txt", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/earlycasualcaiman_tidditcov.bed", - "qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_chromographcov", - "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.per-base.d4", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.summary.txt", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.bw", - "qc_bam/hugelymodelbat_tidditcov.wig", - "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_chromographcov", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "rank_and_filter", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", - "smncopynumbercaller", - "smncopynumbercaller/out", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv" + "pipeline_info/nf_core_raredisease_software_mqc_versions.yml" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:06:28.721832727" + "timestamp": "2025-12-03T09:27:25.22699938" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 68148d358..6f804840a 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,539 +1,21 @@ { "-profile test_bam": { "content": [ - 274, + 0, { - "ADD_VARCALLER_TO_BED": { - "tabix": 1.12 - }, - "BCFTOOLS_ANNOTATE": { - "bcftools": 1.22 - }, - "BCFTOOLS_CONCAT": { - "bcftools": 1.2 - }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.2 - }, - "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.21 - }, - "BCFTOOLS_ROH": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_CNVNATOR": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_MANTA": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_RHOCALL": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_TIDDIT": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_UNCOMPRESS": { - "bcftools": 1.2 - }, - "BEDTOOLS_PAD_TARGET_BED": { - "bedtools": "2.31.1" - }, - "BWAMEM2_INDEX_GENOME": { - "bwamem2": "2.2.1" - }, - "BWAMEM2_INDEX_MT": { - "bwamem2": "2.2.1" - }, - "BWAMEM2_INDEX_MT_SHIFT": { - "bwamem2": "2.2.1" - }, - "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, - "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" - }, - "CAT_CAT_BAIT": { - "pigz": "2.3.4" - }, - "CHROMOGRAPH_AUTOZYG": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_COV": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, - "CNVNATOR_CALL": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_HIST": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_RD": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_STAT": { - "CNVnator": "0.4.1" - }, - "CREATE_PEDIGREE_FILE": { - "create_pedigree_file": "v1.0", - "python": "3.8.3" - }, - 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"qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_chromographcov", - "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.per-base.d4", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.summary.txt", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.bw", - "qc_bam/hugelymodelbat_tidditcov.wig", - "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_chromographcov", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "rank_and_filter", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", - "smncopynumbercaller", - "smncopynumbercaller/out", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv" + "pipeline_info/nf_core_raredisease_software_mqc_versions.yml" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:14:53.307227004" + "timestamp": "2025-12-03T09:05:32.542055259" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e920e634e..de541d181 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,41 +1,11 @@ { "-profile test_singleton": { "content": [ - 148, + 37, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, - "BCFTOOLS_ANNOTATE": { - "bcftools": 1.22 - }, - "BCFTOOLS_CONCAT": { - "bcftools": 1.2 - }, - "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.21 - }, - "BCFTOOLS_ROH": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_CNVNATOR": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_MANTA": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_RHOCALL": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_TIDDIT": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_UNCOMPRESS": { - "bcftools": 1.2 - }, "BEDTOOLS_PAD_TARGET_BED": { "bedtools": "2.31.1" }, @@ -45,198 +15,32 @@ "BWAMEM2_INDEX_MT": { "bwamem2": "2.2.1" }, - "BWAMEM2_INDEX_MT_SHIFT": { - "bwamem2": "2.2.1" - }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", "samtools": "1.19.2" }, - "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, "BWA_INDEX_GENOME": { "bwa": "0.7.18-r1243-dirty" }, - "CAT_CAT_BAIT": { - "pigz": "2.3.4" - }, - "CHROMOGRAPH_AUTOZYG": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_COV": { - "chromograph": "1.3.1" - }, - "CNVNATOR_CALL": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_HIST": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_RD": { - "CNVnator": "0.4.1" - }, - "CNVNATOR_STAT": { - "CNVnator": "0.4.1" - }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", "python": "3.8.3" }, - "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, - "bgzip": 1.21 - }, - "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, - "bgzip": 1.21 - }, - "DEEPVARIANT": { - "deepvariant": "1.8.0" - }, - "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 - }, - "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 - }, - "EXPANSIONHUNTER": { - "expansionhunter": "5.0.0", - "bgzip": 1.18 - }, "FASTQC": { "fastqc": "0.12.1" }, - "GATK4_FILTERMUTECTCALLS_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MERGEBAMALIGNMENT_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_MUTECT2_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_PRINTREADS_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_REVERTSAM_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_SAMTOFASTQ_MT": { - "gatk4": "4.5.0.0" - }, - "GATK4_SELECTVARIANTS": { - "gatk4": "4.5.0.0" - }, - "GATK4_VARIANTFILTRATION_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_BILT": { - "gatk4": "4.5.0.0" - }, - "GATK_ILT": { - "gatk4": "4.5.0.0" - }, "GATK_SD": { "gatk4": "4.5.0.0" }, "GATK_SD_MT": { "gatk4": "4.5.0.0" }, - "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" - }, - "GENMOD_ANNOTATE": { - "genmod": 3.9 - }, - "GENMOD_COMPOUND": { - "genmod": 3.9 - }, - "GENMOD_MODELS": { - "genmod": 3.9 - }, - "GENMOD_SCORE": { - "genmod": 3.9 - }, "GET_CHROM_SIZES": { "coreutils": 8.31 }, - "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" - }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, - "INDEX_CNVNATOR": { - "tabix": 1.2 - }, - "INDEX_TIDDIT": { - "tabix": 1.2 - }, - "MANTA": { - "manta": "1.6.0" - }, "MARKDUPLICATES": { "picard": "3.3.0" }, - "MOSDEPTH": { - "mosdepth": "0.3.10" - }, - "MT_DELETION": { - "samtools": "1.19.2" - }, - "PICARD_ADDORREPLACEREADGROUPS_MT": { - "picard": "3.3.0" - }, - "PICARD_COLLECTHSMETRICS": { - "picard": "3.3.0" - }, - "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.3.0" - }, - "PICARD_COLLECTWGSMETRICS_WG": { - "picard": "3.3.0" - }, - "PICARD_COLLECTWGSMETRICS_Y": { - "picard": "3.3.0" - }, - "PICARD_LIFTOVERVCF": { - "picard": "3.3.0" - }, - "PICARD_MARKDUPLICATES_MT": { - "picard": "3.3.0" - }, - "REMOVE_DUPLICATES_GL": { - "bcftools": 1.21 - }, - "REMOVE_DUPLICATES_MT": { - "bcftools": 1.21 - }, - "RENAMESAMPLE_EXP": { - "picard": "3.3.0" - }, - "RENAME_BAI": { - "coreutils": 8.31 - }, - "RENAME_BAM": { - "coreutils": 8.31 - }, - "RHOCALL_ANNOTATE": { - "rhocall": "0.5.1" - }, - "RHOCALL_VIZ": { - "rhocall": "0.5.1" - }, "SAMTOOLS_EXTRACT_MT": { "samtools": 1.21 }, @@ -249,115 +53,26 @@ "SAMTOOLS_INDEX_MARKDUP": { "samtools": 1.21 }, - "SAMTOOLS_SORT": { - "samtools": "1.22.1" - }, - "SAMTOOLS_SORT_MT": { - "samtools": "1.22.1" - }, "SAMTOOLS_STATS": { "samtools": 1.21 }, - "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" - }, - "SPLIT_MULTIALLELICS_EXP": { - "bcftools": 1.21 - }, - "SPLIT_MULTIALLELICS_GL": { - "bcftools": 1.21 - }, - "SPLIT_MULTIALLELICS_MT": { - "bcftools": 1.21 - }, - "STRANGER": { - "stranger": "0.9.4", - "tabix": 1.21 - }, - "SVDB_MERGE": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_CNVNATOR": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_REPEATS": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "SVDB_MERGE_TIDDIT": { - "svdb": "2.8.2", - "bcftools": 1.21 - }, - "TABIX_ANNOTATE": { - "tabix": 1.21 - }, - "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.21 - }, - "TABIX_BGZIP": { - "tabix": 1.2 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, - "TABIX_BGZIPTABIX": { - "tabix": 1.2 - }, "TABIX_DBSNP": { "tabix": 1.21 }, - "TABIX_EXP_RENAME": { - "tabix": 1.21 - }, - "TABIX_GL": { - "tabix": 1.21 - }, "TABIX_GNOMAD_AF": { "tabix": 1.21 }, "TABIX_PBT": { "tabix": 1.2 }, - "TABIX_TABIX": { - "tabix": 1.21 - }, - "TABIX_TABIX_MERGE": { - "tabix": 1.21 - }, - "TABIX_TABIX_MT2": { - "tabix": 1.21 - }, - "TABIX_TABIX_MT": { - "tabix": 1.21 - }, - "TABIX_VEP": { - "tabix": 1.21 - }, - "TIDDIT_COV": { - "tiddit": "3.6.1" - }, - "TIDDIT_SV": { - "tiddit": "3.6.1" - }, - "UCSC_WIGTOBIGWIG": { - "ucsc": 447 - }, "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "VCFANNO": { - "vcfanno": "0.3.5" - }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" - }, - "ZIP_TABIX_ROHCALL": { - "tabix": 1.2 - }, - "ZIP_TABIX_VCFANNO": { - "tabix": 1.2 } }, [ @@ -365,100 +80,23 @@ "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", - "annotate_snv", - "annotate_snv/genome", - "annotate_snv/genome/hugelymodelbat_rhocallviz", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", - "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.csi", - "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.csi", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.csi", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", - "haplocheck", - "haplocheck/hugelymodelbat.raw.txt", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_plots", - "multiqc/multiqc_report.html", "pedigree", "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/hugelymodelbat_chromographcov", - "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.per-base.d4", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.summary.txt", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.bw", - "qc_bam/hugelymodelbat_tidditcov.wig", - "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "rank_and_filter", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "smncopynumbercaller", - "smncopynumbercaller/out", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv" + "qc_bam/hugelymodelbat_tidditcov.wig" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-27T16:22:08.027799973" + "timestamp": "2025-12-03T09:31:28.426779437" } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 7dce8c96a..8d6a09f98 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -395,7 +395,9 @@ workflow RAREDISEASE { params.platform, params.samtools_sort_threads, params.aligner, + params.mt_aligner, analysis_type, + params.extract_alignments, params.save_mapped_as_cram, skip_fastp ) From 49fb97142b4f5cc9d0694d558490be2fd5558bf3 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 4 Dec 2025 10:27:09 +0100 Subject: [PATCH 131/872] review suggestions --- subworkflows/local/align/main.nf | 4 ++-- subworkflows/local/annotate_genome_snvs.nf | 4 ++-- subworkflows/local/annotate_mt_snvs.nf | 4 ++-- workflows/raredisease.nf | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index d11967e5c..b802e721a 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -61,7 +61,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { meta, bam, bai -> [meta, bam] } + .map { meta, bam, _bai -> [meta, bam] } .set{ch_input_bam} ch_alignments.map { meta, files -> @@ -69,7 +69,7 @@ workflow ALIGN { def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') return [new_meta, files].flatten() } - .map { meta, bam, bai -> [meta, bai] } + .map { meta, _bam, bai -> [meta, bai] } .set{ch_input_bai} if (params.aligner.matches("bwamem2|bwa|bwameme")) { diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 10fcb3203..88067cadb 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -126,9 +126,9 @@ workflow ANNOTATE_GENOME_SNVS { cadd: !(cadd.equals(null)) return [meta + [prefix: meta.prefix + "_filter_cadd"], cadd] } - .set { ch_for_mix } + .set { ch_annotated_vcfs } - ch_for_mix.selvar.mix(ch_for_mix.cadd) + ch_annotated_vcfs.selvar.mix(ch_annotated_vcfs.cadd) .map { meta, vcf -> return [meta, vcf, []] } .set { ch_vep_in } diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index e8b3cf559..3258c8d41 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -77,9 +77,9 @@ workflow ANNOTATE_MT_SNVS { cadd: !(cadd.equals(null)) return [meta + [prefix: meta.prefix + "_cadd_vep"], cadd] } - .set { ch_for_mix } + .set { ch_annotated_vcfs } - ch_for_mix.vcfanno.mix(ch_for_mix.cadd) + ch_annotated_vcfs.vcfanno.mix(ch_annotated_vcfs.cadd) .tap { ch_haplogrep_in } .map { meta, vcf -> return [meta, vcf, []] } .set { ch_vep_in } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 9c7e293d3..1a68caf81 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -301,7 +301,7 @@ workflow RAREDISEASE { // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) // - ch_input_by_sample_type = ch_reads.branch{ meta, reads -> + ch_input_by_sample_type = ch_reads.branch{ meta, _reads -> fastq_gz: meta.data_type == "fastq_gz" interleaved_spring: meta.data_type == "interleaved_spring" separate_spring: meta.data_type == "separate_spring" From 63d3685439119e14cfde154ae07dae4cb64718e8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 4 Dec 2025 12:27:06 +0100 Subject: [PATCH 132/872] align --- conf/modules/align_bwa_bwamem2_bwameme.config | 1 - subworkflows/local/align/main.nf | 2 +- .../local/align/tests/main.nf.test.snap | 140 +++++++++++++++++- .../local/align/tests/nextflow.config | 1 - 4 files changed, 137 insertions(+), 7 deletions(-) diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index ce28d4380..d3dab330f 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -33,7 +33,6 @@ process { ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } ext.args2 = { "-T ./samtools_sort_tmp" } ext.prefix = { "${meta.id}_sorted" } - ext.when = { params.aligner.equals("bwameme") } } withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWA' { diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 85a0ae1d3..08cfd40c8 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -77,7 +77,7 @@ workflow ALIGN { } .map { it -> [it[0], it[2]] } .set{ch_input_bai} - println(val_aligner) + if (val_aligner.matches("bwamem2|bwa|bwameme")) { ALIGN_BWA_BWAMEM2_BWAMEME ( // Triggered when params.aligner is set as bwamem2 or bwa or bwameme ch_reads, diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 1d2a46918..39bb67d3f 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -273,23 +273,155 @@ "align bwameme - wgs": { "content": [ [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "9266e8231917cc16ff9845e50ed22801", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "1df3c2e109a79ba4e7b8293aefbad8", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "645db4b1d55d6d42cba2b55eee1a630", + "slowlycivilbuck_sorted_md.bam.bai" + ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "c55f8bf7b7c42ad8dcef6565eff4440b", + "earlycasualcaiman.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "7fc6a7a47e90fb46daeff00093c7c498", + "hugelymodelbat.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "f0b3fe7d566ae0db56bb85e17d8ec28f", + "slowlycivilbuck.bam.bai" + ] ], [ ], [ - + "versions.yml:md5,04cb590a101237e8d8726039ee466819", + "versions.yml:md5,210790d64830e81c512ff898e8d888db", + "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", + "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", + "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", + "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", + "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", + "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", + "versions.yml:md5,914929705542ec69faf26ad6c672e2af", + "versions.yml:md5,9c218b25dd02dc279b1ce6fad9ae182b", + "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", + "versions.yml:md5,b1c46403177c797d5fc304eebf16731c", + "versions.yml:md5,b511e8fd8c8b46c5470d3e3e79673502", + "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", + "versions.yml:md5,c31eb465488334212645bd43296d8bd7", + "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", + "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", + "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-12-03T16:19:51.543625396" + "timestamp": "2025-12-03T17:04:26.065011032" }, "align bwamem2 - wes": { "content": [ diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index 402477f76..4f13ba425 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -33,7 +33,6 @@ process { ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } ext.args2 = { "-T ./samtools_sort_tmp" } ext.prefix = { "${meta.id}_sorted" } - ext.when = { params.aligner.equals("bwameme") } } withName: 'BWA' { From e562923f4175bcfefa3bd1209f05ca65ef4ed5af Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 4 Dec 2025 12:35:07 +0100 Subject: [PATCH 133/872] align bwameme --- .../tests/main.nf.test.snap | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 8b6bdcef2..879f7dbf8 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "17f8c2ac941e887d9470f69453c08ea5" + "13f1d6d13abf640bc42f5692510b9a7a" ] ], [ @@ -32,18 +32,20 @@ ] ], [ + "versions.yml:md5,22d2871963a6cdc14c58d98fc3c3c9c3", "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", + "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-05-23T16:03:29.762040277" + "timestamp": "2025-12-04T12:30:00.835976838" }, "align bwameme": { "content": [ @@ -59,7 +61,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "144054510dda19100c4274a7db41bd8" + "2b9969e02527b37fdfb5852fc2583bc5" ] ], [ @@ -78,17 +80,19 @@ ] ], [ + "versions.yml:md5,22d2871963a6cdc14c58d98fc3c3c9c3", "versions.yml:md5,390a09ae83280da84de93856149cc3a1", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", + "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-05-23T16:04:03.379890309" + "timestamp": "2025-12-04T12:30:47.082179053" } } \ No newline at end of file From 4684ec0dfb7a422294ffd14593e9d79f614329b9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 4 Dec 2025 13:42:02 +0100 Subject: [PATCH 134/872] qc_bam --- conf/modules/qc_bam.config | 4 -- subworkflows/local/qc_bam/main.nf | 40 +++++++++++-------- subworkflows/local/qc_bam/tests/main.nf.test | 16 ++++---- .../local/qc_bam/tests/nextflow.config | 4 -- workflows/raredisease.nf | 1 + 5 files changed, 33 insertions(+), 32 deletions(-) diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index bd38111a2..a943b3556 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -72,23 +72,19 @@ process { withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' { ext.args = "--TMP_DIR ." - ext.when = { !params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics" } } withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' { ext.args = "--TMP_DIR ." - ext.when = { !params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics_y" } } withName: '.*QC_BAM:SENTIEON_WGSMETRICS_WG' { - ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics" } } withName: '.*QC_BAM:SENTIEON_WGSMETRICS_Y' { - ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics_y" } } } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index bd230d196..130f94196 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -33,6 +33,7 @@ workflow QC_BAM { ch_svd_ud // channel: [optional] [ path(ud) ] ngsbits_samplegender_method // channel: [val(method)] val_analysis_type // string: "wes", "wgs", or "mito" + val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" skip_ngsbits // boolean skip_qualimap // boolean @@ -53,7 +54,7 @@ workflow QC_BAM { PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]) if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results - ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) + ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions) } TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input @@ -67,32 +68,37 @@ workflow QC_BAM { // COLLECT WGS METRICS if (!val_analysis_type.equals("wes")) { - PICARD_COLLECTWGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs ) - PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y ) - SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} ) - SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} ) - ch_cov = channel.empty().mix(PICARD_COLLECTWGSMETRICS_WG.out.metrics, SENTIEON_WGSMETRICS_WG.out.wgs_metrics) - ch_cov_y = channel.empty().mix(PICARD_COLLECTWGSMETRICS_Y.out.metrics, SENTIEON_WGSMETRICS_Y.out.wgs_metrics) - ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_WG.out.versions.first(), SENTIEON_WGSMETRICS_WG.out.versions.first()) - ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_Y.out.versions.first(), SENTIEON_WGSMETRICS_Y.out.versions.first()) + if (val_aligner.matches("bwa|bwameme|bwamem2")) { + PICARD_COLLECTWGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs ) + PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y ) + ch_cov = PICARD_COLLECTWGSMETRICS_WG.out.metrics + ch_cov_y = PICARD_COLLECTWGSMETRICS_Y.out.metrics + ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_WG.out.versions, PICARD_COLLECTWGSMETRICS_Y.out.versions) + } else if (val_aligner.equals("sentieon")) { + SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} ) + SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} ) + ch_cov = SENTIEON_WGSMETRICS_WG.out.wgs_metrics + ch_cov_y = SENTIEON_WGSMETRICS_Y.out.wgs_metrics + ch_versions = ch_versions.mix(SENTIEON_WGSMETRICS_WG.out.versions, SENTIEON_WGSMETRICS_Y.out.versions) + } } // Check sex if (!skip_ngsbits) { NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ngsbits_samplegender_method) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv - ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions.first()) + ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions) } // Check contamination ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {it-> it[1]}) - ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions.first()) - ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first()) - ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first()) - ch_versions = ch_versions.mix(TIDDIT_COV.out.versions.first()) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first()) - ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first()) - ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions.first()) + ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions) + ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions) + ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions) + ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) + ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) + ch_versions = ch_versions.mix(MOSDEPTH.out.versions) + ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 67ec36233..5f6344a46 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -11,8 +11,8 @@ nextflow_workflow { when { params { - aligner = "bwamem2" skip_tools = null + outdir = "$outputDir" } workflow { """ @@ -36,13 +36,14 @@ nextflow_workflow { input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() input[8] = channel.empty() - input[9] = channel.empty() + input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() input[12] = 'xy' input[13] = 'wgs' - input[14] = true - input[15] = false + input[14] = 'bwamem2' + input[15] = true + input[16] = false """ } } @@ -85,7 +86,7 @@ nextflow_workflow { when { params { - aligner = "sentieon" + outdir = "$outputDir" skip_tools = null } workflow { @@ -115,8 +116,9 @@ nextflow_workflow { input[11] = channel.empty() input[12] = 'xy' input[13] = 'wgs' - input[14] = true - input[15] = false + input[14] = 'sentieon' + input[15] = true + input[16] = false """ } } diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config index bd4ae2d5d..785869e7a 100644 --- a/subworkflows/local/qc_bam/tests/nextflow.config +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -42,23 +42,19 @@ process { withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' { ext.args = "--TMP_DIR ." - ext.when = { !params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics" } } withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' { ext.args = "--TMP_DIR ." - ext.when = { !params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics_y" } } withName: '.*QC_BAM:SENTIEON_WGSMETRICS_WG' { - ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics" } } withName: '.*QC_BAM:SENTIEON_WGSMETRICS_Y' { - ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics_y" } } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8d6a09f98..21da546f7 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -438,6 +438,7 @@ workflow RAREDISEASE { ch_svd_ud, channel.value(params.ngsbits_samplegender_method), analysis_type, + params.aligner, skip_ngsbits, skip_qualimap ) From 91c0a0f56c232577475c0dc114c4d4776ba7ad6e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 4 Dec 2025 18:22:52 +0100 Subject: [PATCH 135/872] fix tests --- .../local/call_structural_variants.nf | 2 +- tests/default.nf.test | 1 + tests/default.nf.test.snap | 818 +++++++++++++++++- tests/test_bam.nf.test.snap | 659 +++++++++++++- tests/test_singleton.nf.test.snap | 496 ++++++++++- 5 files changed, 1967 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index ba3fa992f..b3f3f8bc5 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -59,7 +59,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(CALL_SV_CNVNATOR.out.versions) } - if (skip_germlinecnvcaller) { + if (!skip_germlinecnvcaller) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf .collect{ _meta, vcf -> vcf } diff --git a/tests/default.nf.test b/tests/default.nf.test index 20a2bdc98..50792315c 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -11,6 +11,7 @@ nextflow_pipeline { when { params { outdir = "$outputDir" + skip_tools = "germlinecnvcaller,gens" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index af61d3bf6..2c5cf1608 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -5,6 +5,54 @@ "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, + "BCFTOOLS_ANNOTATE": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT": { + "bcftools": 1.2 + }, + "BCFTOOLS_CONCAT_ME": { + "bcftools": 1.2 + }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.2 + }, + "BCFTOOLS_REHEADER_EXP": { + "bcftools": 1.21 + }, + "BCFTOOLS_REHEADER_ME": { + "bcftools": 1.21 + }, + "BCFTOOLS_ROH": { + "bcftools": 1.2 + }, + "BCFTOOLS_SORT": { + "bcftools": 1.2 + }, + "BCFTOOLS_SORT_ME": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_CNVNATOR": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_FILTER": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_MANTA": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_RHOCALL": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_TIDDIT": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_UNCOMPRESS": { + "bcftools": 1.2 + }, "BEDTOOLS_PAD_TARGET_BED": { "bedtools": "2.31.1" }, @@ -14,29 +62,256 @@ "BWAMEM2_INDEX_MT": { "bwamem2": "2.2.1" }, + "BWAMEM2_INDEX_MT_SHIFT": { + "bwamem2": "2.2.1" + }, "BWAMEM2_MEM": { "bwamem2": "2.2.1", "samtools": "1.19.2" }, + "BWAMEM2_MEM_MT": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, "BWA_INDEX_GENOME": { "bwa": "0.7.18-r1243-dirty" }, + "CAT_CAT_BAIT": { + "pigz": "2.3.4" + }, + "CHROMOGRAPH_AUTOZYG": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_COV": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, + "CNVNATOR_CALL": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_CONVERT2VCF": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_HIST": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_PARTITION": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_RD": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_STAT": { + "CNVnator": "0.4.1" + }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", "python": 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"2025-12-04T18:15:10.207423904" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index de541d181..9877cb839 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,11 +1,56 @@ { "-profile test_singleton": { "content": [ - 37, + 362, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 }, + "BCFTOOLS_ANNOTATE": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT": { + "bcftools": 1.2 + }, + "BCFTOOLS_CONCAT_ME": { + "bcftools": 1.2 + }, + "BCFTOOLS_REHEADER_EXP": { + "bcftools": 1.21 + }, + "BCFTOOLS_REHEADER_ME": { + "bcftools": 1.21 + }, + "BCFTOOLS_ROH": { + "bcftools": 1.2 + }, + "BCFTOOLS_SORT": { + "bcftools": 1.2 + }, + "BCFTOOLS_SORT_ME": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_CNVNATOR": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_FILTER": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_MANTA": { + "bcftools": 1.2 + }, + "BCFTOOLS_VIEW_RHOCALL": { + 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"qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.summary.txt", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.wig" + "qc_bam/hugelymodelbat_tidditcov.bw", + "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "rank_and_filter", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.csi", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.gzi", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.csi", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.gzi", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.csi", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.csi", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", + "repeat_expansions", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "smncopynumbercaller", + "smncopynumbercaller/out", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "vcf2cytosure", + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-12-03T09:31:28.426779437" + "timestamp": "2025-12-04T18:21:22.86599878" } } \ No newline at end of file From 7e294f77f437782a8088bdb0a474e954350b8f82 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 5 Dec 2025 10:05:23 +0100 Subject: [PATCH 136/872] add sambamba --- CHANGELOG.md | 1 + conf/modules/qc_bam.config | 15 +++ modules.json | 5 + .../nf-core/sambamba/depth/environment.yml | 7 ++ modules/nf-core/sambamba/depth/main.nf | 56 +++++++++ modules/nf-core/sambamba/depth/meta.yml | 70 ++++++++++++ .../nf-core/sambamba/depth/tests/main.nf.test | 92 +++++++++++++++ .../sambamba/depth/tests/main.nf.test.snap | 107 ++++++++++++++++++ nextflow.config | 1 + nextflow_schema.json | 8 ++ subworkflows/local/qc_bam/main.nf | 7 ++ workflows/raredisease.nf | 3 + 12 files changed, 372 insertions(+) create mode 100644 modules/nf-core/sambamba/depth/environment.yml create mode 100644 modules/nf-core/sambamba/depth/main.nf create mode 100644 modules/nf-core/sambamba/depth/meta.yml create mode 100644 modules/nf-core/sambamba/depth/tests/main.nf.test create mode 100644 modules/nf-core/sambamba/depth/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index fbf446e8e..9fbcab225 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717) - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) - Feature to subsample mitochondrial alignments based on number of reads. [#748](https://github.com/nf-core/raredisease/pull/748) +- Functionality to generate coverage information using Sambamba depth ### `Changed` diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index bd38111a2..f440ae6b8 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -82,6 +82,21 @@ process { ext.prefix = { "${meta.id}_wgsmetrics_y" } } + withName: '.*:QC_BAM:SAMBAMBA_DEPTH' { + ext.prefix = { "${meta.id}_sambamba_depth" } + ext.args = { + [ + "--cov-threshold 10", + "--cov-threshold 15", + "--cov-threshold 20", + "--cov-threshold 50", + "--cov-threshold 100", + "--min-base-quality 10", + "--filter 'mapping_quality >= 10'", + ].join(' ') + } + } + withName: '.*QC_BAM:SENTIEON_WGSMETRICS_WG' { ext.when = { params.aligner.equals("sentieon") } ext.prefix = { "${meta.id}_wgsmetrics" } diff --git a/modules.json b/modules.json index cad5d31c6..f4fb639d8 100644 --- a/modules.json +++ b/modules.json @@ -393,6 +393,11 @@ "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", "installed_by": ["modules"] }, + "sambamba/depth": { + "branch": "master", + "git_sha": "b093f74ddc3ada57a84a209f0e4fb3871bacf2ad", + "installed_by": ["modules"] + }, "samtools/collate": { "branch": "master", "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", diff --git a/modules/nf-core/sambamba/depth/environment.yml b/modules/nf-core/sambamba/depth/environment.yml new file mode 100644 index 000000000..a26092351 --- /dev/null +++ b/modules/nf-core/sambamba/depth/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::sambamba=1.0.1 diff --git a/modules/nf-core/sambamba/depth/main.nf b/modules/nf-core/sambamba/depth/main.nf new file mode 100644 index 000000000..e1404c7b0 --- /dev/null +++ b/modules/nf-core/sambamba/depth/main.nf @@ -0,0 +1,56 @@ +process SAMBAMBA_DEPTH { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/sambamba:1.0.1--he614052_3': + 'biocontainers/sambamba:1.0.1--he614052_3' }" + + input: + tuple val(meta), path(bam), path(bai) + tuple val(meta2), path(bed) + val(mode) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if (!['region','window','base'].contains(mode)) { + error "Mode needs to be one of: region, window, base" + } + def bed_arg = bed ? "--regions ${bed}" : '' + + """ + sambamba \\ + depth \\ + $mode \\ + $bed_arg \\ + $args \\ + -t $task.cpus \\ + -o ${prefix}.bed \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sambamba: \$(echo \$(sambamba --version 2>&1) | awk '{print \$2}' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sambamba: \$(sambamba --version) + END_VERSIONS + """ +} diff --git a/modules/nf-core/sambamba/depth/meta.yml b/modules/nf-core/sambamba/depth/meta.yml new file mode 100644 index 000000000..c16ce3a72 --- /dev/null +++ b/modules/nf-core/sambamba/depth/meta.yml @@ -0,0 +1,70 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "sambamba_depth" +description: Outputs a coverage file from bam files +keywords: + - depth + - coverage + - sambamba +tools: + - "sambamba": + description: "Tools for working with SAM/BAM data" + homepage: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" + documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" + tool_dev_url: "https://github.com/biod/sambamba" + doi: 10.1093/bioinformatics/btv098 + licence: ["GPL v2"] + identifier: biotools:sambamba +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + ontologies: + - edam: "http://edamontology.org/format_2572" + - bai: + type: file + description: BAI file + pattern: "*.{bai}" + ontologies: + - edam: "http://edamontology.org/format_2572" + - - meta2: + type: map + description: | + Groovy Map containing regions information + - bed: + type: file + description: bed file + pattern: "*.{bed}" + ontologies: + - edam: "http://edamontology.org/format_3003" # BED + - mode: + type: string + description: Analysis mode can be region, window, base + pattern: "region|window|base" +output: + bed: + - - meta: + type: map + description: Groovy Map containing sample information + - "*.bed": + type: file + description: bed file + pattern: "*.bed" + ontologies: + - edam: "http://edamontology.org/format_3586" # bed12 + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@peterpru" +maintainers: + - "@peterpru" diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test b/modules/nf-core/sambamba/depth/tests/main.nf.test new file mode 100644 index 000000000..3f5105986 --- /dev/null +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test @@ -0,0 +1,92 @@ + +nextflow_process { + + name "Test Process SAMBAMBA_DEPTH" + script "../main.nf" + process "SAMBAMBA_DEPTH" + + tag "modules" + tag "modules_nfcore" + tag "sambamba" + tag "sambamba/depth" + + test("test-sambamba-depth") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[], []] + input[2] = 'base' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-sambamba-depth-with-region-bed") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'test2' ], // meta2 map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[2] = 'region' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-sambamba-depth-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[], []] + input[2] = 'base' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap new file mode 100644 index 000000000..7f4951e62 --- /dev/null +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "test-sambamba-depth-with-region-bed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,e312edd2c0a9f63b833b5a8913952ba6" + ] + ], + "1": [ + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,e312edd2c0a9f63b833b5a8913952ba6" + ] + ], + "versions": [ + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-12-03T15:57:58.097957" + }, + "test-sambamba-depth": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,430bc921fe8a56d4a47a692a708dfb96" + ] + ], + "1": [ + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,430bc921fe8a56d4a47a692a708dfb96" + ] + ], + "versions": [ + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-12-03T15:57:42.031913" + }, + "test-sambamba-depth-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-12-03T15:58:13.647811" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 65ed2f62a..159a6cbd3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,6 +66,7 @@ params { reduced_penetrance = null readcount_intervals = null rtg_truthvcfs = null + sambamba_regions = null sample_id_map = null sequence_dictionary = null score_config_mt = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 582a23423..128ccd626 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -323,6 +323,14 @@ "pattern": "^\\S+\\.(csv|tsv|json|yaml|yml)$", "schema": "assets/rtg_truthvcfs_schema.json" }, + "sambamba_regions": { + "type": "string", + "exists": true, + "pattern": "^\\S+\\.bed$", + "fa_icon": "fas fa-file", + "format": "file-path", + "description": "A BED file with regions of interest used in sambamba depth.", + }, "save_reference": { "type": "boolean", "description": "If generated by the pipeline save the required indices/references in the results directory.", diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 831fdd854..6a688a5d2 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -8,6 +8,7 @@ include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../.. include { QUALIMAP_BAMQC } from '../../../modules/nf-core/qualimap/bamqc/main' include { TIDDIT_COV } from '../../../modules/nf-core/tiddit/cov/main' include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' +include { SAMBAMBA_DEPTH } from '../../../modules/nf-core/sambamba/depth/main' include { UCSC_WIGTOBIGWIG } from '../../../modules/nf-core/ucsc/wigtobigwig/main' include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG } from '../../../modules/nf-core/picard/collectwgsmetrics/main' include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../../modules/nf-core/picard/collectwgsmetrics/main' @@ -31,6 +32,7 @@ workflow QC_BAM { ch_svd_bed // channel: [optional] [ path(bed) ] ch_svd_mu // channel: [optional] [ path(meanpath) ] ch_svd_ud // channel: [optional] [ path(ud) ] + ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] ngsbits_samplegender_method // channel: [val(method)] main: @@ -62,6 +64,9 @@ workflow QC_BAM { ch_bam_bai.map{ meta, bam, bai -> [meta, bam, bai, []]}.set{ch_mosdepth_in} MOSDEPTH (ch_mosdepth_in, ch_genome_fasta) + + SAMBAMBA_DEPTH(ch_bam_bai, ch_sambamba_bed, 'region') + // COLLECT WGS METRICS if (!params.analysis_type.equals("wes")) { PICARD_COLLECTWGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs ) @@ -90,6 +95,8 @@ workflow QC_BAM { ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first()) ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first()) ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions.first()) + ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions.first()) + emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 43ecdb494..63a5c6356 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -198,6 +198,8 @@ workflow RAREDISEASE { : channel.value([]) ch_rtg_truthvcfs = params.rtg_truthvcfs ? channel.fromPath(params.rtg_truthvcfs).collect() : channel.value([]) + ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() + : channel.empty() ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) : channel.empty() ch_score_config_mt = params.score_config_mt ? channel.fromPath(params.score_config_mt).collect() @@ -407,6 +409,7 @@ workflow RAREDISEASE { ch_svd_bed, ch_svd_mu, ch_svd_ud, + ch_sambamba_bed, channel.value(params.ngsbits_samplegender_method) ) ch_versions = ch_versions.mix(QC_BAM.out.versions) From 209579f2d3ae17702b82838f6e6d5da19015e8e6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 5 Dec 2025 10:09:37 +0100 Subject: [PATCH 137/872] prettier --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 128ccd626..357b122e6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -329,7 +329,7 @@ "pattern": "^\\S+\\.bed$", "fa_icon": "fas fa-file", "format": "file-path", - "description": "A BED file with regions of interest used in sambamba depth.", + "description": "A BED file with regions of interest used in sambamba depth." }, "save_reference": { "type": "boolean", From db1e8eb282b64d72abf12e67a8350e17352110f6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 5 Dec 2025 10:10:35 +0100 Subject: [PATCH 138/872] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9fbcab225..c52e06c34 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Interval parameter in the default retroseq call [#717](https://github.com/nf-core/raredisease/pull/717) - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) -- Feature to subsample mitochondrial alignments based on number of reads. [#748](https://github.com/nf-core/raredisease/pull/748) -- Functionality to generate coverage information using Sambamba depth +- Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) +- Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) ### `Changed` From 1971d59091c8ca5722564de6157d92bb2f670ec6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 5 Dec 2025 11:09:18 +0100 Subject: [PATCH 139/872] update snap for qc_bam --- subworkflows/local/qc_bam/main.nf | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 10 ++++++---- subworkflows/local/qc_bam/tests/main.nf.test.snap | 8 ++++---- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 6a688a5d2..d1d78644e 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -32,7 +32,7 @@ workflow QC_BAM { ch_svd_bed // channel: [optional] [ path(bed) ] ch_svd_mu // channel: [optional] [ path(meanpath) ] ch_svd_ud // channel: [optional] [ path(ud) ] - ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] + ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] ngsbits_samplegender_method // channel: [val(method)] main: diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 329814674..9d996c8f5 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -36,10 +36,11 @@ nextflow_workflow { input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() input[8] = channel.empty() - input[9] = channel.empty() + input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = 'xy' + input[12] = channel.empty() + input[13] = 'xy' """ } } @@ -107,10 +108,11 @@ nextflow_workflow { input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() input[8] = channel.empty() - input[9] = channel.empty() + input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = 'xy' + input[12] = channel.empty() + input[13] = 'xy' """ } } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 28d846441..1a3514045 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -73,10 +73,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-07-10T16:16:06.053312997" + "timestamp": "2025-12-05T11:04:56.134850832" }, "QC_BAM - test, sentieon": { "content": [ @@ -155,6 +155,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-11-15T10:54:27.243271854" + "timestamp": "2025-12-05T11:05:33.520337099" } } \ No newline at end of file From b85c7f4aa01684ee471f4e1bcf8d47e7fe8d53e6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 5 Dec 2025 11:25:31 +0000 Subject: [PATCH 140/872] [automated] Fix code linting --- subworkflows/local/call_snv.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index ae02181ba..f5d16884b 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -57,7 +57,7 @@ workflow CALL_SNV { ch_sentieon_gtbi = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { - CALL_SNV_DEEPVARIANT ( + CALL_SNV_DEEPVARIANT ( ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, @@ -74,7 +74,7 @@ workflow CALL_SNV { ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) } else if (val_variant_caller.equals("sentieon")) { - CALL_SNV_SENTIEON( + CALL_SNV_SENTIEON( ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, From 90770404dfd0962aa4ead9590a292976e31fabe2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 5 Dec 2025 13:37:30 +0100 Subject: [PATCH 141/872] add tool and parameter info --- CHANGELOG.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c52e06c34..0dc4f4afb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,9 +29,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------- | ------------- | -| | | +| Old parameter | New parameter | +| ------------- | ---------------- | +| | sambamba_regions | ### Tool updates @@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | | gens-preproc | 1.0.11 | 1.1.2 | | samtools (sort & view) | 1.21 | 1.22.1 | +| sambamba | | 1.0.1 | ## 2.6.0 - Cacofonix [2025-06-25] From 90f5f19f11163c45948eca1994dd078dc8f6dea6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 8 Dec 2025 15:44:11 +0100 Subject: [PATCH 142/872] review suggestions --- modules/local/replace_spaces_in_vcfinfo/main.nf | 4 ++-- subworkflows/local/align/tests/main.nf.test | 7 ++++++- tests/default.nf.test.snap | 4 ++-- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/modules/local/replace_spaces_in_vcfinfo/main.nf b/modules/local/replace_spaces_in_vcfinfo/main.nf index afd660292..7027e02df 100644 --- a/modules/local/replace_spaces_in_vcfinfo/main.nf +++ b/modules/local/replace_spaces_in_vcfinfo/main.nf @@ -35,7 +35,7 @@ process REPLACE_SPACES_IN_VCFINFO { cat <<-END_VERSIONS > versions.yml "${task.process}": - replace_spaces_in_vcfinfo: v1.0 + replace_spaces_in_vcfinfo: 1.0 python: \$(python --version | sed 's/Python //g') END_VERSIONS """ @@ -52,7 +52,7 @@ process REPLACE_SPACES_IN_VCFINFO { cat <<-END_VERSIONS > versions.yml "${task.process}": - replace_spaces_in_vcfinfo: v1.0 + replace_spaces_in_vcfinfo: 1.0 python: \$(python --version | sed 's/Python //g') END_VERSIONS """ diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index e07048cc9..a183c4f48 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -217,7 +217,12 @@ nextflow_workflow { { assert snapshot( workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.versions + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mt_bam_bai_gatksubwf + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mtshift_bam_bai_gatksubwf + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions ).match() } ) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2c5cf1608..8ba4f8080 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -294,7 +294,7 @@ "coreutils": 8.31 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": "v1.0", + "replace_spaces_in_vcfinfo": 1.0, "python": "3.8.3" }, "RETROSEQ_CALL": { @@ -919,6 +919,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.0" }, - "timestamp": "2025-12-04T17:20:17.784028039" + "timestamp": "2025-12-08T10:42:54.212910271" } } \ No newline at end of file From 46099c139ffcaec5c43c2e70b64f4bc2b06abb4a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 8 Dec 2025 16:16:52 +0100 Subject: [PATCH 143/872] update haplogrep3 --- modules.json | 2 +- .../haplogrep3/classify/environment.yml | 2 + modules/nf-core/haplogrep3/classify/main.nf | 14 +------ modules/nf-core/haplogrep3/classify/meta.yml | 32 +++++++++++---- .../classify/tests/main.nf.test.snap | 40 +++++++++++++------ 5 files changed, 58 insertions(+), 32 deletions(-) diff --git a/modules.json b/modules.json index f4fb639d8..56535bc9b 100644 --- a/modules.json +++ b/modules.json @@ -294,7 +294,7 @@ }, "haplogrep3/classify": { "branch": "master", - "git_sha": "6af333190d76295671e4374df74513bdd7d1c596", + "git_sha": "c95c60597ce23da23ac21f4e6c5d7c0cdb711b8f", "installed_by": ["modules"] }, "hmtnote/annotate": { diff --git a/modules/nf-core/haplogrep3/classify/environment.yml b/modules/nf-core/haplogrep3/classify/environment.yml index ca0c7e691..c219ac43c 100644 --- a/modules/nf-core/haplogrep3/classify/environment.yml +++ b/modules/nf-core/haplogrep3/classify/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/haplogrep3/classify/main.nf b/modules/nf-core/haplogrep3/classify/main.nf index 056b0635f..712146369 100644 --- a/modules/nf-core/haplogrep3/classify/main.nf +++ b/modules/nf-core/haplogrep3/classify/main.nf @@ -11,8 +11,8 @@ process HAPLOGREP3_CLASSIFY { tuple val(meta), path(inputfile) output: - tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions + tuple val(meta) , path("*.txt") , emit: txt + tuple val("${task.process}"), val('haplogrep3'), eval("haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'"), emit: versions_haplogrep3, topic: versions when: task.ext.when == null || task.ext.when @@ -26,22 +26,12 @@ process HAPLOGREP3_CLASSIFY { $args \\ --in $inputfile \\ --out ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //')) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //')) - END_VERSIONS """ } diff --git a/modules/nf-core/haplogrep3/classify/meta.yml b/modules/nf-core/haplogrep3/classify/meta.yml index 4c5c925d2..53e40aa64 100644 --- a/modules/nf-core/haplogrep3/classify/meta.yml +++ b/modules/nf-core/haplogrep3/classify/meta.yml @@ -22,9 +22,10 @@ input: type: file description: valid options are hsd, vcf, or fasta files pattern: "*.{vcf,vcf.gz,fasta,hsd}" + ontologies: [] output: - - txt: - - meta: + txt: + - - meta: type: map description: | Groovy Map containing sample information @@ -33,11 +34,28 @@ output: type: file description: text file with classification information pattern: "*.{txt}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_haplogrep3: + - - ${task.process}: + type: string + description: The process the versions were collected from + - haplogrep3: + type: string + description: The tool name + - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - haplogrep3: + type: string + description: The tool name + - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': + type: string + description: The command used to generate the version of the tool authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap b/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap index d1a276d25..cce1f8715 100644 --- a/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap +++ b/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60" + [ + "HAPLOGREP3_CLASSIFY", + "haplogrep3", + "3.2.2" + ] ], "txt": [ [ @@ -23,16 +27,20 @@ "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60" + "versions_haplogrep3": [ + [ + "HAPLOGREP3_CLASSIFY", + "haplogrep3", + "3.2.2" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-28T15:34:35.106097277" + "timestamp": "2025-12-08T14:14:20.562672125" }, "test-haplogrep3-classify": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60" + [ + "HAPLOGREP3_CLASSIFY", + "haplogrep3", + "3.2.2" + ] ], "txt": [ [ @@ -58,15 +70,19 @@ "test.txt:md5,fb242df629aa6168371d1d742f0fb179" ] ], - "versions": [ - "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60" + "versions_haplogrep3": [ + [ + "HAPLOGREP3_CLASSIFY", + "haplogrep3", + "3.2.2" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-28T15:36:19.954363253" + "timestamp": "2025-12-08T14:14:10.117489085" } } \ No newline at end of file From 22c408ee703210d0ccc5a8c6821d779274f80e9f Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Dec 2025 08:21:57 +0100 Subject: [PATCH 144/872] remove eklipse --- modules.json | 7 -- modules/local/saltshaker/call/main.nf | 6 -- modules/nf-core/eklipse/environment.yml | 5 -- modules/nf-core/eklipse/main.nf | 59 -------------- modules/nf-core/eklipse/meta.yml | 78 ------------------- modules/nf-core/eklipse/tests/main.nf.test | 36 --------- .../nf-core/eklipse/tests/main.nf.test.snap | 11 --- modules/nf-core/eklipse/tests/tags.yml | 2 - 8 files changed, 204 deletions(-) delete mode 100644 modules/local/saltshaker/call/main.nf delete mode 100644 modules/nf-core/eklipse/environment.yml delete mode 100644 modules/nf-core/eklipse/main.nf delete mode 100644 modules/nf-core/eklipse/meta.yml delete mode 100644 modules/nf-core/eklipse/tests/main.nf.test delete mode 100644 modules/nf-core/eklipse/tests/main.nf.test.snap delete mode 100644 modules/nf-core/eklipse/tests/tags.yml diff --git a/modules.json b/modules.json index edc23cb80..9de004593 100644 --- a/modules.json +++ b/modules.json @@ -182,13 +182,6 @@ "modules" ] }, - "eklipse": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] - }, "ensemblvep/filtervep": { "branch": "master", "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf deleted file mode 100644 index 59cf6461a..000000000 --- a/modules/local/saltshaker/call/main.nf +++ /dev/null @@ -1,6 +0,0 @@ -process SS_CALL { - tag "$meta.id" - label 'process_single' - - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - ' diff --git a/modules/nf-core/eklipse/environment.yml b/modules/nf-core/eklipse/environment.yml deleted file mode 100644 index b638fba1d..000000000 --- a/modules/nf-core/eklipse/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::eklipse=1.8 diff --git a/modules/nf-core/eklipse/main.nf b/modules/nf-core/eklipse/main.nf deleted file mode 100644 index 98c577895..000000000 --- a/modules/nf-core/eklipse/main.nf +++ /dev/null @@ -1,59 +0,0 @@ - -process EKLIPSE { - tag "$meta.id" - label 'process_single' - - // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/eklipse:1.8--hdfd78af_1': - 'biocontainers/eklipse:1.8--hdfd78af_1' }" - - input: - tuple val(meta), path(bam), path(bai) - path ref_gb - - output: - tuple val(meta), path("*deletions.csv") , emit: deletions - tuple val(meta), path("*genes.csv") , emit: genes - tuple val(meta), path("*.png") , emit: circos - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def ref_gb = ref_gb ? "$ref_gb" : "/usr/local/bin/data/NC_012920.1.gb" - def VERSION = "1.8" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - echo "$bam\t${prefix}" > infile.txt - eKLIPse.py \\ - -in infile.txt \\ - $args \\ - -ref $ref_gb - mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_${prefix}_deletions.csv - mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_${prefix}_genes.csv - mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - eklipse: $VERSION - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.8" - """ - touch eKLIPse_${prefix}_deletions.csv - touch eKLIPse_${prefix}_genes.csv - touch eKLIPse_${prefix}.png - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - eklipse: $VERSION - END_VERSIONS - """ -} diff --git a/modules/nf-core/eklipse/meta.yml b/modules/nf-core/eklipse/meta.yml deleted file mode 100644 index cf3191959..000000000 --- a/modules/nf-core/eklipse/meta.yml +++ /dev/null @@ -1,78 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: "eklipse" -description: tool for detection and quantification of large mtDNA rearrangements. -keywords: - - eklipse - - mitochondria - - mtDNA - - circos - - deletion - - SV -tools: - - "eklipse": - description: "tool for detection and quantification of large mtDNA rearrangements." - homepage: "https://github.com/dooguypapua/eKLIPse/tree/master" - documentation: "https://github.com/dooguypapua/eKLIPse/tree/master" - tool_dev_url: "https://github.com/dooguypapua/eKLIPse/tree/master" - doi: "10.1038/s41436-018-0350-8" - licence: ["GNU General Public v3 or later (GPL v3+)"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: MT BAM/SAM file - pattern: "*.{bam,sam}" - - bai: - type: file - description: MT BAM/SAM index file - pattern: "*.{bai,sai}" - - - ref_gb: - type: file - description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb - will be used - pattern: "*.{gb}" -output: - - deletions: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*deletions.csv": - type: file - description: csv file with deletion information - pattern: "*deletions.csv" - - genes: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*genes.csv": - type: file - description: csv file with gene information - pattern: "*genes.csv" - - circos: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.png": - type: file - description: png file with circos plot of mt - pattern: "*.{png}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@Lucpen" -maintainers: - - "@Lucpen" diff --git a/modules/nf-core/eklipse/tests/main.nf.test b/modules/nf-core/eklipse/tests/main.nf.test deleted file mode 100644 index fb0be6d43..000000000 --- a/modules/nf-core/eklipse/tests/main.nf.test +++ /dev/null @@ -1,36 +0,0 @@ -nextflow_process { - - name "Test Process EKLIPSE" - script "../main.nf" - process "EKLIPSE" - tag "modules" - tag "modules_nfcore" - tag "eklipse" - - test("homo_sapiens [bam]") { - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai', checkIfExists: true) - ] - input[1] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.NC_012920_1.gb', checkIfExists: true) ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(file(process.out.deletions[0][1]), - file(process.out.genes[0][1]), - file(process.out.circos[0][1]), - file(process.out.versions[0])).match() - } - ) - } - } -} diff --git a/modules/nf-core/eklipse/tests/main.nf.test.snap b/modules/nf-core/eklipse/tests/main.nf.test.snap deleted file mode 100644 index 5969a1da0..000000000 --- a/modules/nf-core/eklipse/tests/main.nf.test.snap +++ /dev/null @@ -1,11 +0,0 @@ -{ - "homo_sapiens [bam]": { - "content": [ - "eKLIPse_test_deletions.csv:md5,8bcfdb8f3e8a63dcd211c2a53b6ca0a7", - "eKLIPse_test_genes.csv:md5,ec1a1f31d018ca66a46d8a2d17bc8d18", - "eKLIPse_test.png:md5,d1ea2a548bc4f8d321b1128a61ea8b0a", - "versions.yml:md5,8e6ebaa9abf72ced91c1f56acd10f131" - ], - "timestamp": "2024-02-11T14:55:25.205208435" - } -} \ No newline at end of file diff --git a/modules/nf-core/eklipse/tests/tags.yml b/modules/nf-core/eklipse/tests/tags.yml deleted file mode 100644 index eb91ee81f..000000000 --- a/modules/nf-core/eklipse/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -eklipse: - - modules/nf-core/eklipse/** From 0ceda253052c5856787e7a997a95a3086c4bd33d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 9 Dec 2025 10:17:01 +0100 Subject: [PATCH 145/872] update snaps --- subworkflows/local/align/tests/main.nf.test.snap | 13 +++++++++++-- subworkflows/local/annotate_mt_snvs.nf | 1 - subworkflows/local/qc_bam/tests/main.nf.test.snap | 4 ++-- tests/default.nf.test.snap | 6 +++--- tests/test_bam.nf.test.snap | 6 +++--- tests/test_singleton.nf.test.snap | 6 +++--- 6 files changed, 22 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 39bb67d3f..42f495bb1 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -483,6 +483,15 @@ "d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck_sorted_md.bam.bai" ] + ], + [ + + ], + [ + + ], + [ + ], [ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", @@ -497,8 +506,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-03T16:17:55.899272968" + "timestamp": "2025-12-08T16:34:03.159847454" } } \ No newline at end of file diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 6d78e207a..f2cc1d8e2 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -103,7 +103,6 @@ workflow ANNOTATE_MT_SNVS { if (!skip_haplogrep3) { HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in) ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt - ch_versions = ch_versions.mix(HAPLOGREP3_CLASSIFY_MT.out.versions) } ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 1a3514045..ae47dfe52 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -153,8 +153,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-05T11:05:33.520337099" + "timestamp": "2025-12-08T20:32:43.970984019" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8ba4f8080..a302513ac 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -219,7 +219,7 @@ "haplocheck": "1.3.3" }, "HAPLOGREP3_CLASSIFY_MT": { - "haplogrep3": null + "haplogrep3": "3.2.2" }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" @@ -917,8 +917,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-08T10:42:54.212910271" + "timestamp": "2025-12-09T10:05:22.987340316" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 100b947f5..86975e020 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -270,7 +270,7 @@ "coreutils": 8.31 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": "v1.0", + "replace_spaces_in_vcfinfo": 1.0, "python": "3.8.3" }, "RETROSEQ_CALL": { @@ -667,8 +667,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-04T18:15:10.207423904" + "timestamp": "2025-12-08T16:34:48.46542842" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 9877cb839..e6c0d8568 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -268,7 +268,7 @@ "coreutils": 8.31 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": "v1.0", + "replace_spaces_in_vcfinfo": 1.0, "python": "3.8.3" }, "RETROSEQ_CALL": { @@ -585,8 +585,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-04T18:21:22.86599878" + "timestamp": "2025-12-08T16:41:21.487778607" } } \ No newline at end of file From 33a03dd2c82625abeb3df9ff38000b96c8961af0 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Dec 2025 10:45:22 +0100 Subject: [PATCH 146/872] refactor mitosalt --- .../resources/usr/bin}/MitoSAlt1.1.1.pl | 0 nextflow.config | 27 +++---- nextflow_schema.json | 2 +- subworkflows/local/call_sv_MT/main.nf | 78 +++++++++---------- workflows/raredisease.nf | 42 ++++------ 5 files changed, 68 insertions(+), 81 deletions(-) rename {bin => modules/local/mitosalt/resources/usr/bin}/MitoSAlt1.1.1.pl (100%) diff --git a/bin/MitoSAlt1.1.1.pl b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl similarity index 100% rename from bin/MitoSAlt1.1.1.pl rename to modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl diff --git a/nextflow.config b/nextflow.config index e185a9ab6..d86042353 100644 --- a/nextflow.config +++ b/nextflow.config @@ -143,19 +143,20 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = System.getenv('HOOK_URL') - help = false - help_full = false - show_hidden = false - version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = System.getenv('HOOK_URL') + help = false + help_full = false + nextflow.enable.moduleBinaries = true + show_hidden = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 459e1bee9..3dec6e7cc 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -592,7 +592,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified tools.", "help_text": "Multiple tools can be specified, separated by commas.", - "pattern": "^((fastp|gens|germlinecnvcaller|haplogrep3|peddy|smncopynumbercaller|vcf2cytosure|fastqc|qualimap|ngsbits|mitosalt)?,?)*(? [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) - ch_cluster_threshold = Channel.value(params.cluster_threshold) ch_dbsnp_tbi = params.known_dbsnp_tbi ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) - ch_deletion_threshold_max = Channel.value(params.deletion_threshold_max) - ch_deletion_threshold_min = Channel.value(params.deletion_threshold_min) - ch_evalue_threshold = Channel.value(params.evalue_threshold) - ch_exclude = Channel.value(params.exclude) - ch_flank = Channel.value(params.flank) ch_foundin_header = Channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_gcnvcaller_model = params.gcnvcaller_model ? Channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> @@ -175,7 +167,6 @@ workflow RAREDISEASE { : ch_references.gnomad_af_idx ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() : Channel.empty() - ch_hplimit = Channel.value(params.hplimit) ch_intervals_wgs = params.intervals_wgs ? Channel.fromPath(params.intervals_wgs).collect() : Channel.empty() ch_intervals_y = params.intervals_y ? Channel.fromPath(params.intervals_y).collect() @@ -202,7 +193,6 @@ workflow RAREDISEASE { ch_mtshift_fai = ch_references.mtshift_fai ch_mtshift_fasta = ch_references.mtshift_fasta ch_mtshift_intervals = ch_references.mtshift_intervals - ch_paired_distance = Channel.value(params.paired_distance) ch_par_bed = params.par_bed ? Channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : Channel.value([[],[]]) ch_ploidy_model = params.ploidy_model ? Channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() @@ -221,12 +211,8 @@ workflow RAREDISEASE { : Channel.value([]) ch_score_config_sv = params.score_config_sv ? Channel.fromPath(params.score_config_sv).collect() : Channel.value([]) - ch_score_threshold = Channel.value(params.score_threshold) ch_sdf = params.sdf ? Channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf - ch_sizelimit = Channel.value(params.sizelimit) - ch_split_distance_threshold = Channel.value(params.split_distance_threshold) - ch_split_length = Channel.value(params.split_length) ch_subdepth = params.mitosalt_depth ? channel.value(params.mitosalt_depth) : channel.value([]) ch_sv_dbs = params.svdb_query_dbs ? Channel.fromPath(params.svdb_query_dbs) @@ -755,22 +741,22 @@ workflow RAREDISEASE { ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta, - ch_score_threshold, - ch_evalue_threshold, - ch_split_length, - ch_paired_distance, - ch_deletion_threshold_min, - ch_deletion_threshold_max, - ch_breakthreshold, - ch_cluster_threshold, - ch_breakspan, - ch_sizelimit, - ch_hplimit, - ch_flank, - ch_split_distance_threshold, + params.score_threshold, + params.evalue_threshold, + params.split_length, + params.paired_distance, + params.deletion_threshold_min, + params.deletion_threshold_max, + params.breakthreshold, + params.cluster_threshold, + params.breakspan, + params.sizelimit, + params.hplimit, + params.flank, + params.split_distance_threshold, ch_subdepth, ch_mito_name, - ch_exclude + params.exclude ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) From 14c9851fa0b588c3bb9b84755e92693de441931c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 11:45:31 +0100 Subject: [PATCH 147/872] move prep ref wf to main.nf --- main.nf | 286 +++++++++++++++++++++++++++++++++++++-- tests/nextflow.config | 17 ++- workflows/raredisease.nf | 279 +++++++++++--------------------------- 3 files changed, 364 insertions(+), 218 deletions(-) diff --git a/main.nf b/main.nf index 4f3da900a..88587dca6 100644 --- a/main.nf +++ b/main.nf @@ -14,12 +14,13 @@ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { RAREDISEASE } from './workflows/raredisease' +include { samplesheetToList } from 'plugin/nf-schema' +include { CREATE_HGNCIDS_FILE } from './modules/local/create_hgncids_file' +include { CREATE_PEDIGREE_FILE } from './modules/local/create_pedigree_file' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' - - +include { PREPARE_REFERENCES } from './subworkflows/local/prepare_references' +include { RAREDISEASE } from './workflows/raredisease' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -33,10 +34,10 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rare workflow NFCORE_RAREDISEASE { take: - fastq - alignment - samples - case_info + ch_alignments + ch_case_info + ch_reads + ch_samples main: @@ -44,6 +45,189 @@ workflow NFCORE_RAREDISEASE { // WORKFLOW: Run pipeline // + ch_versions = channel.empty() + ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() + ch_genome_fai = params.fai ? channel.fromPath(params.fai).map {it -> [[id:it.simpleName], it]}.collect() + : channel.empty() + ch_genome_dictionary = params.sequence_dictionary ? channel.fromPath(params.sequence_dictionary).map {it -> [[id:it.simpleName], it]}.collect() + : channel.empty() + ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_dbsnp = params.known_dbsnp ? channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_mt_fasta = params.mt_fasta ? channel.fromPath(params.mt_fasta).map { it -> [[id:it.simpleName], it] }.collect() + : channel.empty() + ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.value([[],[]]) + ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() + : channel.empty() + ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() + : channel.value([[],[]]) + + PREPARE_REFERENCES ( + ch_genome_fasta, + ch_genome_fai, + ch_genome_dictionary, + ch_mt_fasta, + ch_gnomad_af_tab, + ch_dbsnp, + ch_target_bed_unprocessed, + ch_vcfanno_extra_unprocessed, + ch_vep_cache_unprocessed + ) + .set { ch_references } + + ch_bait_intervals = ch_references.bait_intervals + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() + ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() + : channel.value([]) + ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() + : channel.value([[:],[]]) + ch_dbsnp_tbi = params.known_dbsnp_tbi ? channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() + : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) + ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() + ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) + .map { row -> + return [[id:file(row.models).simpleName], row.models] + } + : channel.empty() + ch_genome_bwaindex = params.bwa ? channel.fromPath(params.bwa).map {it -> [[id:it.simpleName], it]}.collect() + : ch_references.genome_bwa_index + ch_genome_bwamem2index = params.bwamem2 ? channel.fromPath(params.bwamem2).map {it -> [[id:it.simpleName], it]}.collect() + : ch_references.genome_bwamem2_index + ch_genome_bwamemeindex = params.bwameme ? channel.fromPath(params.bwameme).map {it -> [[id:it.simpleName], it]}.collect() + : ch_references.genome_bwameme_index + ch_genome_chrsizes = ch_references.genome_chrom_sizes + ch_genome_fai = ch_references.genome_fai + ch_genome_dictionary = ch_references.genome_dict + ch_gens_gnomad_pos = params.gens_gnomad_pos ? channel.fromPath(params.gens_gnomad_pos).collect() + : channel.empty() + ch_gens_interval_list = params.gens_interval_list ? channel.fromPath(params.gens_interval_list).collect() + : channel.empty() + ch_gens_pon_female = params.gens_pon_female ? channel.fromPath(params.gens_pon_female).map { it -> [ [id:it.simpleName], it ] }.collect() + : channel.empty() + ch_gens_pon_male = params.gens_pon_male ? channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() + : channel.empty() + ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() + : ch_references.gnomad_af_idx + ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() + : channel.empty() + ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() + : channel.empty() + ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() + : channel.empty() + ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) + : channel.empty() + ch_me_svdb_resources = params.mobile_element_svdb_annotations ? channel.fromPath(params.mobile_element_svdb_annotations) + : channel.empty() + ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() + : channel.value([[:],[]]) + ch_mt_intervals = ch_references.mt_intervals + ch_mt_bwaindex = ch_references.mt_bwa_index + ch_mt_bwamem2index = ch_references.mt_bwamem2_index + ch_mt_dictionary = ch_references.mt_dict + ch_mt_fai = ch_references.mt_fai + ch_mt_fasta = ch_references.mt_fasta + ch_mtshift_backchain = ch_references.mtshift_backchain + ch_mtshift_bwaindex = ch_references.mtshift_bwa_index + ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index + ch_mtshift_dictionary = ch_references.mtshift_dict + ch_mtshift_fai = ch_references.mtshift_fai + ch_mtshift_fasta = ch_references.mtshift_fasta + ch_mtshift_intervals = ch_references.mtshift_intervals + ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() + : channel.value([[],[]]) + ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() + : channel.empty() + ch_readcount_intervals = params.readcount_intervals ? channel.fromPath(params.readcount_intervals).collect() + : channel.empty() + ch_reduced_penetrance = params.reduced_penetrance ? channel.fromPath(params.reduced_penetrance).collect() + : channel.value([]) + ch_rtg_truthvcfs = params.rtg_truthvcfs ? channel.fromPath(params.rtg_truthvcfs).collect() + : channel.value([]) + ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() + : channel.empty() + ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) + : channel.empty() + ch_score_config_mt = params.score_config_mt ? channel.fromPath(params.score_config_mt).collect() + : channel.value([]) + ch_score_config_snv = params.score_config_snv ? channel.fromPath(params.score_config_snv).collect() + : channel.value([]) + ch_score_config_sv = params.score_config_sv ? channel.fromPath(params.score_config_sv).collect() + : channel.value([]) + ch_sdf = params.sdf ? channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() + : ch_references.sdf + ch_sv_dbs = params.svdb_query_dbs ? channel.fromPath(params.svdb_query_dbs) + : channel.empty() + ch_sv_bedpedbs = params.svdb_query_bedpedbs ? channel.fromPath(params.svdb_query_bedpedbs) + : channel.empty() + ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) + : channel.empty() + ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) + : channel.empty() + ch_svd_ud = params.verifybamid_svd_ud ? channel.fromPath(params.verifybamid_svd_ud) + : channel.empty() + ch_target_bed = ch_references.target_bed + ch_target_intervals = ch_references.target_intervals + ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) + ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) + ch_variant_consequences_sv = params.variant_consequences_sv ? channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() + : channel.value([[],[]]) + ch_vcfanno_extra = ch_references.vcfanno_extra + ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() + : channel.value([]) + ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? channel.fromPath(params.vcf2cytosure_blacklist).collect() + : channel.value([]) + ch_vcfanno_lua = params.vcfanno_lua ? channel.fromPath(params.vcfanno_lua).collect() + : channel.value([]) + ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() + : channel.value([]) + ch_vep_cache = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") ) ? ch_references.vep_resources + : ( params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([]) ) + ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() + : channel.empty() + ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() + : channel.empty() + ch_versions = ch_versions.mix(ch_references.versions) + + // + // Read and store paths in the vep_plugin_files file + // + ch_vep_extra_files = channel.empty() + if (params.vep_plugin_files) { + channel.fromPath(params.vep_plugin_files) + .collect() + .splitCsv ( header:true ) + .map { row -> + def f = file(row.vep_files[0]) + if(f.isFile() || f.isDirectory()){ + return [f] + } else { + error("\nVep database file ${f} does not exist.") + } + } + .collect() + .set {ch_vep_extra_files} + } + + // + // Dump all HGNC ids in a file + // + ch_vep_filters_scout_fmt + .mix (ch_vep_filters_std_fmt) + .set {ch_vep_filters} + + CREATE_HGNCIDS_FILE(ch_vep_filters) + .txt + .set {ch_hgnc_ids} + + // + // Generate pedigree file + // + ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped + if (params.skip_tools) { skip_eklipse = params.skip_tools.split(',').contains('eklipse') skip_fastp = params.skip_tools.split(',').contains('fastp') @@ -73,10 +257,82 @@ workflow NFCORE_RAREDISEASE { } RAREDISEASE ( - fastq, - alignment, - samples, - case_info, + ch_alignments, + ch_bait_intervals, + ch_cadd_header, + ch_cadd_resources, + ch_call_interval, + ch_case_info, + ch_dbsnp, + ch_dbsnp_tbi, + ch_foundin_header, + ch_gcnvcaller_model, + ch_genome_bwaindex, + ch_genome_bwamem2index, + ch_genome_bwamemeindex, + ch_genome_chrsizes, + ch_genome_dictionary, + ch_genome_fai, + ch_genome_fasta, + ch_gens_gnomad_pos, + ch_gens_interval_list, + ch_gens_pon_female, + ch_gens_pon_male, + ch_gnomad_af, + ch_gnomad_af_tab, + ch_gnomad_afidx, + ch_hgnc_ids, + ch_intervals_wgs, + ch_intervals_y, + ch_me_references, + ch_me_svdb_resources, + ch_ml_model, + ch_mt_bwaindex, + ch_mt_bwamem2index, + ch_mt_dictionary, + ch_mt_fai, + ch_mt_fasta, + ch_mt_intervals, + ch_mtshift_backchain, + ch_mtshift_bwaindex, + ch_mtshift_bwamem2index, + ch_mtshift_dictionary, + ch_mtshift_fai, + ch_mtshift_fasta, + ch_mtshift_intervals, + ch_par_bed, + ch_pedfile, + ch_ploidy_model, + ch_readcount_intervals, + ch_reads, + ch_reduced_penetrance, + ch_rtg_truthvcfs, + ch_sambamba_bed, + ch_sample_id_map, + ch_samples, + ch_score_config_mt, + ch_score_config_snv, + ch_score_config_sv, + ch_sdf, + ch_sv_bedpedbs, + ch_sv_dbs, + ch_svd_bed, + ch_svd_mu, + ch_svd_ud, + ch_target_bed, + ch_target_intervals, + ch_variant_catalog, + ch_variant_consequences_snv, + ch_variant_consequences_sv, + ch_vcf2cytosure_blacklist, + ch_vcfanno_extra, + ch_vcfanno_lua, + ch_vcfanno_resources, + ch_vcfanno_toml, + ch_vep_cache, + ch_vep_extra_files, + ch_vep_filters, + ch_versions, params.analysis_type, skip_me_calling, skip_me_annotation, @@ -131,10 +387,10 @@ workflow { // WORKFLOW: Run main workflow // NFCORE_RAREDISEASE ( - PIPELINE_INITIALISATION.out.reads, PIPELINE_INITIALISATION.out.align, - PIPELINE_INITIALISATION.out.samples, - PIPELINE_INITIALISATION.out.case_info + PIPELINE_INITIALISATION.out.case_info, + PIPELINE_INITIALISATION.out.reads, + PIPELINE_INITIALISATION.out.samples ) // // SUBWORKFLOW: Run completion tasks diff --git a/tests/nextflow.config b/tests/nextflow.config index fef7084f8..b61089b40 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -24,8 +24,21 @@ env { // NOTE This is how pipeline users will use Sentieon in real world use SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + //SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + //SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA // NOTE This is how pipeline users will test out Sentieon with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } + +singularity { + autoMounts = true + runOptions = '-B /home/ramprasad.neethiraj/tmp -B /home/ramprasad.neethiraj/nextflow -B /home/ramprasad.neethiraj/tmp:/rdds/tmp' +} +// Set bash options +process.shell = [ + "bash", + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 6adcfa3e7..46ea7de21 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -3,10 +3,10 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryMap;samplesheetToList } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_raredisease_pipeline' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_raredisease_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -34,8 +34,6 @@ include { STRANGER } from '../modules/n include { RENAME_ALIGN_FILES as RENAME_BAM } from '../modules/local/rename_align_files' include { RENAME_ALIGN_FILES as RENAME_BAI } from '../modules/local/rename_align_files' -include { CREATE_HGNCIDS_FILE } from '../modules/local/create_hgncids_file' -include { CREATE_PEDIGREE_FILE } from '../modules/local/create_pedigree_file' // // SUBWORKFLOWS @@ -79,10 +77,82 @@ include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SV } from '.. workflow RAREDISEASE { take: - ch_reads ch_alignments - ch_samples + ch_bait_intervals + ch_cadd_header + ch_cadd_resources + ch_call_interval ch_case_info + ch_dbsnp + ch_dbsnp_tbi + ch_foundin_header + ch_gcnvcaller_model + ch_genome_bwaindex + ch_genome_bwamem2index + ch_genome_bwamemeindex + ch_genome_chrsizes + ch_genome_dictionary + ch_genome_fai + ch_genome_fasta + ch_gens_gnomad_pos + ch_gens_interval_list + ch_gens_pon_female + ch_gens_pon_male + ch_gnomad_af + ch_gnomad_af_tab + ch_gnomad_afidx + ch_hgnc_ids + ch_intervals_wgs + ch_intervals_y + ch_me_references + ch_me_svdb_resources + ch_ml_model + ch_mt_bwaindex + ch_mt_bwamem2index + ch_mt_dictionary + ch_mt_fai + ch_mt_fasta + ch_mt_intervals + ch_mtshift_backchain + ch_mtshift_bwaindex + ch_mtshift_bwamem2index + ch_mtshift_dictionary + ch_mtshift_fai + ch_mtshift_fasta + ch_mtshift_intervals + ch_par_bed + ch_pedfile + ch_ploidy_model + ch_readcount_intervals + ch_reads + ch_reduced_penetrance + ch_rtg_truthvcfs + ch_sambamba_bed + ch_sample_id_map + ch_samples + ch_score_config_mt + ch_score_config_snv + ch_score_config_sv + ch_sdf + ch_sv_bedpedbs + ch_sv_dbs + ch_svd_bed + ch_svd_mu + ch_svd_ud + ch_target_bed + ch_target_intervals + ch_variant_catalog + ch_variant_consequences_snv + ch_variant_consequences_sv + ch_vcf2cytosure_blacklist + ch_vcfanno_extra + ch_vcfanno_lua + ch_vcfanno_resources + ch_vcfanno_toml + ch_vep_cache + ch_vep_extra_files + ch_vep_filters + ch_versions analysis_type skip_me_calling skip_me_annotation @@ -109,167 +179,9 @@ workflow RAREDISEASE { main: - ch_versions = channel.empty() ch_multiqc_files = channel.empty() ch_mt_txt = channel.empty() - // - // Initialize file channels for PREPARE_REFERENCES subworkflow - // - ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() - ch_genome_fai = params.fai ? channel.fromPath(params.fai).map {it -> [[id:it.simpleName], it]}.collect() - : channel.empty() - ch_genome_dictionary = params.sequence_dictionary ? channel.fromPath(params.sequence_dictionary).map {it -> [[id:it.simpleName], it]}.collect() - : channel.empty() - ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) - ch_dbsnp = params.known_dbsnp ? channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) - ch_mt_fasta = params.mt_fasta ? channel.fromPath(params.mt_fasta).map { it -> [[id:it.simpleName], it] }.collect() - : channel.empty() - ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) - ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() - : channel.empty() - ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() - : channel.value([[],[]]) - - // - // Prepare references and indices. - // - PREPARE_REFERENCES ( - ch_genome_fasta, - ch_genome_fai, - ch_genome_dictionary, - ch_mt_fasta, - ch_gnomad_af_tab, - ch_dbsnp, - ch_target_bed_unprocessed, - ch_vcfanno_extra_unprocessed, - ch_vep_cache_unprocessed - ) - .set { ch_references } - - // - // Gather built indices or get them from the params - // - ch_bait_intervals = ch_references.bait_intervals - ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() - ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() - : channel.value([]) - ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() - : channel.value([[:],[]]) - ch_dbsnp_tbi = params.known_dbsnp_tbi ? channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) - ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() - ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) - .map { row -> - return [[id:file(row.models).simpleName], row.models] - } - : channel.empty() - ch_genome_bwaindex = params.bwa ? channel.fromPath(params.bwa).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwa_index - ch_genome_bwamem2index = params.bwamem2 ? channel.fromPath(params.bwamem2).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwamem2_index - ch_genome_bwamemeindex = params.bwameme ? channel.fromPath(params.bwameme).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwameme_index - ch_genome_chrsizes = ch_references.genome_chrom_sizes - ch_genome_fai = ch_references.genome_fai - ch_genome_dictionary = ch_references.genome_dict - ch_gens_gnomad_pos = params.gens_gnomad_pos ? channel.fromPath(params.gens_gnomad_pos).collect() - : channel.empty() - ch_gens_interval_list = params.gens_interval_list ? channel.fromPath(params.gens_interval_list).collect() - : channel.empty() - ch_gens_pon_female = params.gens_pon_female ? channel.fromPath(params.gens_pon_female).map { it -> [ [id:it.simpleName], it ] }.collect() - : channel.empty() - ch_gens_pon_male = params.gens_pon_male ? channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() - : channel.empty() - ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() - : ch_references.gnomad_af_idx - ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() - : channel.empty() - ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() - : channel.empty() - ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() - : channel.empty() - ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) - : channel.empty() - ch_me_svdb_resources = params.mobile_element_svdb_annotations ? channel.fromPath(params.mobile_element_svdb_annotations) - : channel.empty() - ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() - : channel.value([[:],[]]) - ch_mt_intervals = ch_references.mt_intervals - ch_mt_bwaindex = ch_references.mt_bwa_index - ch_mt_bwamem2index = ch_references.mt_bwamem2_index - ch_mt_dictionary = ch_references.mt_dict - ch_mt_fai = ch_references.mt_fai - ch_mt_fasta = ch_references.mt_fasta - ch_mtshift_backchain = ch_references.mtshift_backchain - ch_mtshift_bwaindex = ch_references.mtshift_bwa_index - ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index - ch_mtshift_dictionary = ch_references.mtshift_dict - ch_mtshift_fai = ch_references.mtshift_fai - ch_mtshift_fasta = ch_references.mtshift_fasta - ch_mtshift_intervals = ch_references.mtshift_intervals - ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() - : channel.value([[],[]]) - ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.empty() - ch_readcount_intervals = params.readcount_intervals ? channel.fromPath(params.readcount_intervals).collect() - : channel.empty() - ch_reduced_penetrance = params.reduced_penetrance ? channel.fromPath(params.reduced_penetrance).collect() - : channel.value([]) - ch_rtg_truthvcfs = params.rtg_truthvcfs ? channel.fromPath(params.rtg_truthvcfs).collect() - : channel.value([]) - ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() - : channel.empty() - ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) - : channel.empty() - ch_score_config_mt = params.score_config_mt ? channel.fromPath(params.score_config_mt).collect() - : channel.value([]) - ch_score_config_snv = params.score_config_snv ? channel.fromPath(params.score_config_snv).collect() - : channel.value([]) - ch_score_config_sv = params.score_config_sv ? channel.fromPath(params.score_config_sv).collect() - : channel.value([]) - ch_sdf = params.sdf ? channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() - : ch_references.sdf - ch_sv_dbs = params.svdb_query_dbs ? channel.fromPath(params.svdb_query_dbs) - : channel.empty() - ch_sv_bedpedbs = params.svdb_query_bedpedbs ? channel.fromPath(params.svdb_query_bedpedbs) - : channel.empty() - ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) - : channel.empty() - ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) - : channel.empty() - ch_svd_ud = params.verifybamid_svd_ud ? channel.fromPath(params.verifybamid_svd_ud) - : channel.empty() - ch_target_bed = ch_references.target_bed - ch_target_intervals = ch_references.target_intervals - ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) - ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) - ch_variant_consequences_sv = params.variant_consequences_sv ? channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) - ch_vcfanno_extra = ch_references.vcfanno_extra - ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() - : channel.value([]) - ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? channel.fromPath(params.vcf2cytosure_blacklist).collect() - : channel.value([]) - ch_vcfanno_lua = params.vcfanno_lua ? channel.fromPath(params.vcfanno_lua).collect() - : channel.value([]) - ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() - : channel.value([]) - ch_vep_cache = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") ) ? ch_references.vep_resources - : ( params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([]) ) - ch_vep_extra_files_unsplit = params.vep_plugin_files ? channel.fromPath(params.vep_plugin_files).collect() - : channel.value([]) - ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() - : channel.empty() - ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() - : channel.empty() - ch_versions = ch_versions.mix(ch_references.versions) - // // SV caller priority // @@ -287,41 +199,6 @@ workflow RAREDISEASE { } } - // - // Generate pedigree file - // - ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped - ch_versions = ch_versions.mix(CREATE_PEDIGREE_FILE.out.versions) - - // - // Read and store paths in the vep_plugin_files file - // - ch_vep_extra_files = channel.empty() - if (params.vep_plugin_files) { - ch_vep_extra_files_unsplit.splitCsv ( header:true ) - .map { row -> - def f = file(row.vep_files[0]) - if(f.isFile() || f.isDirectory()){ - return [f] - } else { - error("\nVep database file ${f} does not exist.") - } - } - .collect() - .set {ch_vep_extra_files} - } - - // - // Dump all HGNC ids in a file - // - ch_vep_filters_scout_fmt - .mix (ch_vep_filters_std_fmt) - .set {ch_vep_filters} - - CREATE_HGNCIDS_FILE(ch_vep_filters) - .txt - .set {ch_hgnc_ids} - // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) // From 6007b1f0c936c3b619268f6d464e7d840b94b0ba Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 11:51:54 +0100 Subject: [PATCH 148/872] parser stuff --- workflows/raredisease.nf | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 6adcfa3e7..a4f07cba6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -186,7 +186,7 @@ workflow RAREDISEASE { : channel.empty() ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() : ch_references.gnomad_af_idx - ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() + ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {_meta, tab, idx -> [tab,idx]}.collect() : channel.empty() ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() : channel.empty() @@ -987,22 +987,22 @@ workflow RAREDISEASE { ) if (!skip_fastqc) { - ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{_meta, reports -> reports}.ifEmpty([])) } - ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{it[1]}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) if (!skip_peddy) { - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{it[1]}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{_meta, reports -> reports}.collect().ifEmpty([])) } MULTIQC ( From 3f6f3a2b572bf28fe0b17197dc8e9c6876b02051 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 14:47:08 +0100 Subject: [PATCH 149/872] move more items from raredisease.nf to main.nf --- main.nf | 86 ++++++++++++------- .../utils_nfcore_raredisease_pipeline/main.nf | 21 +++-- workflows/raredisease.nf | 35 +------- 3 files changed, 73 insertions(+), 69 deletions(-) diff --git a/main.nf b/main.nf index 88587dca6..ed02778c4 100644 --- a/main.nf +++ b/main.nf @@ -17,10 +17,12 @@ include { samplesheetToList } from 'plugin/nf-schema' include { CREATE_HGNCIDS_FILE } from './modules/local/create_hgncids_file' include { CREATE_PEDIGREE_FILE } from './modules/local/create_pedigree_file' +include { parseSkipList } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PREPARE_REFERENCES } from './subworkflows/local/prepare_references' include { RAREDISEASE } from './workflows/raredisease' +include { SCATTER_GENOME } from './subworkflows/local/scatter_genome' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -110,7 +112,7 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() : ch_references.gnomad_af_idx - ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect() + ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {_meta, tab, idx -> [tab,idx]}.collect() : channel.empty() ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() : channel.empty() @@ -228,32 +230,60 @@ workflow NFCORE_RAREDISEASE { // ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped - if (params.skip_tools) { - skip_eklipse = params.skip_tools.split(',').contains('eklipse') - skip_fastp = params.skip_tools.split(',').contains('fastp') - skip_fastqc = params.skip_tools.split(',').contains('fastqc') - skip_gens = params.skip_tools.split(',').contains('gens') - skip_germlinecnvcaller = params.skip_tools.split(',').contains('germlinecnvcaller') - skip_haplogrep3 = params.skip_tools.split(',').contains('haplogrep3') - skip_ngsbits = params.skip_tools.split(',').contains('ngsbits') - skip_peddy = params.skip_tools.split(',').contains('peddy') - skip_qualimap = params.skip_tools.split(',').contains('qualimap') - skip_smncopynumbercaller = params.skip_tools.split(',').contains('smncopynumbercaller') - skip_vcf2cytosure = params.skip_tools.split(',').contains('vcf2cytosure') + // Tools + skip_eklipse = parseSkipList(params.skip_tools, 'eklipse') + skip_fastp = parseSkipList(params.skip_tools, 'fastp') + skip_fastqc = parseSkipList(params.skip_tools, 'fastqc') + skip_gens = parseSkipList(params.skip_tools, 'gens') + skip_germlinecnvcaller = parseSkipList(params.skip_tools, 'germlinecnvcaller') + skip_haplogrep3 = parseSkipList(params.skip_tools, 'haplogrep3') + skip_ngsbits = parseSkipList(params.skip_tools, 'ngsbits') + skip_peddy = parseSkipList(params.skip_tools, 'peddy') + skip_qualimap = parseSkipList(params.skip_tools, 'qualimap') + skip_smncopynumbercaller = parseSkipList(params.skip_tools, 'smncopynumbercaller') + skip_vcf2cytosure = parseSkipList(params.skip_tools, 'vcf2cytosure') + + // Subworkflows + skip_me_annotation = parseSkipList(params.skip_subworkflows, 'me_annotation') + skip_me_calling = parseSkipList(params.skip_subworkflows, 'me_calling') + skip_mt_annotation = parseSkipList(params.skip_subworkflows, 'mt_annotation') + skip_mt_subsample = parseSkipList(params.skip_subworkflows, 'mt_subsample') + skip_repeat_annotation = parseSkipList(params.skip_subworkflows, 'repeat_annotation') + skip_repeat_calling = parseSkipList(params.skip_subworkflows, 'repeat_calling') + skip_snv_annotation = parseSkipList(params.skip_subworkflows, 'snv_annotation') + skip_snv_calling = parseSkipList(params.skip_subworkflows, 'snv_calling') + skip_sv_annotation = parseSkipList(params.skip_subworkflows, 'sv_annotation') + skip_sv_calling = parseSkipList(params.skip_subworkflows, 'sv_calling') + skip_generate_clinical_set = parseSkipList(params.skip_subworkflows, 'generate_clinical_set') + + // + // SV caller priority + // + if (skip_germlinecnvcaller) { + if (params.analysis_type.equals("wgs")) { + ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) + } else { + ch_svcaller_priority = channel.value([]) + } + } else { + if (params.analysis_type.equals("wgs")) { + ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) + } else { + ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) + } } - if (params.skip_subworkflows) { - skip_me_annotation = params.skip_tools.split(',').contains('me_annotation') - skip_me_calling = params.skip_tools.split(',').contains('me_calling') - skip_mt_annotation = params.skip_tools.split(',').contains('mt_annotation') - skip_mt_subsample = params.skip_tools.split(',').contains('mt_subsample') - skip_repeat_annotation = params.skip_tools.split(',').contains('repeat_annotation') - skip_repeat_calling = params.skip_tools.split(',').contains('repeat_calling') - skip_snv_annotation = params.skip_tools.split(',').contains('snv_annotation') - skip_snv_calling = params.skip_tools.split(',').contains('snv_calling') - skip_sv_annotation = params.skip_tools.split(',').contains('sv_annotation') - skip_sv_calling = params.skip_tools.split(',').contains('sv_calling') - skip_generate_clinical_set = params.skip_tools.split(',').contains('generate_clinical_set') + // + // Create chromosome bed and intervals for splitting and gathering operations + // + ch_scatter_split_intervals = channel.empty() + if (!skip_snv_annotation) { + SCATTER_GENOME ( + ch_genome_dictionary, + ch_genome_fai, + ch_genome_fasta + ).split_intervals + .set { ch_scatter_split_intervals } } RAREDISEASE ( @@ -279,8 +309,6 @@ workflow NFCORE_RAREDISEASE { ch_gens_pon_female, ch_gens_pon_male, ch_gnomad_af, - ch_gnomad_af_tab, - ch_gnomad_afidx, ch_hgnc_ids, ch_intervals_wgs, ch_intervals_y, @@ -310,12 +338,14 @@ workflow NFCORE_RAREDISEASE { ch_sambamba_bed, ch_sample_id_map, ch_samples, + ch_scatter_split_intervals, ch_score_config_mt, ch_score_config_snv, ch_score_config_sv, ch_sdf, ch_sv_bedpedbs, ch_sv_dbs, + ch_svcaller_priority, ch_svd_bed, ch_svd_mu, ch_svd_ud, @@ -331,7 +361,6 @@ workflow NFCORE_RAREDISEASE { ch_vcfanno_toml, ch_vep_cache, ch_vep_extra_files, - ch_vep_filters, ch_versions, params.analysis_type, skip_me_calling, @@ -375,7 +404,6 @@ workflow { PIPELINE_INITIALISATION ( params.version, params.validate_params, - params.monochrome_logs, args, params.outdir, params.input, diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index f6696f133..0f64fd518 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -29,7 +29,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet @@ -102,9 +101,9 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .tap { ch_original_input } - .map { meta, fastq1, fastq2, spring1, spring2, bam, bai -> meta.id } + .map { meta, _fastq1, _fastq2, _spring1, _spring2, _bam, _bai -> meta.id } .reduce([:]) { counts, sample -> //get counts of each sample in the samplesheet - for groupTuple counts[sample] = (counts[sample] ?: 0) + 1 counts @@ -130,7 +129,7 @@ workflow PIPELINE_INITIALISATION { } } .tap{ ch_input_counts } - .map { meta, files -> files } + .map { _meta, files -> files } .reduce([:]) { counts, files -> //get line number for each row to construct unique sample ids counts[files] = counts.size() + 1 return counts @@ -149,13 +148,13 @@ workflow PIPELINE_INITIALISATION { } .set {ch_samplesheet_by_type} - ch_samples = ch_samplesheet.map { meta, files -> + ch_samples = ch_samplesheet.map { meta, _files -> def new_id = meta.sample def new_meta = meta - meta.subMap('lane', 'read_group') + [id:new_id] return new_meta }.unique() - ch_case_info = ch_samples.toList().map { createCaseChannel(it) } + ch_case_info = ch_samples.toList().map { it -> createCaseChannel(it) } emit: reads = ch_samplesheet_by_type.fastq @@ -266,6 +265,14 @@ def validateInputParameters() { genomeExistsError() } + +// +// Initialize skip parameters +// +def parseSkipList(paramValue, toolName) { + return paramValue ? paramValue.split(',').contains(toolName) : false +} + // // Validate parameters // @@ -314,7 +321,7 @@ def checkRequiredParameters(params) { } } - all_skips = params.skip_subworkflows+","+params.skip_tools + def all_skips = params.skip_subworkflows+","+params.skip_tools dynamicRequirements.each { condition, paramsList -> if (!all_skips.split(',').contains(condition)) { mandatoryParams += paramsList diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3c3498a1c..bf0c44eaa 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -59,7 +59,6 @@ include { QC_BAM } from '.. include { RANK_VARIANTS as RANK_VARIANTS_MT } from '../subworkflows/local/rank_variants' include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' -include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' include { SUBSAMPLE_MT_FRAC } from '../subworkflows/local/subsample_mt_frac' include { SUBSAMPLE_MT_READS } from '../subworkflows/local/subsample_mt_reads' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' @@ -99,8 +98,6 @@ workflow RAREDISEASE { ch_gens_pon_female ch_gens_pon_male ch_gnomad_af - ch_gnomad_af_tab - ch_gnomad_afidx ch_hgnc_ids ch_intervals_wgs ch_intervals_y @@ -130,12 +127,14 @@ workflow RAREDISEASE { ch_sambamba_bed ch_sample_id_map ch_samples + ch_scatter_split_intervals ch_score_config_mt ch_score_config_snv ch_score_config_sv ch_sdf ch_sv_bedpedbs ch_sv_dbs + ch_svcaller_priority ch_svd_bed ch_svd_mu ch_svd_ud @@ -151,7 +150,6 @@ workflow RAREDISEASE { ch_vcfanno_toml ch_vep_cache ch_vep_extra_files - ch_vep_filters ch_versions analysis_type skip_me_calling @@ -182,22 +180,6 @@ workflow RAREDISEASE { ch_multiqc_files = channel.empty() ch_mt_txt = channel.empty() - // SV caller priority - // - if (skip_germlinecnvcaller) { - if (analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) - } else { - ch_svcaller_priority = channel.value([]) - } - } else { - if (analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) - } else { - ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) - } - } - // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) // @@ -221,19 +203,6 @@ workflow RAREDISEASE { ch_input_fastqs = ch_input_by_sample_type.fastq_gz.mix(ch_one_fastq_gz_pair_from_spring).mix(ch_two_fastq_gz_from_spring) - // - // Create chromosome bed and intervals for splitting and gathering operations - // - ch_scatter_split_intervals = channel.empty() - if (!skip_snv_annotation) { - SCATTER_GENOME ( - ch_genome_dictionary, - ch_genome_fai, - ch_genome_fasta - ).split_intervals - .set { ch_scatter_split_intervals } - } - // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is nott fastq) // From 9195330a0dd885ca41c9a0e85fff87433ee7c772 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 14:49:27 +0100 Subject: [PATCH 150/872] update env for sentieon test --- .../local/align_sentieon/tests/nextflow.config | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/nextflow.config b/subworkflows/local/align_sentieon/tests/nextflow.config index 76615ae41..f1ecc67a5 100644 --- a/subworkflows/local/align_sentieon/tests/nextflow.config +++ b/subworkflows/local/align_sentieon/tests/nextflow.config @@ -1,12 +1,10 @@ env { - // NOTE This is how nf-core/raredisease users will use Sentieon in real world use with an IP - // SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" - - // NOTE This is how nf-core/raredisease users will test out Sentieon in raredisease with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) + // NOTE This is how pipeline users will use Sentieon in real world use + SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA } From e5d25247e712b8fabe5f5e4b424db21cc0df9450 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 14:57:26 +0100 Subject: [PATCH 151/872] pre-commit --- subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index 0f64fd518..e711d5c55 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -268,7 +268,7 @@ def validateInputParameters() { // // Initialize skip parameters -// +// def parseSkipList(paramValue, toolName) { return paramValue ? paramValue.split(',').contains(toolName) : false } From fe0c8444e2de758f66499f602deb7975ebdd020f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Dec 2025 15:35:03 +0100 Subject: [PATCH 152/872] update config --- .../align_sentieon/tests/nextflow.config | 10 --------- tests/nextflow.config | 21 ++++--------------- 2 files changed, 4 insertions(+), 27 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/nextflow.config b/subworkflows/local/align_sentieon/tests/nextflow.config index f1ecc67a5..bb4c7f5bc 100644 --- a/subworkflows/local/align_sentieon/tests/nextflow.config +++ b/subworkflows/local/align_sentieon/tests/nextflow.config @@ -1,13 +1,3 @@ -env { - // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') - - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') - - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA -} - process { withName: 'SENTIEON_BWAMEM' { diff --git a/tests/nextflow.config b/tests/nextflow.config index b61089b40..5d388a7f6 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -22,23 +22,10 @@ aws.client.anonymous = true // fixes S3 access issues on self-hosted runners env { // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') ?: false + // NOTE This should only happen in GitHub actions or nf-core MegaTests - //SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - //SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how pipeline users will test out Sentieon with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} + SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') ?: false -singularity { - autoMounts = true - runOptions = '-B /home/ramprasad.neethiraj/tmp -B /home/ramprasad.neethiraj/nextflow -B /home/ramprasad.neethiraj/tmp:/rdds/tmp' + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA ?: false } -// Set bash options -process.shell = [ - "bash", - "-e", // Exit if a tool returns a non-zero status/exit code - "-u", // Treat unset variables and parameters as an error - "-o", // Returns the status of the last command to exit.. - "pipefail" // ..with a non-zero status or zero if all successfully execute -] From b5168cd1b6849843e3eec0e4e69439f6249cceb8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 08:27:10 +0100 Subject: [PATCH 153/872] update tests --- conf/test.config | 3 +- conf/test_bam.config | 3 - conf/test_sentieon.config | 2 - conf/test_singleton.config | 3 - main.nf | 1 + tests/default.nf.test | 2 +- tests/test_bam.nf.test | 3 +- tests/test_bam.nf.test.snap | 195 +++++++++++++++++++++++++++++- tests/test_singleton.nf.test | 3 +- tests/test_singleton.nf.test.snap | 95 ++++++++++++++- 10 files changed, 293 insertions(+), 17 deletions(-) diff --git a/conf/test.config b/conf/test.config index 0c01b1035..843c89bad 100644 --- a/conf/test.config +++ b/conf/test.config @@ -36,8 +36,7 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' - skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' - skip_subworkflows = "mt_annotation,mt_subsample,sv_annotation" + skip_tools = 'gens,germlinecnvcaller' input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' diff --git a/conf/test_bam.config b/conf/test_bam.config index 3e164ab46..f66191c3c 100644 --- a/conf/test_bam.config +++ b/conf/test_bam.config @@ -36,9 +36,6 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse' - skip_subworkflows = "mt_annotation,mt_subsample,me_calling,me_annotation,sv_annotation" - input = params.pipelines_testdata_base_path + 'testdata/samplesheet_bam.csv' fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config index 5349641d6..a2a5ad710 100644 --- a/conf/test_sentieon.config +++ b/conf/test_sentieon.config @@ -35,8 +35,6 @@ params { igenomes_ignore = true mito_name = 'MT' - skip_tools = 'gens,haplogrep3,peddy,germlinecnvcaller' - // Input data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' input = params.pipelines_testdata_base_path + 'testdata/samplesheet_trio.csv' diff --git a/conf/test_singleton.config b/conf/test_singleton.config index 615f16a68..1c885ab39 100644 --- a/conf/test_singleton.config +++ b/conf/test_singleton.config @@ -36,9 +36,6 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' - skip_subworkflows = "mt_annotation,mt_subsample,me_calling,me_annotation,sv_annotation" - input = params.pipelines_testdata_base_path + 'testdata/samplesheet_single.csv' fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' fai = params.pipelines_testdata_base_path + 'reference/reference.fasta.fai' diff --git a/main.nf b/main.nf index ed02778c4..440fa257a 100644 --- a/main.nf +++ b/main.nf @@ -229,6 +229,7 @@ workflow NFCORE_RAREDISEASE { // Generate pedigree file // ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped + ch_versions = ch_versions.mix(CREATE_PEDIGREE_FILE.out.versions) // Tools skip_eklipse = parseSkipList(params.skip_tools, 'eklipse') diff --git a/tests/default.nf.test b/tests/default.nf.test index 50792315c..59e505297 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" skip_tools = "germlinecnvcaller,gens" } } diff --git a/tests/test_bam.nf.test b/tests/test_bam.nf.test index 82487c3eb..20c314c84 100644 --- a/tests/test_bam.nf.test +++ b/tests/test_bam.nf.test @@ -11,7 +11,8 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" + skip_tools = "germlinecnvcaller,gens" } } diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 86975e020..3c92e4efd 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 794, + 802, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -121,6 +121,9 @@ "DEEPVARIANT": { "deepvariant": "1.8.0" }, + "EKLIPSE": { + "eklipse": 1.8 + }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -206,6 +209,9 @@ "HAPLOCHECK_MT": { "haplocheck": "1.3.3" }, + "HAPLOGREP3_CLASSIFY_MT": { + "haplogrep3": "3.2.2" + }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" }, @@ -230,6 +236,9 @@ "NGSBITS_SAMPLEGENDER": { "ngs-bits": 202411 }, + "PEDDY": { + "peddy": "0.4.8" + }, "PICARD_ADDORREPLACEREADGROUPS_MT": { "picard": "3.3.0" }, @@ -254,6 +263,9 @@ "PICARD_SORTVCF": { "picard": "3.3.0" }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.21 }, @@ -488,6 +500,7 @@ "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.json.gz", "annotate_sv/justhusky_svdbquery_vep.summary.html", @@ -513,6 +526,15 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman.png", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman_deletions.csv", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman_genes.csv", + "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck.png", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck_deletions.csv", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck_genes.csv", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", @@ -528,11 +550,72 @@ "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", + "peddy", + "peddy/justhusky.het_check.csv", + "peddy/justhusky.html", + "peddy/justhusky.ped_check.csv", + "peddy/justhusky.peddy.ped", + "peddy/justhusky.sex_check.csv", + "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman", + "qc_bam/earlycasualcaiman/css", + "qc_bam/earlycasualcaiman/css/agogo.css", + "qc_bam/earlycasualcaiman/css/ajax-loader.gif", + "qc_bam/earlycasualcaiman/css/basic.css", + "qc_bam/earlycasualcaiman/css/bgfooter.png", + "qc_bam/earlycasualcaiman/css/bgtop.png", + "qc_bam/earlycasualcaiman/css/comment-bright.png", + "qc_bam/earlycasualcaiman/css/comment-close.png", + "qc_bam/earlycasualcaiman/css/comment.png", + "qc_bam/earlycasualcaiman/css/doctools.js", + "qc_bam/earlycasualcaiman/css/down-pressed.png", + "qc_bam/earlycasualcaiman/css/down.png", + "qc_bam/earlycasualcaiman/css/file.png", + "qc_bam/earlycasualcaiman/css/jquery.js", + "qc_bam/earlycasualcaiman/css/minus.png", + "qc_bam/earlycasualcaiman/css/plus.png", + "qc_bam/earlycasualcaiman/css/pygments.css", + "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", + "qc_bam/earlycasualcaiman/css/report.css", + "qc_bam/earlycasualcaiman/css/searchtools.js", + "qc_bam/earlycasualcaiman/css/underscore.js", + "qc_bam/earlycasualcaiman/css/up-pressed.png", + "qc_bam/earlycasualcaiman/css/up.png", + "qc_bam/earlycasualcaiman/css/websupport.js", + "qc_bam/earlycasualcaiman/genome_results.txt", + "qc_bam/earlycasualcaiman/images_qualimapReport", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/earlycasualcaiman/qualimapReport.html", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/earlycasualcaiman_chromographcov", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", @@ -562,6 +645,60 @@ "qc_bam/earlycasualcaiman_tidditcov.wig", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat", + "qc_bam/hugelymodelbat/css", + "qc_bam/hugelymodelbat/css/agogo.css", + "qc_bam/hugelymodelbat/css/ajax-loader.gif", + "qc_bam/hugelymodelbat/css/basic.css", + "qc_bam/hugelymodelbat/css/bgfooter.png", + "qc_bam/hugelymodelbat/css/bgtop.png", + "qc_bam/hugelymodelbat/css/comment-bright.png", + "qc_bam/hugelymodelbat/css/comment-close.png", + "qc_bam/hugelymodelbat/css/comment.png", + "qc_bam/hugelymodelbat/css/doctools.js", + "qc_bam/hugelymodelbat/css/down-pressed.png", + "qc_bam/hugelymodelbat/css/down.png", + "qc_bam/hugelymodelbat/css/file.png", + "qc_bam/hugelymodelbat/css/jquery.js", + "qc_bam/hugelymodelbat/css/minus.png", + "qc_bam/hugelymodelbat/css/plus.png", + "qc_bam/hugelymodelbat/css/pygments.css", + "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", + "qc_bam/hugelymodelbat/css/report.css", + "qc_bam/hugelymodelbat/css/searchtools.js", + "qc_bam/hugelymodelbat/css/underscore.js", + "qc_bam/hugelymodelbat/css/up-pressed.png", + "qc_bam/hugelymodelbat/css/up.png", + "qc_bam/hugelymodelbat/css/websupport.js", + "qc_bam/hugelymodelbat/genome_results.txt", + "qc_bam/hugelymodelbat/images_qualimapReport", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/hugelymodelbat/qualimapReport.html", + "qc_bam/hugelymodelbat/raw_data_qualimapReport", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/hugelymodelbat_chromographcov", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", @@ -591,6 +728,60 @@ "qc_bam/hugelymodelbat_tidditcov.wig", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck", + "qc_bam/slowlycivilbuck/css", + "qc_bam/slowlycivilbuck/css/agogo.css", + "qc_bam/slowlycivilbuck/css/ajax-loader.gif", + "qc_bam/slowlycivilbuck/css/basic.css", + "qc_bam/slowlycivilbuck/css/bgfooter.png", + "qc_bam/slowlycivilbuck/css/bgtop.png", + "qc_bam/slowlycivilbuck/css/comment-bright.png", + "qc_bam/slowlycivilbuck/css/comment-close.png", + "qc_bam/slowlycivilbuck/css/comment.png", + "qc_bam/slowlycivilbuck/css/doctools.js", + "qc_bam/slowlycivilbuck/css/down-pressed.png", + "qc_bam/slowlycivilbuck/css/down.png", + "qc_bam/slowlycivilbuck/css/file.png", + "qc_bam/slowlycivilbuck/css/jquery.js", + "qc_bam/slowlycivilbuck/css/minus.png", + "qc_bam/slowlycivilbuck/css/plus.png", + "qc_bam/slowlycivilbuck/css/pygments.css", + "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", + "qc_bam/slowlycivilbuck/css/report.css", + "qc_bam/slowlycivilbuck/css/searchtools.js", + "qc_bam/slowlycivilbuck/css/underscore.js", + "qc_bam/slowlycivilbuck/css/up-pressed.png", + "qc_bam/slowlycivilbuck/css/up.png", + "qc_bam/slowlycivilbuck/css/websupport.js", + "qc_bam/slowlycivilbuck/genome_results.txt", + "qc_bam/slowlycivilbuck/images_qualimapReport", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/slowlycivilbuck/qualimapReport.html", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/slowlycivilbuck_chromographcov", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", @@ -669,6 +860,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-08T16:34:48.46542842" + "timestamp": "2025-12-10T22:49:15.518602316" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test b/tests/test_singleton.nf.test index 235365090..245921098 100644 --- a/tests/test_singleton.nf.test +++ b/tests/test_singleton.nf.test @@ -11,7 +11,8 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" + skip_tools = "germlinecnvcaller,gens" } } diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e6c0d8568..8f39a08ed 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 362, + 368, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -116,6 +116,9 @@ "DEEPVARIANT": { "deepvariant": "1.8.0" }, + "EKLIPSE": { + "eklipse": 1.8 + }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -135,6 +138,9 @@ "expansionhunter": "5.0.0", "bgzip": 1.18 }, + "FASTP": { + "fastp": "0.23.4" + }, "FASTQC": { "fastqc": "0.12.1" }, @@ -204,6 +210,9 @@ "HAPLOCHECK_MT": { "haplocheck": "1.3.3" }, + "HAPLOGREP3_CLASSIFY_MT": { + "haplogrep3": "3.2.2" + }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" }, @@ -228,6 +237,12 @@ "MT_DELETION": { "samtools": "1.19.2" }, + "NGSBITS_SAMPLEGENDER": { + "ngs-bits": 202411 + }, + "PEDDY": { + "peddy": "0.4.8" + }, "PICARD_ADDORREPLACEREADGROUPS_MT": { "picard": "3.3.0" }, @@ -252,6 +267,9 @@ "PICARD_SORTVCF": { "picard": "3.3.0" }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.21 }, @@ -476,6 +494,7 @@ "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.json.gz", "annotate_sv/justhusky_svdbquery_vep.summary.html", @@ -501,6 +520,9 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", + "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", @@ -512,11 +534,74 @@ "multiqc/multiqc_data", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "peddy", + "peddy/justhusky.het_check.csv", + "peddy/justhusky.html", + "peddy/justhusky.ped_check.csv", + "peddy/justhusky.peddy.ped", + "peddy/justhusky.sex_check.csv", + "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/hugelymodelbat", + "qc_bam/hugelymodelbat/css", + "qc_bam/hugelymodelbat/css/agogo.css", + "qc_bam/hugelymodelbat/css/ajax-loader.gif", + "qc_bam/hugelymodelbat/css/basic.css", + "qc_bam/hugelymodelbat/css/bgfooter.png", + "qc_bam/hugelymodelbat/css/bgtop.png", + "qc_bam/hugelymodelbat/css/comment-bright.png", + "qc_bam/hugelymodelbat/css/comment-close.png", + "qc_bam/hugelymodelbat/css/comment.png", + "qc_bam/hugelymodelbat/css/doctools.js", + "qc_bam/hugelymodelbat/css/down-pressed.png", + "qc_bam/hugelymodelbat/css/down.png", + "qc_bam/hugelymodelbat/css/file.png", + "qc_bam/hugelymodelbat/css/jquery.js", + "qc_bam/hugelymodelbat/css/minus.png", + "qc_bam/hugelymodelbat/css/plus.png", + "qc_bam/hugelymodelbat/css/pygments.css", + "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", + "qc_bam/hugelymodelbat/css/report.css", + "qc_bam/hugelymodelbat/css/searchtools.js", + "qc_bam/hugelymodelbat/css/underscore.js", + "qc_bam/hugelymodelbat/css/up-pressed.png", + "qc_bam/hugelymodelbat/css/up.png", + "qc_bam/hugelymodelbat/css/websupport.js", + "qc_bam/hugelymodelbat/genome_results.txt", + "qc_bam/hugelymodelbat/images_qualimapReport", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/hugelymodelbat/qualimapReport.html", + "qc_bam/hugelymodelbat/raw_data_qualimapReport", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/hugelymodelbat_chromographcov", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", @@ -579,6 +664,12 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/hugelymodelbat.cgh" ] @@ -587,6 +678,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-08T16:41:21.487778607" + "timestamp": "2025-12-10T23:01:52.852603616" } } \ No newline at end of file From 1cf6bb57cec7a157314adb15a297d8c265f6d149 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 08:28:24 +0100 Subject: [PATCH 154/872] update config --- tests/nextflow.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 5d388a7f6..45062503b 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -22,10 +22,10 @@ aws.client.anonymous = true // fixes S3 access issues on self-hosted runners env { // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') ?: false + SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') ?: false + SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA ?: false + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA } From e636c925b438180d4f3b100b5bf7002a4f6e9772 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 11 Dec 2025 07:32:49 +0000 Subject: [PATCH 155/872] [automated] Fix code linting --- tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 45062503b..34b695ee4 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -22,7 +22,7 @@ aws.client.anonymous = true // fixes S3 access issues on self-hosted runners env { // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') + SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') From a6bb463d2c15005fe7060df65410c8c60e23cc1f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 13:19:20 +0100 Subject: [PATCH 156/872] Update test.config --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 843c89bad..3fd5ceb32 100644 --- a/conf/test.config +++ b/conf/test.config @@ -36,7 +36,7 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' - skip_tools = 'gens,germlinecnvcaller' + skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits' input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' From 75c0b2944876342350282867da6734725ba94f19 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 13:20:42 +0100 Subject: [PATCH 157/872] Update test_bam.config --- conf/test_bam.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/test_bam.config b/conf/test_bam.config index f66191c3c..0173ea483 100644 --- a/conf/test_bam.config +++ b/conf/test_bam.config @@ -36,6 +36,8 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + input = params.pipelines_testdata_base_path + 'testdata/samplesheet_bam.csv' fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' From 99819aba1ee25adb80cdd4d5818c7dea65b229ef Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 13:21:27 +0100 Subject: [PATCH 158/872] Update test_sentieon.config --- conf/test_sentieon.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config index a2a5ad710..e34a7f9c1 100644 --- a/conf/test_sentieon.config +++ b/conf/test_sentieon.config @@ -35,6 +35,8 @@ params { igenomes_ignore = true mito_name = 'MT' + skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + // Input data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' input = params.pipelines_testdata_base_path + 'testdata/samplesheet_trio.csv' From a8819f55d6aeaf0e37b767a0d0b71c3e70df0db4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 13:21:54 +0100 Subject: [PATCH 159/872] Update test_singleton.config --- conf/test_singleton.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/test_singleton.config b/conf/test_singleton.config index 1c885ab39..180bfc0a1 100644 --- a/conf/test_singleton.config +++ b/conf/test_singleton.config @@ -36,6 +36,8 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + input = params.pipelines_testdata_base_path + 'testdata/samplesheet_single.csv' fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' fai = params.pipelines_testdata_base_path + 'reference/reference.fasta.fai' From 8848b5476a93dda02d09098f77d67154fcd14ef1 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Thu, 11 Dec 2025 16:10:08 +0100 Subject: [PATCH 160/872] Update modules/local/mitosalt/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- modules/local/mitosalt/main.nf | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 9f06ae402..9c4375ad0 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -7,11 +7,6 @@ process MITOSALT { 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" -// container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -// 'https://depot.galaxyproject.org/singularity/mitosalt:1.1.1--hdfd78af_2': -// 'quay.io/biocontainers/mitosalt:1.1.1--hdfd78af_2' }" - -// container 'docker://ieduba/mitosalt:latest' input: tuple val(meta), path(reads) From 75a7db9aeeed31904301c632392d56708fbbcf7f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:10:09 +0100 Subject: [PATCH 161/872] few fixes --- conf/modules/annotate_genome_snvs.config | 1 - .../annotate_structural_variants.config | 2 - conf/modules/call_snv_deepvariant.config | 4 - main.nf | 8 +- subworkflows/local/annotate_genome_snvs.nf | 8 +- .../local/annotate_rhocallviz/main.nf | 13 +- .../local/annotate_structural_variants.nf | 126 ++++++++---------- workflows/raredisease.nf | 8 +- 8 files changed, 80 insertions(+), 90 deletions(-) diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index de3b4210b..6ec08c8b7 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -18,7 +18,6 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH' { - ext.when = { meta.probands.size()>0 } ext.args = { "--samples ${meta.probands.unique().first()} --skip-indels " } ext.prefix = { "${meta.id}_roh" } } diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config index b8af1e888..dd737e3bb 100644 --- a/conf/modules/annotate_structural_variants.config +++ b/conf/modules/annotate_structural_variants.config @@ -18,12 +18,10 @@ process { withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_BEDPE' { - ext.when = {!params.svdb_query_bedpedbs.equals(null)} ext.prefix = { "${meta.id}_bedpedb" } } withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB' { - ext.when = {!params.svdb_query_dbs.equals(null)} ext.prefix = { "${meta.id}_vcfdb" } } diff --git a/conf/modules/call_snv_deepvariant.config b/conf/modules/call_snv_deepvariant.config index 3bbf26061..140de6d95 100644 --- a/conf/modules/call_snv_deepvariant.config +++ b/conf/modules/call_snv_deepvariant.config @@ -17,10 +17,6 @@ process { - withName: '.*CALL_SNV_DEEPVARIANT:.*' { - ext.when = params.variant_caller.equals("deepvariant") - } - withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT' { ext.args = { [ "--model_type=${params.analysis_type.toUpperCase()}", diff --git a/main.nf b/main.nf index 440fa257a..366191925 100644 --- a/main.nf +++ b/main.nf @@ -159,10 +159,6 @@ workflow NFCORE_RAREDISEASE { : channel.value([]) ch_sdf = params.sdf ? channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() : ch_references.sdf - ch_sv_dbs = params.svdb_query_dbs ? channel.fromPath(params.svdb_query_dbs) - : channel.empty() - ch_sv_bedpedbs = params.svdb_query_bedpedbs ? channel.fromPath(params.svdb_query_bedpedbs) - : channel.empty() ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) : channel.empty() ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) @@ -344,8 +340,6 @@ workflow NFCORE_RAREDISEASE { ch_score_config_snv, ch_score_config_sv, ch_sdf, - ch_sv_bedpedbs, - ch_sv_dbs, ch_svcaller_priority, ch_svd_bed, ch_svd_mu, @@ -364,6 +358,8 @@ workflow NFCORE_RAREDISEASE { ch_vep_extra_files, ch_versions, params.analysis_type, + params.svdb_query_bedpedbs, + params.svdb_query_dbs, skip_me_calling, skip_me_annotation, skip_mt_annotation, diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 88067cadb..2f3587320 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -48,7 +48,13 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcf_scatter_in = channel.empty() ch_vep_in = channel.empty() - BCFTOOLS_ROH (ch_vcf, ch_gnomad_af, [], [], [], []) + ch_vcf + .filter { meta, _vcf, _tbi -> + meta.probands.size() > 0 + } + .set { ch_roh_in } + + BCFTOOLS_ROH (ch_roh_in, ch_gnomad_af, [], [], [], []) RHOCALL_ANNOTATE (ch_vcf, BCFTOOLS_ROH.out.roh, []) diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 3a32da956..af527cf09 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -37,7 +37,18 @@ workflow ANNOTATE_RHOCALLVIZ { BCFTOOLS_VIEW_UNCOMPRESS(ch_roh_in,[],[],[]) - RHOCALL_VIZ(BCFTOOLS_VIEW_UNCOMPRESS.out.vcf, BCFTOOLS_ROH.out.roh) + BCFTOOLS_VIEW_UNCOMPRESS.out.vcf + .join(BCFTOOLS_ROH.out.roh) + .multiMap { meta, vcf, roh -> + vcf: [meta, vcf] + roh: [meta, roh] + } + .set { ch_rhocall_viz_input } + + RHOCALL_VIZ( + ch_rhocall_viz_input.vcf, + ch_rhocall_viz_input.roh + ) CHROMOGRAPH_AUTOZYG(RHOCALL_VIZ.out.bed, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 2de52d0d1..a6ec70f5e 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -13,8 +13,8 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { take: ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_sv_dbs // channel: [mandatory] [ val(csv) ] - ch_sv_bedpedbs // channel: [mandatory] [ val(csv) ] + svdb_query_bedpedbs // String: [optional] params.svdb_query_bedpedbs + svdb_query_dbs // String: [optional] params.svdb_query_dbs val_vep_genome // string: [mandatory] GRCh37 or GRCh38 val_vep_cache_version // string: [mandatory] default: 107 ch_vep_cache // channel: [mandatory] [ path(cache) ] @@ -27,73 +27,59 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_svdb_dbs = channel.empty() ch_svdb_bedpedbs = channel.empty() - ch_sv_dbs - .splitCsv ( header:true ) - .multiMap { row -> - vcf_dbs: row.filename - in_frqs: row.in_freq_info_key - in_occs: row.in_allele_count_info_key - out_frqs: row.out_freq_info_key - out_occs: row.out_allele_count_info_key - } - .set { ch_svdb_dbs } - - ch_sv_bedpedbs - .splitCsv ( header:true ) - .multiMap { row -> - bedpedbs: row.filename - in_frqs: row.in_freq_info_key - in_occs: row.in_allele_count_info_key - out_frqs: row.out_freq_info_key - out_occs: row.out_allele_count_info_key - } - .set { ch_svdb_bedpedbs } - - SVDB_QUERY_DB ( - ch_vcf, - ch_svdb_dbs.in_occs.toList(), - ch_svdb_dbs.in_frqs.toList(), - ch_svdb_dbs.out_occs.toList(), - ch_svdb_dbs.out_frqs.toList(), - ch_svdb_dbs.vcf_dbs.toList(), - [] - ) - - ch_vcf - .join(SVDB_QUERY_DB.out.vcf, remainder: true) - .branch { meta, vcfcalls, annotatedvcf -> - original_call: annotatedvcf.equals(null) - return [meta, vcfcalls] - annotated_with_db: !(annotatedvcf.equals(null)) - return [meta, annotatedvcf] - } - .set { ch_for_mix_querydb } - - ch_querydb_out = ch_for_mix_querydb.original_call.mix(ch_for_mix_querydb.annotated_with_db) - - SVDB_QUERY_BEDPE ( - ch_querydb_out, - ch_svdb_bedpedbs.in_occs.toList(), - ch_svdb_bedpedbs.in_frqs.toList(), - ch_svdb_bedpedbs.out_occs.toList(), - ch_svdb_bedpedbs.out_frqs.toList(), - [], - ch_svdb_bedpedbs.bedpedbs.toList() - ) - - ch_querydb_out - .join(SVDB_QUERY_BEDPE.out.vcf, remainder: true) - .branch { meta, annotated_db, annotated_bedped -> - querydb_out: annotated_bedped.equals(null) - return [meta, annotated_db] - querybedped_out: !(annotated_bedped.equals(null)) - return [meta, annotated_bedped] - } - .set { ch_for_mix_querybedpedb } - - ch_querypedbed_out = ch_for_mix_querybedpedb.querydb_out.mix(ch_for_mix_querybedpedb.querybedped_out) - - PICARD_SORTVCF(ch_querypedbed_out, ch_genome_fasta, ch_genome_dictionary) + if (svdb_query_dbs) { + channel.fromPath(svdb_query_dbs) + .splitCsv ( header:true ) + .multiMap { row -> + vcf_dbs: row.filename + in_frqs: row.in_freq_info_key + in_occs: row.in_allele_count_info_key + out_frqs: row.out_freq_info_key + out_occs: row.out_allele_count_info_key + } + .set { ch_svdb_dbs } + + SVDB_QUERY_DB ( + ch_vcf, + ch_svdb_dbs.in_occs.toList(), + ch_svdb_dbs.in_frqs.toList(), + ch_svdb_dbs.out_occs.toList(), + ch_svdb_dbs.out_frqs.toList(), + ch_svdb_dbs.vcf_dbs.toList(), + [] + ) + + ch_vcf = SVDB_QUERY_DB.out.vcf + ch_versions = ch_versions.mix(SVDB_QUERY_DB.out.versions) + } + + if (svdb_query_bedpedbs) { + channel.fromPath(svdb_query_bedpedbs) + .splitCsv ( header:true ) + .multiMap { row -> + bedpedbs: row.filename + in_frqs: row.in_freq_info_key + in_occs: row.in_allele_count_info_key + out_frqs: row.out_freq_info_key + out_occs: row.out_allele_count_info_key + } + .set { ch_svdb_bedpedbs } + + SVDB_QUERY_BEDPE ( + ch_vcf, + ch_svdb_bedpedbs.in_occs.toList(), + ch_svdb_bedpedbs.in_frqs.toList(), + ch_svdb_bedpedbs.out_occs.toList(), + ch_svdb_bedpedbs.out_frqs.toList(), + [], + ch_svdb_bedpedbs.bedpedbs.toList() + ) + + ch_vcf = SVDB_QUERY_BEDPE.out.vcf + ch_versions = ch_versions.mix(SVDB_QUERY_BEDPE.out.versions) + } + + PICARD_SORTVCF(ch_vcf, ch_genome_fasta, ch_genome_dictionary) PICARD_SORTVCF.out.vcf .map { meta, vcf -> return [meta,vcf,[]] } @@ -116,8 +102,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) - ch_versions = ch_versions.mix(SVDB_QUERY_DB.out.versions) - ch_versions = ch_versions.mix(SVDB_QUERY_BEDPE.out.versions) ch_versions = ch_versions.mix(PICARD_SORTVCF.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(ENSEMBLVEP_SV.out.versions) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index bf0c44eaa..bf2b624a6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -132,8 +132,6 @@ workflow RAREDISEASE { ch_score_config_snv ch_score_config_sv ch_sdf - ch_sv_bedpedbs - ch_sv_dbs ch_svcaller_priority ch_svd_bed ch_svd_mu @@ -152,6 +150,8 @@ workflow RAREDISEASE { ch_vep_extra_files ch_versions analysis_type + svdb_query_bedpedbs + svdb_query_dbs skip_me_calling skip_me_annotation skip_mt_annotation @@ -551,8 +551,8 @@ workflow RAREDISEASE { if (!skip_sv_annotation) { ANNOTATE_STRUCTURAL_VARIANTS ( CALL_STRUCTURAL_VARIANTS.out.vcf, - ch_sv_dbs, - ch_sv_bedpedbs, + svdb_query_bedpedbs, + svdb_query_dbs, params.genome, params.vep_cache_version, ch_vep_cache, From 203dd24c8d6ff7200980d0a07a79a8a5d587d27f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:17:02 +0100 Subject: [PATCH 162/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0dc4f4afb..574d74bc2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) +- Fixed mismatch between VCF and ROH calls when running multiple samples [#739](https://github.com/nf-core/raredisease/issues/739) ### Parameters From 6a0ed280b9f4247f3f912a7602a3c43ea164eb00 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 17:19:43 +0100 Subject: [PATCH 163/872] fix 739 --- CHANGELOG.md | 1 + subworkflows/local/annotate_rhocallviz/main.nf | 13 ++++++++++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fbf446e8e..e9bda2041 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) +- Fixed mismatch between VCF and ROH calls when analysing multiple samples [#739](https://github.com/nf-core/raredisease/issues/739) ### Parameters diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 3a32da956..5d85c9e17 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -37,7 +37,18 @@ workflow ANNOTATE_RHOCALLVIZ { BCFTOOLS_VIEW_UNCOMPRESS(ch_roh_in,[],[],[]) - RHOCALL_VIZ(BCFTOOLS_VIEW_UNCOMPRESS.out.vcf, BCFTOOLS_ROH.out.roh) + BCFTOOLS_VIEW_UNCOMPRESS.out.vcf + .join(BCFTOOLS_ROH.out.roh) + .multiMap { meta, vcf, roh -> + vcf: [meta, vcf] + roh: [meta, roh] + } + .set { ch_rhocall_viz_input } + + RHOCALL_VIZ( + ch_rhocall_viz_input.vcf, + ch_rhocall_viz_input.roh, + ) CHROMOGRAPH_AUTOZYG(RHOCALL_VIZ.out.bed, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) From cc3afe283b6017d88a8c820b65e963b964da1bd9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Dec 2025 20:50:15 +0100 Subject: [PATCH 164/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d8a3caa5..5631c6844 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) -- Fixed mismatch between VCF and ROH calls when analysing multiple samples [#739](https://github.com/nf-core/raredisease/issues/739) +- Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) ### Parameters From 59ef7c218a7fb4f4c213645217f4a1d63f8fcaa7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 11 Dec 2025 22:42:22 +0000 Subject: [PATCH 165/872] [automated] Fix code linting --- subworkflows/local/annotate_genome_snvs.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 2f3587320..4e4f66b1e 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -49,8 +49,8 @@ workflow ANNOTATE_GENOME_SNVS { ch_vep_in = channel.empty() ch_vcf - .filter { meta, _vcf, _tbi -> - meta.probands.size() > 0 + .filter { meta, _vcf, _tbi -> + meta.probands.size() > 0 } .set { ch_roh_in } From 12ae427621a7760af3cdb710978c623fa135e259 Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Fri, 12 Dec 2025 09:50:38 +0100 Subject: [PATCH 166/872] Remove deepvariant_parabricks config inclusion --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 6715f1c22..020228ee0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -466,7 +466,6 @@ includeConfig 'conf/modules/align_sentieon.config' includeConfig 'conf/modules/annotate_cadd.config' includeConfig 'conf/modules/call_snv_MT.config' includeConfig 'conf/modules/call_snv_deepvariant.config' -includeConfig 'conf/modules/call_snv_deepvariant_parabricks.config' includeConfig 'conf/modules/call_snv_sentieon.config' includeConfig 'conf/modules/call_sv_MT.config' includeConfig 'conf/modules/call_sv_cnvnator.config' From 65de84424a3c8f8cf9f1b442440c5bd30549c9b3 Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Fri, 12 Dec 2025 10:10:00 +0100 Subject: [PATCH 167/872] Fix trailing whitespace and EOF newlines --- assets/multiqc_config.yml | 2 +- conf/modules/align_bwa_bwamem2_bwameme.config | 4 ++-- conf/modules/contamination.config | 6 +++--- .../local/parse_contamination/environment.yml | 2 +- modules/local/parse_contamination/main.nf | 10 +++++----- modules/local/parse_contamination/meta.yml | 2 +- modules/nf-core/svdb/merge/main.nf | 2 +- subworkflows/local/contamination_check/main.nf | 18 +++++++++--------- .../local/contamination_check/meta.yml | 2 +- workflows/raredisease.nf | 14 +++++++------- 10 files changed, 31 insertions(+), 31 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 960470155..6bff5169c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -102,4 +102,4 @@ extra_fn_clean_exts: - type: regex pattern: "_LNUMBER[0-9]{1,}" -disable_version_detection: true \ No newline at end of file +disable_version_detection: true diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index ce28d4380..708d45671 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -59,7 +59,7 @@ process { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_sorted_md" } publishDir = [ - enabled: !params.save_mapped_as_cram, + enabled: true, path: { "${params.outdir}/alignment" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } @@ -68,7 +68,7 @@ process { withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' { publishDir = [ - enabled: !params.save_mapped_as_cram, + enabled: true, path: { "${params.outdir}/alignment" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } diff --git a/conf/modules/contamination.config b/conf/modules/contamination.config index 4fc09327d..f07ebeca2 100644 --- a/conf/modules/contamination.config +++ b/conf/modules/contamination.config @@ -18,7 +18,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - + // // GATK CalculateContamination // @@ -31,7 +31,7 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - + // // Parse contamination results for MultiQC // @@ -43,4 +43,4 @@ process { pattern: '*_mqc.tsv' ] } -} \ No newline at end of file +} diff --git a/modules/local/parse_contamination/environment.yml b/modules/local/parse_contamination/environment.yml index 1f07535d3..b5260d32d 100644 --- a/modules/local/parse_contamination/environment.yml +++ b/modules/local/parse_contamination/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - python=3.11 \ No newline at end of file + - python=3.11 diff --git a/modules/local/parse_contamination/main.nf b/modules/local/parse_contamination/main.nf index f811175d2..ad957390b 100644 --- a/modules/local/parse_contamination/main.nf +++ b/modules/local/parse_contamination/main.nf @@ -21,9 +21,9 @@ process PARSE_CONTAMINATION { def prefix = task.ext.prefix ?: "${meta.id}" """ #!/usr/bin/env python3 - + import csv - + # Read GATK contamination table with open("${contamination_table}", 'r') as f: lines = f.readlines() @@ -32,7 +32,7 @@ process PARSE_CONTAMINATION { sample = data_line[0] contamination = float(data_line[1]) contamination_pct = contamination * 100 - + # Write MultiQC custom content file with open("${prefix}_contamination_mqc.tsv", 'w') as out: # Header with MultiQC configuration @@ -52,10 +52,10 @@ process PARSE_CONTAMINATION { # Data out.write("Sample\\tcontamination_pct\\n") out.write(f"${meta.id}\\t{contamination_pct:.4f}\\n") - + # Create versions file with open("versions.yml", 'w') as v: v.write('"${task.process}":\\n') v.write(' python: "3.11"\\n') """ -} \ No newline at end of file +} diff --git a/modules/local/parse_contamination/meta.yml b/modules/local/parse_contamination/meta.yml index 2739258c8..6018fd2df 100644 --- a/modules/local/parse_contamination/meta.yml +++ b/modules/local/parse_contamination/meta.yml @@ -26,4 +26,4 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "56053vujinovic" \ No newline at end of file + - "56053vujinovic" diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 104f5ad79..75b1373b6 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -102,4 +102,4 @@ process SVDB_MERGE { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ -} +} \ No newline at end of file diff --git a/subworkflows/local/contamination_check/main.nf b/subworkflows/local/contamination_check/main.nf index 8ff0d4e90..e9ef9c757 100644 --- a/subworkflows/local/contamination_check/main.nf +++ b/subworkflows/local/contamination_check/main.nf @@ -6,7 +6,7 @@ include { GATK4_GETPILEUPSUMMARIES } from '../../../modules/nf-core/gatk4/ge include { GATK4_CALCULATECONTAMINATION } from '../../../modules/nf-core/gatk4/calculatecontamination/main' workflow CONTAMINATION_CHECK { - + take: ch_bam // channel: [ val(meta), path(bam), path(bai) ] ch_fasta // channel: [ val(meta), path(fasta) ] @@ -17,26 +17,26 @@ workflow CONTAMINATION_CHECK { main: ch_versions = Channel.empty() - + // Prepare BAM with intervals - conditionally based on analysis type // For WGS: intervals will be empty [], for WES: intervals will contain the BED file ch_bam_with_intervals = ch_bam .combine(ch_intervals.ifEmpty([[]])) - .map { meta, bam, bai, bed -> + .map { meta, bam, bai, bed -> // If bed is an empty list, pass empty list; otherwise pass bed file def intervals = (bed instanceof List && bed.isEmpty()) ? [] : (bed ?: []) [ meta, bam, bai, intervals ] } - + // Separate VCF and TBI - collect them to make value channels ch_variants_vcf = ch_contamination_vcf .map { vcf, tbi -> vcf } .collect() - + ch_variants_tbi = ch_contamination_vcf .map { vcf, tbi -> tbi } .collect() - + // Run GetPileupSummaries GATK4_GETPILEUPSUMMARIES ( ch_bam_with_intervals, // [meta, bam, bai, intervals] @@ -47,13 +47,13 @@ workflow CONTAMINATION_CHECK { ch_variants_tbi // path(tbi) ) ch_versions = ch_versions.mix(GATK4_GETPILEUPSUMMARIES.out.versions.first()) - + // Run CalculateContamination (tumor-only, no matched normal) // Format: [meta, pileup_table, matched_normal_table] // matched_normal_table is empty [] for tumor-only mode ch_contamination_input = GATK4_GETPILEUPSUMMARIES.out.table .map { meta, table -> [ meta, table, [] ] } - + GATK4_CALCULATECONTAMINATION ( ch_contamination_input ) @@ -64,4 +64,4 @@ workflow CONTAMINATION_CHECK { segmentation_table = GATK4_CALCULATECONTAMINATION.out.segmentation pileup_table = GATK4_GETPILEUPSUMMARIES.out.table versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/contamination_check/meta.yml b/subworkflows/local/contamination_check/meta.yml index 9a26869a0..ab7f5937b 100644 --- a/subworkflows/local/contamination_check/meta.yml +++ b/subworkflows/local/contamination_check/meta.yml @@ -38,4 +38,4 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "56053vujinovic" \ No newline at end of file + - "56053vujinovic" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 476a8fb69..005e2a800 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -411,16 +411,16 @@ workflow RAREDISEASE { ch_contamination_mqc = Channel.empty() if (params.run_contamination && params.contamination_sites) { - + log.info "=== CONTAMINATION CHECK ENABLED ===" log.info "Analysis type: ${params.analysis_type}" - + // Prepare contamination sites channel ch_contamination_sites = Channel.of([ file(params.contamination_sites, checkIfExists: true), file(params.contamination_sites_tbi, checkIfExists: true) ]).collect() - + // Prepare intervals channel - CRITICAL: Use Channel.empty() for WGS, not Channel.of([]) if (params.analysis_type == 'wes' && params.target_bed) { ch_intervals_contamination = Channel.fromPath(params.target_bed).collect() @@ -429,11 +429,11 @@ workflow RAREDISEASE { ch_intervals_contamination = Channel.empty() log.info "No intervals for WGS contamination check (genome-wide)" } - + // Prepare BAM input with BAI ch_bam_for_contamination = ch_mapped.genome_marked_bam .join(ch_mapped.genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) - + CONTAMINATION_CHECK ( ch_bam_for_contamination, ch_genome_fasta, @@ -442,12 +442,12 @@ workflow RAREDISEASE { ch_contamination_sites, ch_intervals_contamination ) - + // Parse for MultiQC PARSE_CONTAMINATION ( CONTAMINATION_CHECK.out.contamination_table ) - + ch_contamination_mqc = PARSE_CONTAMINATION.out.mqc_table ch_versions = ch_versions.mix(CONTAMINATION_CHECK.out.versions) ch_versions = ch_versions.mix(PARSE_CONTAMINATION.out.versions) From 269381975bf7ef4a92d0e0dae9595419b7602aba Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Fri, 12 Dec 2025 10:15:53 +0100 Subject: [PATCH 168/872] Refactor GATK contamination settings in YAML Updated GATK contamination configuration for clarity and consistency. --- assets/multiqc_config.yml | 32 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6bff5169c..bd604186a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -6,7 +6,6 @@ report_comment: > target="_blank">nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. - report_section_order: "nf-core-raredisease-methods-description": order: -1000 @@ -16,9 +15,7 @@ report_section_order: order: -1002 gatk_contamination: order: 1050 - export_plots: true - run_modules: - fastqc - fastp @@ -30,7 +27,6 @@ run_modules: - peddy - verifybamid - custom_content - module_order: - fastqc: name: "FastQC" @@ -56,38 +52,38 @@ module_order: # Custom content configuration for GATK contamination custom_data: gatk_contamination: - id: 'gatk_contamination' - section_name: 'GATK Contamination' - description: 'Sample contamination estimates from GATK CalculateContamination based on common variant allele frequencies' - plot_type: 'generalstats' + id: "gatk_contamination" + section_name: "GATK Contamination" + description: "Sample contamination estimates from GATK CalculateContamination based on common variant allele frequencies" + plot_type: "generalstats" pconfig: contamination_pct: - title: 'Contamination' - description: 'Estimated sample contamination percentage' + title: "Contamination" + description: "Estimated sample contamination percentage" max: 10 min: 0 - scale: 'RdYlGn-rev' - suffix: '%' - format: '{:,.2f}' - shared_key: 'contamination' + scale: "RdYlGn-rev" + suffix: "%" + format: "{:,.2f}" + shared_key: "contamination" # Make contamination visible in general stats by default table_columns_visible: gatk_contamination: - contamination_pct: True + contamination_pct: true # Color coding thresholds for contamination table_cond_formatting_rules: contamination_pct: pass: - - s_eq: 'pass' + - s_eq: "pass" - lt: 2.0 warn: - - s_eq: 'warn' + - s_eq: "warn" - lt: 5.0 - gte: 2.0 fail: - - s_eq: 'fail' + - s_eq: "fail" - gte: 5.0 # Add to General Statistics table configuration From 879655b26f0aa200dc90ee7d39d78dbcbfa155ea Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Fri, 12 Dec 2025 10:38:34 +0100 Subject: [PATCH 169/872] Change default test branch from 'dev' to 'master' --- .github/workflows/download_pipeline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 999bcc382..91d253370 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -10,7 +10,7 @@ on: testbranch: description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true - default: "dev" + default: "master" pull_request: branches: - main @@ -32,7 +32,7 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'master' }}" >> "$GITHUB_OUTPUT" download: runs-on: ubuntu-latest From 3fcffb5bcaba9687596fdc3e47b720f4bdc994f4 Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 12 Dec 2025 13:32:45 +0100 Subject: [PATCH 170/872] allow bait padding 0 --- conf/modules/prepare_references.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 50e441017..28336c7bc 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -105,7 +105,7 @@ process { } withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' { - ext.when = { params.target_bed && params.bait_padding > 0 } + ext.when = { params.target_bed } ext.prefix = { "${meta.id}_pad${params.bait_padding}" } ext.args = { "-b ${params.bait_padding}" } } From 03af0c5d5e928f54f484b6fa9e118391b2fe630c Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 12 Dec 2025 13:38:10 +0100 Subject: [PATCH 171/872] add changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5631c6844..208aa1061 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) +- Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) ### Parameters From 88d16643cce89fae639056f3c2c0cca67c16c25e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 12 Dec 2025 16:46:11 +0100 Subject: [PATCH 172/872] move svdb query database channel initialization to main.nf --- main.nf | 6 ++++ .../local/annotate_structural_variants.nf | 34 +++++++++---------- workflows/raredisease.nf | 4 +++ 3 files changed, 26 insertions(+), 18 deletions(-) diff --git a/main.nf b/main.nf index 366191925..a991a808c 100644 --- a/main.nf +++ b/main.nf @@ -165,6 +165,10 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_svd_ud = params.verifybamid_svd_ud ? channel.fromPath(params.verifybamid_svd_ud) : channel.empty() + ch_svdb_bedpedbs = params.svdb_query_bedpedbs ? channel.fromList(samplesheetToList(params.svdb_query_bedpedbs, "assets/svdb_query_bedpe_schema.json")).collect() + : channel.empty() + ch_svdb_dbs = params.svdb_query_dbs ? channel.fromList(samplesheetToList(params.svdb_query_dbs, "assets/svdb_query_vcf_schema.json")).collect() + : channel.empty() ch_target_bed = ch_references.target_bed ch_target_intervals = ch_references.target_intervals ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() @@ -344,6 +348,8 @@ workflow NFCORE_RAREDISEASE { ch_svd_bed, ch_svd_mu, ch_svd_ud, + ch_svdb_bedpedbs, + ch_svdb_dbs, ch_target_bed, ch_target_intervals, ch_variant_catalog, diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index a6ec70f5e..4237f2651 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -17,6 +17,8 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { svdb_query_dbs // String: [optional] params.svdb_query_dbs val_vep_genome // string: [mandatory] GRCh37 or GRCh38 val_vep_cache_version // string: [mandatory] default: 107 + ch_svdb_bedpedbs // channel: [optional] + ch_svdb_dbs // channel: [optional] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] @@ -24,18 +26,15 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { main: ch_versions = channel.empty() - ch_svdb_dbs = channel.empty() - ch_svdb_bedpedbs = channel.empty() if (svdb_query_dbs) { - channel.fromPath(svdb_query_dbs) - .splitCsv ( header:true ) - .multiMap { row -> - vcf_dbs: row.filename - in_frqs: row.in_freq_info_key - in_occs: row.in_allele_count_info_key - out_frqs: row.out_freq_info_key - out_occs: row.out_allele_count_info_key + ch_svdb_dbs + .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> + vcf_dbs: file + in_frqs: in_freq_info_key + in_occs: in_allele_count_info_key + out_frqs: out_freq_info_key + out_occs: out_allele_count_info_key } .set { ch_svdb_dbs } @@ -54,14 +53,13 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { } if (svdb_query_bedpedbs) { - channel.fromPath(svdb_query_bedpedbs) - .splitCsv ( header:true ) - .multiMap { row -> - bedpedbs: row.filename - in_frqs: row.in_freq_info_key - in_occs: row.in_allele_count_info_key - out_frqs: row.out_freq_info_key - out_occs: row.out_allele_count_info_key + ch_svdb_bedpedbs + .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> + bedpedbs: file + in_frqs: in_freq_info_key + in_occs: in_allele_count_info_key + out_frqs: out_freq_info_key + out_occs: out_allele_count_info_key } .set { ch_svdb_bedpedbs } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index bf2b624a6..7d7bd3d24 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -136,6 +136,8 @@ workflow RAREDISEASE { ch_svd_bed ch_svd_mu ch_svd_ud + ch_svdb_bedpedbs + ch_svdb_dbs ch_target_bed ch_target_intervals ch_variant_catalog @@ -555,6 +557,8 @@ workflow RAREDISEASE { svdb_query_dbs, params.genome, params.vep_cache_version, + ch_svdb_bedpedbs, + ch_svdb_dbs, ch_vep_cache, ch_genome_fasta, ch_genome_dictionary, From 0fc617bc553049e180ceb9b32e7655b509364b5e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 12 Dec 2025 15:51:41 +0000 Subject: [PATCH 173/872] [automated] Fix code linting --- subworkflows/local/annotate_structural_variants.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 4237f2651..052aac96d 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -17,8 +17,8 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { svdb_query_dbs // String: [optional] params.svdb_query_dbs val_vep_genome // string: [mandatory] GRCh37 or GRCh38 val_vep_cache_version // string: [mandatory] default: 107 - ch_svdb_bedpedbs // channel: [optional] - ch_svdb_dbs // channel: [optional] + ch_svdb_bedpedbs // channel: [optional] + ch_svdb_dbs // channel: [optional] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] From c90b425427747a2e83fd85d38bac674747cf7a1c Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Mon, 15 Dec 2025 14:29:54 +0100 Subject: [PATCH 174/872] Change default branch from 'master' to 'dev' --- .github/workflows/download_pipeline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 91d253370..999bcc382 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -10,7 +10,7 @@ on: testbranch: description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true - default: "master" + default: "dev" pull_request: branches: - main @@ -32,7 +32,7 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'master' }}" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" download: runs-on: ubuntu-latest From 2bdd2c3087762f095eca26d858ebb028af8f85d7 Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Mon, 15 Dec 2025 14:38:10 +0100 Subject: [PATCH 175/872] Update CHANGELOG with GATK contamination features Introduced GATK contamination check for WES/WGS samples, added new parameters and subworkflow, and updated MultiQC configuration. --- CHANGELOG.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cb7fb320b..35c9f2220 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [Unreleased] + +### Added + +- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2 +- New parameters: `run_contamination`, `contamination_sites`, `contamination_sites_tbi` +- CONTAMINATION_CHECK subworkflow using GATK4 GetPileupSummaries and CalculateContamination +- PARSE_CONTAMINATION module for MultiQC integration +- Contamination results displayed in MultiQC with color-coded thresholds + +### Changed + +- Updated MultiQC configuration to include GATK contamination metrics + ## 2.6.0 - Cacofonix [2025-06-25] ### `Added` From 2cb578fdc8e48ff097ed88316aa8c7a87daad845 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 15 Dec 2025 16:01:42 +0100 Subject: [PATCH 176/872] remove ext.when from prepare_references --- conf/modules/prepare_references.config | 42 ----- main.nf | 21 +-- subworkflows/local/prepare_references/main.nf | 159 +++++++++++------- 3 files changed, 111 insertions(+), 111 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 28336c7bc..47469fc4a 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -25,37 +25,8 @@ process { ] } - withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME' { - ext.when = {!params.bwamem2 && (params.aligner == "bwamem2" || params.mt_aligner == "bwamem2")} - } - withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { ext.args = '-a meme' - ext.when = {!params.bwameme && params.aligner == "bwameme"} - } - - withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' { - ext.when = {!params.bwa && (!(params.aligner == "sentieon") || params.mt_aligner == "bwa")} - } - - withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' { - ext.when = {!params.bwa && (params.aligner == "sentieon" || params.mt_aligner == "sentieon")} - } - - withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} - } - - withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} - } - - withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} - } - - withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' { - ext.when = {!params.fai} } withName: '.*PREPARE_REFERENCES:RTGTOOLS_FORMAT' { @@ -64,25 +35,12 @@ process { withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' { ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" } - ext.when = {!params.mt_fasta} - } - - withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) } - } - - withName: '.*PREPARE_REFERENCES:GATK_SD' { - ext.when = {!params.sequence_dictionary} } withName: '.*PREPARE_REFERENCES:GATK_SHIFTFASTA' { ext.args = { "--interval-file-name ${meta.id}_mt" } } - withName: '.*PREPARE_REFERENCES:GATK_SD_MT' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes)} - } - withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { ext.when = {params.known_dbsnp && !params.known_dbsnp_tbi} } diff --git a/main.nf b/main.nf index a991a808c..4b7d742c8 100644 --- a/main.nf +++ b/main.nf @@ -49,16 +49,10 @@ workflow NFCORE_RAREDISEASE { ch_versions = channel.empty() ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() - ch_genome_fai = params.fai ? channel.fromPath(params.fai).map {it -> [[id:it.simpleName], it]}.collect() - : channel.empty() - ch_genome_dictionary = params.sequence_dictionary ? channel.fromPath(params.sequence_dictionary).map {it -> [[id:it.simpleName], it]}.collect() - : channel.empty() ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) ch_dbsnp = params.known_dbsnp ? channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) - ch_mt_fasta = params.mt_fasta ? channel.fromPath(params.mt_fasta).map { it -> [[id:it.simpleName], it] }.collect() - : channel.empty() ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() @@ -68,14 +62,21 @@ workflow NFCORE_RAREDISEASE { PREPARE_REFERENCES ( ch_genome_fasta, - ch_genome_fai, - ch_genome_dictionary, - ch_mt_fasta, ch_gnomad_af_tab, ch_dbsnp, ch_target_bed_unprocessed, ch_vcfanno_extra_unprocessed, - ch_vep_cache_unprocessed + ch_vep_cache_unprocessed, + params.aligner, + params.analysis_type, + params.bwa, + params.bwamem2, + params.bwameme, + params.fai, + params.mt_aligner, + params.mt_fasta, + params.run_mt_for_wes, + params.sequence_dictionary ) .set { ch_references } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 8dd3c5c0f..05b09c153 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -36,54 +36,111 @@ include { UNTAR as UNTAR_VEP_CACHE } from '../../../mo workflow PREPARE_REFERENCES { take: ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(fai) ] - ch_mt_fasta // channel: [mandatory for dedicated mt analysis] [ val(meta), path(fasta) ] ch_gnomad_af_tab // channel: [optional; used in for snv annotation] [ val(meta), path(tab) ] ch_known_dbsnp // channel: [optional; used only by sentieon] [ val(meta), path(vcf) ] ch_target_bed // channel: [mandatory for WES] [ path(bed) ] ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] + val_aligner + val_analysis_type + val_bwa + val_bwamem2 + val_bwameme + val_fai + val_mtaligner + val_mtfasta + val_run_mt_for_wes + val_genome_dict main: - ch_versions = channel.empty() - ch_bgzip_tbi = channel.empty() - ch_bwa = channel.empty() - ch_sentieonbwa = channel.empty() - ch_vcfanno_extra = channel.empty() - ch_vcfanno_bgzip = channel.empty() - ch_vcfanno_index = channel.empty() + ch_versions = channel.empty() + ch_bgzip_tbi = channel.empty() + ch_bwa = channel.empty() + ch_genome_bwameme_index = channel.empty() + ch_genome_bwamem2_index = channel.empty() + ch_mt_bwa_index = channel.empty() + ch_mt_bwamem2_index = channel.empty() + ch_mtshift_bwa_index = channel.empty() + ch_mtshift_bwamem2_index = channel.empty() + ch_mt_dict = channel.empty() + ch_mt_fai = channel.empty() + ch_mt_fasta = channel.empty() + ch_sentieonbwa = channel.empty() + ch_vcfanno_extra = channel.empty() + ch_vcfanno_bgzip = channel.empty() + ch_vcfanno_index = channel.empty() // Genome indices - SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]) - GATK_SD(ch_genome_fasta) - ch_fai = channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect() - ch_dict = channel.empty().mix(ch_genome_dictionary, GATK_SD.out.dict).collect() + if (!val_fai) { + ch_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]).fai.collect() + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) + } else { + ch_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() + } + + if (!val_genome_dict) { + ch_genome_dict = GATK_SD(ch_genome_fasta).dict.collect() + ch_versions = ch_versions.mix(GATK_SD.out.versions) + } else { + ch_genome_dict = channel.fromPath(val_genome_dict).map {it -> [[id:it.simpleName], it]}.collect() + } + GET_CHROM_SIZES( ch_fai ) // Genome alignment indices - BWA_INDEX_GENOME(ch_genome_fasta).index.set{ch_bwa} - BWAMEM2_INDEX_GENOME(ch_genome_fasta) - BWAMEME_INDEX_GENOME(ch_genome_fasta) - SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} + if (!val_bwa) { + if (!val_aligner.equals("sentieon") || val_mtaligner.equals("bwa")) { + BWA_INDEX_GENOME(ch_genome_fasta).index.set{ch_bwa} + ch_versions = ch_versions.mix(BWA_INDEX_GENOME.out.versions) + } + if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { + SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} + ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) + } + } + if (!val_bwamem2 && (val_aligner.equals("bwamem2") || val_mtaligner.equals("bwamem2"))) { + ch_genome_bwamem2_index = BWAMEM2_INDEX_GENOME(ch_genome_fasta).index.collect() + ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) + } + if (!val_bwamem2 && val_aligner.equals("bwameme")) { + ch_genome_bwameme_index = BWAMEME_INDEX_GENOME(ch_genome_fasta).index.collect() + ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) + } // MT genome indices - SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) - ch_mt_fasta_in = channel.empty().mix(ch_mt_fasta, SAMTOOLS_EXTRACT_MT.out.fa).collect() - SAMTOOLS_FAIDX_MT(ch_mt_fasta_in, [[],[]]) - GATK_SD_MT(ch_mt_fasta_in) - GATK_SHIFTFASTA(ch_mt_fasta_in, SAMTOOLS_FAIDX_MT.out.fai, GATK_SD_MT.out.dict) + + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { + if (!val_mtfasta) { + ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai).fa.collect() + ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) + } else { + ch_mt_fasta = channel.fromPath(val_mtfasta).map { it -> [[id:it.simpleName], it] }.collect() + } + + ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() + ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() + GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) + + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions,GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) + } // MT alignment indices - BWAMEM2_INDEX_MT(ch_mt_fasta_in) - BWA_INDEX_MT(ch_mt_fasta_in) - SENTIEON_BWAINDEX_MT(ch_mt_fasta_in) - ch_bwa_mt = channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() - - BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) - BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) - SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) - ch_bwa_mtshift = channel.empty().mix(SENTIEON_BWAINDEX_MT_SHIFT.out.index, BWA_INDEX_MT_SHIFT.out.index).collect() + if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwamem2")) { + ch_mt_bwamem2_index = BWAMEM2_INDEX_MT(ch_mt_fasta).index.collect() + ch_mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions, BWAMEM2_INDEX_MT_SHIFT.out.versions) + } + if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwa")) { + ch_mt_bwa_index = BWA_INDEX_MT(ch_mt_fasta).index.collect() + ch_mtshift_bwa_index = BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions, BWA_INDEX_MT_SHIFT.out.versions) + } + if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("sentieon")) { + ch_mt_bwa_index = SENTIEON_BWAINDEX_MT(ch_mt_fasta).index.collect() + ch_mtshift_bwa_index = SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions, SENTIEON_BWAINDEX_MT_SHIFT.out.versions) + } + GATK_SHIFTFASTA.out.intervals .multiMap{ _meta, files -> shift_intervals: @@ -142,7 +199,7 @@ workflow PREPARE_REFERENCES { .set { ch_target_bed_gz_tbi } // Generate bait and target intervals - GATK_BILT(ch_target_bed, ch_dict).interval_list + GATK_BILT(ch_target_bed, ch_genome_dict).interval_list GATK_ILT(GATK_BILT.out.interval_list) GATK_ILT.out.interval_list .collect{ _meta, list -> list } @@ -160,23 +217,7 @@ workflow PREPARE_REFERENCES { RTGTOOLS_FORMAT(ch_rtgformat_in) // Gather versions - ch_versions = ch_versions.mix(BWA_INDEX_GENOME.out.versions) - ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) - ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) - ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) - ch_versions = ch_versions.mix(GATK_SD.out.versions) ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions) - ch_versions = ch_versions.mix(GATK_SD_MT.out.versions) - ch_versions = ch_versions.mix(GATK_SHIFTFASTA.out.versions) - ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions) - ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions) - ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions) - ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT_SHIFT.out.versions) - ch_versions = ch_versions.mix(BWA_INDEX_MT_SHIFT.out.versions) - ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT_SHIFT.out.versions) ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions) ch_versions = ch_versions.mix(TABIX_PT.out.versions) ch_versions = ch_versions.mix(TABIX_PBT.out.versions) @@ -193,25 +234,25 @@ workflow PREPARE_REFERENCES { emit: genome_bwa_index = channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] - genome_bwamem2_index = BWAMEM2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] - genome_bwameme_index = BWAMEME_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] + genome_bwamem2_index = ch_genome_bwamem2_index // channel: [ val(meta), path(index) ] + genome_bwameme_index = ch_genome_bwameme_index // channel: [ val(meta), path(index) ] genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] genome_fai = ch_fai // channel: [ val(meta), path(fai) ] - genome_dict = ch_dict // channel: [ val(meta), path(dict) ] + genome_dict = ch_genome_dict // channel: [ val(meta), path(dict) ] sdf = RTGTOOLS_FORMAT.out.sdf // channel: [ val (meta), path(intervals) ] mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] - mt_bwa_index = ch_bwa_mt // channel: [ val(meta), path(index) ] - mt_bwamem2_index = BWAMEM2_INDEX_MT.out.index.collect() // channel: [ val(meta), path(index) ] - mt_dict = GATK_SD_MT.out.dict.collect() // channel: [ val(meta), path(dict) ] - mt_fasta = ch_mt_fasta_in.collect() // channel: [ val(meta), path(fasta) ] - mt_fai = SAMTOOLS_FAIDX_MT.out.fai.collect() // channel: [ val(meta), path(fai) ] + mt_bwa_index = ch_mt_bwa_index // channel: [ val(meta), path(index) ] + mt_bwamem2_index = ch_mt_bwamem2_index // channel: [ val(meta), path(index) ] + mt_dict = ch_mt_dict // channel: [ val(meta), path(dict) ] + mt_fai = ch_mt_fai // channel: [ val(meta), path(fai) ] + mt_fasta = ch_mt_fasta // channel: [ val(meta), path(fasta) ] mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel: [ path(intervals) ] mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() // channel: [ val(meta), path(backchain) ] mtshift_dict = GATK_SHIFTFASTA.out.dict // channel: [ val(meta), path(dict) ] mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() // channel: [ val(meta), path(fai) ] mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel: [ val(meta), path(fasta) ] - mtshift_bwa_index = ch_bwa_mtshift // channel: [ val(meta), path(index) ] - mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect() // channel: [ val(meta), path(index) ] + mtshift_bwa_index = ch_mtshift_bwa_index // channel: [ val(meta), path(index) ] + mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel: [ val(meta), path(index) ] gnomad_af_idx = TABIX_GNOMAD_AF.out.tbi.collect() // channel: [ val(meta), path(fasta) ] known_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() // channel: [ val(meta), path(fasta) ] target_bed = ch_target_bed_gz_tbi.collect() // channel: [ val(meta), path(bed), path(tbi) ] From 7a6e4fb81983e61f7782232ab9458de432435a3b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 15 Dec 2025 15:04:04 +0000 Subject: [PATCH 177/872] [automated] Fix code linting --- subworkflows/local/prepare_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 05b09c153..f310f27f5 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -84,7 +84,7 @@ workflow PREPARE_REFERENCES { } else { ch_genome_dict = channel.fromPath(val_genome_dict).map {it -> [[id:it.simpleName], it]}.collect() } - + GET_CHROM_SIZES( ch_fai ) // Genome alignment indices From 574b6495a307e5246dfe2bd25f1c712f52b0926f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 15 Dec 2025 16:36:22 +0100 Subject: [PATCH 178/872] update test --- .../prepare_references/tests/main.nf.test | 27 +++++++----- .../tests/main.nf.test.snap | 16 ++++--- .../prepare_references/tests/nextflow.config | 44 +------------------ 3 files changed, 26 insertions(+), 61 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 774194923..2ae360e03 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -9,22 +9,27 @@ nextflow_workflow { when { params { - aligner = "bwamem2" - mt_aligner = "bwa" variant_caller = "deepvariant" mito_name = "MT" } workflow { """ - input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai').map {it -> [[id:'genome'], it]}.collect() - input[2] = channel.empty() - input[3] = channel.empty() - input[4] = channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() - input[5] = channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() - input[6] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() - input[7] = channel.empty() - input[8] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() + input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() + input[2] = channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() + input[3] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() + input[4] = channel.empty() + input[5] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[6] = "bwamem2" + input[7] = "wgs" + input[8] = null + input[9] = null + input[10] = null + input[11] = null + input[12] = "bwa" + input[13] = null + input[14] = false + input[15] = null """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index fe5c7e7d8..9f8d74df2 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -43,7 +43,7 @@ { "id": "genome" }, - "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "12": [ @@ -51,7 +51,7 @@ { "id": "genome" }, - "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], "13": [ @@ -389,6 +389,7 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", + "versions.yml:md5,3d14ad719ad5095ae199e915140148b6", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", @@ -415,7 +416,7 @@ { "id": "genome" }, - "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai" + "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ], "5": [ @@ -505,7 +506,7 @@ { "id": "genome" }, - "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai" + "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ], "gnomad_af_idx": [ @@ -884,6 +885,7 @@ "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", + "versions.yml:md5,3d14ad719ad5095ae199e915140148b6", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", @@ -903,9 +905,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-07-10T22:52:01.91651849" + "timestamp": "2025-12-15T16:15:07.860328132" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/nextflow.config b/subworkflows/local/prepare_references/tests/nextflow.config index 451952698..61d96724b 100644 --- a/subworkflows/local/prepare_references/tests/nextflow.config +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -17,37 +17,8 @@ process { - withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME' { - ext.when = {!params.bwamem2 && (params.aligner == "bwamem2" || params.mt_aligner == "bwamem2")} - } - withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { ext.args = '-a meme' - ext.when = {!params.bwameme && params.aligner == "bwameme"} - } - - withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' { - ext.when = {!params.bwa && (!(params.aligner == "sentieon") || params.mt_aligner == "bwa")} - } - - withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' { - ext.when = {!params.bwa && (params.aligner == "sentieon" || params.mt_aligner == "sentieon")} - } - - withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwamem2"} - } - - withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "sentieon"} - } - - withName: '.*PREPARE_REFERENCES:BWA_INDEX_MT.*' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) && params.mt_aligner == "bwa"} - } - - withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME' { - ext.when = {!params.fai} } withName: '.*PREPARE_REFERENCES:RTGTOOLS_FORMAT' { @@ -56,25 +27,12 @@ process { withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' { ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" } - ext.when = {!params.mt_fasta} - } - - withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes) } - } - - withName: '.*PREPARE_REFERENCES:GATK_SD' { - ext.when = {!params.sequence_dictionary} } withName: '.*PREPARE_REFERENCES:GATK_SHIFTFASTA' { ext.args = { "--interval-file-name ${meta.id}_mt" } } - withName: '.*PREPARE_REFERENCES:GATK_SD_MT' { - ext.when = { (params.analysis_type.matches("wgs|mito") || params.run_mt_for_wes)} - } - withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { ext.when = {params.known_dbsnp && !params.known_dbsnp_tbi} } @@ -97,7 +55,7 @@ process { } withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' { - ext.when = { params.target_bed && params.bait_padding > 0 } + ext.when = { params.target_bed } ext.prefix = { "${meta.id}_pad${params.bait_padding}" } ext.args = { "-b ${params.bait_padding}" } } From 22381b40d5db1f21086200d2b6ffcd1fdc5391af Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Dec 2025 10:20:31 +0100 Subject: [PATCH 179/872] gnomad and dbsnp --- conf/modules/prepare_references.config | 5 - main.nf | 14 +- subworkflows/local/prepare_references/main.nf | 90 ++++++---- .../prepare_references/tests/main.nf.test | 22 +-- .../tests/main.nf.test.snap | 168 ++++++++++-------- .../prepare_references/tests/nextflow.config | 5 - 6 files changed, 165 insertions(+), 139 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 47469fc4a..f7b63ae8e 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -41,12 +41,7 @@ process { ext.args = { "--interval-file-name ${meta.id}_mt" } } - withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { - ext.when = {params.known_dbsnp && !params.known_dbsnp_tbi} - } - withName: '.*PREPARE_REFERENCES:TABIX_GNOMAD_AF' { - ext.when = {params.gnomad_af && !params.gnomad_af_idx} ext.args = '-s 1 -b 2 -e 2' } diff --git a/main.nf b/main.nf index 4b7d742c8..70dbab516 100644 --- a/main.nf +++ b/main.nf @@ -51,8 +51,6 @@ workflow NFCORE_RAREDISEASE { ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) - ch_dbsnp = params.known_dbsnp ? channel.fromPath(params.known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() @@ -63,7 +61,6 @@ workflow NFCORE_RAREDISEASE { PREPARE_REFERENCES ( ch_genome_fasta, ch_gnomad_af_tab, - ch_dbsnp, ch_target_bed_unprocessed, ch_vcfanno_extra_unprocessed, ch_vep_cache_unprocessed, @@ -73,6 +70,10 @@ workflow NFCORE_RAREDISEASE { params.bwamem2, params.bwameme, params.fai, + params.gnomad_af, + params.gnomad_af_idx, + params.known_dbsnp, + params.known_dbsnp_tbi, params.mt_aligner, params.mt_fasta, params.run_mt_for_wes, @@ -86,8 +87,8 @@ workflow NFCORE_RAREDISEASE { : channel.value([]) ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_dbsnp_tbi = params.known_dbsnp_tbi ? channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.known_dbsnp_tbi.ifEmpty([[],[]]) + ch_dbsnp = ch_references.dbsnp + ch_dbsnp_tbi = ch_references.dbsnp_tbi ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> @@ -113,8 +114,7 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() : ch_references.gnomad_af_idx - ch_gnomad_af = params.gnomad_af ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {_meta, tab, idx -> [tab,idx]}.collect() - : channel.empty() + ch_gnomad_af = ch_references.gnomad_af_idx ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() : channel.empty() ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index f310f27f5..9a276b36c 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -36,8 +36,6 @@ include { UNTAR as UNTAR_VEP_CACHE } from '../../../mo workflow PREPARE_REFERENCES { take: ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_gnomad_af_tab // channel: [optional; used in for snv annotation] [ val(meta), path(tab) ] - ch_known_dbsnp // channel: [optional; used only by sentieon] [ val(meta), path(vcf) ] ch_target_bed // channel: [mandatory for WES] [ path(bed) ] ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] @@ -47,28 +45,36 @@ workflow PREPARE_REFERENCES { val_bwamem2 val_bwameme val_fai + val_gnomad_af + val_gnomad_af_idx + val_known_dbsnp + val_known_dbsnp_tbi val_mtaligner val_mtfasta val_run_mt_for_wes val_genome_dict main: - ch_versions = channel.empty() - ch_bgzip_tbi = channel.empty() - ch_bwa = channel.empty() - ch_genome_bwameme_index = channel.empty() - ch_genome_bwamem2_index = channel.empty() - ch_mt_bwa_index = channel.empty() - ch_mt_bwamem2_index = channel.empty() - ch_mtshift_bwa_index = channel.empty() - ch_mtshift_bwamem2_index = channel.empty() - ch_mt_dict = channel.empty() - ch_mt_fai = channel.empty() - ch_mt_fasta = channel.empty() - ch_sentieonbwa = channel.empty() - ch_vcfanno_extra = channel.empty() - ch_vcfanno_bgzip = channel.empty() - ch_vcfanno_index = channel.empty() + ch_versions = channel.empty() + ch_bgzip_tbi = channel.empty() + ch_bwa = channel.empty() + ch_genome_bwameme_index = channel.empty() + ch_genome_bwamem2_index = channel.empty() + ch_gnomad_af_idx = channel.empty() + ch_dbsnp = channel.value([[:],[]]) + ch_dbsnp_tbi = channel.value([[:],[]]) + ch_mt_bwa_index = channel.empty() + ch_mt_bwamem2_index = channel.empty() + ch_mtshift_bwa_index = channel.empty() + ch_mtshift_bwamem2_index = channel.empty() + ch_mt_dict = channel.empty() + ch_mt_fai = channel.empty() + ch_mt_fasta = channel.empty() + ch_sentieonbwa = channel.empty() + ch_shiftfasta_mtintervals = channel.empty() + ch_vcfanno_extra = channel.empty() + ch_vcfanno_bgzip = channel.empty() + ch_vcfanno_index = channel.empty() // Genome indices if (!val_fai) { @@ -120,6 +126,16 @@ workflow PREPARE_REFERENCES { ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) + GATK_SHIFTFASTA.out.intervals + .multiMap{ _meta, files -> + shift_intervals: + def ind = files.findIndexValues {file -> file.toString().endsWith("shifted.intervals")} + files[ind] + intervals: + ind = files.findIndexValues {file -> !(file.toString().endsWith("shifted.intervals"))} + files[ind] + } + .set {ch_shiftfasta_mtintervals} ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions,GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) } @@ -141,20 +157,27 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions, SENTIEON_BWAINDEX_MT_SHIFT.out.versions) } - GATK_SHIFTFASTA.out.intervals - .multiMap{ _meta, files -> - shift_intervals: - def ind = files.findIndexValues {file -> file.toString().endsWith("shifted.intervals")} - files[ind] - intervals: - ind = files.findIndexValues {file -> !(file.toString().endsWith("shifted.intervals"))} - files[ind] + // Vcf, tab and bed indices + if (val_known_dbsnp) { + ch_dbsnp = channel.fromPath(val_known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() + if (val_known_dbsnp_tbi) { + ch_dbsnp_tbi = channel.fromPath(val_known_dbsnp_tbi).map{ it -> [[id:it.simpleName], it] }.collect() + } else { + ch_dbsnp_tbi = TABIX_DBSNP(ch_dbsnp).tbi.collect() + ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) } - .set {ch_shiftfasta_mtintervals} + } - // Vcf, tab and bed indices - TABIX_DBSNP(ch_known_dbsnp) - TABIX_GNOMAD_AF(ch_gnomad_af_tab) + if (val_gnomad_af) { + ch_gnomad_af = channel.fromPath(val_gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() + if (val_gnomad_af_idx) { + ch_gnomad_idx = channel.fromPath(val_gnomad_af_idx).map{ it -> [[id:it.simpleName], it] }.collect() + } else { + ch_gnomad_idx = TABIX_GNOMAD_AF(ch_gnomad_af).tbi.collect() + ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions) + } + ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() + } // Index target bed file in case of gz input TABIX_PT(ch_target_bed) @@ -218,12 +241,10 @@ workflow PREPARE_REFERENCES { // Gather versions ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) - ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions) ch_versions = ch_versions.mix(TABIX_PT.out.versions) ch_versions = ch_versions.mix(TABIX_PBT.out.versions) ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) - ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions) ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions) ch_versions = ch_versions.mix(GATK_BILT.out.versions) @@ -233,12 +254,15 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) emit: + dbsnp = ch_dbsnp // channel: [ val(meta), path(dbsnp) ] + dbsnp_tbi = ch_dbsnp_tbi // channel: [ val(meta), path(dbsnp_idx) ] genome_bwa_index = channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] genome_bwamem2_index = ch_genome_bwamem2_index // channel: [ val(meta), path(index) ] genome_bwameme_index = ch_genome_bwameme_index // channel: [ val(meta), path(index) ] genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] genome_fai = ch_fai // channel: [ val(meta), path(fai) ] genome_dict = ch_genome_dict // channel: [ val(meta), path(dict) ] + gnomad_af_idx = ch_gnomad_af_idx // channel: [ val(gnomad), path(idx) ] sdf = RTGTOOLS_FORMAT.out.sdf // channel: [ val (meta), path(intervals) ] mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] mt_bwa_index = ch_mt_bwa_index // channel: [ val(meta), path(index) ] @@ -253,8 +277,6 @@ workflow PREPARE_REFERENCES { mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel: [ val(meta), path(fasta) ] mtshift_bwa_index = ch_mtshift_bwa_index // channel: [ val(meta), path(index) ] mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel: [ val(meta), path(index) ] - gnomad_af_idx = TABIX_GNOMAD_AF.out.tbi.collect() // channel: [ val(meta), path(fasta) ] - known_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() // channel: [ val(meta), path(fasta) ] target_bed = ch_target_bed_gz_tbi.collect() // channel: [ val(meta), path(bed), path(tbi) ] vcfanno_extra = ch_vcfanno_extra.ifEmpty([[]]) // channel: [ [path(vcf), path(tbi)] ] bait_intervals = CAT_CAT_BAIT.out.file_out.map{ _meta, inter -> inter}.collect().ifEmpty([[]])// channel: [ path(intervals) ] diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 2ae360e03..aa79f0c6e 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -15,21 +15,23 @@ nextflow_workflow { workflow { """ input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz').map {it -> [[id:'genome'], it]}.collect() - input[2] = channel.of(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz').map {it -> [[id:'genome'], it]}.collect() - input[3] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() - input[4] = channel.empty() - input[5] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() - input[6] = "bwamem2" - input[7] = "wgs" + input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() + input[2] = channel.empty() + input[3] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[4] = "bwamem2" + input[5] = "wgs" + input[6] = null + input[7] = null input[8] = null input[9] = null - input[10] = null + input[10] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' input[11] = null - input[12] = "bwa" + input[12] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' input[13] = null - input[14] = false + input[14] = "bwa" input[15] = null + input[16] = false + input[17] = null """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 9f8d74df2..6943777e1 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -5,32 +5,42 @@ "0": [ [ { - "id": "genome" + "id": "dbsnp_-138-" }, - [ - "reference.amb:md5,0a85644af00f9a856d874381d24e7803", - "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", - "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", - "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", - "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" - ] + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], "1": [ + [ + { + "id": "dbsnp_-138-" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + ] + ], + "10": [ + [ + "genome_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" + ] + ], + "11": [ [ { "id": "genome" }, [ - "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b", - "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803", - "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", - "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0", - "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2" + "genome_mt.amb:md5,6749f645487281112c254ab829ea048c", + "genome_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "genome_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", + "genome_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", + "genome_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" ] ] ], - "10": [ + "12": [ + + ], + "13": [ [ { "id": "genome" @@ -38,7 +48,7 @@ "genome_mt.dict:md5,249ad4680360e4a9fc1e3b44ed54f568" ] ], - "11": [ + "14": [ [ { "id": "genome" @@ -46,7 +56,7 @@ "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], - "12": [ + "15": [ [ { "id": "genome" @@ -54,12 +64,12 @@ "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], - "13": [ + "16": [ [ "genome_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" ] ], - "14": [ + "17": [ [ { "id": "genome" @@ -67,7 +77,7 @@ "genome_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ], - "15": [ + "18": [ [ { "id": "genome" @@ -75,7 +85,7 @@ "genome_shift.dict:md5,a714408661d0f6403f417304342574fc" ] ], - "16": [ + "19": [ [ { "id": "genome" @@ -83,40 +93,26 @@ "genome_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], - "17": [ - [ - { - "id": "genome" - }, - "genome_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" - ] - ], - "18": [ + "2": [ [ { "id": "genome" }, [ - "genome_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", - "genome_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", - "genome_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", - "genome_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + "reference.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", + "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", + "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" ] ] - ], - "19": [ - - ], - "2": [ - ], "20": [ [ { "id": "genome" }, - "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + "genome_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" ] ], "21": [ @@ -124,10 +120,19 @@ { "id": "genome" }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + [ + "genome_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "genome_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "genome_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "genome_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "genome_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + ] ] ], "22": [ + + ], + "23": [ [ { "id": "genome" @@ -136,24 +141,24 @@ "genome_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" ] ], - "23": [ + "24": [ [ [ ] ] ], - "24": [ + "25": [ [ "genome_bait.intervals_list:md5,1f3d445e6e53260510710a8333d29cfe" ] ], - "25": [ + "26": [ [ "genome_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" ] ], - "26": [ + "27": [ [ [ "LoFtool_scores.txt:md5,d9abd640ef22c790583b4b15d144ea6f", @@ -384,7 +389,7 @@ ] ] ], - "27": [ + "28": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", @@ -408,10 +413,27 @@ ], "3": [ [ - "reference.fasta.fai.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" + { + "id": "genome" + }, + [ + "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b", + "reference.fasta.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.fasta.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.fasta.bwt.2bit.64:md5,3c0df9450afc5cb0ad5e85870829d9d0", + "reference.fasta.pac:md5,96b449e1316067fdfba91b1399687bc2" + ] ] ], "4": [ + + ], + "5": [ + [ + "reference.fasta.fai.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" + ] + ], + "6": [ [ { "id": "genome" @@ -419,7 +441,7 @@ "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ], - "5": [ + "7": [ [ { "id": "genome" @@ -427,34 +449,34 @@ "reference.dict:md5,81abd0fc051c084405024e0927f7b436" ] ], - "6": [ + "8": [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + ] + ], + "9": [ ], - "7": [ + "bait_intervals": [ [ - "genome_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" + "genome_bait.intervals_list:md5,1f3d445e6e53260510710a8333d29cfe" ] ], - "8": [ + "dbsnp": [ [ { - "id": "genome" + "id": "dbsnp_-138-" }, - [ - "genome_mt.amb:md5,6749f645487281112c254ab829ea048c", - "genome_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", - "genome_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", - "genome_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" - ] + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], - "9": [ - - ], - "bait_intervals": [ + "dbsnp_tbi": [ [ - "genome_bait.intervals_list:md5,1f3d445e6e53260510710a8333d29cfe" + { + "id": "dbsnp_-138-" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" ] ], "genome_bwa_index": [ @@ -511,20 +533,10 @@ ], "gnomad_af_idx": [ [ - { - "id": "genome" - }, + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ], - "known_dbsnp_tbi": [ - [ - { - "id": "genome" - }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" - ] - ], "mt_bwa_index": [ [ { @@ -908,6 +920,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-15T16:15:07.860328132" + "timestamp": "2025-12-16T10:16:04.746173646" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/nextflow.config b/subworkflows/local/prepare_references/tests/nextflow.config index 61d96724b..bbc72e400 100644 --- a/subworkflows/local/prepare_references/tests/nextflow.config +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -33,12 +33,7 @@ process { ext.args = { "--interval-file-name ${meta.id}_mt" } } - withName: '.*PREPARE_REFERENCES:TABIX_DBSNP' { - ext.when = {params.known_dbsnp && !params.known_dbsnp_tbi} - } - withName: '.*PREPARE_REFERENCES:TABIX_GNOMAD_AF' { - ext.when = {params.gnomad_af && !params.gnomad_af_idx} ext.args = '-s 1 -b 2 -e 2' } From d1cf1348d8a1c1fc7cc6a9cce7f64e3978be2c44 Mon Sep 17 00:00:00 2001 From: dorotejavujinovic <66911549+dorotejavujinovic@users.noreply.github.com> Date: Tue, 16 Dec 2025 10:28:48 +0100 Subject: [PATCH 180/872] Refactor workflow includes and MultiQC file handling --- workflows/raredisease.nf | 97 +++++++++++++++++++++------------------- 1 file changed, 50 insertions(+), 47 deletions(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 005e2a800..741784f46 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -41,35 +41,34 @@ include { PARSE_CONTAMINATION } from '../modules/local/parse_contam // SUBWORKFLOWS // -include { ALIGN } from '../subworkflows/local/align' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli.nf' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_MT } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SV } from '../subworkflows/local/annotate_consequence_pli' -include { ANNOTATE_GENOME_SNVS } from '../subworkflows/local/annotate_genome_snvs' -include { ANNOTATE_MOBILE_ELEMENTS } from '../subworkflows/local/annotate_mobile_elements' -include { ANNOTATE_MT_SNVS } from '../subworkflows/local/annotate_mt_snvs' -include { ANNOTATE_STRUCTURAL_VARIANTS } from '../subworkflows/local/annotate_structural_variants' -include { CALL_MOBILE_ELEMENTS } from '../subworkflows/local/call_mobile_elements' -include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' -include { CALL_SNV } from '../subworkflows/local/call_snv' -include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_ME } from '../subworkflows/local/generate_clinical_set.nf' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_MT } from '../subworkflows/local/generate_clinical_set' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/local/generate_clinical_set' -include { GENERATE_CLINICAL_SET as GENERATE_CLINICAL_SET_SV } from '../subworkflows/local/generate_clinical_set' -include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' -include { GENS } from '../subworkflows/local/gens' -include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' -include { QC_BAM } from '../subworkflows/local/qc_bam' -include { RANK_VARIANTS as RANK_VARIANTS_MT } from '../subworkflows/local/rank_variants' -include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' -include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' -include { SCATTER_GENOME } from '../subworkflows/local/scatter_genome' -include { SUBSAMPLE_MT } from '../subworkflows/local/subsample_mt' -include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' -include { CONTAMINATION_CHECK } from '../subworkflows/local/contamination_check/main' - +include { ALIGN } from '../subworkflows/local/align' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli.nf' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_MT } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SV } from '../subworkflows/local/annotate_consequence_pli' +include { ANNOTATE_GENOME_SNVS } from '../subworkflows/local/annotate_genome_snvs' +include { ANNOTATE_MOBILE_ELEMENTS } from '../subworkflows/local/annotate_mobile_elements' +include { ANNOTATE_MT_SNVS } from '../subworkflows/local/annotate_mt_snvs' +include { ANNOTATE_STRUCTURAL_VARIANTS } from '../subworkflows/local/annotate_structural_variants' +include { CALL_MOBILE_ELEMENTS } from '../subworkflows/local/call_mobile_elements' +include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' +include { CALL_SNV } from '../subworkflows/local/call_snv' +include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' +include { CONTAMINATION_CHECK } from '../subworkflows/local/contamination_check/main' +include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' +include { GENS } from '../subworkflows/local/gens' +include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' +include { QC_BAM } from '../subworkflows/local/qc_bam' +include { RANK_VARIANTS as RANK_VARIANTS_MT } from '../subworkflows/local/rank_variants' +include { RANK_VARIANTS as RANK_VARIANTS_SNV } from '../subworkflows/local/rank_variants' +include { RANK_VARIANTS as RANK_VARIANTS_SV } from '../subworkflows/local/rank_variants' +include { SUBSAMPLE_MT_FRAC } from '../subworkflows/local/subsample_mt_frac' +include { SUBSAMPLE_MT_READS } from '../subworkflows/local/subsample_mt_reads' +include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -957,25 +956,29 @@ workflow RAREDISEASE { sort: true ) ) - - ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{it[1]}.collect().ifEmpty([])) -// Add contamination results to MultiQC - ch_multiqc_files = ch_multiqc_files.mix(ch_contamination_mqc.map { meta, file -> file }) - - if (!(params.skip_tools && params.skip_tools.split(',').contains('peddy'))) { - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{it[1]}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{it[1]}.collect().ifEmpty([])) + if (!skip_fastqc) { + ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{_meta, reports -> reports}.ifEmpty([])) } + ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) + + // Add contamination results to MultiQC + ch_multiqc_files = ch_multiqc_files.mix(ch_contamination_mqc.map { _meta, file -> file }) + + if (!skip_peddy) { + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + } + + MULTIQC ( MULTIQC ( ch_multiqc_files.collect(), From 00bc48762c9fbf5fefcdf74a40dd8fad2c18dfe3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Dec 2025 11:33:16 +0100 Subject: [PATCH 181/872] padding target bed --- conf/modules/prepare_references.config | 9 ----- main.nf | 6 +-- nextflow_schema.json | 2 +- subworkflows/local/prepare_references/main.nf | 38 +++++++------------ .../prepare_references/tests/main.nf.test | 29 +++++++------- .../tests/main.nf.test.snap | 24 ++++++------ .../prepare_references/tests/nextflow.config | 9 ----- 7 files changed, 43 insertions(+), 74 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index f7b63ae8e..593e72518 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -45,20 +45,11 @@ process { ext.args = '-s 1 -b 2 -e 2' } - withName: '.*PREPARE_REFERENCES:TABIX_PT' { - ext.when = { !params.target_bed.equals(null) && params.target_bed.endsWith(".gz") } - } - - withName: '.*PREPARE_REFERENCES:TABIX_PBT' { - ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") } - } - withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_VCFANNOEXTRA' { ext.args2 = '--csi' } withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' { - ext.when = { params.target_bed } ext.prefix = { "${meta.id}_pad${params.bait_padding}" } ext.args = { "-b ${params.bait_padding}" } } diff --git a/main.nf b/main.nf index 70dbab516..01215b01f 100644 --- a/main.nf +++ b/main.nf @@ -51,8 +51,6 @@ workflow NFCORE_RAREDISEASE { ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() : channel.value([[],[]]) - ch_target_bed_unprocessed = params.target_bed ? channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() : channel.empty() ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() @@ -61,7 +59,6 @@ workflow NFCORE_RAREDISEASE { PREPARE_REFERENCES ( ch_genome_fasta, ch_gnomad_af_tab, - ch_target_bed_unprocessed, ch_vcfanno_extra_unprocessed, ch_vep_cache_unprocessed, params.aligner, @@ -77,7 +74,8 @@ workflow NFCORE_RAREDISEASE { params.mt_aligner, params.mt_fasta, params.run_mt_for_wes, - params.sequence_dictionary + params.sequence_dictionary, + params.target_bed ) .set { ch_references } diff --git a/nextflow_schema.json b/nextflow_schema.json index 357b122e6..cd756f526 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -399,7 +399,7 @@ "exists": true, "format": "path", "fa_icon": "fas fa-file", - "pattern": "^\\S+\\.bed(\\.gz)?$", + "pattern": "^\\S+\\.bed$", "description": "Path to directory for target bed file.", "help_text": "If you would like to limit your analysis to specific regions of the genome, you can pass those regions in a bed file using this option" }, diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 9a276b36c..b52ce1eda 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -24,19 +24,16 @@ include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../../mo include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../../modules/nf-core/sentieon/bwaindex/main' include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../../modules/nf-core/sentieon/bwaindex/main' include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../../modules/nf-core/sentieon/bwaindex/main' -include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_PT } from '../../../modules/nf-core/tabix/tabix/main' include { UNTAR as UNTAR_VEP_CACHE } from '../../../modules/nf-core/untar/main' workflow PREPARE_REFERENCES { take: ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_target_bed // channel: [mandatory for WES] [ path(bed) ] ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] val_aligner @@ -53,6 +50,7 @@ workflow PREPARE_REFERENCES { val_mtfasta val_run_mt_for_wes val_genome_dict + val_target_bed main: ch_versions = channel.empty() @@ -72,6 +70,7 @@ workflow PREPARE_REFERENCES { ch_mt_fasta = channel.empty() ch_sentieonbwa = channel.empty() ch_shiftfasta_mtintervals = channel.empty() + ch_target_bed_gz_tbi = channel.value([[:],[],[]]) ch_vcfanno_extra = channel.empty() ch_vcfanno_bgzip = channel.empty() ch_vcfanno_index = channel.empty() @@ -179,16 +178,18 @@ workflow PREPARE_REFERENCES { ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() } - // Index target bed file in case of gz input - TABIX_PT(ch_target_bed) - ch_target_bed - .join(TABIX_PT.out.tbi) - .set{ ch_trgt_bed_tbi } - // Compress and index target bed file in case of uncompressed input - TABIX_PBT(ch_target_bed).gz_tbi - .set { ch_bgzip_tbi } - ch_target_bed_gz_tbi = channel.empty() - .mix(ch_trgt_bed_tbi, ch_bgzip_tbi) + // Index target bed file + if (val_target_bed) { + ch_target_bed = channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() + BEDTOOLS_PAD_TARGET_BED( + ch_target_bed, + ch_fai.map { _meta, fai -> return fai } + ) + TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi + .set { ch_target_bed_gz_tbi } + ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions) + ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions) + } ch_vcfanno_extra_unprocessed .branch { _meta, vcf -> @@ -213,13 +214,6 @@ workflow PREPARE_REFERENCES { .collect() .set{ch_vcfanno_extra} - // Pad bed file - BEDTOOLS_PAD_TARGET_BED( - ch_target_bed, - ch_fai.map { _meta, fai -> return fai } - ) - TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi - .set { ch_target_bed_gz_tbi } // Generate bait and target intervals GATK_BILT(ch_target_bed, ch_genome_dict).interval_list @@ -241,12 +235,8 @@ workflow PREPARE_REFERENCES { // Gather versions ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) - ch_versions = ch_versions.mix(TABIX_PT.out.versions) - ch_versions = ch_versions.mix(TABIX_PBT.out.versions) ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) - ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions) - ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions) ch_versions = ch_versions.mix(GATK_BILT.out.versions) ch_versions = ch_versions.mix(GATK_ILT.out.versions) ch_versions = ch_versions.mix(CAT_CAT_BAIT.out.versions) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index aa79f0c6e..d7fd6dbb7 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -11,27 +11,28 @@ nextflow_workflow { params { variant_caller = "deepvariant" mito_name = "MT" + bait_padding = 100 } workflow { """ input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = channel.of(params.pipelines_testdata_base_path + 'reference/target.bed').map {it -> [[id:'genome'], it]}.collect() - input[2] = channel.empty() - input[3] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() - input[4] = "bwamem2" - input[5] = "wgs" + input[1] = channel.empty() + input[2] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() + input[3] = "bwamem2" + input[4] = "wgs" + input[5] = null input[6] = null input[7] = null input[8] = null - input[9] = null - input[10] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' - input[11] = null - input[12] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' - input[13] = null - input[14] = "bwa" - input[15] = null - input[16] = false - input[17] = null + input[9] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[10] = null + input[11] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[12] = null + input[13] = "bwa" + input[14] = null + input[15] = false + input[16] = null + input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 6943777e1..df8fe39b5 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -135,10 +135,10 @@ "23": [ [ { - "id": "genome" + "id": "target" }, - "genome_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", - "genome_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" + "target_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", + "target_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" ] ], "24": [ @@ -150,12 +150,12 @@ ], "25": [ [ - "genome_bait.intervals_list:md5,1f3d445e6e53260510710a8333d29cfe" + "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" ] ], "26": [ [ - "genome_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" + "target_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" ] ], "27": [ @@ -404,7 +404,6 @@ "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", - "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", @@ -460,7 +459,7 @@ ], "bait_intervals": [ [ - "genome_bait.intervals_list:md5,1f3d445e6e53260510710a8333d29cfe" + "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" ] ], "dbsnp": [ @@ -643,15 +642,15 @@ "target_bed": [ [ { - "id": "genome" + "id": "target" }, - "genome_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", - "genome_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" + "target_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", + "target_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" ] ], "target_intervals": [ [ - "genome_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" + "target_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" ] ], "vcfanno_extra": [ @@ -907,7 +906,6 @@ "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", - "versions.yml:md5,b426ba6290d3f2ccd5c547854d9e2b75", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", @@ -920,6 +918,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T10:16:04.746173646" + "timestamp": "2025-12-16T11:12:17.45974749" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/nextflow.config b/subworkflows/local/prepare_references/tests/nextflow.config index bbc72e400..cafc2e1c8 100644 --- a/subworkflows/local/prepare_references/tests/nextflow.config +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -37,20 +37,11 @@ process { ext.args = '-s 1 -b 2 -e 2' } - withName: '.*PREPARE_REFERENCES:TABIX_PT' { - ext.when = { !params.target_bed.equals(null) && params.target_bed.endsWith(".gz") } - } - - withName: '.*PREPARE_REFERENCES:TABIX_PBT' { - ext.when = { !params.target_bed.equals(null) && !params.target_bed.endsWith(".gz") } - } - withName: '.*PREPARE_REFERENCES:TABIX_BGZIPINDEX_VCFANNOEXTRA' { ext.args2 = '--csi' } withName: '.*PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED' { - ext.when = { params.target_bed } ext.prefix = { "${meta.id}_pad${params.bait_padding}" } ext.args = { "-b ${params.bait_padding}" } } From 15a89da909cb9977974f131a8fe8d612c588257b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Dec 2025 11:59:22 +0100 Subject: [PATCH 182/872] move interval list generation logic --- conf/modules/prepare_references.config | 3 -- subworkflows/local/prepare_references/main.nf | 42 ++++++++++--------- .../prepare_references/tests/nextflow.config | 3 -- 3 files changed, 22 insertions(+), 26 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 593e72518..7e4cd2c1c 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -59,17 +59,14 @@ process { } withName: '.*PREPARE_REFERENCES:GATK_BILT' { - ext.when = { !params.target_bed.equals(null) } ext.prefix = { "${meta.id}_target" } } withName: '.*PREPARE_REFERENCES:GATK_ILT' { - ext.when = { !params.target_bed.equals(null) } ext.args = { "--PADDING ${params.bait_padding} -SUBDIVISION_MODE INTERVAL_SUBDIVISION --SCATTER_COUNT 2" } } withName: '.*PREPARE_REFERENCES:CAT_CAT_BAIT' { - ext.when = { !params.target_bed.equals(null) } ext.prefix = { "${meta.id}" } } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index b52ce1eda..6aa7aaf68 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -55,6 +55,7 @@ workflow PREPARE_REFERENCES { main: ch_versions = channel.empty() ch_bgzip_tbi = channel.empty() + ch_bait_intervals = channel.empty() ch_bwa = channel.empty() ch_genome_bwameme_index = channel.empty() ch_genome_bwamem2_index = channel.empty() @@ -71,6 +72,7 @@ workflow PREPARE_REFERENCES { ch_sentieonbwa = channel.empty() ch_shiftfasta_mtintervals = channel.empty() ch_target_bed_gz_tbi = channel.value([[:],[],[]]) + ch_target_intervals = channel.empty() ch_vcfanno_extra = channel.empty() ch_vcfanno_bgzip = channel.empty() ch_vcfanno_index = channel.empty() @@ -181,14 +183,28 @@ workflow PREPARE_REFERENCES { // Index target bed file if (val_target_bed) { ch_target_bed = channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() + BEDTOOLS_PAD_TARGET_BED( ch_target_bed, ch_fai.map { _meta, fai -> return fai } ) - TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi - .set { ch_target_bed_gz_tbi } - ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions) - ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions) + ch_target_bed_gz_tbi = TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi + + ch_target_intervals = GATK_BILT(ch_target_bed, ch_genome_dict).interval_list.map{ _meta, inter -> inter}.collect() + + GATK_ILT(GATK_BILT.out.interval_list) + + GATK_ILT.out.interval_list + .collect{ _meta, list -> list } + .map { list -> + def meta = list.toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" + return [[id:meta], list] + } + .set { ch_bait_intervals_cat_in } + + ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) + + ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, TABIX_BGZIPINDEX_PADDED_BED.out.versions, GATK_BILT.out.versions, GATK_ILT.out.versions, CAT_CAT_BAIT.out.versions) } ch_vcfanno_extra_unprocessed @@ -214,18 +230,7 @@ workflow PREPARE_REFERENCES { .collect() .set{ch_vcfanno_extra} - // Generate bait and target intervals - GATK_BILT(ch_target_bed, ch_genome_dict).interval_list - GATK_ILT(GATK_BILT.out.interval_list) - GATK_ILT.out.interval_list - .collect{ _meta, list -> list } - .map { list -> - def meta = list.toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" - return [[id:meta], list] - } - .set { ch_bait_intervals_cat_in } - CAT_CAT_BAIT ( ch_bait_intervals_cat_in ) UNTAR_VEP_CACHE (ch_vep_cache) // RTG tools @@ -237,9 +242,6 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) - ch_versions = ch_versions.mix(GATK_BILT.out.versions) - ch_versions = ch_versions.mix(GATK_ILT.out.versions) - ch_versions = ch_versions.mix(CAT_CAT_BAIT.out.versions) ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) @@ -269,8 +271,8 @@ workflow PREPARE_REFERENCES { mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel: [ val(meta), path(index) ] target_bed = ch_target_bed_gz_tbi.collect() // channel: [ val(meta), path(bed), path(tbi) ] vcfanno_extra = ch_vcfanno_extra.ifEmpty([[]]) // channel: [ [path(vcf), path(tbi)] ] - bait_intervals = CAT_CAT_BAIT.out.file_out.map{ _meta, inter -> inter}.collect().ifEmpty([[]])// channel: [ path(intervals) ] - target_intervals = GATK_BILT.out.interval_list.map{ _meta, inter -> inter}.collect() // channel: [ path(interval_list) ] + bait_intervals = ch_bait_intervals // channel: [ path(intervals) ] + target_intervals = ch_target_intervals // channel: [ path(interval_list) ] vep_resources = UNTAR_VEP_CACHE.out.untar.map{ _meta, files -> [files]}.collect() // channel: [ path(cache) ] versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/prepare_references/tests/nextflow.config b/subworkflows/local/prepare_references/tests/nextflow.config index cafc2e1c8..17503f419 100644 --- a/subworkflows/local/prepare_references/tests/nextflow.config +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -51,17 +51,14 @@ process { } withName: '.*PREPARE_REFERENCES:GATK_BILT' { - ext.when = { !params.target_bed.equals(null) } ext.prefix = { "${meta.id}_target" } } withName: '.*PREPARE_REFERENCES:GATK_ILT' { - ext.when = { !params.target_bed.equals(null) } ext.args = { "--PADDING ${params.bait_padding} -SUBDIVISION_MODE INTERVAL_SUBDIVISION --SCATTER_COUNT 2" } } withName: '.*PREPARE_REFERENCES:CAT_CAT_BAIT' { - ext.when = { !params.target_bed.equals(null) } ext.prefix = { "${meta.id}" } } From e8fa560134e3effcbbb6472f81aa28cd42225b90 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Dec 2025 12:25:12 +0100 Subject: [PATCH 183/872] remove gnomad from call --- main.nf | 3 --- 1 file changed, 3 deletions(-) diff --git a/main.nf b/main.nf index 01215b01f..1f5aceda7 100644 --- a/main.nf +++ b/main.nf @@ -49,8 +49,6 @@ workflow NFCORE_RAREDISEASE { ch_versions = channel.empty() ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() - ch_gnomad_af_tab = params.gnomad_af ? channel.fromPath(params.gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.value([[],[]]) ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() : channel.empty() ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() @@ -58,7 +56,6 @@ workflow NFCORE_RAREDISEASE { PREPARE_REFERENCES ( ch_genome_fasta, - ch_gnomad_af_tab, ch_vcfanno_extra_unprocessed, ch_vep_cache_unprocessed, params.aligner, From 18ef763b0a589def339accfc3c488c883eecc385 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 09:35:04 +0100 Subject: [PATCH 184/872] refactor remaining steps of prepare references --- conf/modules/prepare_references.config | 8 - main.nf | 19 +- subworkflows/local/prepare_references/main.nf | 212 ++++++++------- .../prepare_references/tests/main.nf.test | 26 +- .../tests/main.nf.test.snap | 242 +++++++++--------- .../prepare_references/tests/nextflow.config | 8 - 6 files changed, 273 insertions(+), 242 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 7e4cd2c1c..e433191ad 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -29,10 +29,6 @@ process { ext.args = '-a meme' } - withName: '.*PREPARE_REFERENCES:RTGTOOLS_FORMAT' { - ext.when = { !params.sdf && params.run_rtgvcfeval } - } - withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' { ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" } } @@ -70,8 +66,4 @@ process { ext.prefix = { "${meta.id}" } } - withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' { - ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) } - } - } diff --git a/main.nf b/main.nf index 1f5aceda7..f0963601e 100644 --- a/main.nf +++ b/main.nf @@ -48,22 +48,15 @@ workflow NFCORE_RAREDISEASE { // ch_versions = channel.empty() - ch_genome_fasta = channel.fromPath(params.fasta).map { it -> [[id:it.simpleName], it] }.collect() - ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect() - : channel.empty() - ch_vep_cache_unprocessed = params.vep_cache ? channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect() - : channel.value([[],[]]) PREPARE_REFERENCES ( - ch_genome_fasta, - ch_vcfanno_extra_unprocessed, - ch_vep_cache_unprocessed, params.aligner, params.analysis_type, params.bwa, params.bwamem2, params.bwameme, params.fai, + params.fasta, params.gnomad_af, params.gnomad_af_idx, params.known_dbsnp, @@ -71,11 +64,16 @@ workflow NFCORE_RAREDISEASE { params.mt_aligner, params.mt_fasta, params.run_mt_for_wes, + params.run_rtgvcfeval, + params.sdf, params.sequence_dictionary, - params.target_bed + params.target_bed, + params.vcfanno_extra_resources, + params.vep_cache ) .set { ch_references } + ch_genome_fasta = ch_references.genome_fasta ch_bait_intervals = ch_references.bait_intervals ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() @@ -182,8 +180,7 @@ workflow NFCORE_RAREDISEASE { : channel.value([]) ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() : channel.value([]) - ch_vep_cache = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") ) ? ch_references.vep_resources - : ( params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([]) ) + ch_vep_cache = ch_references.vep_resources ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() : channel.empty() ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 6aa7aaf68..4c25c03a7 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -33,15 +33,13 @@ include { UNTAR as UNTAR_VEP_CACHE } from '../../../mo workflow PREPARE_REFERENCES { take: - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ] - ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] val_aligner val_analysis_type val_bwa val_bwamem2 val_bwameme val_fai + val_fasta val_gnomad_af val_gnomad_af_idx val_known_dbsnp @@ -49,8 +47,12 @@ workflow PREPARE_REFERENCES { val_mtaligner val_mtfasta val_run_mt_for_wes + val_run_rtgvcfeval + val_sdf val_genome_dict val_target_bed + val_vcfanno_extra + val_vep_cache main: ch_versions = channel.empty() @@ -66,59 +68,76 @@ workflow PREPARE_REFERENCES { ch_mt_bwamem2_index = channel.empty() ch_mtshift_bwa_index = channel.empty() ch_mtshift_bwamem2_index = channel.empty() + ch_mtshift_backchain = channel.empty() + ch_mtshift_dict = channel.empty() + ch_mtshift_fai = channel.empty() + ch_mtshift_fasta = channel.empty() + ch_mt_dict = channel.empty() ch_mt_fai = channel.empty() ch_mt_fasta = channel.empty() + ch_sdf = channel.empty() ch_sentieonbwa = channel.empty() ch_shiftfasta_mtintervals = channel.empty() ch_target_bed_gz_tbi = channel.value([[:],[],[]]) ch_target_intervals = channel.empty() - ch_vcfanno_extra = channel.empty() - ch_vcfanno_bgzip = channel.empty() - ch_vcfanno_index = channel.empty() + ch_vcfanno_extra = channel.value([]) + ch_vep_resources = channel.value([]) + ch_genome_fasta = channel.fromPath(val_fasta).map { it -> [[id:it.simpleName], it] }.collect() + // // Genome indices + // if (!val_fai) { - ch_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]).fai.collect() - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) + ch_genome_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]).fai.collect() + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) } else { - ch_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() + ch_genome_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() } + GET_CHROM_SIZES( ch_genome_fai ) + if (!val_genome_dict) { ch_genome_dict = GATK_SD(ch_genome_fasta).dict.collect() - ch_versions = ch_versions.mix(GATK_SD.out.versions) + ch_versions = ch_versions.mix(GATK_SD.out.versions) } else { ch_genome_dict = channel.fromPath(val_genome_dict).map {it -> [[id:it.simpleName], it]}.collect() } - - GET_CHROM_SIZES( ch_fai ) - + // // Genome alignment indices + // if (!val_bwa) { if (!val_aligner.equals("sentieon") || val_mtaligner.equals("bwa")) { - BWA_INDEX_GENOME(ch_genome_fasta).index.set{ch_bwa} + ch_bwa = BWA_INDEX_GENOME(ch_genome_fasta).index.collect() ch_versions = ch_versions.mix(BWA_INDEX_GENOME.out.versions) } if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { - SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} + ch_bwa = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) } + } else if (val_bwa) { + ch_bwa = channel.fromPath(val_bwa).map {it -> [[id:it.simpleName], it]}.collect() } + if (!val_bwamem2 && (val_aligner.equals("bwamem2") || val_mtaligner.equals("bwamem2"))) { ch_genome_bwamem2_index = BWAMEM2_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) + ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) + } else if (val_bwamem2) { + ch_genome_bwamem2_index = channel.fromPath(val_bwamem2).map {it -> [[id:it.simpleName], it]}.collect() } + if (!val_bwamem2 && val_aligner.equals("bwameme")) { ch_genome_bwameme_index = BWAMEME_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) + ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) + } else if (val_bwameme) { + ch_genome_bwameme_index = channel.fromPath(val_bwameme).map {it -> [[id:it.simpleName], it]}.collect() } - + // // MT genome indices - + // if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { if (!val_mtfasta) { - ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai).fa.collect() + ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_genome_fai).fa.collect() ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) } else { ch_mt_fasta = channel.fromPath(val_mtfasta).map { it -> [[id:it.simpleName], it] }.collect() @@ -126,7 +145,14 @@ workflow PREPARE_REFERENCES { ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() + GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) + + ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() // channel:[ val(meta), path(backchain) ] + ch_mtshift_dict = GATK_SHIFTFASTA.out.dict // channel:[ val(meta), path(dict) ] + ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() // channel:[ val(meta), path(fai) ] + ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel:[ val(meta), path(fasta) ] + GATK_SHIFTFASTA.out.intervals .multiMap{ _meta, files -> shift_intervals: @@ -140,25 +166,27 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions,GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) } - + // // MT alignment indices + // if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwamem2")) { ch_mt_bwamem2_index = BWAMEM2_INDEX_MT(ch_mt_fasta).index.collect() - ch_mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions, BWAMEM2_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwa")) { ch_mt_bwa_index = BWA_INDEX_MT(ch_mt_fasta).index.collect() - ch_mtshift_bwa_index = BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_mtshift_bwa_index = BWA_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions, BWA_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("sentieon")) { ch_mt_bwa_index = SENTIEON_BWAINDEX_MT(ch_mt_fasta).index.collect() - ch_mtshift_bwa_index = SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa).index.collect() + ch_mtshift_bwa_index = SENTIEON_BWAINDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions, SENTIEON_BWAINDEX_MT_SHIFT.out.versions) } - + // // Vcf, tab and bed indices + // if (val_known_dbsnp) { ch_dbsnp = channel.fromPath(val_known_dbsnp).map{ it -> [[id:it.simpleName], it] }.collect() if (val_known_dbsnp_tbi) { @@ -179,14 +207,15 @@ workflow PREPARE_REFERENCES { } ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() } - + // // Index target bed file + // if (val_target_bed) { ch_target_bed = channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() BEDTOOLS_PAD_TARGET_BED( ch_target_bed, - ch_fai.map { _meta, fai -> return fai } + ch_genome_fai.map { _meta, fai -> return fai } ) ch_target_bed_gz_tbi = TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi @@ -206,74 +235,81 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, TABIX_BGZIPINDEX_PADDED_BED.out.versions, GATK_BILT.out.versions, GATK_ILT.out.versions, CAT_CAT_BAIT.out.versions) } + // + // Prepare vcfanno extra files + // + if (val_vcfanno_extra) { + ch_vcfanno_tabix_in = channel.fromPath(val_vcfanno_extra).map { it -> [[id:it.baseName], it] } - ch_vcfanno_extra_unprocessed - .branch { _meta, vcf -> - bgzipindex: !vcf.toString().endsWith(".gz") - index: vcf.toString().endsWith(".gz") + if (val_vcfanno_extra.endsWith(".gz")) { + TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in).tbi + .join(ch_vcfanno_tabix_in) + .map { _meta, tbi, vcf -> return [[vcf,tbi]]} + .set {ch_vcfanno_extra} + ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) + } else { + TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in) + channel.empty() + .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) + .map { _meta, vcf, index -> return [[vcf,index]] } + .set {ch_vcfanno_extra} + ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) } - .set { ch_vcfanno_tabix_in } - - TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in.index).tbi - .join(ch_vcfanno_tabix_in.index) - .map { _meta, tbi, vcf -> return [[vcf,tbi]]} - .set {ch_vcfanno_index} - - TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex) - channel.empty() - .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) - .map { _meta, vcf, index -> return [[vcf,index]] } - .set {ch_vcfanno_bgzip} - - channel.empty() - .mix(ch_vcfanno_bgzip, ch_vcfanno_index) - .collect() - .set{ch_vcfanno_extra} - - // Generate bait and target intervals - UNTAR_VEP_CACHE (ch_vep_cache) - + } + // + // Prepare vep cache files + // + if (val_vep_cache) { + if (val_vep_cache.endsWith("tar.gz")) { + ch_vep_resources = UNTAR_VEP_CACHE (channel.fromPath(val_vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()).untar.map{ _meta, files -> [files]}.collect() + ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) + } else { + ch_vep_resources = channel.fromPath(params.vep_cache).collect() + } + } + // // RTG tools - ch_genome_fasta.map { meta, fasta -> return [meta, fasta, [], [] ] } - .set {ch_rtgformat_in} - RTGTOOLS_FORMAT(ch_rtgformat_in) + // + if (!val_sdf && val_run_rtgvcfeval) { + ch_genome_fasta.map { meta, fasta -> return [meta, fasta, [], [] ] } + .set {ch_rtgformat_in} + ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf + ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) + } // Gather versions ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) - ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) - ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) - ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) - ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) emit: - dbsnp = ch_dbsnp // channel: [ val(meta), path(dbsnp) ] - dbsnp_tbi = ch_dbsnp_tbi // channel: [ val(meta), path(dbsnp_idx) ] - genome_bwa_index = channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] - genome_bwamem2_index = ch_genome_bwamem2_index // channel: [ val(meta), path(index) ] - genome_bwameme_index = ch_genome_bwameme_index // channel: [ val(meta), path(index) ] - genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] - genome_fai = ch_fai // channel: [ val(meta), path(fai) ] - genome_dict = ch_genome_dict // channel: [ val(meta), path(dict) ] - gnomad_af_idx = ch_gnomad_af_idx // channel: [ val(gnomad), path(idx) ] - sdf = RTGTOOLS_FORMAT.out.sdf // channel: [ val (meta), path(intervals) ] - mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] - mt_bwa_index = ch_mt_bwa_index // channel: [ val(meta), path(index) ] - mt_bwamem2_index = ch_mt_bwamem2_index // channel: [ val(meta), path(index) ] - mt_dict = ch_mt_dict // channel: [ val(meta), path(dict) ] - mt_fai = ch_mt_fai // channel: [ val(meta), path(fai) ] - mt_fasta = ch_mt_fasta // channel: [ val(meta), path(fasta) ] - mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel: [ path(intervals) ] - mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() // channel: [ val(meta), path(backchain) ] - mtshift_dict = GATK_SHIFTFASTA.out.dict // channel: [ val(meta), path(dict) ] - mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() // channel: [ val(meta), path(fai) ] - mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel: [ val(meta), path(fasta) ] - mtshift_bwa_index = ch_mtshift_bwa_index // channel: [ val(meta), path(index) ] - mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel: [ val(meta), path(index) ] - target_bed = ch_target_bed_gz_tbi.collect() // channel: [ val(meta), path(bed), path(tbi) ] - vcfanno_extra = ch_vcfanno_extra.ifEmpty([[]]) // channel: [ [path(vcf), path(tbi)] ] - bait_intervals = ch_bait_intervals // channel: [ path(intervals) ] - target_intervals = ch_target_intervals // channel: [ path(interval_list) ] - vep_resources = UNTAR_VEP_CACHE.out.untar.map{ _meta, files -> [files]}.collect() // channel: [ path(cache) ] - versions = ch_versions // channel: [ path(versions.yml) ] + bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] + dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] + dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] + genome_bwa_index = ch_bwa // channel:[ val(meta), path(index) ] + genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] + genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] + genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel:[ path(sizes) ] + genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] + genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] + genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] + gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] + mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel:[ path(intervals) ] + mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] + mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] + mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] + mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] + mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] + mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel:[ path(intervals) ] + mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] + mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] + mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] + mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] + mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] + mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] + sdf = ch_sdf // channel:[ val (meta), path(sdf) ] + target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] + target_intervals = ch_target_intervals // channel:[ path(interval_list) ] + vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] + vep_resources = ch_vep_resources // channel:[ path(cache) ] + versions = ch_versions // channel:[ path(versions.yml) ] } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index d7fd6dbb7..85d94b7e8 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -15,24 +15,26 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of(params.pipelines_testdata_base_path + 'reference/reference.fasta').map {it -> [[id:'genome'], it]}.collect() - input[1] = channel.empty() - input[2] = channel.of(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz').map {it -> [[id:'genome'], it]}.collect() - input[3] = "bwamem2" - input[4] = "wgs" + input[0] = "bwamem2" + input[1] = "wgs" + input[2] = null + input[3] = null + input[4] = null input[5] = null - input[6] = null - input[7] = null + input[6] = params.pipelines_testdata_base_path + 'reference/reference.fasta' + input[7] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' input[8] = null - input[9] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[9] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' input[10] = null - input[11] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[11] = "bwa" input[12] = null - input[13] = "bwa" - input[14] = null - input[15] = false + input[13] = false + input[14] = false + input[15] = null input[16] = null input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[18] = null + input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index df8fe39b5..56d4bba38 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -4,10 +4,7 @@ { "0": [ [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" ] ], "1": [ @@ -15,142 +12,133 @@ { "id": "dbsnp_-138-" }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], "10": [ [ - "genome_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ], "11": [ [ - { - "id": "genome" - }, - [ - "genome_mt.amb:md5,6749f645487281112c254ab829ea048c", - "genome_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", - "genome_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", - "genome_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" - ] + "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ], "12": [ - - ], - "13": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.dict:md5,249ad4680360e4a9fc1e3b44ed54f568" + [ + "reference_mt.amb:md5,6749f645487281112c254ab829ea048c", + "reference_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", + "reference_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", + "reference_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" + ] ] + ], + "13": [ + ], "14": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" ] ], "15": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "16": [ [ - "genome_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + { + "id": "reference" + }, + "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], "17": [ [ - { - "id": "genome" - }, - "genome_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" ] ], "18": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.dict:md5,a714408661d0f6403f417304342574fc" + "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ], "19": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" ] ], "2": [ [ { - "id": "genome" + "id": "dbsnp_-138-" }, - [ - "reference.amb:md5,0a85644af00f9a856d874381d24e7803", - "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", - "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", - "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", - "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" - ] + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" ] ], "20": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "21": [ [ { - "id": "genome" + "id": "reference" }, - [ - "genome_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", - "genome_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", - "genome_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", - "genome_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" - ] + "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" ] ], "22": [ - - ], - "23": [ [ { - "id": "target" + "id": "reference" }, - "target_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", - "target_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" - ] - ], - "24": [ - [ [ - + "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" ] ] + ], + "23": [ + + ], + "24": [ + ], "25": [ [ - "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" + { + "id": "target" + }, + "target_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", + "target_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" ] ], "26": [ @@ -159,6 +147,11 @@ ] ], "27": [ + [ + + ] + ], + "28": [ [ [ "LoFtool_scores.txt:md5,d9abd640ef22c790583b4b15d144ea6f", @@ -389,7 +382,7 @@ ] ] ], - "28": [ + "29": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", @@ -413,7 +406,21 @@ "3": [ [ { - "id": "genome" + "id": "reference" + }, + [ + "reference.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", + "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", + "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" + ] + ] + ], + "4": [ + [ + { + "id": "reference" }, [ "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b", @@ -424,38 +431,37 @@ ] ] ], - "4": [ + "5": [ ], - "5": [ + "6": [ [ "reference.fasta.fai.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" ] ], - "6": [ + "7": [ [ { - "id": "genome" + "id": "reference" }, "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ], - "7": [ + "8": [ [ { - "id": "genome" + "id": "reference" }, - "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ], - "8": [ + "9": [ [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + { + "id": "reference" + }, + "reference.dict:md5,81abd0fc051c084405024e0927f7b436" ] - ], - "9": [ - ], "bait_intervals": [ [ @@ -481,7 +487,7 @@ "genome_bwa_index": [ [ { - "id": "genome" + "id": "reference" }, [ "reference.amb:md5,0a85644af00f9a856d874381d24e7803", @@ -495,7 +501,7 @@ "genome_bwamem2_index": [ [ { - "id": "genome" + "id": "reference" }, [ "reference.fasta.0123:md5,0f0ff4414949e6787a25a563f19e2a3b", @@ -517,7 +523,7 @@ "genome_dict": [ [ { - "id": "genome" + "id": "reference" }, "reference.dict:md5,81abd0fc051c084405024e0927f7b436" ] @@ -525,11 +531,19 @@ "genome_fai": [ [ { - "id": "genome" + "id": "reference" }, "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ], + "genome_fasta": [ + [ + { + "id": "reference" + }, + "/nf-core/test-datasets/raredisease/reference/reference.fasta" + ] + ], "gnomad_af_idx": [ [ "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", @@ -539,14 +553,14 @@ "mt_bwa_index": [ [ { - "id": "genome" + "id": "reference" }, [ - "genome_mt.amb:md5,6749f645487281112c254ab829ea048c", - "genome_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", - "genome_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", - "genome_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" + "reference_mt.amb:md5,6749f645487281112c254ab829ea048c", + "reference_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", + "reference_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", + "reference_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" ] ] ], @@ -556,51 +570,51 @@ "mt_dict": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.dict:md5,249ad4680360e4a9fc1e3b44ed54f568" + "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" ] ], "mt_fai": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "mt_fasta": [ [ { - "id": "genome" + "id": "reference" }, - "genome_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], "mt_intervals": [ [ - "genome_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" + "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ], "mtshift_backchain": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ], "mtshift_bwa_index": [ [ { - "id": "genome" + "id": "reference" }, [ - "genome_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", - "genome_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "genome_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", - "genome_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", - "genome_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" ] ] ], @@ -610,30 +624,30 @@ "mtshift_dict": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.dict:md5,a714408661d0f6403f417304342574fc" + "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" ] ], "mtshift_fai": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "mtshift_fasta": [ [ { - "id": "genome" + "id": "reference" }, - "genome_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" ] ], "mtshift_intervals": [ [ - "genome_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" ] ], "sdf": [ @@ -655,9 +669,7 @@ ], "vcfanno_extra": [ [ - [ - - ] + ] ], "vep_resources": [ @@ -918,6 +930,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T11:12:17.45974749" + "timestamp": "2025-12-17T09:21:48.119185152" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/nextflow.config b/subworkflows/local/prepare_references/tests/nextflow.config index 17503f419..5f820e8b8 100644 --- a/subworkflows/local/prepare_references/tests/nextflow.config +++ b/subworkflows/local/prepare_references/tests/nextflow.config @@ -21,10 +21,6 @@ process { ext.args = '-a meme' } - withName: '.*PREPARE_REFERENCES:RTGTOOLS_FORMAT' { - ext.when = { !params.sdf && params.run_rtgvcfeval } - } - withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' { ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" } } @@ -62,8 +58,4 @@ process { ext.prefix = { "${meta.id}" } } - withName: '.*PREPARE_REFERENCES:UNTAR_VEP_CACHE' { - ext.when = { (params.vep_cache && params.vep_cache.endsWith("tar.gz")) } - } - } From 01064c88ed4ff70f855782d7a34ee7c0239ec186 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 09:45:57 +0100 Subject: [PATCH 185/872] refactor channel initialization order in main.nf --- main.nf | 65 +++++++++---------- subworkflows/local/prepare_references/main.nf | 8 +-- 2 files changed, 34 insertions(+), 39 deletions(-) diff --git a/main.nf b/main.nf index f0963601e..8f46f2968 100644 --- a/main.nf +++ b/main.nf @@ -73,30 +73,48 @@ workflow NFCORE_RAREDISEASE { ) .set { ch_references } - ch_genome_fasta = ch_references.genome_fasta ch_bait_intervals = ch_references.bait_intervals + ch_dbsnp = ch_references.dbsnp + ch_dbsnp_tbi = ch_references.dbsnp_tbi + ch_genome_bwaindex = ch_references.genome_bwa_index + ch_genome_bwamem2index = ch_references.genome_bwamem2_index + ch_genome_bwamemeindex = ch_references.genome_bwameme_index + ch_genome_chrsizes = ch_references.genome_chrom_sizes + ch_genome_fai = ch_references.genome_fai + ch_genome_fasta = ch_references.genome_fasta + ch_genome_dictionary = ch_references.genome_dict + ch_gnomad_af = ch_references.gnomad_af_idx + ch_mt_bwaindex = ch_references.mt_bwa_index + ch_mt_bwamem2index = ch_references.mt_bwamem2_index + ch_mt_dictionary = ch_references.mt_dict + ch_mt_fai = ch_references.mt_fai + ch_mt_fasta = ch_references.mt_fasta + ch_mt_intervals = ch_references.mt_intervals + ch_mtshift_backchain = ch_references.mtshift_backchain + ch_mtshift_bwaindex = ch_references.mtshift_bwa_index + ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index + ch_mtshift_dictionary = ch_references.mtshift_dict + ch_mtshift_fai = ch_references.mtshift_fai + ch_mtshift_fasta = ch_references.mtshift_fasta + ch_mtshift_intervals = ch_references.mtshift_intervals + ch_sdf = ch_references.sdf + ch_target_bed = ch_references.target_bed + ch_target_intervals = ch_references.target_intervals + ch_vcfanno_extra = ch_references.vcfanno_extra + ch_vep_cache = ch_references.vep_resources + ch_versions = ch_versions.mix(ch_references.versions) + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() : channel.value([]) ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_dbsnp = ch_references.dbsnp - ch_dbsnp_tbi = ch_references.dbsnp_tbi ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> return [[id:file(row.models).simpleName], row.models] } : channel.empty() - ch_genome_bwaindex = params.bwa ? channel.fromPath(params.bwa).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwa_index - ch_genome_bwamem2index = params.bwamem2 ? channel.fromPath(params.bwamem2).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwamem2_index - ch_genome_bwamemeindex = params.bwameme ? channel.fromPath(params.bwameme).map {it -> [[id:it.simpleName], it]}.collect() - : ch_references.genome_bwameme_index - ch_genome_chrsizes = ch_references.genome_chrom_sizes - ch_genome_fai = ch_references.genome_fai - ch_genome_dictionary = ch_references.genome_dict ch_gens_gnomad_pos = params.gens_gnomad_pos ? channel.fromPath(params.gens_gnomad_pos).collect() : channel.empty() ch_gens_interval_list = params.gens_interval_list ? channel.fromPath(params.gens_interval_list).collect() @@ -105,9 +123,6 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_gens_pon_male = params.gens_pon_male ? channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() : channel.empty() - ch_gnomad_afidx = params.gnomad_af_idx ? channel.fromPath(params.gnomad_af_idx).collect() - : ch_references.gnomad_af_idx - ch_gnomad_af = ch_references.gnomad_af_idx ch_intervals_wgs = params.intervals_wgs ? channel.fromPath(params.intervals_wgs).collect() : channel.empty() ch_intervals_y = params.intervals_y ? channel.fromPath(params.intervals_y).collect() @@ -118,19 +133,6 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_mt_intervals = ch_references.mt_intervals - ch_mt_bwaindex = ch_references.mt_bwa_index - ch_mt_bwamem2index = ch_references.mt_bwamem2_index - ch_mt_dictionary = ch_references.mt_dict - ch_mt_fai = ch_references.mt_fai - ch_mt_fasta = ch_references.mt_fasta - ch_mtshift_backchain = ch_references.mtshift_backchain - ch_mtshift_bwaindex = ch_references.mtshift_bwa_index - ch_mtshift_bwamem2index = ch_references.mtshift_bwamem2_index - ch_mtshift_dictionary = ch_references.mtshift_dict - ch_mtshift_fai = ch_references.mtshift_fai - ch_mtshift_fasta = ch_references.mtshift_fasta - ch_mtshift_intervals = ch_references.mtshift_intervals ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() @@ -151,8 +153,6 @@ workflow NFCORE_RAREDISEASE { : channel.value([]) ch_score_config_sv = params.score_config_sv ? channel.fromPath(params.score_config_sv).collect() : channel.value([]) - ch_sdf = params.sdf ? channel.fromPath(params.sdf).map{it -> [[id:it.simpleName],it]}.collect() - : ch_references.sdf ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) : channel.empty() ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) @@ -163,15 +163,12 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_svdb_dbs = params.svdb_query_dbs ? channel.fromList(samplesheetToList(params.svdb_query_dbs, "assets/svdb_query_vcf_schema.json")).collect() : channel.empty() - ch_target_bed = ch_references.target_bed - ch_target_intervals = ch_references.target_intervals ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() : channel.value([[],[]]) ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() : channel.value([[],[]]) ch_variant_consequences_sv = params.variant_consequences_sv ? channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() : channel.value([[],[]]) - ch_vcfanno_extra = ch_references.vcfanno_extra ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() : channel.value([]) ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? channel.fromPath(params.vcf2cytosure_blacklist).collect() @@ -180,12 +177,10 @@ workflow NFCORE_RAREDISEASE { : channel.value([]) ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() : channel.value([]) - ch_vep_cache = ch_references.vep_resources ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() : channel.empty() ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() : channel.empty() - ch_versions = ch_versions.mix(ch_references.versions) // // Read and store paths in the vep_plugin_files file diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 4c25c03a7..2f9faff51 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -292,19 +292,19 @@ workflow PREPARE_REFERENCES { genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] - mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel:[ path(intervals) ] mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] - mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel:[ path(intervals) ] + mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel:[ path(intervals) ] mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] + mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] + mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] - mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] - mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] + mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel:[ path(intervals) ] sdf = ch_sdf // channel:[ val (meta), path(sdf) ] target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] target_intervals = ch_target_intervals // channel:[ path(interval_list) ] From 725d2ea61bea288180ed467181ed008d5ec8ccb1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 09:53:47 +0100 Subject: [PATCH 186/872] update snaps --- .../tests/main.nf.test.snap | 50 +++++++++---------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 56d4bba38..81912ead4 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -22,11 +22,6 @@ ] ], "11": [ - [ - "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" - ] - ], - "12": [ [ { "id": "reference" @@ -40,10 +35,10 @@ ] ] ], - "13": [ + "12": [ ], - "14": [ + "13": [ [ { "id": "reference" @@ -51,7 +46,7 @@ "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" ] ], - "15": [ + "14": [ [ { "id": "reference" @@ -59,7 +54,7 @@ "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], - "16": [ + "15": [ [ { "id": "reference" @@ -67,12 +62,12 @@ "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], - "17": [ + "16": [ [ - "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ], - "18": [ + "17": [ [ { "id": "reference" @@ -80,13 +75,22 @@ "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ], - "19": [ + "18": [ [ { "id": "reference" }, - "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" + [ + "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + ] ] + ], + "19": [ + ], "2": [ [ @@ -101,7 +105,7 @@ { "id": "reference" }, - "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" ] ], "21": [ @@ -109,7 +113,7 @@ { "id": "reference" }, - "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], "22": [ @@ -117,17 +121,13 @@ { "id": "reference" }, - [ - "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", - "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", - "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", - "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" - ] + "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" ] ], "23": [ - + [ + "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + ] ], "24": [ @@ -930,6 +930,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T09:21:48.119185152" + "timestamp": "2025-12-17T09:51:07.657949096" } } \ No newline at end of file From cbe7cc8eed73b876f8c9c3ed9806813f8e29b6e4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 10:02:04 +0100 Subject: [PATCH 187/872] add comments --- subworkflows/local/prepare_references/main.nf | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index f310f27f5..8ecb607a5 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -41,16 +41,16 @@ workflow PREPARE_REFERENCES { ch_target_bed // channel: [mandatory for WES] [ path(bed) ] ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ] - val_aligner - val_analysis_type - val_bwa - val_bwamem2 - val_bwameme - val_fai - val_mtaligner - val_mtfasta - val_run_mt_for_wes - val_genome_dict + val_aligner // String: "bwa", "bwamem2", "sentieon" or "bwameme" + val_analysis_type // String: "wgs", "wes", or "mito" + val_bwa // String: path to bwa index + val_bwamem2 // String: path to bwamem2 index + val_bwameme // String: path to bwameme index + val_fai // String: path to genome fasta index + val_mtaligner // String: "bwa", "bwamem2", or "sentieon" + val_mtfasta // String: path to mitochondrial fasta + val_run_mt_for_wes // Boolean + val_genome_dict // String: path to genome dictionary main: ch_versions = channel.empty() From 2bf4556b0b35daa8b14403e5380e436acf7feb10 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 10:11:35 +0100 Subject: [PATCH 188/872] parser --- subworkflows/local/prepare_references/main.nf | 23 +++++++++++-------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 2f9faff51..481cf1dc9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -56,7 +56,6 @@ workflow PREPARE_REFERENCES { main: ch_versions = channel.empty() - ch_bgzip_tbi = channel.empty() ch_bait_intervals = channel.empty() ch_bwa = channel.empty() ch_genome_bwameme_index = channel.empty() @@ -72,12 +71,10 @@ workflow PREPARE_REFERENCES { ch_mtshift_dict = channel.empty() ch_mtshift_fai = channel.empty() ch_mtshift_fasta = channel.empty() - ch_mt_dict = channel.empty() ch_mt_fai = channel.empty() ch_mt_fasta = channel.empty() ch_sdf = channel.empty() - ch_sentieonbwa = channel.empty() ch_shiftfasta_mtintervals = channel.empty() ch_target_bed_gz_tbi = channel.value([[:],[],[]]) ch_target_intervals = channel.empty() @@ -148,10 +145,10 @@ workflow PREPARE_REFERENCES { GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) - ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() // channel:[ val(meta), path(backchain) ] - ch_mtshift_dict = GATK_SHIFTFASTA.out.dict // channel:[ val(meta), path(dict) ] - ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() // channel:[ val(meta), path(fai) ] - ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() // channel:[ val(meta), path(fasta) ] + ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() + ch_mtshift_dict = GATK_SHIFTFASTA.out.dict + ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() + ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() GATK_SHIFTFASTA.out.intervals .multiMap{ _meta, files -> @@ -164,7 +161,9 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions,GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions, + GATK_SD_MT.out.versions, + GATK_SHIFTFASTA.out.versions) } // // MT alignment indices @@ -212,7 +211,7 @@ workflow PREPARE_REFERENCES { // if (val_target_bed) { ch_target_bed = channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() - + BEDTOOLS_PAD_TARGET_BED( ch_target_bed, ch_genome_fai.map { _meta, fai -> return fai } @@ -233,7 +232,11 @@ workflow PREPARE_REFERENCES { ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) - ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, TABIX_BGZIPINDEX_PADDED_BED.out.versions, GATK_BILT.out.versions, GATK_ILT.out.versions, CAT_CAT_BAIT.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, + TABIX_BGZIPINDEX_PADDED_BED.out.versions, + GATK_BILT.out.versions, + GATK_ILT.out.versions, + CAT_CAT_BAIT.out.versions) } // // Prepare vcfanno extra files From 3b587534ca20bd4f8869b708c614a8b08592e671 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 11:53:59 +0100 Subject: [PATCH 189/872] update value channel defs --- subworkflows/local/prepare_references/main.nf | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 45b206548..a4189adf9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -1,3 +1,4 @@ + // // Prepare reference files // @@ -79,8 +80,8 @@ workflow PREPARE_REFERENCES { ch_shiftfasta_mtintervals = channel.empty() ch_target_bed_gz_tbi = channel.value([[:],[],[]]) ch_target_intervals = channel.empty() - ch_vcfanno_extra = channel.value([]) - ch_vep_resources = channel.value([]) + ch_vcfanno_extra = channel.value([[]]) + ch_vep_resources = channel.value([[]]) ch_genome_fasta = channel.fromPath(val_fasta).map { it -> [[id:it.simpleName], it] }.collect() // From c9f93a72b2ef4138011fc074051ae986a98d1c67 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 17 Dec 2025 11:02:50 +0000 Subject: [PATCH 190/872] [automated] Fix code linting --- subworkflows/local/prepare_references/main.nf | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a4189adf9..7b362d1cd 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -40,7 +40,7 @@ workflow PREPARE_REFERENCES { val_bwamem2 // String: path to bwamem2 index val_bwameme // String: path to bwameme index val_fai // String: path to genome fasta index - val_fasta // String: path to genome fasta + val_fasta // String: path to genome fasta val_gnomad_af // String: path to gnomad allele frequency file val_gnomad_af_idx // String: path to gnomad allele frequency file's index val_known_dbsnp // String: path to dbsnp file @@ -52,7 +52,7 @@ workflow PREPARE_REFERENCES { val_sdf // String: path to sdf file val_genome_dict // String: path to genome dictionary val_target_bed // String: path to target bed file - val_vcfanno_extra // String: path to additional annotation files used by vcfanno + val_vcfanno_extra // String: path to additional annotation files used by vcfanno val_vep_cache // String: path to vep cache folder @@ -69,10 +69,10 @@ workflow PREPARE_REFERENCES { ch_mt_bwamem2_index = channel.empty() ch_mtshift_bwa_index = channel.empty() ch_mtshift_bwamem2_index = channel.empty() - ch_mtshift_backchain = channel.empty() - ch_mtshift_dict = channel.empty() - ch_mtshift_fai = channel.empty() - ch_mtshift_fasta = channel.empty() + ch_mtshift_backchain = channel.empty() + ch_mtshift_dict = channel.empty() + ch_mtshift_fai = channel.empty() + ch_mtshift_fasta = channel.empty() ch_mt_dict = channel.empty() ch_mt_fai = channel.empty() ch_mt_fasta = channel.empty() @@ -147,10 +147,10 @@ workflow PREPARE_REFERENCES { GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) - ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() - ch_mtshift_dict = GATK_SHIFTFASTA.out.dict - ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() - ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() + ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() + ch_mtshift_dict = GATK_SHIFTFASTA.out.dict + ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() + ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() GATK_SHIFTFASTA.out.intervals .multiMap{ _meta, files -> @@ -163,8 +163,8 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions, - GATK_SD_MT.out.versions, + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions, + GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) } // @@ -196,7 +196,7 @@ workflow PREPARE_REFERENCES { ch_dbsnp_tbi = TABIX_DBSNP(ch_dbsnp).tbi.collect() ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) } - } + } if (val_gnomad_af) { ch_gnomad_af = channel.fromPath(val_gnomad_af).map{ it -> [[id:it.simpleName], it] }.collect() @@ -206,7 +206,7 @@ workflow PREPARE_REFERENCES { ch_gnomad_idx = TABIX_GNOMAD_AF(ch_gnomad_af).tbi.collect() ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions) } - ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() + ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() } // // Index target bed file @@ -234,10 +234,10 @@ workflow PREPARE_REFERENCES { ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) - ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, - TABIX_BGZIPINDEX_PADDED_BED.out.versions, - GATK_BILT.out.versions, - GATK_ILT.out.versions, + ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, + TABIX_BGZIPINDEX_PADDED_BED.out.versions, + GATK_BILT.out.versions, + GATK_ILT.out.versions, CAT_CAT_BAIT.out.versions) } // From a32cd38067435fae4f9267f0725eb355242c7f4b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 14:32:32 +0100 Subject: [PATCH 191/872] update snaps --- .../local/prepare_references/tests/main.nf.test.snap | 10 +++++++--- tests/default.nf.test.snap | 5 +---- tests/test_bam.nf.test.snap | 7 ++----- tests/test_singleton.nf.test.snap | 7 ++----- 4 files changed, 12 insertions(+), 17 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 81912ead4..d7aab6732 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -148,7 +148,9 @@ ], "27": [ [ - + [ + + ] ] ], "28": [ @@ -669,7 +671,9 @@ ], "vcfanno_extra": [ [ - + [ + + ] ] ], "vep_resources": [ @@ -930,6 +934,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T09:51:07.657949096" + "timestamp": "2025-12-17T13:36:20.294622928" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a302513ac..af31f3a58 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -417,9 +417,6 @@ "TABIX_ME_SPLIT": { "tabix": 1.21 }, - "TABIX_PBT": { - "tabix": 1.2 - }, "TABIX_TABIX": { "tabix": 1.21 }, @@ -919,6 +916,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-09T10:05:22.987340316" + "timestamp": "2025-12-17T13:47:44.773905542" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 3c92e4efd..a008b7006 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 802, + 801, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -393,9 +393,6 @@ "TABIX_ME_SPLIT": { "tabix": 1.21 }, - "TABIX_PBT": { - "tabix": 1.2 - }, "TABIX_TABIX": { "tabix": 1.21 }, @@ -860,6 +857,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-10T22:49:15.518602316" + "timestamp": "2025-12-17T13:34:43.907963783" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 8f39a08ed..9d76182c4 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 368, + 367, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -406,9 +406,6 @@ "TABIX_ME_SPLIT": { "tabix": 1.21 }, - "TABIX_PBT": { - "tabix": 1.2 - }, "TABIX_TABIX": { "tabix": 1.21 }, @@ -678,6 +675,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-10T23:01:52.852603616" + "timestamp": "2025-12-17T14:03:35.94640986" } } \ No newline at end of file From c78c4534a24e78f98c1791137754496165be4db5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 17 Dec 2025 17:12:44 +0100 Subject: [PATCH 192/872] remove ext.when conditionals from the workflow --- conf/modules/qc_bam.config | 1 - conf/modules/rank_variants.config | 12 ------------ conf/modules/variant_evaluation.config | 5 ----- main.nf | 1 + subworkflows/local/qc_bam/main.nf | 10 +++++++--- subworkflows/local/qc_bam/tests/main.nf.test | 10 ++++++---- subworkflows/local/rank_variants.nf | 17 ++++++++++------- workflows/raredisease.nf | 12 ++++++++++-- 8 files changed, 34 insertions(+), 34 deletions(-) diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 019cf8657..08653e936 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -31,7 +31,6 @@ process { withName: '.*QC_BAM:PICARD_COLLECTHSMETRICS' { ext.args = "--TMP_DIR ." - ext.when = { !params.target_bed.equals(null) } ext.prefix = { "${meta.id}_hsmetrics" } } diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config index cd5ab7c98..6f08ef886 100644 --- a/conf/modules/rank_variants.config +++ b/conf/modules/rank_variants.config @@ -51,10 +51,6 @@ process { ] } - withName: '.*RANK_VARIANTS_SV:TABIX_BGZIP' { - ext.when = false - } - withName: '.*RANK_VARIANTS_SV:TABIX_TABIX' { publishDir = [ path: { "${params.outdir}/rank_and_filter" }, @@ -94,10 +90,6 @@ process { ext.args = "--temp_dir ./" } - withName: '.*RANK_VARIANTS_SNV:BCFTOOLS_SORT' { - ext.when = false - } - withName: '.*RANK_VARIANTS_SNV:TABIX_BGZIP' { ext.prefix = { "${meta.id}_snv_ranked_${meta.set}" } publishDir = [ @@ -146,10 +138,6 @@ process { ext.args = "--temp_dir ./" } - withName: '.*RANK_VARIANTS_MT:BCFTOOLS_SORT' { - ext.when = false - } - withName: '.*RANK_VARIANTS_MT:TABIX_BGZIP' { ext.prefix = { "${meta.id}_mt_ranked_${meta.set}" } publishDir = [ diff --git a/conf/modules/variant_evaluation.config b/conf/modules/variant_evaluation.config index 4059b3a72..905a1d4d1 100644 --- a/conf/modules/variant_evaluation.config +++ b/conf/modules/variant_evaluation.config @@ -16,21 +16,16 @@ // process { - withName: '.*VARIANT_EVALUATION.*' { - ext.when = { params.run_rtgvcfeval } - } withName: '.*VARIANT_EVALUATION:BCFTOOLS_REHEADER' { beforeScript = { "echo ${meta.samplename} > ${meta.samplename}.txt" } ext.args = { "--samples ${meta.samplename}.txt" } ext.args2 = "--output-type z" - ext.when = { params.run_rtgvcfeval } ext.prefix = { "${meta.samplename}_truthvcf" } } withName: '.*VARIANT_EVALUATION:RTGTOOLS_VCFEVAL' { ext.args = { "--sample ${meta.samplename} --output-mode=split" } - ext.when = { params.run_rtgvcfeval } ext.prefix = { "${meta.samplename}_vcfeval" } publishDir = [ path: { "${params.outdir}/rtgvcfeval" }, diff --git a/main.nf b/main.nf index 8f46f2968..8d423c8d7 100644 --- a/main.nf +++ b/main.nf @@ -354,6 +354,7 @@ workflow NFCORE_RAREDISEASE { params.analysis_type, params.svdb_query_bedpedbs, params.svdb_query_dbs, + params.target_bed, skip_me_calling, skip_me_annotation, skip_mt_annotation, diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index ba597fdd4..6d13e4ac4 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -36,6 +36,7 @@ workflow QC_BAM { ngsbits_samplegender_method // channel: [val(method)] val_analysis_type // string: "wes", "wgs", or "mito" val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" + val_target_bed // string: path to target bed file skip_ngsbits // boolean skip_qualimap // boolean @@ -43,6 +44,7 @@ workflow QC_BAM { ch_cov = channel.empty() ch_cov_y = channel.empty() ch_versions = channel.empty() + ch_hsmetrics= channel.empty() ch_qualimap = channel.empty() ch_ngsbits = channel.empty() @@ -53,7 +55,10 @@ workflow QC_BAM { .combine(ch_target_intervals) .set { ch_hsmetrics_in} - PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]) + if (val_target_bed) { + ch_hsmetrics = PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]).metrics + ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions) + } if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions) @@ -99,7 +104,6 @@ workflow QC_BAM { ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions) ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions) - ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions) ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) ch_versions = ch_versions.mix(MOSDEPTH.out.versions) @@ -108,7 +112,7 @@ workflow QC_BAM { emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] - hs_metrics = PICARD_COLLECTHSMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] + hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] qualimap_results = ch_qualimap // channel: [ val(meta), path(qualimap_dir) ] tiddit_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] bigwig = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index bbe7119c4..32707daf4 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -43,8 +43,9 @@ nextflow_workflow { input[13] = 'xy' input[14] = 'wgs' input[15] = 'bwamem2' - input[16] = true - input[17] = false + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + input[18] = false """ } } @@ -119,8 +120,9 @@ nextflow_workflow { input[13] = 'xy' input[14] = 'wgs' input[15] = 'sentieon' - input[16] = true - input[17] = false + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + input[18] = false """ } } diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 1c64def08..7abe816f6 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -17,6 +17,8 @@ workflow RANK_VARIANTS { ch_pedfile // channel: [mandatory] [ path(ped) ] ch_reduced_penetrance // channel: [mandatory] [ path(pentrance) ] ch_score_config // channel: [mandatory] [ path(ini) ] + process_with_sort // Boolean + process_with_tabix // Boolean main: ch_versions = channel.empty() @@ -33,11 +35,14 @@ workflow RANK_VARIANTS { GENMOD_COMPOUND(GENMOD_SCORE.out.vcf) - BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf) // SV file needs to be sorted before indexing - - TABIX_BGZIP(GENMOD_COMPOUND.out.vcf) //run only for SNVs - - ch_vcf = TABIX_BGZIP.out.output.mix(BCFTOOLS_SORT.out.vcf) + if (process_with_sort) { + ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf) // SV file needs to be sorted before indexing + ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) + } + if (process_with_tabix) { + ch_vcf = TABIX_BGZIP(GENMOD_COMPOUND.out.vcf) //run only for SNVs + ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) + } TABIX_TABIX (ch_vcf) @@ -45,8 +50,6 @@ workflow RANK_VARIANTS { ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions) ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions) ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) - ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 7d7bd3d24..88c386d02 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -176,6 +176,7 @@ workflow RAREDISEASE { skip_qualimap skip_smncopynumbercaller skip_vcf2cytosure + val_target_bed main: @@ -289,6 +290,7 @@ workflow RAREDISEASE { channel.value(params.ngsbits_samplegender_method), analysis_type, params.aligner, + val_target_bed, skip_ngsbits, skip_qualimap ) @@ -442,6 +444,8 @@ workflow RAREDISEASE { ch_pedfile, ch_reduced_penetrance, ch_score_config_snv + false, + true ) ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) } @@ -512,7 +516,9 @@ workflow RAREDISEASE { ch_ranksnv_mt_in, ch_pedfile, ch_reduced_penetrance, - ch_score_config_mt + ch_score_config_mt, + false, + true ) ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions) } @@ -608,7 +614,9 @@ workflow RAREDISEASE { ch_ranksnv_sv_in, ch_pedfile, ch_reduced_penetrance, - ch_score_config_sv + ch_score_config_sv, + true, + false ) ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) } From b7db393f0cc03f53f9401ffc2af798f772c376c7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Dec 2025 14:45:21 +0100 Subject: [PATCH 193/872] remove suggestion --- subworkflows/local/prepare_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 7b362d1cd..68e42e837 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -148,7 +148,7 @@ workflow PREPARE_REFERENCES { GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) ch_mtshift_backchain = GATK_SHIFTFASTA.out.shift_back_chain.collect() - ch_mtshift_dict = GATK_SHIFTFASTA.out.dict + ch_mtshift_dict = GATK_SHIFTFASTA.out.dict.collect() ch_mtshift_fai = GATK_SHIFTFASTA.out.shift_fai.collect() ch_mtshift_fasta = GATK_SHIFTFASTA.out.shift_fa.collect() From 9660c2255335e0ae452e57dd39eda2d68214acc9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Dec 2025 15:37:23 +0100 Subject: [PATCH 194/872] fix spacing --- subworkflows/local/qc_bam/main.nf | 12 ++++++------ workflows/raredisease.nf | 5 +++-- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 6d13e4ac4..2d831935a 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -41,12 +41,12 @@ workflow QC_BAM { skip_qualimap // boolean main: - ch_cov = channel.empty() - ch_cov_y = channel.empty() - ch_versions = channel.empty() - ch_hsmetrics= channel.empty() - ch_qualimap = channel.empty() - ch_ngsbits = channel.empty() + ch_cov = channel.empty() + ch_cov_y = channel.empty() + ch_versions = channel.empty() + ch_hsmetrics = channel.empty() + ch_qualimap = channel.empty() + ch_ngsbits = channel.empty() PICARD_COLLECTMULTIPLEMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 88c386d02..b8fc9c554 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -154,6 +154,7 @@ workflow RAREDISEASE { analysis_type svdb_query_bedpedbs svdb_query_dbs + target_bed skip_me_calling skip_me_annotation skip_mt_annotation @@ -176,7 +177,7 @@ workflow RAREDISEASE { skip_qualimap skip_smncopynumbercaller skip_vcf2cytosure - val_target_bed + main: @@ -290,7 +291,7 @@ workflow RAREDISEASE { channel.value(params.ngsbits_samplegender_method), analysis_type, params.aligner, - val_target_bed, + target_bed, skip_ngsbits, skip_qualimap ) From a4134dbe7b6c82b5d43925db6969dd6a9fe7cd66 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Dec 2025 19:14:32 +0100 Subject: [PATCH 195/872] fix error --- conf/modules/rank_variants.config | 29 +++++------------------------ subworkflows/local/rank_variants.nf | 16 +++++----------- tests/default.nf.test.snap | 15 +-------------- tests/test_bam.nf.test.snap | 17 ++--------------- tests/test_singleton.nf.test.snap | 17 ++--------------- workflows/raredisease.nf | 11 ++++------- 6 files changed, 19 insertions(+), 86 deletions(-) diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config index 6f08ef886..878ebe6f9 100644 --- a/conf/modules/rank_variants.config +++ b/conf/modules/rank_variants.config @@ -42,7 +42,7 @@ process { } withName: '.*RANK_VARIANTS_SV:BCFTOOLS_SORT' { - ext.args = "--output-type z" + ext.args = "--output-type z --write-index=tbi" ext.prefix = { "${meta.id}_sv_ranked_${meta.set}" } publishDir = [ path: { "${params.outdir}/rank_and_filter" }, @@ -51,13 +51,6 @@ process { ] } - withName: '.*RANK_VARIANTS_SV:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } // @@ -90,7 +83,8 @@ process { ext.args = "--temp_dir ./" } - withName: '.*RANK_VARIANTS_SNV:TABIX_BGZIP' { + withName: '.*RANK_VARIANTS_SNV:TABIX_BGZIPTABIX' { + ext.args2 = '-p vcf' ext.prefix = { "${meta.id}_snv_ranked_${meta.set}" } publishDir = [ path: { "${params.outdir}/rank_and_filter" }, @@ -99,13 +93,6 @@ process { ] } - withName: '.*RANK_VARIANTS_SNV:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } // @@ -138,7 +125,8 @@ process { ext.args = "--temp_dir ./" } - withName: '.*RANK_VARIANTS_MT:TABIX_BGZIP' { + withName: '.*RANK_VARIANTS_MT:TABIX_BGZIPTABIX' { + ext.args2 = '-p vcf' ext.prefix = { "${meta.id}_mt_ranked_${meta.set}" } publishDir = [ path: { "${params.outdir}/rank_and_filter" }, @@ -147,11 +135,4 @@ process { ] } - withName: '.*RANK_VARIANTS_MT:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 7abe816f6..e80a22a3a 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -7,8 +7,7 @@ include { GENMOD_MODELS } from '../../modules/nf-core/genmod/models/main' include { GENMOD_SCORE } from '../../modules/nf-core/genmod/score/main' include { GENMOD_COMPOUND } from '../../modules/nf-core/genmod/compound/main' include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort/main' -include { TABIX_BGZIP } from '../../modules/nf-core/tabix/bgzip/main' -include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' workflow RANK_VARIANTS { @@ -18,7 +17,6 @@ workflow RANK_VARIANTS { ch_reduced_penetrance // channel: [mandatory] [ path(pentrance) ] ch_score_config // channel: [mandatory] [ path(ini) ] process_with_sort // Boolean - process_with_tabix // Boolean main: ch_versions = channel.empty() @@ -36,21 +34,17 @@ workflow RANK_VARIANTS { GENMOD_COMPOUND(GENMOD_SCORE.out.vcf) if (process_with_sort) { - ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf) // SV file needs to be sorted before indexing + ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf).vcf // SV file needs to be sorted before indexing ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) + } else { + ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_tbi.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs + ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) } - if (process_with_tabix) { - ch_vcf = TABIX_BGZIP(GENMOD_COMPOUND.out.vcf) //run only for SNVs - ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) - } - - TABIX_TABIX (ch_vcf) ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions) ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions) ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions) ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: vcf = ch_vcf // channel: [ val(meta), path(vcf) ] diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index af31f3a58..bebce756d 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -390,9 +390,6 @@ "TABIX_BCFTOOLS_CONCAT": { "tabix": 1.21 }, - "TABIX_BGZIP": { - "tabix": 1.2 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, @@ -853,26 +850,16 @@ "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", @@ -916,6 +903,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T13:47:44.773905542" + "timestamp": "2025-12-18T17:13:55.314547424" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index a008b7006..7ce7c0353 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 801, + 795, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -366,9 +366,6 @@ "TABIX_BCFTOOLS_CONCAT": { "tabix": 1.21 }, - "TABIX_BGZIP": { - "tabix": 1.2 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, @@ -810,26 +807,16 @@ "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", @@ -857,6 +844,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T13:34:43.907963783" + "timestamp": "2025-12-18T17:30:21.579519047" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 9d76182c4..a537d5f6c 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 367, + 361, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -379,9 +379,6 @@ "TABIX_BCFTOOLS_CONCAT": { "tabix": 1.21 }, - "TABIX_BGZIP": { - "tabix": 1.2 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "tabix": 1.2 }, @@ -630,26 +627,16 @@ "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.csi", - "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.gzi", "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", - "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.csi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", @@ -675,6 +662,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T14:03:35.94640986" + "timestamp": "2025-12-18T17:37:33.421833397" } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b8fc9c554..b4e57ad9d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -444,9 +444,8 @@ workflow RAREDISEASE { ch_ranksnv_nuclear_in, ch_pedfile, ch_reduced_penetrance, - ch_score_config_snv - false, - true + ch_score_config_snv, + false ) ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) } @@ -518,8 +517,7 @@ workflow RAREDISEASE { ch_pedfile, ch_reduced_penetrance, ch_score_config_mt, - false, - true + false ) ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions) } @@ -616,8 +614,7 @@ workflow RAREDISEASE { ch_pedfile, ch_reduced_penetrance, ch_score_config_sv, - true, - false + true ) ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) } From 20a7f1b9f5fddf6542722cae7dd62568a862d6a1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 18 Dec 2025 18:18:59 +0000 Subject: [PATCH 196/872] [automated] Fix code linting --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b4e57ad9d..109e6425c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -177,7 +177,7 @@ workflow RAREDISEASE { skip_qualimap skip_smncopynumbercaller skip_vcf2cytosure - + main: From 1cdddde93c9905dbaf9465aa1f560cdf3e205b01 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Dec 2025 20:13:11 +0100 Subject: [PATCH 197/872] remove option to bwamem as fallback aligner --- CHANGELOG.md | 8 +++++--- nextflow.config | 1 - nextflow_schema.json | 6 ------ .../local/align_bwa_bwamem2_bwameme/main.nf | 16 ---------------- 4 files changed, 5 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 208aa1061..bb93606b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741) - Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742) - Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747) +- Removed parameter `bwa_as_fallback` ### `Fixed` @@ -31,9 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------- | ---------------- | -| | sambamba_regions | +| Old parameter | New parameter | +| --------------- | ---------------- | +| | sambamba_regions | +| bwa_as_fallback | | ### Tool updates diff --git a/nextflow.config b/nextflow.config index 159a6cbd3..f5d3e0a28 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,6 @@ params { // Main options analysis_type = 'wgs' - bwa_as_fallback = false bait_padding = 100 concatenate_snv_calls = false extract_alignments = false diff --git a/nextflow_schema.json b/nextflow_schema.json index cd756f526..c074a13d6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -531,12 +531,6 @@ "fa_icon": "fas fa-align-center", "enum": ["wgs", "wes", "mito"] }, - "bwa_as_fallback": { - "type": "boolean", - "description": "Specifies whether or not to use bwa as a fallback aligner in case bwamem2 throws an error.", - "help_text": "errorStrategy needs to be set to ignore for the bwamem2 process for the fallback to work. Turned off by default.", - "fa_icon": "fas fa-toggle-on" - }, "concatenate_snv_calls": { "type": "boolean", "description": "Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls", diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 62466d6a7..34625caa2 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -45,22 +45,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first()) - - if (params.bwa_as_fallback) { - ch_reads_input - .join(BWAMEM2_MEM.out.bam, remainder: true) - .branch { meta, reads, bam -> - ERROR: bam.equals(null) - return [meta, reads] // return reads - SUCCESS: !bam.equals(null) - return [meta, bam] // return bam - } - .set { ch_fallback } - - BWAMEM_FALLBACK ( ch_fallback.ERROR, ch_bwa_index, ch_genome_fasta, true ) - ch_align = ch_fallback.SUCCESS.mix(BWAMEM_FALLBACK.out.bam) - ch_versions = ch_versions.mix(BWAMEM_FALLBACK.out.versions.first()) - } } SAMTOOLS_INDEX_ALIGN ( ch_align ) From 27396e97af9387127d7b718619cd18a74777d976 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 18 Dec 2025 20:14:11 +0100 Subject: [PATCH 198/872] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb93606b6..e41bc0aa1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Don't call mobile elements in mitochondrial DNA. [#741](https://github.com/nf-core/raredisease/pull/741) - Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742) - Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747) -- Removed parameter `bwa_as_fallback` +- Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763) ### `Fixed` From d708ee8674cb1a8b587e536fbfeaf47c47ff5aab Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 09:26:02 +0100 Subject: [PATCH 199/872] Update main.nf --- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 34625caa2..5236a1f9d 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -3,7 +3,6 @@ // include { BWA_MEM as BWA } from '../../../modules/nf-core/bwa/mem/main' -include { BWA_MEM as BWAMEM_FALLBACK } from '../../../modules/nf-core/bwa/mem/main' include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main' include { BWAMEME_MEM } from '../../../modules/nf-core/bwameme/mem/main' include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGN } from '../../../modules/nf-core/samtools/index/main' From a335e76daf769652c3d294da46f3cb0b672f6c68 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 10:45:53 +0100 Subject: [PATCH 200/872] part 1 --- main.nf | 22 +++-- subworkflows/local/align/main.nf | 23 ++--- subworkflows/local/align/tests/main.nf.test | 55 ++++++------ .../local/align_bwa_bwamem2_bwameme/main.nf | 24 +++--- .../tests/main.nf.test | 44 +++++----- subworkflows/local/annotate_genome_snvs.nf | 7 +- subworkflows/local/annotate_mt_snvs.nf | 7 +- subworkflows/local/generate_cytosure_files.nf | 13 +-- workflows/raredisease.nf | 85 +++++++++++-------- 9 files changed, 157 insertions(+), 123 deletions(-) diff --git a/main.nf b/main.nf index 8d423c8d7..645413b49 100644 --- a/main.nf +++ b/main.nf @@ -351,10 +351,6 @@ workflow NFCORE_RAREDISEASE { ch_vep_cache, ch_vep_extra_files, ch_versions, - params.analysis_type, - params.svdb_query_bedpedbs, - params.svdb_query_dbs, - params.target_bed, skip_me_calling, skip_me_annotation, skip_mt_annotation, @@ -376,7 +372,23 @@ workflow NFCORE_RAREDISEASE { skip_peddy, skip_qualimap, skip_smncopynumbercaller, - skip_vcf2cytosure + skip_vcf2cytosure, + params.aligner, + params.analysis_type, + params.cadd_resources, + params.extract_alignments, + params.genome, + params.mbuffer_mem, + params.mt_aligner, + params.platform, + params.run_mt_for_wes, + params.sample_id_map, + params.samtools_sort_threads, + params.save_mapped_as_cram, + params.svdb_query_bedpedbs, + params.svdb_query_dbs, + params.target_bed, + params.vep_cache_version ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 1e6532e49..c883e3fe1 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -30,15 +30,16 @@ workflow ALIGN { ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + skip_fastp // boolean + val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_extract_alignments // boolean val_mbuffer_mem // integer: [mandatory] memory in megabytes + val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' val_platform // string: [mandatory] illumina or a different technology + val_run_mt_for_wes // boolean val_sort_threads // integer: [mandatory] number of sorting threads - val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' - val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' - val_analysis_type // string: 'wgs', 'wes', or 'mito' - extract_alignments // boolean - save_mapped_as_cram // boolean - skip_fastp // boolean + val_save_mapped_as_cram // boolean main: ch_bwamem2_bam = channel.empty() @@ -86,11 +87,11 @@ workflow ALIGN { ch_genome_bwamemeindex, ch_genome_fasta, ch_genome_fai, + val_aligner, + val_extract_alignments, val_mbuffer_mem, val_platform, - val_sort_threads, - val_aligner, - extract_alignments + val_sort_threads ) ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai @@ -115,7 +116,7 @@ workflow ALIGN { // PREPARING READS FOR MT ALIGNMENT - if (val_analysis_type.matches("wgs|mito") || params.run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CONVERT_MT_BAM_TO_FASTQ ( ch_genome_marked_bam_bai, ch_genome_fasta, @@ -154,7 +155,7 @@ workflow ALIGN { .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) } - if (save_mapped_as_cram) { + if (val_save_mapped_as_cram) { SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index a183c4f48..1c43236d2 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -98,15 +98,16 @@ nextflow_workflow { input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = 3072 - input[19] = "illumina" - input[20] = 4 - input[21] = "bwamem2" - input[22] = "bwamem2" - input[23] = "wgs" - input[24] = false - input[25] = true - input[26] = false + input[18] = false + input[19] = "bwamem2" + input[20] = "wgs" + input[21] = false + input[22] = 3072 + input[23] = "bwamem2" + input[24] = "illumina" + input[25] = false + input[26] = 4 + input[27] = true """ } } @@ -198,15 +199,16 @@ nextflow_workflow { input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = 3072 - input[19] = "illumina" - input[20] = 4 - input[21] = "bwamem2" - input[22] = "bwamem2" - input[23] = "wes" - input[24] = false + input[18] = false + input[19] = "bwamem2" + input[20] = "wes" + input[21] = false + input[22] = 3072 + input[23] = "bwamem2" + input[24] = "illumina" input[25] = false - input[26] = false + input[26] = 4 + input[27] = false """ } } @@ -289,15 +291,16 @@ nextflow_workflow { input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = 3072 - input[19] = "illumina" - input[20] = 4 - input[21] = "bwameme" - input[22] = "bwamem2" - input[23] = "wgs" - input[24] = false - input[25] = true - input[26] = true + input[18] = true + input[19] = "bwameme" + input[20] = "wgs" + input[21] = false + input[22] = 3072 + input[23] = "bwamem2" + input[24] = "illumina" + input[25] = false + input[26] = 4 + input[27] = true """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 34625caa2..ceefc89f6 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -17,17 +17,17 @@ include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-c workflow ALIGN_BWA_BWAMEM2_BWAMEME { take: - ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] - ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] - ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] - ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - val_mbuffer_mem // integer: [mandatory] default: 3072 - val_platform // string: [mandatory] default: illumina - val_sort_threads // integer: [mandatory] default: 4 - val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' - extract_alignments // boolean + ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] + ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] + ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] + ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_extract_alignments // boolean + val_mbuffer_mem // integer: [mandatory] default: 3072 + val_platform // string: [mandatory] default: illumina + val_sort_threads // integer: [mandatory] default: 4 main: ch_versions = channel.empty() @@ -72,7 +72,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS - if (extract_alignments) { + if (val_extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 49c87d1bb..45285021e 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -30,23 +30,23 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ + input[0] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = [[:],[]] - input[2] = BWAMEM2_INDEX.out.index - input[3] = [[:],[]] - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[6] = 3072 - input[7] = "illumina" - input[8] = 4 - input[9] = "bwamem2" - input[10] = true + input[1] = [[:],[]] + input[2] = BWAMEM2_INDEX.out.index + input[3] = [[:],[]] + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[6] = "bwamem2" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 """ } } @@ -87,23 +87,23 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ + input[0] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = [[:],[]] - input[2] = [[:],[]] - input[3] = BWAMEME_INDEX.out.index - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[6] = 3072 - input[7] = "illumina" - input[8] = 4 - input[9] = "bwameme" - input[10] = true + input[1] = [[:],[]] + input[2] = [[:],[]] + input[3] = BWAMEME_INDEX.out.index + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[6] = "bwameme" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 """ } } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 4e4f66b1e..926834634 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -31,8 +31,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] - val_vep_genome // string: [mandatory] GRCh37 or GRCh38 - val_vep_cache_version // string: [mandatory] default: 107 ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_gnomad_af // channel: [optional] [ path(tab), path(tbi) ] @@ -41,6 +39,9 @@ workflow ANNOTATE_GENOME_SNVS { ch_vep_extra_files // channel: [mandatory] [ path(files) ] ch_genome_fai // channel: [mandatory] [ path(fai) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + val_cadd_resources // string: path to cadd resources file + val_vep_genome // string: GRCh37 or GRCh38 + val_vep_cache_version // string: vep version ex: 107 main: ch_cadd_vcf = channel.empty() @@ -106,7 +107,7 @@ workflow ANNOTATE_GENOME_SNVS { BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_tbi, [], [], []) // filter on frequencies // Annotating with CADD - if (params.cadd_resources != null) { + if (!val_cadd_resources.equals(null)) { TABIX_BCFTOOLS_VIEW (BCFTOOLS_VIEW.out.vcf) BCFTOOLS_VIEW.out.vcf diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 5287e6aa5..74c6ece01 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -22,12 +22,13 @@ workflow ANNOTATE_MT_SNVS { ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] - val_vep_genome // string: [mandatory] GRCh37 or GRCh38 - val_vep_cache_version // string: [mandatory] 107 ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] ch_fai // channel: [mandatory] [ path(fai) ] skip_haplogrep3 // boolean + val_cadd_resources // string: path to cadd resources file + val_vep_genome // string: GRCh37 or GRCh38 + val_vep_cache_version // string: vep version ex: 107 main: ch_versions = channel.empty() @@ -57,7 +58,7 @@ workflow ANNOTATE_MT_SNVS { ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, _tbi -> return [meta, vcf]} // Annotating with CADD - if (params.cadd_resources != null) { + if (!val_cadd_resources.equals(null)) { ANNOTATE_CADD ( ZIP_TABIX_VCFANNO_MT.out.gz_tbi, ch_cadd_header, diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 69ff98f86..98604419c 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -9,11 +9,12 @@ include { VCF2CYTOSURE } from '../../modules/nf workflow GENERATE_CYTOSURE_FILES { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_sample_id_map // channel: [optional] [val(id), val(id)] - ch_blacklist // channel: [optional] [path(blacklist)] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] + ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_sample_id_map // channel: [optional] [val(id), val(id)] + ch_blacklist // channel: [optional] [path(blacklist)] + val_sample_id_map // string: path to sample_id_map file main: ch_versions = channel.empty() @@ -48,7 +49,7 @@ workflow GENERATE_CYTOSURE_FILES { // Split vcf into sample vcf:s and frequency filter SPLIT_AND_FILTER_SV_VCF ( ch_sample_vcf, [], [], [] ) - if (params.sample_id_map != null) { + if (!val_sample_id_map.equals(null)) { SPLIT_AND_FILTER_SV_VCF.out.vcf .map { meta, vcf -> return [meta, vcf, [], []]} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 109e6425c..a54928960 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -151,10 +151,6 @@ workflow RAREDISEASE { ch_vep_cache ch_vep_extra_files ch_versions - analysis_type - svdb_query_bedpedbs - svdb_query_dbs - target_bed skip_me_calling skip_me_annotation skip_mt_annotation @@ -177,7 +173,22 @@ workflow RAREDISEASE { skip_qualimap skip_smncopynumbercaller skip_vcf2cytosure - + val_aligner + val_analysis_type + val_cadd_resources + val_extract_alignments + val_genome + val_mbuffer_mem + val_mt_aligner + val_platform + val_run_mt_for_wes + val_sample_id_map + val_samtools_sort_threads + val_save_mapped_as_cram + val_svdb_query_bedpedbs + val_svdb_query_dbs + val_target_bed + val_vep_cache_version main: @@ -242,20 +253,21 @@ workflow RAREDISEASE { ch_mtshift_dictionary, ch_mtshift_fai, ch_mtshift_fasta, - params.mbuffer_mem, - params.platform, - params.samtools_sort_threads, - params.aligner, - params.mt_aligner, - analysis_type, - params.extract_alignments, - params.save_mapped_as_cram, - skip_fastp + skip_fastp, + val_aligner, + val_analysis_type, + val_extract_alignments, + val_mbuffer_mem, + val_mt_aligner, + val_platform, + val_run_mt_for_wes, + val_samtools_sort_threads, + val_save_mapped_as_cram ) .set { ch_mapped } ch_versions = ch_versions.mix(ALIGN.out.versions) - if (!(skip_mt_subsample) && (analysis_type.equals("wgs") || params.run_mt_for_wes)) { + if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || params.run_mt_for_wes)) { if (params.mt_subsample_approach.equals("fraction")) { SUBSAMPLE_MT_FRAC( ch_mapped.mt_bam_bai, @@ -289,9 +301,9 @@ workflow RAREDISEASE { ch_svd_ud, ch_sambamba_bed, channel.value(params.ngsbits_samplegender_method), - analysis_type, + val_analysis_type, params.aligner, - target_bed, + val_target_bed, skip_ngsbits, skip_qualimap ) @@ -303,7 +315,7 @@ workflow RAREDISEASE { RENAME ALIGNMENT FILES FOR SMNCOPYNUMBERCALLER & REPEATCALLING ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if ( analysis_type.equals("wgs") && (!skip_smncopynumbercaller || !skip_repeat_calling)) { + if ( val_analysis_type.equals("wgs") && (!skip_smncopynumbercaller || !skip_repeat_calling)) { RENAME_BAM(ch_mapped.genome_marked_bam, "bam") RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai") ch_versions = ch_versions.mix(RENAME_BAM.out.versions) @@ -316,7 +328,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!skip_repeat_calling && analysis_type.equals("wgs") ) { + if (!skip_repeat_calling && val_analysis_type.equals("wgs") ) { CALL_REPEAT_EXPANSIONS ( RENAME_BAM.out.output.join(RENAME_BAI.out.output, failOnMismatch:true, failOnDuplicate:true), ch_variant_catalog, @@ -368,9 +380,9 @@ workflow RAREDISEASE { ch_case_info, ch_foundin_header, channel.value(params.sentieon_dnascope_pcr_indel_model), - analysis_type, + val_analysis_type, params.variant_caller, - params.run_mt_for_wes, + val_run_mt_for_wes, params.concatenate_snv_calls ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) @@ -389,8 +401,6 @@ workflow RAREDISEASE { ch_vcfanno_resources, ch_vcfanno_lua, ch_vcfanno_toml, - params.genome, - params.vep_cache_version, ch_vep_cache, ch_genome_fasta, ch_gnomad_af, @@ -398,7 +408,10 @@ workflow RAREDISEASE { ch_scatter_split_intervals, ch_vep_extra_files, ch_genome_fai, - ch_genome_chrsizes + ch_genome_chrsizes, + val_cadd_resources, + val_genome, + val_vep_cache_version ).set { ch_snv_annotate } ch_versions = ch_versions.mix(ch_snv_annotate.versions) @@ -453,7 +466,7 @@ workflow RAREDISEASE { // // ANNOTATE MT SNVs // - if (!(skip_mt_annotation) && (params.run_mt_for_wes || analysis_type.matches("wgs|mito"))) { + if (!(skip_mt_annotation) && (params.run_mt_for_wes || val_analysis_type.matches("wgs|mito"))) { ANNOTATE_MT_SNVS ( CALL_SNV.out.mt_vcf, @@ -464,12 +477,13 @@ workflow RAREDISEASE { ch_vcfanno_lua, ch_vcfanno_resources, ch_vcfanno_toml, - params.genome, - params.vep_cache_version, ch_vep_cache, ch_vep_extra_files, ch_genome_fai, - skip_haplogrep3 + skip_haplogrep3, + val_cadd_resources, + val_genome, + val_vep_cache_version ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) @@ -545,7 +559,7 @@ workflow RAREDISEASE { ch_readcount_intervals, ch_ploidy_model, ch_gcnvcaller_model, - analysis_type, + val_analysis_type, params.run_mt_for_wes, skip_germlinecnvcaller, skip_eklipse @@ -558,8 +572,8 @@ workflow RAREDISEASE { if (!skip_sv_annotation) { ANNOTATE_STRUCTURAL_VARIANTS ( CALL_STRUCTURAL_VARIANTS.out.vcf, - svdb_query_bedpedbs, - svdb_query_dbs, + val_svdb_query_bedpedbs, + val_svdb_query_dbs, params.genome, params.vep_cache_version, ch_svdb_bedpedbs, @@ -626,7 +640,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!skip_me_calling && analysis_type.equals("wgs")) { + if (!skip_me_calling && val_analysis_type.equals("wgs")) { CALL_MOBILE_ELEMENTS( ch_mapped.genome_marked_bam_bai, ch_genome_fasta, @@ -687,7 +701,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if ( analysis_type.equals("wgs") && !skip_smncopynumbercaller ) { + if ( val_analysis_type.equals("wgs") && !skip_smncopynumbercaller ) { RENAME_BAM.out.output .collect{_meta, bam -> bam} @@ -728,13 +742,14 @@ workflow RAREDISEASE { Generate CGH files from sequencing data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!skip_vcf2cytosure && analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { + if (!skip_vcf2cytosure && val_analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { GENERATE_CYTOSURE_FILES ( ch_sv_annotate.vcf_ann, ch_sv_annotate.tbi, ch_mapped.genome_marked_bam, ch_sample_id_map, - ch_vcf2cytosure_blacklist + ch_vcf2cytosure_blacklist, + val_sample_id_map ) ch_versions = ch_versions.mix(GENERATE_CYTOSURE_FILES.out.versions) } From abd61d0b31c182b193366e2d4e834f59addb7a81 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 11:25:38 +0100 Subject: [PATCH 201/872] more changes --- main.nf | 1 + subworkflows/local/align/main.nf | 1 + subworkflows/local/align_sentieon/main.nf | 13 +++++++------ .../local/align_sentieon/tests/main.nf.test | 3 ++- subworkflows/local/annotate_cadd/main.nf | 3 ++- subworkflows/local/annotate_genome_snvs.nf | 4 +++- subworkflows/local/annotate_mt_snvs.nf | 4 +++- workflows/raredisease.nf | 3 +++ 8 files changed, 22 insertions(+), 10 deletions(-) diff --git a/main.nf b/main.nf index 645413b49..067bf91c9 100644 --- a/main.nf +++ b/main.nf @@ -388,6 +388,7 @@ workflow NFCORE_RAREDISEASE { params.svdb_query_bedpedbs, params.svdb_query_dbs, params.target_bed, + params.vep_genome, params.vep_cache_version ) emit: diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index c883e3fe1..52bd70651 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -103,6 +103,7 @@ workflow ALIGN { ch_genome_fasta, ch_genome_fai, ch_genome_bwaindex, + val_extract_alignments, val_platform ) ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index e14edc40f..44f3d6981 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -10,11 +10,12 @@ include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-c workflow ALIGN_SENTIEON { take: - ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] - val_platform // string: [mandatory] default: illumina + ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] + val_extract_alignments // string: boolean + val_platform // string: [mandatory] default: illumina main: ch_versions = channel.empty() @@ -39,7 +40,7 @@ workflow ALIGN_SENTIEON { ch_bam_bai = merge_bams_in.single.mix(SENTIEON_READWRITER.out.output_index) // GET ALIGNMENT FROM SELECTED CONTIGS - if (params.extract_alignments) { + if (val_extract_alignments) { EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions.first()) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 01868bc39..e516861bf 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -41,7 +41,8 @@ nextflow_workflow { input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[3] = SENTIEON_BWAINDEX.out.index - input[4] = "illumina" + input[4] = false + input[5] = "illumina" """ } } diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 57b2145d1..d2684ea8f 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -19,12 +19,13 @@ workflow ANNOTATE_CADD { ch_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(dir) ] ch_fai // channel: [optional] [ path(fai) ] + val_genome // string: GRCh37 or GRCh37 main: ch_versions = channel.empty() ch_rename_chrs = channel.empty() - if (params.genome_build == 'GRCh38') { + if (val_genome.equals('GRCh38')) { REFERENCE_TO_CADD_CHRNAMES ( ch_fai , [], false ) ch_versions = ch_versions.mix(REFERENCE_TO_CADD_CHRNAMES.out.versions) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 926834634..1a5e296af 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -40,6 +40,7 @@ workflow ANNOTATE_GENOME_SNVS { ch_genome_fai // channel: [mandatory] [ path(fai) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] val_cadd_resources // string: path to cadd resources file + val_genome // string: GRCh37 or GRCh38 val_vep_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 @@ -118,7 +119,8 @@ workflow ANNOTATE_GENOME_SNVS { ch_cadd_in, ch_cadd_header, ch_cadd_resources, - ch_genome_fai + ch_genome_fai, + val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 74c6ece01..c2e1b4a82 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -27,6 +27,7 @@ workflow ANNOTATE_MT_SNVS { ch_fai // channel: [mandatory] [ path(fai) ] skip_haplogrep3 // boolean val_cadd_resources // string: path to cadd resources file + val_genome // string: GRCh37 or GRCh38 val_vep_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 @@ -63,7 +64,8 @@ workflow ANNOTATE_MT_SNVS { ZIP_TABIX_VCFANNO_MT.out.gz_tbi, ch_cadd_header, ch_cadd_resources, - ch_fai + ch_fai, + val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a54928960..af31ce2b5 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -188,6 +188,7 @@ workflow RAREDISEASE { val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed + val_vep_genome val_vep_cache_version main: @@ -411,6 +412,7 @@ workflow RAREDISEASE { ch_genome_chrsizes, val_cadd_resources, val_genome, + val_vep_genome, val_vep_cache_version ).set { ch_snv_annotate } ch_versions = ch_versions.mix(ch_snv_annotate.versions) @@ -483,6 +485,7 @@ workflow RAREDISEASE { skip_haplogrep3, val_cadd_resources, val_genome, + val_vep_genome, val_vep_cache_version ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) From b61984c9e872ab0e65832986b9ef323d7637c22b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 19:16:34 +0100 Subject: [PATCH 202/872] align suwbwf --- main.nf | 8 ++ subworkflows/local/align/main.nf | 96 +++++++++---------- subworkflows/local/align/tests/main.nf.test | 52 +++++----- subworkflows/local/align_MT/main.nf | 8 +- .../local/align_MT/tests/main.nf.test | 28 +++--- .../local/align_MT/tests/main.nf.test.snap | 32 +++---- .../local/align_bwa_bwamem2_bwameme/main.nf | 16 ++-- .../tests/main.nf.test | 24 ++--- subworkflows/local/align_sentieon/main.nf | 8 +- .../local/align_sentieon/tests/main.nf.test | 8 +- subworkflows/local/annotate_genome_snvs.nf | 3 +- .../local/annotate_mobile_elements.nf | 4 +- subworkflows/local/annotate_mt_snvs.nf | 3 +- .../local/annotate_structural_variants.nf | 28 +++--- .../local/convert_mt_bam_to_fastq/main.nf | 6 +- subworkflows/local/prepare_references/main.nf | 4 +- subworkflows/local/qc_bam/main.nf | 40 ++++---- workflows/raredisease.nf | 55 ++++++----- 18 files changed, 217 insertions(+), 206 deletions(-) diff --git a/main.nf b/main.nf index 067bf91c9..3b35acc70 100644 --- a/main.nf +++ b/main.nf @@ -376,18 +376,26 @@ workflow NFCORE_RAREDISEASE { params.aligner, params.analysis_type, params.cadd_resources, + params.concatenate_snv_calls, params.extract_alignments, params.genome, params.mbuffer_mem, params.mt_aligner, + params.mt_subsample_approach, + params.mt_subsample_rd, + params.mt_subsample_seed, + params.ngsbits_samplegender_method, params.platform, params.run_mt_for_wes, + params.run_rtgvcfeval, params.sample_id_map, params.samtools_sort_threads, params.save_mapped_as_cram, + params.sentieon_dnascope_pcr_indel_model, params.svdb_query_bedpedbs, params.svdb_query_dbs, params.target_bed, + params.variant_caller, params.vep_genome, params.vep_cache_version ) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 52bd70651..b338ad30b 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -12,34 +12,34 @@ include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' workflow ALIGN { take: - ch_reads // channel: [optional] [ val(meta), [path(reads)] ] - ch_alignments // channel: [optional] [ val(meta), [path(bam),path(bai)] ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_genome_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_bwamemeindex // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_mt_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_mt_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_mt_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_mtshift_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_mtshift_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - skip_fastp // boolean - val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' - val_analysis_type // string: 'wgs', 'wes', or 'mito' - val_extract_alignments // boolean - val_mbuffer_mem // integer: [mandatory] memory in megabytes - val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' - val_platform // string: [mandatory] illumina or a different technology - val_run_mt_for_wes // boolean - val_sort_threads // integer: [mandatory] number of sorting threads - val_save_mapped_as_cram // boolean + ch_alignments // channel: [optional] [ val(meta), [path(bam),path(bai)] ] + ch_genome_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_bwamemeindex // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_input_reads // channel: [optional] [ val(meta), [path(reads)] ] + ch_mt_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_mtshift_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_mtshift_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + skip_fastp // boolean + val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_extract_alignments // boolean + val_mbuffer_mem // integer: [mandatory] memory in megabytes + val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' + val_platform // string: [mandatory] illumina or a different technology + val_run_mt_for_wes // boolean + val_samtools_sort_threads // integer: [mandatory] number of sorting threads + val_save_mapped_as_cram // boolean main: ch_bwamem2_bam = channel.empty() @@ -54,10 +54,10 @@ workflow ALIGN { ch_versions = channel.empty() if (!skip_fastp) { - FASTP (ch_reads, [], false, false, false) - ch_reads = FASTP.out.reads - ch_versions = ch_versions.mix(FASTP.out.versions) - ch_fastp_json = FASTP.out.json + FASTP (ch_input_reads, [], false, false, false) + ch_input_reads = FASTP.out.reads + ch_versions = ch_versions.mix(FASTP.out.versions) + ch_fastp_json = FASTP.out.json } // @@ -80,29 +80,29 @@ workflow ALIGN { .set{ch_input_bai} if (val_aligner.matches("bwamem2|bwa|bwameme")) { - ALIGN_BWA_BWAMEM2_BWAMEME ( // Triggered when params.aligner is set as bwamem2 or bwa or bwameme - ch_reads, + ALIGN_BWA_BWAMEM2_BWAMEME ( ch_genome_bwaindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, - ch_genome_fasta, ch_genome_fai, + ch_genome_fasta, + ch_input_reads, val_aligner, val_extract_alignments, val_mbuffer_mem, val_platform, - val_sort_threads + val_samtools_sort_threads ) ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics ch_versions = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions) } else if (val_aligner.equals("sentieon")) { - ALIGN_SENTIEON ( // Triggered when params.aligner is set as sentieon - ch_reads, - ch_genome_fasta, - ch_genome_fai, + ALIGN_SENTIEON ( ch_genome_bwaindex, + ch_genome_fai, + ch_genome_fasta, + ch_input_reads, val_extract_alignments, val_platform ) @@ -120,30 +120,30 @@ workflow ALIGN { if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CONVERT_MT_BAM_TO_FASTQ ( ch_genome_marked_bam_bai, - ch_genome_fasta, + ch_genome_dictionary, ch_genome_fai, - ch_genome_dictionary + ch_genome_fasta ) ALIGN_MT ( - CONVERT_MT_BAM_TO_FASTQ.out.fastq, - CONVERT_MT_BAM_TO_FASTQ.out.ubam, ch_mt_bwaindex, ch_mt_bwamem2index, - ch_mt_fasta, ch_mt_dictionary, ch_mt_fai, + ch_mt_fasta, + CONVERT_MT_BAM_TO_FASTQ.out.fastq, + CONVERT_MT_BAM_TO_FASTQ.out.ubam, val_mt_aligner ) ALIGN_MT_SHIFT ( - CONVERT_MT_BAM_TO_FASTQ.out.fastq, - CONVERT_MT_BAM_TO_FASTQ.out.ubam, ch_mtshift_bwaindex, ch_mtshift_bwamem2index, - ch_mtshift_fasta, ch_mtshift_dictionary, ch_mtshift_fai, + ch_mtshift_fasta, + CONVERT_MT_BAM_TO_FASTQ.out.fastq, + CONVERT_MT_BAM_TO_FASTQ.out.ubam, val_mt_aligner ) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 1c43236d2..8577d471e 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -58,7 +58,14 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of( + input[0] = channel.empty() + input[1] = channel.empty() + input[2] = GENOME_MEM2.out.index.collect() + input[3] = channel.empty() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[7] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -80,14 +87,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ] ] - ) - input[1] = channel.empty() - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = channel.empty() - input[5] = GENOME_MEM2.out.index.collect() - input[6] = channel.empty() - input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + ) input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() @@ -159,7 +159,14 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of( + input[0] = channel.empty() + input[1] = channel.empty() + input[2] = GENOME_MEM2.out.index.collect() + input[3] = channel.empty() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[7] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -182,16 +189,9 @@ nextflow_workflow { ] ] ) - input[1] = channel.empty() - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = channel.empty() - input[5] = GENOME_MEM2.out.index.collect() - input[6] = channel.empty() - input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() - input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() input[13] = channel.empty() @@ -257,7 +257,14 @@ nextflow_workflow { } workflow { """ - input[0] = channel.fromList([ + input[0] = channel.empty() + input[1] = channel.empty() + input[2] = channel.empty() + input[3] = GENOME_MEME.out.index.collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[7] = channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), @@ -274,13 +281,6 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) - input[1] = channel.empty() - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = channel.empty() - input[5] = channel.empty() - input[6] = GENOME_MEME.out.index.collect() - input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index fae1c7998..334c75f0f 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -12,13 +12,13 @@ include { SAMTOOLS_SORT as SAMTOOLS_SORT_MT } fr workflow ALIGN_MT { take: - ch_fastq // channel: [mandatory] [ val(meta), [ path(reads) ] ] - ch_ubam // channel: [mandatory] [ val(meta), path(bam) ] ch_bwaindex // channel: [mandatory for sentieon] [ val(meta), path(index) ] ch_bwamem2index // channel: [mandatory for bwamem2] [ val(meta), path(index) ] - ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_dict // channel: [mandatory] [ val(meta), path(dict) ] ch_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_fastq // channel: [mandatory] [ val(meta), [ path(reads) ] ] + ch_ubam // channel: [mandatory] [ val(meta), path(bam) ] val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' main: @@ -55,7 +55,7 @@ workflow ALIGN_MT { ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions.first()) emit: - marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] + marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 04186df9b..6deaaba85 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -29,7 +29,12 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of( + input[0] = [[:],[]] + input[1] = MT_MEM2.out.index.collect() + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] @@ -43,7 +48,7 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) - input[1] = channel.of( + input[6] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] @@ -57,11 +62,6 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) - input[2] = [[:],[]] - input[3] = MT_MEM2.out.index.collect() - input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) input[7] = "bwamem2" """ } @@ -96,7 +96,12 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of( + input[0] = MT_BWA.out.index.collect() + input[1] = [[:],[]] + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] @@ -110,7 +115,7 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] ] ) - input[1] = channel.of( + input[6] = channel.of( [ [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] @@ -124,11 +129,6 @@ nextflow_workflow { [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] ] ) - input[2] = MT_BWA.out.index.collect() - input[3] = [[:],[]] - input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) - input[5] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) - input[6] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) input[7] = 'bwa' """ } diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 791238c66..a417a4330 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" ], [ { @@ -33,7 +33,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" ], [ { @@ -49,7 +49,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" ] ], "1": [ @@ -67,7 +67,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" ], [ { @@ -83,7 +83,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" ], [ { @@ -99,7 +99,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" ] ], "2": [ @@ -220,9 +220,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T16:19:27.352451428" + "timestamp": "2025-12-19T17:12:01.590311293" }, "align mt - bwa": { "content": [ @@ -242,7 +242,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" ], [ { @@ -258,7 +258,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" ], [ { @@ -274,7 +274,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" ] ], "1": [ @@ -292,7 +292,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" ], [ { @@ -308,7 +308,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" ], [ { @@ -324,7 +324,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" ] ], "2": [ @@ -445,8 +445,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-11-27T16:22:50.087959667" + "timestamp": "2025-12-19T17:14:00.976440705" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index ceefc89f6..f28559db6 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -17,12 +17,12 @@ include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-c workflow ALIGN_BWA_BWAMEM2_BWAMEME { take: - ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_input_reads // channel: [mandatory] [ val(meta), path(reads_input) ] val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' val_extract_alignments // boolean val_mbuffer_mem // integer: [mandatory] default: 3072 @@ -34,15 +34,15 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { // Map, sort, and index if (val_aligner.equals("bwa")) { - BWA ( ch_reads_input, ch_bwa_index, ch_genome_fasta, true ) + BWA ( ch_input_reads, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam ch_versions = ch_versions.mix(BWA.out.versions.first()) } else if (val_aligner.equals("bwameme")) { - BWAMEME_MEM ( ch_reads_input, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) + BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions.first()) } else { - BWAMEM2_MEM ( ch_reads_input, ch_bwamem2_index, ch_genome_fasta, true ) + BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first()) } @@ -92,9 +92,9 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions.first()) emit: - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] - marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] + marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] + metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 45285021e..a9d3a12f1 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -30,18 +30,18 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ + input[0] = [[:],[]] + input[1] = BWAMEM2_INDEX.out.index + input[2] = [[:],[]] + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = [[:],[]] - input[2] = BWAMEM2_INDEX.out.index - input[3] = [[:],[]] - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = "bwamem2" input[7] = true input[8] = 3072 @@ -87,18 +87,18 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ + input[0] = [[:],[]] + input[1] = [[:],[]] + input[2] = BWAMEME_INDEX.out.index + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = [[:],[]] - input[2] = [[:],[]] - input[3] = BWAMEME_INDEX.out.index - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) input[6] = "bwameme" input[7] = true input[8] = 3072 diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 44f3d6981..92f85563a 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -10,17 +10,17 @@ include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-c workflow ALIGN_SENTIEON { take: - ch_reads_input // channel: [mandatory] [ val(meta), path(reads_input) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_input_reads // channel: [mandatory] [ val(meta), path(reads_input) ] val_extract_alignments // string: boolean val_platform // string: [mandatory] default: illumina main: ch_versions = channel.empty() - SENTIEON_BWAMEM ( ch_reads_input, ch_bwa_index, ch_genome_fasta, ch_genome_fai ) + SENTIEON_BWAMEM ( ch_input_reads, ch_bwa_index, ch_genome_fasta, ch_genome_fai ) SENTIEON_BWAMEM.out .bam_and_bai diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index e516861bf..9c36901c8 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -31,16 +31,16 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ + input[0] = SENTIEON_BWAINDEX.out.index + input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[3] = SENTIEON_BWAINDEX.out.index input[4] = false input[5] = "illumina" """ diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 1a5e296af..65e8ae337 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -41,7 +41,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 - val_vep_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 main: @@ -144,7 +143,7 @@ workflow ANNOTATE_GENOME_SNVS { // Annotating with ensembl Vep ENSEMBLVEP_SNV( ch_vep_in, - val_vep_genome, + val_genome, "homo_sapiens", val_vep_cache_version, ch_vep_cache, diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index 9e8c4d179..a9a0fc09e 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -16,7 +16,7 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] - val_vep_genome // string: [mandatory] GRCh37 or GRCh38 + val_genome // string: [mandatory] GRCh37 or GRCh38 val_vep_cache_version // string: [mandatory] default: 107 ch_vep_extra_files // channel: [mandatory] [ path(files) ] @@ -56,7 +56,7 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ENSEMBLVEP_ME( ch_vep_in, - val_vep_genome, + val_genome, "homo_sapiens", val_vep_cache_version, ch_vep_cache, diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index c2e1b4a82..c362d7f29 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -28,7 +28,6 @@ workflow ANNOTATE_MT_SNVS { skip_haplogrep3 // boolean val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 - val_vep_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 main: @@ -91,7 +90,7 @@ workflow ANNOTATE_MT_SNVS { // Annotating with ensembl Vep ENSEMBLVEP_MT( ch_vep_in, - val_vep_genome, + val_genome, "homo_sapiens", val_vep_cache_version, ch_vep_cache, diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 052aac96d..d106f3138 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -12,22 +12,22 @@ include { TABIX_TABIX as TABIX_VEP } from '../../modules/nf-core/tabix/ta workflow ANNOTATE_STRUCTURAL_VARIANTS { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - svdb_query_bedpedbs // String: [optional] params.svdb_query_bedpedbs - svdb_query_dbs // String: [optional] params.svdb_query_dbs - val_vep_genome // string: [mandatory] GRCh37 or GRCh38 - val_vep_cache_version // string: [mandatory] default: 107 - ch_svdb_bedpedbs // channel: [optional] - ch_svdb_dbs // channel: [optional] - ch_vep_cache // channel: [mandatory] [ path(cache) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_vep_extra_files // channel: [mandatory] [ path(files) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_svdb_bedpedbs // channel: [optional] + ch_svdb_dbs // channel: [optional] + ch_vep_cache // channel: [mandatory] [ path(cache) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_vep_extra_files // channel: [mandatory] [ path(files) ] + val_svdb_query_bedpedbs // String: [optional] params.svdb_query_bedpedbs + val_svdb_query_dbs // String: [optional] params.svdb_query_dbs + val_genome // string: [mandatory] GRCh37 or GRCh38 + val_vep_cache_version // string: [mandatory] default: 107 main: ch_versions = channel.empty() - if (svdb_query_dbs) { + if (val_svdb_query_dbs) { ch_svdb_dbs .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> vcf_dbs: file @@ -52,7 +52,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(SVDB_QUERY_DB.out.versions) } - if (svdb_query_bedpedbs) { + if (val_svdb_query_bedpedbs) { ch_svdb_bedpedbs .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> bedpedbs: file @@ -90,7 +90,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ENSEMBLVEP_SV( ch_vep_in, - val_vep_genome, + val_genome, "homo_sapiens", val_vep_cache_version, ch_vep_cache, diff --git a/subworkflows/local/convert_mt_bam_to_fastq/main.nf b/subworkflows/local/convert_mt_bam_to_fastq/main.nf index 178aa876e..90167ea82 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/main.nf +++ b/subworkflows/local/convert_mt_bam_to_fastq/main.nf @@ -10,9 +10,9 @@ include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MT } from '../../../modules/nf-co workflow CONVERT_MT_BAM_TO_FASTQ { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_dict // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] main: ch_versions = channel.empty() @@ -33,8 +33,8 @@ workflow CONVERT_MT_BAM_TO_FASTQ { ch_versions = ch_versions.mix(GATK4_SAMTOFASTQ_MT.out.versions.first()) emit: - fastq = GATK4_SAMTOFASTQ_MT.out.fastq // channel: [ val(meta), [ path(fastq) ] ] bam_bai = ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + fastq = GATK4_SAMTOFASTQ_MT.out.fastq // channel: [ val(meta), [ path(fastq) ] ] ubam = GATK4_REVERTSAM_MT.out.bam // channel: [ val(meta), path(bam) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 68e42e837..76ff9391b 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -212,7 +212,7 @@ workflow PREPARE_REFERENCES { // Index target bed file // if (val_target_bed) { - ch_target_bed = channel.fromPath(params.target_bed).map{ it -> [[id:it.simpleName], it] }.collect() + ch_target_bed = channel.fromPath(val_target_bed).map{ it -> [[id:it.simpleName], it] }.collect() BEDTOOLS_PAD_TARGET_BED( ch_target_bed, @@ -269,7 +269,7 @@ workflow PREPARE_REFERENCES { ch_vep_resources = UNTAR_VEP_CACHE (channel.fromPath(val_vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()).untar.map{ _meta, files -> [files]}.collect() ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) } else { - ch_vep_resources = channel.fromPath(params.vep_cache).collect() + ch_vep_resources = channel.fromPath(val_vep_cache).collect() } } // diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 2d831935a..25523b078 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -20,25 +20,25 @@ include { VERIFYBAMID_VERIFYBAMID2 } from '../.. workflow QC_BAM { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_bait_intervals // channel: [mandatory] [ path(intervals_list) ] - ch_target_intervals // channel: [mandatory] [ path(intervals_list) ] - ch_chrom_sizes // channel: [mandatory] [ path(sizes) ] - ch_intervals_wgs // channel: [mandatory] [ path(intervals) ] - ch_intervals_y // channel: [mandatory] [ path(intervals) ] - ch_svd_bed // channel: [optional] [ path(bed) ] - ch_svd_mu // channel: [optional] [ path(meanpath) ] - ch_svd_ud // channel: [optional] [ path(ud) ] - ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] - ngsbits_samplegender_method // channel: [val(method)] - val_analysis_type // string: "wes", "wgs", or "mito" - val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" - val_target_bed // string: path to target bed file - skip_ngsbits // boolean - skip_qualimap // boolean + ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_bait_intervals // channel: [mandatory] [ path(intervals_list) ] + ch_target_intervals // channel: [mandatory] [ path(intervals_list) ] + ch_chrom_sizes // channel: [mandatory] [ path(sizes) ] + ch_intervals_wgs // channel: [mandatory] [ path(intervals) ] + ch_intervals_y // channel: [mandatory] [ path(intervals) ] + ch_svd_bed // channel: [optional] [ path(bed) ] + ch_svd_mu // channel: [optional] [ path(meanpath) ] + ch_svd_ud // channel: [optional] [ path(ud) ] + ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] + val_analysis_type // string: "wes", "wgs", or "mito" + val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" + val_ngsbits_samplegender_method // channel: [val(method)] + val_target_bed // string: path to target bed file + skip_ngsbits // boolean + skip_qualimap // boolean main: ch_cov = channel.empty() @@ -94,7 +94,7 @@ workflow QC_BAM { } // Check sex if (!skip_ngsbits) { - NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ngsbits_samplegender_method) + NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, channel.value(val_ngsbits_samplegender_method)) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions) } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index af31ce2b5..e0b34c583 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -176,19 +176,26 @@ workflow RAREDISEASE { val_aligner val_analysis_type val_cadd_resources + val_concatenate_snv_calls val_extract_alignments val_genome val_mbuffer_mem val_mt_aligner + val_mt_subsample_approach + val_mt_subsample_rd + val_mt_subsample_seed + val_ngsbits_samplegender_method val_platform val_run_mt_for_wes + val_run_rtgvcfeval val_sample_id_map val_samtools_sort_threads val_save_mapped_as_cram + val_sentieon_dnascope_pcr_indel_model val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed - val_vep_genome + val_variant_caller val_vep_cache_version main: @@ -236,14 +243,14 @@ workflow RAREDISEASE { */ ALIGN ( - ch_input_fastqs, ch_alignments, - ch_genome_fasta, - ch_genome_fai, ch_genome_bwaindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, ch_genome_dictionary, + ch_genome_fai, + ch_genome_fasta, + ch_input_fastqs, ch_mt_bwaindex, ch_mt_bwamem2index, ch_mt_dictionary, @@ -268,12 +275,12 @@ workflow RAREDISEASE { .set { ch_mapped } ch_versions = ch_versions.mix(ALIGN.out.versions) - if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || params.run_mt_for_wes)) { - if (params.mt_subsample_approach.equals("fraction")) { + if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { + if (val_mt_subsample_approach.equals("fraction")) { SUBSAMPLE_MT_FRAC( ch_mapped.mt_bam_bai, - params.mt_subsample_rd, - params.mt_subsample_seed + val_mt_subsample_rd, + val_mt_subsample_seed ) ch_versions = ch_versions.mix(SUBSAMPLE_MT_FRAC.out.versions) } else { @@ -301,9 +308,9 @@ workflow RAREDISEASE { ch_svd_mu, ch_svd_ud, ch_sambamba_bed, - channel.value(params.ngsbits_samplegender_method), val_analysis_type, - params.aligner, + val_aligner, + val_ngsbits_samplegender_method, val_target_bed, skip_ngsbits, skip_qualimap @@ -380,11 +387,11 @@ workflow RAREDISEASE { ch_par_bed, ch_case_info, ch_foundin_header, - channel.value(params.sentieon_dnascope_pcr_indel_model), + channel.value(val_sentieon_dnascope_pcr_indel_model), val_analysis_type, - params.variant_caller, + val_variant_caller, val_run_mt_for_wes, - params.concatenate_snv_calls + val_concatenate_snv_calls ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) ch_mt_txt = CALL_SNV.out.mt_txt @@ -412,7 +419,6 @@ workflow RAREDISEASE { ch_genome_chrsizes, val_cadd_resources, val_genome, - val_vep_genome, val_vep_cache_version ).set { ch_snv_annotate } ch_versions = ch_versions.mix(ch_snv_annotate.versions) @@ -468,7 +474,7 @@ workflow RAREDISEASE { // // ANNOTATE MT SNVs // - if (!(skip_mt_annotation) && (params.run_mt_for_wes || val_analysis_type.matches("wgs|mito"))) { + if (!(skip_mt_annotation) && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))) { ANNOTATE_MT_SNVS ( CALL_SNV.out.mt_vcf, @@ -485,7 +491,6 @@ workflow RAREDISEASE { skip_haplogrep3, val_cadd_resources, val_genome, - val_vep_genome, val_vep_cache_version ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) @@ -563,7 +568,7 @@ workflow RAREDISEASE { ch_ploidy_model, ch_gcnvcaller_model, val_analysis_type, - params.run_mt_for_wes, + val_run_mt_for_wes, skip_germlinecnvcaller, skip_eklipse ) @@ -575,16 +580,16 @@ workflow RAREDISEASE { if (!skip_sv_annotation) { ANNOTATE_STRUCTURAL_VARIANTS ( CALL_STRUCTURAL_VARIANTS.out.vcf, - val_svdb_query_bedpedbs, - val_svdb_query_dbs, - params.genome, - params.vep_cache_version, ch_svdb_bedpedbs, ch_svdb_dbs, ch_vep_cache, ch_genome_fasta, ch_genome_dictionary, - ch_vep_extra_files + ch_vep_extra_files, + val_svdb_query_bedpedbs, + val_svdb_query_dbs, + val_genome, + val_vep_cache_version ).set { ch_sv_annotate } ch_versions = ch_versions.mix(ch_sv_annotate.versions) @@ -660,8 +665,8 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_dictionary, ch_vep_cache, - params.genome, - params.vep_cache_version, + val_genome, + val_vep_cache_version, ch_vep_extra_files ).set { ch_me_annotate } ch_versions = ch_versions.mix(ANNOTATE_MOBILE_ELEMENTS.out.versions) @@ -783,7 +788,7 @@ workflow RAREDISEASE { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (params.run_rtgvcfeval) { + if (val_run_rtgvcfeval) { VARIANT_EVALUATION ( CALL_SNV.out.genome_vcf_tabix, ch_rtg_truthvcfs, From 178d2569626dee018a23983851696a5965f4fbb2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 19:52:46 +0100 Subject: [PATCH 203/872] qc_bam --- main.nf | 3 +- subworkflows/local/qc_bam/main.nf | 14 ++++----- subworkflows/local/qc_bam/tests/main.nf.test | 32 ++++++++++---------- workflows/raredisease.nf | 10 +++--- 4 files changed, 30 insertions(+), 29 deletions(-) diff --git a/main.nf b/main.nf index 3b35acc70..75e196499 100644 --- a/main.nf +++ b/main.nf @@ -133,6 +133,7 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) + ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() @@ -317,6 +318,7 @@ workflow NFCORE_RAREDISEASE { ch_mtshift_fai, ch_mtshift_fasta, ch_mtshift_intervals, + ch_ngsbits_method, ch_par_bed, ch_pedfile, ch_ploidy_model, @@ -384,7 +386,6 @@ workflow NFCORE_RAREDISEASE { params.mt_subsample_approach, params.mt_subsample_rd, params.mt_subsample_seed, - params.ngsbits_samplegender_method, params.platform, params.run_mt_for_wes, params.run_rtgvcfeval, diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 25523b078..bc0373405 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -22,20 +22,20 @@ workflow QC_BAM { take: ch_bam // channel: [mandatory] [ val(meta), path(bam) ] ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_bait_intervals // channel: [mandatory] [ path(intervals_list) ] - ch_target_intervals // channel: [mandatory] [ path(intervals_list) ] - ch_chrom_sizes // channel: [mandatory] [ path(sizes) ] + ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_intervals_wgs // channel: [mandatory] [ path(intervals) ] ch_intervals_y // channel: [mandatory] [ path(intervals) ] + ch_ngsbits_method // channel: [val(method)] ch_svd_bed // channel: [optional] [ path(bed) ] ch_svd_mu // channel: [optional] [ path(meanpath) ] ch_svd_ud // channel: [optional] [ path(ud) ] ch_sambamba_bed // channel: [optional] [ val(meta), path(bed) ] + ch_target_intervals // channel: [mandatory] [ path(intervals_list) ] val_analysis_type // string: "wes", "wgs", or "mito" val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" - val_ngsbits_samplegender_method // channel: [val(method)] val_target_bed // string: path to target bed file skip_ngsbits // boolean skip_qualimap // boolean @@ -66,7 +66,7 @@ workflow QC_BAM { TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input - UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_chrom_sizes) + UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_genome_chrsizes) CHROMOGRAPH_COV([[:],[]], TIDDIT_COV.out.wig, [[:],[]], [[:],[]], [[:],[]], [[:],[]], [[:],[]]) @@ -94,7 +94,7 @@ workflow QC_BAM { } // Check sex if (!skip_ngsbits) { - NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, channel.value(val_ngsbits_samplegender_method)) + NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_ngsbits_method) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions) } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 32707daf4..f97d7b47a 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -29,18 +29,18 @@ nextflow_workflow { [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[8] = channel.empty() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() input[12] = channel.empty() - input[13] = 'xy' + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() input[14] = 'wgs' input[15] = 'bwamem2' input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' @@ -106,18 +106,18 @@ nextflow_workflow { [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[8] = channel.empty() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() input[12] = channel.empty() - input[13] = 'xy' + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() input[14] = 'wgs' input[15] = 'sentieon' input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e0b34c583..f159bdb03 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -117,6 +117,7 @@ workflow RAREDISEASE { ch_mtshift_fai ch_mtshift_fasta ch_mtshift_intervals + ch_ngsbits_method ch_par_bed ch_pedfile ch_ploidy_model @@ -184,7 +185,6 @@ workflow RAREDISEASE { val_mt_subsample_approach val_mt_subsample_rd val_mt_subsample_seed - val_ngsbits_samplegender_method val_platform val_run_mt_for_wes val_run_rtgvcfeval @@ -297,20 +297,20 @@ workflow RAREDISEASE { QC_BAM ( ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bam_bai, - ch_genome_fasta, - ch_genome_fai, ch_bait_intervals, - ch_target_intervals, ch_genome_chrsizes, + ch_genome_fai, + ch_genome_fasta, ch_intervals_wgs, ch_intervals_y, + ch_ngsbits_method, ch_svd_bed, ch_svd_mu, ch_svd_ud, ch_sambamba_bed, + ch_target_intervals, val_analysis_type, val_aligner, - val_ngsbits_samplegender_method, val_target_bed, skip_ngsbits, skip_qualimap From 28eebf6488812f24459e393a98b832a80792da8f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 20:46:40 +0100 Subject: [PATCH 204/872] remove vep_genome --- main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/main.nf b/main.nf index 75e196499..aa89904a5 100644 --- a/main.nf +++ b/main.nf @@ -397,7 +397,6 @@ workflow NFCORE_RAREDISEASE { params.svdb_query_dbs, params.target_bed, params.variant_caller, - params.vep_genome, params.vep_cache_version ) emit: From 7b0f6b01e9eb665b54bdd2b330e17829e426afed Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 19 Dec 2025 21:15:52 +0100 Subject: [PATCH 205/872] call snv --- main.nf | 4 +- subworkflows/local/call_snv.nf | 108 +++++++++--------- subworkflows/local/call_snv_MT/main.nf | 12 +- .../local/call_snv_deepvariant/main.nf | 12 +- subworkflows/local/call_snv_sentieon/main.nf | 16 +-- .../local/postprocess_MT_calls/main.nf | 20 ++-- workflows/raredisease.nf | 24 ++-- 7 files changed, 98 insertions(+), 98 deletions(-) diff --git a/main.nf b/main.nf index 75e196499..077f7d035 100644 --- a/main.nf +++ b/main.nf @@ -136,6 +136,7 @@ workflow NFCORE_RAREDISEASE { ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) + ch_sentieon_pcr_indel_model = channel.value(params.sentieon_dnascope_pcr_indel_model) ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() : channel.empty() ch_readcount_intervals = params.readcount_intervals ? channel.fromPath(params.readcount_intervals).collect() @@ -334,6 +335,7 @@ workflow NFCORE_RAREDISEASE { ch_score_config_snv, ch_score_config_sv, ch_sdf, + ch_sentieon_pcr_indel_model, ch_svcaller_priority, ch_svd_bed, ch_svd_mu, @@ -392,12 +394,10 @@ workflow NFCORE_RAREDISEASE { params.sample_id_map, params.samtools_sort_threads, params.save_mapped_as_cram, - params.sentieon_dnascope_pcr_indel_model, params.svdb_query_bedpedbs, params.svdb_query_dbs, params.target_bed, params.variant_caller, - params.vep_genome, params.vep_cache_version ) emit: diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index f5d16884b..0d45783c0 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -12,34 +12,34 @@ include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftool workflow CALL_SNV { take: - ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_mtshift_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mt_intervals // channel: [optional] [ path(interval_list) ] - ch_mt_dictionary // channel: [optional] [ val(meta), path(dict) ] - ch_mt_fai // channel: [optional] [ val(meta), path(fai) ] - ch_mt_fasta // channel: [optional] [ val(meta), path(fasta) ] - ch_mtshift_dictionary // channel: [optional] [ val(meta), path(dict) ] - ch_mtshift_fai // channel: [optional] [ val(meta), path(fai) ] - ch_mtshift_fasta // channel: [optional] [ val(meta), path(fasta) ] - ch_mtshift_intervals // channel: [optional] [ path(interval_list) ] - ch_mtshift_backchain // channel: [mandatory] [ val(meta), path(back_chain) ] - ch_dbsnp // channel: [optional] [ val(meta), path(vcf) ] - ch_dbsnp_tbi // channel: [optional] [ val(meta), path(tbi) ] - ch_call_interval // channel: [mandatory] [ path(intervals) ] - ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] - ch_ml_model // channel: [mandatory] [ path(model) ] - ch_par_bed // channel: [optional] [ val(meta), path(bed) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_foundin_header // channel: [mandatory] [ path(header) ] - ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] - val_analysis_type // string: 'wgs', 'wes', or 'mito' - val_variant_caller // string: 'deepvariant' or 'sentieon' - run_mt_for_wes // boolean - concatenate_snv_calls // boolean + ch_call_interval // channel: [mandatory] [ path(intervals) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_dbsnp // channel: [optional] [ val(meta), path(vcf) ] + ch_dbsnp_tbi // channel: [optional] [ val(meta), path(tbi) ] + ch_foundin_header // channel: [mandatory] [ path(header) ] + ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_ml_model // channel: [mandatory] [ path(model) ] + ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_mt_dictionary // channel: [optional] [ val(meta), path(dict) ] + ch_mt_fai // channel: [optional] [ val(meta), path(fai) ] + ch_mt_fasta // channel: [optional] [ val(meta), path(fasta) ] + ch_mt_intervals // channel: [optional] [ path(interval_list) ] + ch_mtshift_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_mtshift_dictionary // channel: [optional] [ val(meta), path(dict) ] + ch_mtshift_fai // channel: [optional] [ val(meta), path(fai) ] + ch_mtshift_fasta // channel: [optional] [ val(meta), path(fasta) ] + ch_mtshift_intervals // channel: [optional] [ path(interval_list) ] + ch_mtshift_backchain // channel: [mandatory] [ val(meta), path(back_chain) ] + ch_par_bed // channel: [optional] [ val(meta), path(bed) ] + ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] + ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_concatenate_snv_calls // boolean + val_run_mt_for_wes // boolean + val_variant_caller // string: 'deepvariant' or 'sentieon' main: ch_versions = channel.empty() @@ -59,13 +59,13 @@ workflow CALL_SNV { if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( ch_genome_bam_bai, - ch_genome_fasta, - ch_genome_fai, - ch_target_bed, - ch_par_bed, ch_case_info, ch_foundin_header, ch_genome_chrsizes, + ch_genome_fai, + ch_genome_fasta, + ch_par_bed, + ch_target_bed, val_analysis_type ) ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf @@ -76,16 +76,16 @@ workflow CALL_SNV { } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, - ch_genome_fasta, - ch_genome_fai, - ch_dbsnp, - ch_dbsnp_tbi, ch_call_interval, - ch_ml_model, ch_case_info, - ch_pcr_indel_model, + ch_dbsnp, + ch_dbsnp_tbi, ch_foundin_header, - ch_genome_chrsizes + ch_genome_chrsizes, + ch_genome_fai, + ch_genome_fasta, + ch_ml_model, + ch_pcr_indel_model ) ch_sentieon_vcf = CALL_SNV_SENTIEON.out.vcf ch_sentieon_tbi = CALL_SNV_SENTIEON.out.tabix @@ -112,30 +112,30 @@ workflow CALL_SNV { if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { CALL_SNV_MT( ch_mt_bam_bai, - ch_mt_fasta, - ch_mt_fai, ch_mt_dictionary, + ch_mt_fai, + ch_mt_fasta, ch_mt_intervals ) CALL_SNV_MT_SHIFT( ch_mtshift_bam_bai, - ch_mtshift_fasta, - ch_mtshift_fai, ch_mtshift_dictionary, + ch_mtshift_fai, + ch_mtshift_fasta, ch_mtshift_intervals ) POSTPROCESS_MT_CALLS( - CALL_SNV_MT.out.vcf, - CALL_SNV_MT_SHIFT.out.vcf, - ch_mt_fasta, + ch_case_info, + ch_foundin_header, + ch_genome_chrsizes, ch_mt_dictionary, ch_mt_fai, + ch_mt_fasta, + CALL_SNV_MT.out.vcf, ch_mtshift_backchain, - ch_case_info, - ch_foundin_header, - ch_genome_chrsizes + CALL_SNV_MT_SHIFT.out.vcf ) ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi @@ -147,7 +147,7 @@ workflow CALL_SNV { ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) } - if (concatenate_snv_calls) { + if (val_concatenate_snv_calls) { ch_concat_vcf_in = ch_genome_vcf_tabix.concat(ch_mt_vcf_tabix).groupTuple() BCFTOOLS_CONCAT ( ch_concat_vcf_in @@ -156,13 +156,13 @@ workflow CALL_SNV { } emit: - genome_vcf = ch_genome_vcf // channel: [ val(meta), path(vcf) ] + genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] + genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] genome_tabix = ch_genome_tabix // channel: [ val(meta), path(tbi) ] + genome_vcf = ch_genome_vcf // channel: [ val(meta), path(vcf) ] genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] - genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] - genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] - mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] + mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] mt_txt = ch_mt_txt // channel: [ val(meta), path(txt) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index c69bc564f..be84e6538 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -9,9 +9,9 @@ include { GATK4_FILTERMUTECTCALLS as GATK4_FILTERMUTECTCALLS_MT } fr workflow CALL_SNV_MT { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_dict // channel: [mandatory] [ val(meta), path(dict) ] + ch_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_intervals // channel: [mandatory] [ path(interval_list) ] main: @@ -38,11 +38,11 @@ workflow CALL_SNV_MT { ch_versions = ch_versions.mix(GATK4_FILTERMUTECTCALLS_MT.out.versions.first()) emit: - vcf = GATK4_FILTERMUTECTCALLS_MT.out.vcf // channel: [ val(meta), path(vcf) ] - tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] - stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] - txt = HAPLOCHECK_MT.out.txt // channel: [ val(meta), path(txt) ] html = HAPLOCHECK_MT.out.html // channel: [ val(meta), path(html) ] + stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] + tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] + txt = HAPLOCHECK_MT.out.txt // channel: [ val(meta), path(txt) ] + vcf = GATK4_FILTERMUTECTCALLS_MT.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index b4eee1e77..896cb78e9 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -15,13 +15,13 @@ include { ADD_VARCALLER_TO_BED } from '../../../modules/lo workflow CALL_SNV_DEEPVARIANT { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] - ch_par_bed // channel: [optional] [ val(meta), path(bed) ] ch_case_info // channel: [mandatory] [ val(case_info) ] ch_foundin_header // channel: [mandatory] [ path(header) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_par_bed // channel: [optional] [ val(meta), path(bed) ] + ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] val_analysis_type // boolean main: @@ -93,9 +93,9 @@ workflow CALL_SNV_DEEPVARIANT { ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] + tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index bff039012..c8f1afa23 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -17,16 +17,16 @@ include { ADD_VARCALLER_TO_BED } from '../../../modules/lo workflow CALL_SNV_SENTIEON { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_dbsnp // channel: [mandatory] [ val(meta), path(vcf) ] - ch_dbsnp_index // channel: [mandatory] [ val(meta), path(tbi) ] ch_call_interval // channel: [mandatory] [ val(meta), path(interval) ] - ch_ml_model // channel: [mandatory] [ val(meta), path(model) ] ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] + ch_dbsnp // channel: [mandatory] [ val(meta), path(vcf) ] + ch_dbsnp_index // channel: [mandatory] [ val(meta), path(tbi) ] ch_foundin_header // channel: [mandatory] [ path(header) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_ml_model // channel: [mandatory] [ val(meta), path(model) ] + ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] main: ch_versions = channel.empty() @@ -121,9 +121,9 @@ workflow CALL_SNV_SENTIEON { ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] gvcf = SENTIEON_DNASCOPE.out.gvcf // channel: [ val(meta), path(gvcf) ] gvcf_tbi = SENTIEON_DNASCOPE.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi) ] + tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index cf1af6edf..1612e9439 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -17,15 +17,15 @@ include { TABIX_TABIX as TABIX_ANNOTATE } from '../../.. workflow POSTPROCESS_MT_CALLS { take: - ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_mtshift_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mtshift_backchain // channel: [mandatory] [ val(meta), path(backchain) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_foundin_header // channel: [mandatory] [ path(header) ] - ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_foundin_header // channel: [mandatory] [ path(header) ] + ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_mtshift_backchain // channel: [mandatory] [ val(meta), path(backchain) ] + ch_mtshift_vcf // channel: [mandatory] [ val(meta), path(vcf) ] main: ch_versions = channel.empty() @@ -135,7 +135,7 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(TABIX_TABIX_MT2.out.versions) emit: - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index f159bdb03..48f613253 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -133,6 +133,7 @@ workflow RAREDISEASE { ch_score_config_snv ch_score_config_sv ch_sdf + ch_sentieon_pcr_indel_model ch_svcaller_priority ch_svd_bed ch_svd_mu @@ -191,7 +192,6 @@ workflow RAREDISEASE { val_sample_id_map val_samtools_sort_threads val_save_mapped_as_cram - val_sentieon_dnascope_pcr_indel_model val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed @@ -364,30 +364,30 @@ workflow RAREDISEASE { if (!skip_snv_calling) { CALL_SNV ( + ch_call_interval, + ch_case_info, + ch_dbsnp, + ch_dbsnp_tbi, + ch_foundin_header, ch_mapped.genome_marked_bam_bai, - ch_mapped.mt_bam_bai_gatksubwf, - ch_mapped.mtshift_bam_bai_gatksubwf, ch_genome_chrsizes, ch_genome_fasta, ch_genome_fai, - ch_mt_intervals, + ch_ml_model, + ch_mapped.mt_bam_bai_gatksubwf, ch_mt_dictionary, ch_mt_fai, ch_mt_fasta, + ch_mt_intervals, + ch_mapped.mtshift_bam_bai_gatksubwf, ch_mtshift_dictionary, ch_mtshift_fai, ch_mtshift_fasta, ch_mtshift_intervals, ch_mtshift_backchain, - ch_dbsnp, - ch_dbsnp_tbi, - ch_call_interval, - ch_target_bed, - ch_ml_model, ch_par_bed, - ch_case_info, - ch_foundin_header, - channel.value(val_sentieon_dnascope_pcr_indel_model), + ch_sentieon_pcr_indel_model, + ch_target_bed, val_analysis_type, val_variant_caller, val_run_mt_for_wes, From 78f4edc1b8b9ac50a83b9dec78f8920325c40327 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 09:15:19 +0100 Subject: [PATCH 206/872] annotate and related swfs --- subworkflows/local/annotate_cadd/main.nf | 6 ++--- .../local/annotate_consequence_pli.nf | 2 +- subworkflows/local/annotate_genome_snvs.nf | 24 +++++++++---------- subworkflows/local/annotate_mt_snvs.nf | 4 ++-- .../local/annotate_rhocallviz/main.nf | 4 ++-- tests/nextflow.config | 18 ++++++++++++-- workflows/raredisease.nf | 24 +++++++++---------- 7 files changed, 48 insertions(+), 34 deletions(-) diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index d2684ea8f..f32e36613 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -15,10 +15,10 @@ include { TABIX_TABIX as TABIX_VIEW } from '../../../modules/nf-core workflow ANNOTATE_CADD { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] - ch_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(dir) ] ch_fai // channel: [optional] [ path(fai) ] + ch_header // channel: [mandatory] [ path(txt) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] val_genome // string: GRCh37 or GRCh37 main: @@ -81,7 +81,7 @@ workflow ANNOTATE_CADD { ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions.first()) emit: - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index 722cd9d8e..c6aa34511 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -8,8 +8,8 @@ include { TABIX_TABIX } from '../../modules/nf-core/tabix/ta workflow ANNOTATE_CSQ_PLI { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_variant_consequences // channel: [mandatory] [ path(consequences) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] val_index // bool main: diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 65e8ae337..4bc6cc3d6 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -24,21 +24,21 @@ include { ANNOTATE_RHOCALLVIZ } from './annotate_rhocallviz' workflow ANNOTATE_GENOME_SNVS { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] ch_cadd_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(annotation) ] - ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] - ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] - ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] - ch_vep_cache // channel: [mandatory] [ path(cache) ] + ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + ch_genome_fai // channel: [mandatory] [ path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_gnomad_af // channel: [optional] [ path(tab), path(tbi) ] ch_samples // channel: [mandatory] [ val(sample_meta) ] ch_split_intervals // channel: [mandatory] [ path(intervals) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] + ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] + ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] + ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] + ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] + ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] - ch_genome_fai // channel: [mandatory] [ path(fai) ] - ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 @@ -115,10 +115,10 @@ workflow ANNOTATE_GENOME_SNVS { .set { ch_cadd_in } ANNOTATE_CADD ( - ch_cadd_in, - ch_cadd_header, ch_cadd_resources, ch_genome_fai, + ch_cadd_header, + ch_cadd_in, val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf @@ -194,7 +194,7 @@ workflow ANNOTATE_GENOME_SNVS { ch_vep_index = TABIX_BCFTOOLS_CONCAT.out.tbi ch_vep_ann_index = ch_concat_out.join(TABIX_BCFTOOLS_CONCAT.out.tbi) //rhocall_viz - ANNOTATE_RHOCALLVIZ(ch_vep_ann_index, ch_samples, ch_genome_chrsizes) + ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions) ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) @@ -214,7 +214,7 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) emit: - vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] + vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index c362d7f29..f74638aab 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -60,10 +60,10 @@ workflow ANNOTATE_MT_SNVS { // Annotating with CADD if (!val_cadd_resources.equals(null)) { ANNOTATE_CADD ( - ZIP_TABIX_VCFANNO_MT.out.gz_tbi, - ch_cadd_header, ch_cadd_resources, ch_fai, + ch_cadd_header, + ZIP_TABIX_VCFANNO_MT.out.gz_tbi, val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 5d85c9e17..8596d5fb0 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -13,9 +13,9 @@ include { CHROMOGRAPH as CHROMOGRAPH_AUTOZYG } from '../../../modules/nf- workflow ANNOTATE_RHOCALLVIZ { take: - ch_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - ch_samples // channel: [mandatory] [ val(sample_meta) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + ch_samples // channel: [mandatory] [ val(sample_meta) ] + ch_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: ch_versions = channel.empty() diff --git a/tests/nextflow.config b/tests/nextflow.config index 34b695ee4..15c9018d2 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -25,7 +25,21 @@ env { SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = System.getenv('SENTIEON_AUTH_MECH') + //SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + //SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how pipeline users will test out Sentieon with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA +singularity { + autoMounts = true + runOptions = '-B /home/ramprasad.neethiraj/tmp -B /home/ramprasad.neethiraj/nextflow -B /home/ramprasad.neethiraj/tmp:/rdds/tmp' } +// Set bash options +process.shell = [ + "bash", + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 48f613253..651fc4f54 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -402,21 +402,21 @@ workflow RAREDISEASE { if (!skip_snv_annotation) { ANNOTATE_GENOME_SNVS ( - CALL_SNV.out.genome_vcf_tabix, ch_cadd_header, ch_cadd_resources, - ch_vcfanno_extra, - ch_vcfanno_resources, - ch_vcfanno_lua, - ch_vcfanno_toml, - ch_vep_cache, + ch_genome_chrsizes, + ch_genome_fai, ch_genome_fasta, ch_gnomad_af, ch_samples, ch_scatter_split_intervals, + CALL_SNV.out.genome_vcf_tabix, + ch_vcfanno_extra, + ch_vcfanno_lua, + ch_vcfanno_resources, + ch_vcfanno_toml, + ch_vep_cache, ch_vep_extra_files, - ch_genome_fai, - ch_genome_chrsizes, val_cadd_resources, val_genome, val_vep_cache_version @@ -446,8 +446,8 @@ workflow RAREDISEASE { ch_ann_csq_snv_in = ch_clinical_snv_vcf.mix(ch_clin_research_snv_vcf.research) ANN_CSQ_PLI_SNV ( - ch_ann_csq_snv_in, ch_variant_consequences_snv, + ch_ann_csq_snv_in, false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) @@ -519,8 +519,8 @@ workflow RAREDISEASE { ch_ann_csq_mtsnv_in = ch_clinical_mtsnv_vcf.mix(ch_clin_research_mt_vcf.research) ANN_CSQ_PLI_MT( - ch_ann_csq_mtsnv_in, ch_variant_consequences_snv, + ch_ann_csq_mtsnv_in, false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions) @@ -616,8 +616,8 @@ workflow RAREDISEASE { ch_ann_csq_sv_in = ch_clinical_sv_vcf.mix(ch_clin_research_sv_vcf.research) ANN_CSQ_PLI_SV ( - ch_ann_csq_sv_in, ch_variant_consequences_sv, + ch_ann_csq_sv_in, false ) ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions) @@ -694,8 +694,8 @@ workflow RAREDISEASE { ch_ann_csq_me_in = ch_clinical_me_vcf.mix(ch_clin_research_me_vcf.research) ANN_CSQ_PLI_ME( - ch_ann_csq_me_in, ch_variant_consequences_sv, + ch_ann_csq_me_in, true ) ch_versions = ch_versions.mix( ANN_CSQ_PLI_ME.out.versions ) From dae9819534d172b479265036abd19b9b11552ee9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 11:28:38 +0100 Subject: [PATCH 207/872] remaining subwfs --- .../local/annotate_mobile_elements.nf | 6 +-- subworkflows/local/annotate_mt_snvs.nf | 8 +-- .../local/annotate_structural_variants.nf | 8 +-- subworkflows/local/call_mobile_elements.nf | 6 +-- subworkflows/local/generate_cytosure_files.nf | 6 +-- subworkflows/local/gens.nf | 10 ++-- subworkflows/local/rank_variants.nf | 2 +- subworkflows/local/variant_evaluation.nf | 2 +- workflows/raredisease.nf | 52 +++++++++---------- 9 files changed, 50 insertions(+), 50 deletions(-) diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index a9a0fc09e..f1064aa91 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -11,10 +11,10 @@ include { SVDB_QUERY as SVDB_QUERY_DB } from '../../modules/nf-core/sv workflow ANNOTATE_MOBILE_ELEMENTS { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_me_svdb_resources // channel: [mandatory] [ path(csv) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_me_svdb_resources // channel: [mandatory] [ path(csv) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] val_genome // string: [mandatory] GRCh37 or GRCh38 val_vep_cache_version // string: [mandatory] default: 107 diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index f74638aab..6c327c1c0 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -14,17 +14,17 @@ include { HMTNOTE_ANNOTATE } from '../../modules/n workflow ANNOTATE_MT_SNVS { take: - ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_cadd_header // channel: [mandatory] [ path(txt) ] ch_cadd_resources // channel: [mandatory] [ path(annotation) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_fai // channel: [mandatory] [ path(fai) ] + ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] - ch_fai // channel: [mandatory] [ path(fai) ] skip_haplogrep3 // boolean val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 @@ -116,8 +116,8 @@ workflow ANNOTATE_MT_SNVS { emit: haplog = ch_haplog // channel: [ val(meta), path(txt) ] - vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] - tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ] report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] + tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ] + vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index d106f3138..9bca4d2fe 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -12,12 +12,12 @@ include { TABIX_TABIX as TABIX_VEP } from '../../modules/nf-core/tabix/ta workflow ANNOTATE_STRUCTURAL_VARIANTS { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_svdb_bedpedbs // channel: [optional] ch_svdb_dbs // channel: [optional] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] val_svdb_query_bedpedbs // String: [optional] params.svdb_query_bedpedbs val_svdb_query_dbs // String: [optional] params.svdb_query_dbs @@ -106,7 +106,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(TABIX_VEP.out.versions) emit: - vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] tbi = TABIX_VEP.out.tbi // channel: [ val(meta), path(tbi) ] + vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 869d15aef..2f5fc695b 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -15,11 +15,11 @@ include { SVDB_MERGE as SVDB_MERGE_ME } from '../../modules/nf-co workflow CALL_MOBILE_ELEMENTS { take: + ch_case_info // channel: [mandatory] [ val(case_info) ] ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_me_references // channel: [mandatory] [path(tsv)] - ch_case_info // channel: [mandatory] [ val(case_info) ] main: ch_versions = channel.empty() @@ -132,7 +132,7 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(TABIX_ME.out.versions) emit: - vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] tbi = TABIX_ME.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 98604419c..d61ca8d27 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -9,11 +9,11 @@ include { VCF2CYTOSURE } from '../../modules/nf workflow GENERATE_CYTOSURE_FILES { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_sample_id_map // channel: [optional] [val(id), val(id)] ch_blacklist // channel: [optional] [path(blacklist)] + ch_sample_id_map // channel: [optional] [val(id), val(id)] + ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] val_sample_id_map // string: path to sample_id_map file main: diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index b72cf0962..08e302b63 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -12,14 +12,14 @@ include { TABIX_BGZIPTABIX as GENS_GENERATE_COV_INDEX } from '../../modu workflow GENS { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_gvcf // channel: [mandatory] [ val(meta), path(gvcf) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_gnomad_pos // channel: [mandatory] [ path(gnomad_pos) ] + ch_gvcf // channel: [mandatory] [ val(meta), path(gvcf) ] ch_interval_list // channel: [mandatory] [ path(interval_list) ] ch_pon_female // channel: [mandatory] [ path(pon) ] ch_pon_male // channel: [mandatory] [ path(pon) ] - ch_gnomad_pos // channel: [mandatory] [ path(gnomad_pos) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] main: ch_versions = channel.empty() @@ -73,7 +73,7 @@ workflow GENS { ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions.first()) emit: - gens_cov_bed_gz = GENS_GENERATE.out.cov // channel: [ val(meta), path(bed) ] gens_baf_bed_gz = GENS_GENERATE.out.baf // channel: [ val(meta), path(bed) ] + gens_cov_bed_gz = GENS_GENERATE.out.cov // channel: [ val(meta), path(bed) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index e80a22a3a..2a425cf87 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -12,10 +12,10 @@ include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' workflow RANK_VARIANTS { take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] ch_pedfile // channel: [mandatory] [ path(ped) ] ch_reduced_penetrance // channel: [mandatory] [ path(pentrance) ] ch_score_config // channel: [mandatory] [ path(ini) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] process_with_sort // Boolean main: diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index e6155b397..0debbdd0c 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -9,9 +9,9 @@ include { TABIX_TABIX as TABIX_TRUTHVCF } from '../../modules/nf-core/tabix/t workflow VARIANT_EVALUATION { take: - ch_snv_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] ch_rtg_truthvcfs // channel: [mandatory] [ val(meta), path(dbs) ] ch_sdf // channel: [mandatory] [ val(meta), path(sdf) ] + ch_snv_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: ch_versions = channel.empty() diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 651fc4f54..225c3d6b6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -389,9 +389,9 @@ workflow RAREDISEASE { ch_sentieon_pcr_indel_model, ch_target_bed, val_analysis_type, - val_variant_caller, + val_concatenate_snv_calls, val_run_mt_for_wes, - val_concatenate_snv_calls + val_variant_caller ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) ch_mt_txt = CALL_SNV.out.mt_txt @@ -462,10 +462,10 @@ workflow RAREDISEASE { .set {ch_ranksnv_nuclear_in} RANK_VARIANTS_SNV ( - ch_ranksnv_nuclear_in, ch_pedfile, ch_reduced_penetrance, ch_score_config_snv, + ch_ranksnv_nuclear_in, false ) ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) @@ -477,17 +477,17 @@ workflow RAREDISEASE { if (!(skip_mt_annotation) && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))) { ANNOTATE_MT_SNVS ( - CALL_SNV.out.mt_vcf, ch_cadd_header, ch_cadd_resources, ch_genome_fasta, + ch_genome_fai, + CALL_SNV.out.mt_vcf, ch_vcfanno_extra, ch_vcfanno_lua, ch_vcfanno_resources, ch_vcfanno_toml, ch_vep_cache, ch_vep_extra_files, - ch_genome_fai, skip_haplogrep3, val_cadd_resources, val_genome, @@ -535,10 +535,10 @@ workflow RAREDISEASE { .set {ch_ranksnv_mt_in} RANK_VARIANTS_MT ( - ch_ranksnv_mt_in, ch_pedfile, ch_reduced_penetrance, ch_score_config_mt, + ch_ranksnv_mt_in, false ) ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions) @@ -579,12 +579,12 @@ workflow RAREDISEASE { // if (!skip_sv_annotation) { ANNOTATE_STRUCTURAL_VARIANTS ( - CALL_STRUCTURAL_VARIANTS.out.vcf, + ch_genome_dictionary, + ch_genome_fasta, ch_svdb_bedpedbs, ch_svdb_dbs, + CALL_STRUCTURAL_VARIANTS.out.vcf, ch_vep_cache, - ch_genome_fasta, - ch_genome_dictionary, ch_vep_extra_files, val_svdb_query_bedpedbs, val_svdb_query_dbs, @@ -632,10 +632,10 @@ workflow RAREDISEASE { .set {ch_ranksnv_sv_in} RANK_VARIANTS_SV ( - ch_ranksnv_sv_in, ch_pedfile, ch_reduced_penetrance, ch_score_config_sv, + ch_ranksnv_sv_in, true ) ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) @@ -650,20 +650,20 @@ workflow RAREDISEASE { if (!skip_me_calling && val_analysis_type.equals("wgs")) { CALL_MOBILE_ELEMENTS( + ch_case_info, ch_mapped.genome_marked_bam_bai, - ch_genome_fasta, ch_genome_fai, - ch_me_references, - ch_case_info + ch_genome_fasta, + ch_me_references ) ch_versions = ch_versions.mix(CALL_MOBILE_ELEMENTS.out.versions) if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( - CALL_MOBILE_ELEMENTS.out.vcf, - ch_me_svdb_resources, - ch_genome_fasta, ch_genome_dictionary, + ch_genome_fasta, + ch_me_svdb_resources, + CALL_MOBILE_ELEMENTS.out.vcf, ch_vep_cache, val_genome, val_vep_cache_version, @@ -752,11 +752,11 @@ workflow RAREDISEASE { */ if (!skip_vcf2cytosure && val_analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { GENERATE_CYTOSURE_FILES ( - ch_sv_annotate.vcf_ann, - ch_sv_annotate.tbi, ch_mapped.genome_marked_bam, - ch_sample_id_map, ch_vcf2cytosure_blacklist, + ch_sample_id_map, + ch_sv_annotate.tbi, + ch_sv_annotate.vcf_ann, val_sample_id_map ) ch_versions = ch_versions.mix(GENERATE_CYTOSURE_FILES.out.versions) @@ -770,14 +770,14 @@ workflow RAREDISEASE { if (!skip_gens && analysis_type.equals("wgs")) { GENS ( ch_mapped.genome_marked_bam_bai, - CALL_SNV.out.genome_gvcf, - ch_genome_fasta, + ch_genome_dictionary, ch_genome_fai, + ch_genome_fasta, + ch_gens_gnomad_pos, + CALL_SNV.out.genome_gvcf, ch_gens_interval_list, ch_gens_pon_female, - ch_gens_pon_male, - ch_gens_gnomad_pos, - ch_genome_dictionary + ch_gens_pon_male ) ch_versions = ch_versions.mix(GENS.out.versions) } @@ -790,9 +790,9 @@ workflow RAREDISEASE { if (val_run_rtgvcfeval) { VARIANT_EVALUATION ( - CALL_SNV.out.genome_vcf_tabix, ch_rtg_truthvcfs, - ch_sdf + ch_sdf, + CALL_SNV.out.genome_vcf_tabix ) ch_versions = ch_versions.mix(VARIANT_EVALUATION.out.versions) } From 50a6e9823a553d25f2257b53c25c395179ca4515 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 13:41:31 +0100 Subject: [PATCH 208/872] add multiqc_samples option --- nextflow.config | 1 + nextflow_schema.json | 12 +++++++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index f5d3e0a28..5e969fe74 100644 --- a/nextflow.config +++ b/nextflow.config @@ -122,6 +122,7 @@ params { // MultiQC options multiqc_config = null + multiqc_samples = null multiqc_title = null multiqc_logo = null max_multiqc_email_size = '25.MB' diff --git a/nextflow_schema.json b/nextflow_schema.json index c074a13d6..b534dc9ee 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -538,7 +538,6 @@ }, "extract_alignments": { "type": "boolean", - "default": "false", "description": "After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.", "help_text": "Set this to true, and specify the contig(s) using `restrict_to_contigs` parameter", "fa_icon": "fas fa-toggle-on" @@ -871,6 +870,17 @@ "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_samples": { + "type": "string", + "exists": true, + "format": "file-path", + "description": "Path to a file containing internal ids and customer ids in tab seperated format.", + "fa_icon": "fas fa-table", + "mimetype": "text/csv", + "schema": "assets/sample_id_map.json", + "help_text": "File for multiqc to group entries by samples", + "pattern": "^\\S+\\.tsv$" + }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", From 17e6277ced103534612dd8ee4a1b5120492e3b79 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 13:44:52 +0100 Subject: [PATCH 209/872] update multiqc config --- assets/multiqc_config.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 034fb00ed..cc29c5c71 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -53,7 +53,13 @@ module_order: extra_fn_clean_exts: - "_sorted_md" + - "_mosdepth" + - "_sorted" - type: regex pattern: "_LNUMBER[0-9]{1,}" +table_sample_merge: + "R1": "_1" + "R2": "_2" + disable_version_detection: true From 0d753233cb3e6e4e2eb614659faad45b3c380885 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 13:49:33 +0100 Subject: [PATCH 210/872] add to module --- main.nf | 3 +++ workflows/raredisease.nf | 3 ++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 077f7d035..fa6556bbe 100644 --- a/main.nf +++ b/main.nf @@ -133,6 +133,8 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) + ch_multiqc_samples = params.multiqc_samples ? channel.value(params.multiqc_samples) + : channel.value([[]]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) @@ -319,6 +321,7 @@ workflow NFCORE_RAREDISEASE { ch_mtshift_fai, ch_mtshift_fasta, ch_mtshift_intervals, + ch_multiqc_samples, ch_ngsbits_method, ch_par_bed, ch_pedfile, diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 225c3d6b6..325dd91ed 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -117,6 +117,7 @@ workflow RAREDISEASE { ch_mtshift_fai ch_mtshift_fasta ch_mtshift_intervals + ch_multiqc_samples ch_ngsbits_method ch_par_bed ch_pedfile @@ -889,7 +890,7 @@ workflow RAREDISEASE { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList(), [], - [] + ch_multiqc_samples ) emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html From 56a8fcb795563604db2703a5a10b80a6692edaba Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 13:52:07 +0100 Subject: [PATCH 211/872] update schema --- main.nf | 2 +- nextflow_schema.json | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/main.nf b/main.nf index fa6556bbe..5eb6a8877 100644 --- a/main.nf +++ b/main.nf @@ -133,7 +133,7 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_multiqc_samples = params.multiqc_samples ? channel.value(params.multiqc_samples) + ch_multiqc_samples = params.multiqc_samples ? channel.value(params.multiqc_samples) : channel.value([[]]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() diff --git a/nextflow_schema.json b/nextflow_schema.json index b534dc9ee..8a3f9eeb5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -877,7 +877,6 @@ "description": "Path to a file containing internal ids and customer ids in tab seperated format.", "fa_icon": "fas fa-table", "mimetype": "text/csv", - "schema": "assets/sample_id_map.json", "help_text": "File for multiqc to group entries by samples", "pattern": "^\\S+\\.tsv$" }, From 73e3ee950807c841e8e65e7fe42fd756d77e371b Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 14:00:12 +0100 Subject: [PATCH 212/872] udpate default --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 5eb6a8877..0c9d5e364 100644 --- a/main.nf +++ b/main.nf @@ -134,7 +134,7 @@ workflow NFCORE_RAREDISEASE { ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) ch_multiqc_samples = params.multiqc_samples ? channel.value(params.multiqc_samples) - : channel.value([[]]) + : channel.value([]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) From a7ad27642ccf8a27bab575edcb517645c6f10ea8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 14:17:19 +0100 Subject: [PATCH 213/872] update config --- assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index cc29c5c71..0fa4b51ef 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -59,7 +59,7 @@ extra_fn_clean_exts: pattern: "_LNUMBER[0-9]{1,}" table_sample_merge: - "R1": "_1" - "R2": "_2" + "(R1)": "_1" + "(R2)": "_2" disable_version_detection: true From feb8eca51d69576ca06aef8c07a395ef80b5cdce Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 14:20:37 +0100 Subject: [PATCH 214/872] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e41bc0aa1..a0c1790e0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) +- Parameter to pass a samples file to multiqc [#764](https://github.com/nf-core/raredisease/pull/764) ### `Changed` @@ -36,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | --------------- | ---------------- | | | sambamba_regions | | bwa_as_fallback | | +| | multiqc_samples | ### Tool updates From b5aafc1987a8c0d4412799dd93ab03b025ba2add Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 14:32:47 +0100 Subject: [PATCH 215/872] updatae help text --- main.nf | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 0c9d5e364..33570d2eb 100644 --- a/main.nf +++ b/main.nf @@ -133,7 +133,7 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_multiqc_samples = params.multiqc_samples ? channel.value(params.multiqc_samples) + ch_multiqc_samples = params.multiqc_samples ? channel.fromPath(params.multiqc_samples) : channel.value([]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() diff --git a/nextflow_schema.json b/nextflow_schema.json index 8a3f9eeb5..feb185aa6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -874,7 +874,7 @@ "type": "string", "exists": true, "format": "file-path", - "description": "Path to a file containing internal ids and customer ids in tab seperated format.", + "description": "Path to a file containing internal ids and customer ids in tab seperated format. For more info check, https://docs.seqera.io/multiqc/reports/customisation#sample-grouping", "fa_icon": "fas fa-table", "mimetype": "text/csv", "help_text": "File for multiqc to group entries by samples", From 96c6437d313f6146b54e90e53a86c6e658f50139 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 14:47:54 +0100 Subject: [PATCH 216/872] fix link --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index feb185aa6..c08645b0b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -874,10 +874,10 @@ "type": "string", "exists": true, "format": "file-path", - "description": "Path to a file containing internal ids and customer ids in tab seperated format. For more info check, https://docs.seqera.io/multiqc/reports/customisation#sample-grouping", + "description": "Path to a file containing internal ids and customer ids in tab seperated format. For more info check, https://docs.seqera.io/multiqc/reports/customisation#sample-name-replacement", "fa_icon": "fas fa-table", "mimetype": "text/csv", - "help_text": "File for multiqc to group entries by samples", + "help_text": "File for multiqc to embed renaming patterns in reports", "pattern": "^\\S+\\.tsv$" }, "validate_params": { From c45add74d6c8c38a98dab46ca2511acfe00b8208 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 22 Dec 2025 13:48:38 +0000 Subject: [PATCH 217/872] [automated] Fix code linting --- subworkflows/local/align/main.nf | 4 ++-- subworkflows/local/align/tests/main.nf.test | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index b338ad30b..d5f96741a 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -80,7 +80,7 @@ workflow ALIGN { .set{ch_input_bai} if (val_aligner.matches("bwamem2|bwa|bwameme")) { - ALIGN_BWA_BWAMEM2_BWAMEME ( + ALIGN_BWA_BWAMEM2_BWAMEME ( ch_genome_bwaindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, @@ -98,7 +98,7 @@ workflow ALIGN { ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics ch_versions = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions) } else if (val_aligner.equals("sentieon")) { - ALIGN_SENTIEON ( + ALIGN_SENTIEON ( ch_genome_bwaindex, ch_genome_fai, ch_genome_fasta, diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 8577d471e..32c053815 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -87,7 +87,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ] ] - ) + ) input[8] = channel.empty() input[9] = MT_MEM2.out.index.collect() input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() From b34bb6187495e3723827f7bc519c865d283634cf Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 16:02:21 +0100 Subject: [PATCH 218/872] update config --- tests/nextflow.config | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 15c9018d2..ef3aeed34 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -25,21 +25,8 @@ env { SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - //SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - //SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA // NOTE This is how pipeline users will test out Sentieon with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} - -singularity { - autoMounts = true - runOptions = '-B /home/ramprasad.neethiraj/tmp -B /home/ramprasad.neethiraj/nextflow -B /home/ramprasad.neethiraj/tmp:/rdds/tmp' -} -// Set bash options -process.shell = [ - "bash", - "-e", // Exit if a tool returns a non-zero status/exit code - "-u", // Treat unset variables and parameters as an error - "-o", // Returns the status of the last command to exit.. - "pipefail" // ..with a non-zero status or zero if all successfully execute -] +} \ No newline at end of file From 5c4e0a7934bfc645932c08d37e0d6a278d84341a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 22 Dec 2025 15:06:02 +0000 Subject: [PATCH 219/872] [automated] Fix code linting --- tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index ef3aeed34..d9f466d55 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -29,4 +29,4 @@ env { SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA // NOTE This is how pipeline users will test out Sentieon with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} \ No newline at end of file +} From d0559296a9c3ca95170d93f41828f6b24df53250 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 19:04:07 +0100 Subject: [PATCH 220/872] Update nextflow_schema.json Co-authored-by: Anders Jemt --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index c08645b0b..8a806a193 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -874,7 +874,7 @@ "type": "string", "exists": true, "format": "file-path", - "description": "Path to a file containing internal ids and customer ids in tab seperated format. For more info check, https://docs.seqera.io/multiqc/reports/customisation#sample-name-replacement", + "description": "Path to a file containing internal ids and alternative ids in tab separated format. Will replace the internal id with the alternative id in the report. For more info check, https://docs.seqera.io/multiqc/reports/customisation#sample-name-replacement", "fa_icon": "fas fa-table", "mimetype": "text/csv", "help_text": "File for multiqc to embed renaming patterns in reports", From 276ee40b81d249f4b2196032b40ae19d2939a3e3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Dec 2025 19:04:28 +0100 Subject: [PATCH 221/872] Update CHANGELOG.md Co-authored-by: Anders Jemt --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a0c1790e0..fae558fc4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) -- Parameter to pass a samples file to multiqc [#764](https://github.com/nf-core/raredisease/pull/764) +- Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) ### `Changed` From 89a83b0f04be195c7c9b2b7d49ef17f0fc3482a7 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 7 Jan 2026 11:46:35 +0100 Subject: [PATCH 222/872] recommended PR edits --- modules.json | 451 +++++++------------------- modules/local/mitosalt/main.nf | 14 + modules/local/prep_mitosalt/main.nf | 7 + nextflow.config | 3 +- subworkflows/local/call_sv_MT/main.nf | 22 +- workflows/raredisease.nf | 42 ++- 6 files changed, 165 insertions(+), 374 deletions(-) diff --git a/modules.json b/modules.json index 9de004593..1fcf56a17 100644 --- a/modules.json +++ b/modules.json @@ -8,764 +8,545 @@ "bcftools/annotate": { "branch": "master", "git_sha": "cb08035150685b11d890d90c9534d4f16869eaec", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/roh": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/slop": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwameme/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwameme/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "chromograph": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - 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"installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "expansionhunter": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ngsbits/samplegender": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "peddy": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/collecthsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/renamesampleinvcf": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "qualimap/bamqc": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rhocall/annotate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rhocall/viz": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/datametrics": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/readwriter": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/sample": { "branch": "master", "git_sha": "af2861c63a6db77168f039ac265d84cfecd9efc2", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stranger": { "branch": "master", "git_sha": "ffe458cbd1208b82e33e607fa43fbe80df191047", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -774,30 +555,22 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 9f06ae402..44de5dd7f 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -43,4 +43,18 @@ process MITOSALT { mitosalt: $VERSION END_VERSIONS """ + + stub: + def VERSION = "1.1.1" + def prefix = task.ext.prefix ?: "${meta.id}" + """ + cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} + touch ${prefix}.breakpoint + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mitosalt: $VERSION + END_VERSIONS + """ + } diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf index 629ebb9b9..18977a932 100644 --- a/modules/local/prep_mitosalt/main.nf +++ b/modules/local/prep_mitosalt/main.nf @@ -79,4 +79,11 @@ process PREP_MITOSALT { echo "i_del = yes" >> mitosalt_config.txt echo "cn_mt = yes" >> mitosalt_config.txt """ + + stub: + """ + echo "hisat2 = hisat2" > mitosalt_config.txt + echo "lastal = lastal" >> mitosalt_config.txt + """ + } diff --git a/nextflow.config b/nextflow.config index d86042353..a730c941f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -51,7 +51,7 @@ params { gens_gnomad_pos = null gnomad_af = null gnomad_af_idx = null - hisat2 = null + hisat2 = null intervals_wgs = null intervals_y = null known_dbsnp = null @@ -152,7 +152,6 @@ params { hook_url = System.getenv('HOOK_URL') help = false help_full = false - nextflow.enable.moduleBinaries = true show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index b113ecbfd..a2eee98ab 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -13,11 +13,11 @@ workflow CALL_SV_MT { ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] - ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] - ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_genome_chrsizes // channel: [mandatory] [ val(meta), path(chrsizes) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] val_score_threshold // string: [mandatory] mitosalt_score_threshold val_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold val_split_length // string: [mandatory] mitosalt_split_length @@ -32,8 +32,8 @@ workflow CALL_SV_MT { val_flank // string: [mandatory] mitosalt_flank val_split_distance_threshold // string: [mandatory] mitosalt_split_dist_threshold ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - ch_mito_name // channel: [mandatory] [ val(mito_name) ] - val_exclude // string: [mandatory] mitosalt_exclude + val_mito_name // string: [mandatory] mito_name + val_exclude // string: [mandatory] mitosalt_exclude main: ch_versions = Channel.empty() @@ -50,8 +50,8 @@ workflow CALL_SV_MT { ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta, - ch_mito_name, - val_exclude, + val_mito_name, + val_exclude, val_score_threshold, val_evalue_threshold, val_split_length, @@ -68,8 +68,8 @@ workflow CALL_SV_MT { ) MITOSALT( - SEQTK_SAMPLE.out.reads, - PREP_MITOSALT.out.msconfig, + SEQTK_SAMPLE.out.reads, + PREP_MITOSALT.out.msconfig, ch_genome_hisat2index, ch_genome_fai, ch_mt_lastdb, diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 6b4d15aa8..997db456f 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -175,8 +175,6 @@ workflow RAREDISEASE { : Channel.empty() ch_me_svdb_resources = params.mobile_element_svdb_annotations ? Channel.fromPath(params.mobile_element_svdb_annotations) : Channel.empty() - ch_mito_name = params.mito_name ? Channel.value(params.mito_name) - : Channel.value([]) ch_ml_model = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : Channel.value([[:],[]]) ch_mt_intervals = ch_references.mt_intervals @@ -735,28 +733,28 @@ workflow RAREDISEASE { ch_reads, ch_mapped.genome_bam_bai, ch_genome_fasta, - ch_genome_hisat2index, - ch_genome_fai, - ch_mt_lastdb, - ch_mt_fai, - ch_genome_chrsizes, - ch_mt_fasta, + ch_genome_hisat2index, + ch_genome_fai, + ch_mt_lastdb, + ch_mt_fai, + ch_genome_chrsizes, + ch_mt_fasta, params.score_threshold, - params.evalue_threshold, - params.split_length, - params.paired_distance, - params.deletion_threshold_min, - params.deletion_threshold_max, - params.breakthreshold, - params.cluster_threshold, - params.breakspan, - params.sizelimit, - params.hplimit, - params.flank, - params.split_distance_threshold, + params.evalue_threshold, + params.split_length, + params.paired_distance, + params.deletion_threshold_min, + params.deletion_threshold_max, + params.breakthreshold, + params.cluster_threshold, + params.breakspan, + params.sizelimit, + params.hplimit, + params.flank, + params.split_distance_threshold, ch_subdepth, - ch_mito_name, - params.exclude + params.mito_name, + params.exclude ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) From 0af6f98bf9caccfcd576f45f9089612a06e195ab Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 20 Jan 2026 09:51:20 +0100 Subject: [PATCH 223/872] fixed indentation --- conf/test.config | 1 - modules/local/mitosalt/main.nf | 8 +++- subworkflows/local/call_sv_MT/main.nf | 48 +++++++++---------- subworkflows/local/prepare_references/main.nf | 12 ++--- 4 files changed, 36 insertions(+), 33 deletions(-) diff --git a/conf/test.config b/conf/test.config index 0c165711e..9ddb93393 100644 --- a/conf/test.config +++ b/conf/test.config @@ -37,7 +37,6 @@ params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,ngsbits' - skip_subworkflows = "sv_annotation,snv_calling" input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 57cd991d3..9dedce623 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -3,8 +3,12 @@ process MITOSALT { label "process_low" conda "${moduleDir}/environment.yml" +// container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +// 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': +// 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': + '/home/proj/production/dropbox/RN/mitosalt.sif': 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" @@ -29,7 +33,7 @@ process MITOSALT { """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} mkdir -p log indel bam tab bw plot - MitoSAlt1.1.1.pl new-${msconfig} $reads $prefix + mitosalt new-${msconfig} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint mv indel/*.cluster ${prefix}.cluster diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index a2eee98ab..9e886fdaa 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -43,29 +43,29 @@ workflow CALL_SV_MT { SEQTK_SAMPLE (ch_reads_subdepth) ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - PREP_MITOSALT( - ch_genome_hisat2index, - ch_genome_fai, - ch_mt_lastdb, - ch_mt_fai, - ch_genome_chrsizes, - ch_mt_fasta, - val_mito_name, - val_exclude, - val_score_threshold, - val_evalue_threshold, - val_split_length, - val_paired_distance, - val_deletion_threshold_min, - val_deletion_threshold_max, - val_breakthreshold, - val_cluster_threshold, - val_breakspan, - val_sizelimit, - val_hplimit, - val_flank, - val_split_distance_threshold - ) + PREP_MITOSALT( + ch_genome_hisat2index, + ch_genome_fai, + ch_mt_lastdb, + ch_mt_fai, + ch_genome_chrsizes, + ch_mt_fasta, + val_mito_name, + val_exclude, + val_score_threshold, + val_evalue_threshold, + val_split_length, + val_paired_distance, + val_deletion_threshold_min, + val_deletion_threshold_max, + val_breakthreshold, + val_cluster_threshold, + val_breakspan, + val_sizelimit, + val_hplimit, + val_flank, + val_split_distance_threshold + ) MITOSALT( SEQTK_SAMPLE.out.reads, @@ -76,7 +76,7 @@ workflow CALL_SV_MT { ch_mt_fai, ch_genome_chrsizes, ch_mt_fasta - ) + ) ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 8506d0f10..81f7d29d8 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -69,7 +69,7 @@ workflow PREPARE_REFERENCES { BWAMEM2_INDEX_GENOME(ch_genome_fasta) BWAMEME_INDEX_GENOME(ch_genome_fasta) SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.set{ch_sentieonbwa} - HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]) + HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]) // MT genome indices SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_fai) @@ -83,7 +83,7 @@ workflow PREPARE_REFERENCES { BWA_INDEX_MT(ch_mt_fasta_in) SENTIEON_BWAINDEX_MT(ch_mt_fasta_in) ch_bwa_mt = Channel.empty().mix(SENTIEON_BWAINDEX_MT.out.index, BWA_INDEX_MT.out.index).collect() - LAST_INDEX_MT(ch_mt_fasta_in) + LAST_INDEX_MT(ch_mt_fasta_in) BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) BWA_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa) @@ -170,7 +170,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) - ch_versions = ch_versions.mix(HISAT2_INDEX_GENOME.out.versions) + ch_versions = ch_versions.mix(HISAT2_INDEX_GENOME.out.versions) ch_versions = ch_versions.mix(GATK_SD.out.versions) ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) @@ -179,7 +179,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(GATK_SHIFTFASTA.out.versions) ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions) ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions) - ch_versions = ch_versions.mix(LAST_INDEX_MT.out.versions) + ch_versions = ch_versions.mix(LAST_INDEX_MT.out.versions) ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions) ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT_SHIFT.out.versions) ch_versions = ch_versions.mix(BWA_INDEX_MT_SHIFT.out.versions) @@ -202,7 +202,7 @@ workflow PREPARE_REFERENCES { genome_bwa_index = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect() // channel: [ val(meta), path(index) ] genome_bwamem2_index = BWAMEM2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_bwameme_index = BWAMEME_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] - genome_hisat2_index = HISAT2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] + genome_hisat2_index = HISAT2_INDEX_GENOME.out.index.collect() // channel: [ val(meta), path(index) ] genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel: [ path(sizes) ] genome_fai = ch_fai // channel: [ val(meta), path(fai) ] genome_dict = ch_dict // channel: [ val(meta), path(dict) ] @@ -210,7 +210,7 @@ workflow PREPARE_REFERENCES { mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel: [ path(intervals) ] mt_bwa_index = ch_bwa_mt // channel: [ val(meta), path(index) ] mt_bwamem2_index = BWAMEM2_INDEX_MT.out.index.collect() // channel: [ val(meta), path(index) ] - mt_last_index = LAST_INDEX_MT.out.index // channel: [ val(meta), path(index) ] + mt_last_index = LAST_INDEX_MT.out.index // channel: [ val(meta), path(index) ] mt_dict = GATK_SD_MT.out.dict.collect() // channel: [ val(meta), path(dict) ] mt_fasta = ch_mt_fasta_in.collect() // channel: [ val(meta), path(fasta) ] mt_fai = SAMTOOLS_FAIDX_MT.out.fai.collect() // channel: [ val(meta), path(fai) ] From 73023056bb74387ed334d107e4c7a6b72a608429 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 20 Jan 2026 17:09:55 +0100 Subject: [PATCH 224/872] fix error --- subworkflows/local/call_sv_MT/main.nf | 17 ++++++++--------- subworkflows/local/prepare_references/main.nf | 6 ++++-- workflows/raredisease.nf | 2 +- 3 files changed, 13 insertions(+), 12 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6164cbf31..9c83ac8d1 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -39,15 +39,12 @@ workflow CALL_SV_MT { ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { - ch_reads_subdepth = ch_reads.concat(ch_subdepth).collect() + ch_reads_subdepth = ch_reads.combine(ch_subdepth) + SEQTK_SAMPLE (ch_reads_subdepth) - ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions.first()) - ch_genome_chrsizes.dump(tag:"chrsizes") - ch_genome_fai.dump(tag:"fai") - ch_genome_hisat2index.dump(tag:"hisat2") - ch_mt_lastdb.dump(tag:"lastdb") + PREP_MITOSALT( - ch_genome_chrsizes, + ch_genome_chrsizes, ch_genome_fai, ch_genome_hisat2index, ch_mt_fai, @@ -80,11 +77,13 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) - ch_versions = ch_versions.mix(MITOSALT.out.versions.first()) + + ch_versions = ch_versions.mix(MITOSALT.out.versions) + ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_versions = ch_versions.mix(MT_DELETION.out.versions.first()) + ch_versions = ch_versions.mix(MT_DELETION.out.versions) emit: mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a9ed545ef..5f889286b 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -64,6 +64,8 @@ workflow PREPARE_REFERENCES { ch_bwa = channel.empty() ch_genome_bwameme_index = channel.empty() ch_genome_bwamem2_index = channel.empty() + ch_genome_hisat2_index = channel.empty() + ch_mt_last_index = channel.empty() ch_gnomad_af_idx = channel.empty() ch_dbsnp = channel.value([[:],[]]) ch_dbsnp_tbi = channel.value([[:],[]]) @@ -147,8 +149,8 @@ workflow PREPARE_REFERENCES { ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() - ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).out.index.collect() - ch_mt_last_index = LAST_INDEX_MT(ch_mt_fasta).out.index + ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).index.collect() + ch_mt_last_index = LAST_INDEX_MT(ch_mt_fasta).index.collect() GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d6d1bb5ca..5cb4ac564 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -659,7 +659,7 @@ workflow RAREDISEASE { ch_mt_fai, ch_mt_fasta, ch_mt_lastdb, - ch_reads, + ch_input_fastqs, ch_subdepth, params.breakspan, params.breakthreshold, From b0a64122b49405dafc97b0ae84580f395d7f8c8e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 11:05:42 +0100 Subject: [PATCH 225/872] add channelFromPathOrValue --- main.nf | 151 ++++++++++++++++++++++++--------- subworkflows/local/call_snv.nf | 2 +- 2 files changed, 110 insertions(+), 43 deletions(-) diff --git a/main.nf b/main.nf index 33570d2eb..4e66e139e 100644 --- a/main.nf +++ b/main.nf @@ -40,6 +40,36 @@ workflow NFCORE_RAREDISEASE { ch_case_info ch_reads ch_samples + val_aligner + val_analysis_type + val_bwa + val_bwamem2 + val_bwameme + val_cadd_resources + val_fai + val_fasta + val_gnomad_af + val_gnomad_af_idx + val_known_dbsnp + val_known_dbsnp_tbi + val_mt_aligner + val_mt_fasta + val_multiqc_samples + val_reduced_penetrance + val_rtg_truthvcfs + val_run_mt_for_wes + val_run_rtgvcfeval + val_score_config_mt + val_score_config_snv + val_score_config_sv + val_sdf + val_sequence_dictionary + val_target_bed + val_vcf2cytosure_blacklist + val_vcfanno_extra_resources + val_vcfanno_lua + val_vcfanno_toml + val_vep_cache main: @@ -47,29 +77,29 @@ workflow NFCORE_RAREDISEASE { // WORKFLOW: Run pipeline // - ch_versions = channel.empty() + ch_versions = channel.empty() PREPARE_REFERENCES ( - params.aligner, - params.analysis_type, - params.bwa, - params.bwamem2, - params.bwameme, - params.fai, - params.fasta, - params.gnomad_af, - params.gnomad_af_idx, - params.known_dbsnp, - params.known_dbsnp_tbi, - params.mt_aligner, - params.mt_fasta, - params.run_mt_for_wes, - params.run_rtgvcfeval, - params.sdf, - params.sequence_dictionary, - params.target_bed, - params.vcfanno_extra_resources, - params.vep_cache + val_aligner, + val_analysis_type, + val_bwa, + val_bwamem2, + val_bwameme, + val_fai, + val_fasta, + val_gnomad_af, + val_gnomad_af_idx, + val_known_dbsnp, + val_known_dbsnp_tbi, + val_mt_aligner, + val_mt_fasta, + val_run_mt_for_wes, + val_run_rtgvcfeval, + val_sdf, + val_sequence_dictionary, + val_target_bed, + val_vcfanno_extra_resources, + val_vep_cache ) .set { ch_references } @@ -104,9 +134,19 @@ workflow NFCORE_RAREDISEASE { ch_vep_cache = ch_references.vep_resources ch_versions = ch_versions.mix(ch_references.versions) + // Using channelFromPathOrValue helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) + ch_cadd_resources = channelFromPathOrValue(val_cadd_resources) + ch_multiqc_samples = channelFromPathOrValue(val_multiqc_samples) + ch_reduced_penetrance = channelFromPathOrValue(val_reduced_penetrance) + ch_rtg_truthvcfs = channelFromPathOrValue(val_rtg_truthvcfs) + ch_score_config_mt = channelFromPathOrValue(val_score_config_mt) + ch_score_config_snv = channelFromPathOrValue(val_score_config_snv) + ch_score_config_sv = channelFromPathOrValue(val_score_config_sv) + ch_vcf2cytosure_blacklist = channelFromPathOrValue(val_vcf2cytosure_blacklist) + ch_vcfanno_lua = channelFromPathOrValue(val_vcfanno_lua) + ch_vcfanno_toml = channelFromPathOrValue(val_vcfanno_toml) + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() - ch_cadd_resources = params.cadd_resources ? channel.fromPath(params.cadd_resources).collect() - : channel.value([]) ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() @@ -133,8 +173,6 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) - ch_multiqc_samples = params.multiqc_samples ? channel.fromPath(params.multiqc_samples) - : channel.value([]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) @@ -143,20 +181,10 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_readcount_intervals = params.readcount_intervals ? channel.fromPath(params.readcount_intervals).collect() : channel.empty() - ch_reduced_penetrance = params.reduced_penetrance ? channel.fromPath(params.reduced_penetrance).collect() - : channel.value([]) - ch_rtg_truthvcfs = params.rtg_truthvcfs ? channel.fromPath(params.rtg_truthvcfs).collect() - : channel.value([]) ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() : channel.empty() ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) : channel.empty() - ch_score_config_mt = params.score_config_mt ? channel.fromPath(params.score_config_mt).collect() - : channel.value([]) - ch_score_config_snv = params.score_config_snv ? channel.fromPath(params.score_config_snv).collect() - : channel.value([]) - ch_score_config_sv = params.score_config_sv ? channel.fromPath(params.score_config_sv).collect() - : channel.value([]) ch_svd_bed = params.verifybamid_svd_bed ? channel.fromPath(params.verifybamid_svd_bed) : channel.empty() ch_svd_mu = params.verifybamid_svd_mu ? channel.fromPath(params.verifybamid_svd_mu) @@ -175,12 +203,6 @@ workflow NFCORE_RAREDISEASE { : channel.value([[],[]]) ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() : channel.value([]) - ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? channel.fromPath(params.vcf2cytosure_blacklist).collect() - : channel.value([]) - ch_vcfanno_lua = params.vcfanno_lua ? channel.fromPath(params.vcfanno_lua).collect() - : channel.value([]) - ch_vcfanno_toml = params.vcfanno_toml ? channel.fromPath(params.vcfanno_toml).collect() - : channel.value([]) ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() : channel.empty() ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() @@ -435,7 +457,37 @@ workflow { PIPELINE_INITIALISATION.out.align, PIPELINE_INITIALISATION.out.case_info, PIPELINE_INITIALISATION.out.reads, - PIPELINE_INITIALISATION.out.samples + PIPELINE_INITIALISATION.out.samples, + params.aligner, + params.analysis_type, + params.bwa, + params.bwamem2, + params.bwameme, + params.cadd_resources, + params.fai, + params.fasta, + params.gnomad_af, + params.gnomad_af_idx, + params.known_dbsnp, + params.known_dbsnp_tbi, + params.mt_aligner, + params.mt_fasta, + params.multiqc_samples, + params.reduced_penetrance, + params.rtg_truthvcfs, + params.run_mt_for_wes, + params.run_rtgvcfeval, + params.score_config_mt, + params.score_config_snv, + params.score_config_sv, + params.sdf, + params.sequence_dictionary, + params.target_bed, + params.vcf2cytosure_blacklist, + params.vcfanno_extra_resources, + params.vcfanno_lua, + params.vcfanno_toml, + params.vep_cache ) // // SUBWORKFLOW: Run completion tasks @@ -451,6 +503,21 @@ workflow { ) } +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + HELPER FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +/** + * Creates a channel from a file path if the parameter is provided, otherwise returns a channel with an empty value + * @param filePath The path to the file (can be null) + * @return Channel with collected file path or channel.value([]) + */ +def channelFromPathOrValue(filePath) { + return filePath ? channel.fromPath(filePath).collect() : channel.value([]) +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 0d45783c0..3b35da14e 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -109,7 +109,7 @@ workflow CALL_SNV { ch_genome_tabix = GATK4_SELECTVARIANTS.out.tbi ch_genome_vcf_tabix = ch_genome_vcf.join(ch_genome_tabix, failOnMismatch:true, failOnDuplicate:true) - if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CALL_SNV_MT( ch_mt_bam_bai, ch_mt_dictionary, From 738cb65d00204a3d46f64d531e9500d49d61b882 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 11:07:31 +0100 Subject: [PATCH 226/872] add changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fae558fc4..321693ba5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) +- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf []() ### `Changed` From 16bb9be10be678f09386462d43285be137e9fca7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 21 Jan 2026 10:12:12 +0000 Subject: [PATCH 227/872] [automated] Fix code linting --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 321693ba5..e5ec2bce8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) -- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf []() +- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf []() ### `Changed` From 81199dfef6a11a5738db74142ff5bb00d280b417 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 11:19:18 +0100 Subject: [PATCH 228/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e5ec2bce8..118693e97 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) -- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf []() +- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) ### `Changed` From 7568873c57a9246cebeec4eefbc51f17cba9110b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 11:21:24 +0100 Subject: [PATCH 229/872] add channelFromPathOrEmpty --- CHANGELOG.md | 3 ++- main.nf | 45 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 47 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 321693ba5..6c3655283 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) -- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf []() +- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) +- A helper function channelFromPathOrEmpty to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) ### `Changed` diff --git a/main.nf b/main.nf index 4e66e139e..70472f03d 100644 --- a/main.nf +++ b/main.nf @@ -48,13 +48,19 @@ workflow NFCORE_RAREDISEASE { val_cadd_resources val_fai val_fasta + val_gens_gnomad_pos + val_gens_interval_list val_gnomad_af val_gnomad_af_idx + val_intervals_wgs + val_intervals_y val_known_dbsnp val_known_dbsnp_tbi + val_mobile_element_svdb_annotations val_mt_aligner val_mt_fasta val_multiqc_samples + val_readcount_intervals val_reduced_penetrance val_rtg_truthvcfs val_run_mt_for_wes @@ -64,11 +70,16 @@ workflow NFCORE_RAREDISEASE { val_score_config_sv val_sdf val_sequence_dictionary + val_svdb_query_bedpedbs + val_svdb_query_dbs val_target_bed val_vcf2cytosure_blacklist val_vcfanno_extra_resources val_vcfanno_lua val_vcfanno_toml + val_verifybamid_svd_bed + val_verifybamid_svd_mu + val_verifybamid_svd_ud val_vep_cache main: @@ -146,6 +157,19 @@ workflow NFCORE_RAREDISEASE { ch_vcfanno_lua = channelFromPathOrValue(val_vcfanno_lua) ch_vcfanno_toml = channelFromPathOrValue(val_vcfanno_toml) + // Using channelFromPathOrEmpty helper (val_x ? channel.fromPath(val_x).collect() : channel.empty()) + ch_gens_gnomad_pos = channelFromPathOrEmpty(val_gens_gnomad_pos) + ch_gens_interval_list = channelFromPathOrEmpty(val_gens_interval_list) + ch_intervals_wgs = channelFromPathOrEmpty(val_intervals_wgs) + ch_intervals_y = channelFromPathOrEmpty(val_intervals_y) + ch_me_svdb_resources = channelFromPathOrEmpty(val_mobile_element_svdb_annotations) + ch_readcount_intervals = channelFromPathOrEmpty(val_readcount_intervals) + ch_svd_bed = channelFromPathOrEmpty(val_verifybamid_svd_bed) + ch_svd_mu = channelFromPathOrEmpty(val_verifybamid_svd_mu) + ch_svd_ud = channelFromPathOrEmpty(val_verifybamid_svd_ud) + ch_svdb_bedpedbs = channelFromPathOrEmpty(val_svdb_query_bedpedbs) + ch_svdb_dbs = channelFromPathOrEmpty(val_svdb_query_dbs) + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) @@ -466,13 +490,19 @@ workflow { params.cadd_resources, params.fai, params.fasta, + params.gens_gnomad_pos, + params.gens_interval_list, params.gnomad_af, params.gnomad_af_idx, + params.intervals_wgs, + params.intervals_y, params.known_dbsnp, params.known_dbsnp_tbi, + params.mobile_element_svdb_annotations, params.mt_aligner, params.mt_fasta, params.multiqc_samples, + params.readcount_intervals, params.reduced_penetrance, params.rtg_truthvcfs, params.run_mt_for_wes, @@ -482,11 +512,16 @@ workflow { params.score_config_sv, params.sdf, params.sequence_dictionary, + params.svdb_query_bedpedbs, + params.svdb_query_dbs, params.target_bed, params.vcf2cytosure_blacklist, params.vcfanno_extra_resources, params.vcfanno_lua, params.vcfanno_toml, + params.verifybamid_svd_bed, + params.verifybamid_svd_mu, + params.verifybamid_svd_ud, params.vep_cache ) // @@ -509,6 +544,16 @@ workflow { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ + +/** + * Creates a channel from a file path if the parameter is provided, otherwise returns an empty channel + * @param filePath The path to the file (can be null) + * @return Channel with collected file path or empty channel + */ +def channelFromPathOrEmpty(filePath) { + return filePath ? channel.fromPath(filePath).collect() : channel.empty() +} + /** * Creates a channel from a file path if the parameter is provided, otherwise returns a channel with an empty value * @param filePath The path to the file (can be null) From 586e6dff39ab940a31487ae0026490aade022baa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 12:03:23 +0100 Subject: [PATCH 230/872] add channelFromPathWithIdOrDoubleEmpty --- CHANGELOG.md | 1 + main.nf | 44 +++++++++++++++++++++++++++++++++----------- 2 files changed, 34 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c3655283..0245d6ea4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) - A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) - A helper function channelFromPathOrEmpty to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) +- A helper function channelFromPathWithIdOrDoubleEmpty to create channels in a readable fashion in main.nf [#768](https://github.com/nf-core/raredisease/pull/768) ### `Changed` diff --git a/main.nf b/main.nf index 25451199f..b276f8600 100644 --- a/main.nf +++ b/main.nf @@ -46,6 +46,7 @@ workflow NFCORE_RAREDISEASE { val_bwamem2 val_bwameme val_cadd_resources + val_call_interval val_fai val_fasta val_gens_gnomad_pos @@ -56,6 +57,7 @@ workflow NFCORE_RAREDISEASE { val_intervals_y val_known_dbsnp val_known_dbsnp_tbi + val_ml_model val_mobile_element_svdb_annotations val_mt_aligner val_mt_fasta @@ -73,6 +75,9 @@ workflow NFCORE_RAREDISEASE { val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed + val_variant_catalog + val_variant_consequences_snv + val_variant_consequences_sv val_vcf2cytosure_blacklist val_vcfanno_extra_resources val_vcfanno_lua @@ -170,9 +175,14 @@ workflow NFCORE_RAREDISEASE { ch_svdb_bedpedbs = channelFromPathOrEmpty(val_svdb_query_bedpedbs) ch_svdb_dbs = channelFromPathOrEmpty(val_svdb_query_dbs) + // Using channelFromPathWithIdOrDoubleEmpty helper (with simpleName) + ch_call_interval = channelFromPathWithIdOrDoubleEmpty(val_call_interval) + ch_ml_model = channelFromPathWithIdOrDoubleEmpty(val_ml_model) + ch_variant_catalog = channelFromPathWithIdOrDoubleEmpty(val_variant_catalog) + ch_variant_consequences_snv = channelFromPathWithIdOrDoubleEmpty(val_variant_consequences_snv) + ch_variant_consequences_sv = channelFromPathWithIdOrDoubleEmpty(val_variant_consequences_sv) + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() - ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() - : channel.value([[:],[]]) ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) .map { row -> @@ -185,8 +195,6 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) : channel.empty() - ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() - : channel.value([[:],[]]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) @@ -197,12 +205,6 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) : channel.empty() - ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) - ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) - ch_variant_consequences_sv = params.variant_consequences_sv ? channel.fromPath(params.variant_consequences_sv).map { it -> [[id:it.simpleName],it]}.collect() - : channel.value([[],[]]) ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() : channel.value([]) ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() @@ -466,6 +468,7 @@ workflow { params.bwamem2, params.bwameme, params.cadd_resources, + params.call_interval, params.fai, params.fasta, params.gens_gnomad_pos, @@ -476,6 +479,7 @@ workflow { params.intervals_y, params.known_dbsnp, params.known_dbsnp_tbi, + params.ml_model, params.mobile_element_svdb_annotations, params.mt_aligner, params.mt_fasta, @@ -493,6 +497,9 @@ workflow { params.svdb_query_bedpedbs, params.svdb_query_dbs, params.target_bed, + params.variant_catalog, + params.variant_consequences_snv, + params.variant_consequences_sv, params.vcf2cytosure_blacklist, params.vcfanno_extra_resources, params.vcfanno_lua, @@ -522,7 +529,6 @@ workflow { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - /** * Creates a channel from a file path if the parameter is provided, otherwise returns an empty channel * @param filePath The path to the file (can be null) @@ -541,6 +547,22 @@ def channelFromPathOrValue(filePath) { return filePath ? channel.fromPath(filePath).collect() : channel.value([]) } + +/** + * Creates a channel from a file path, maps it to [id, file] format, and collects + * Falls back to channel.value([[:], []]) if file path is null + * @param filePath The path to the file (can be null) + * @param useSimpleName Whether to use simpleName for the id (default: true) + * @return Channel with [[id:name], file] format or channel.value([[:], []]) + */ +def channelFromPathWithIdOrDoubleEmpty(filePath) { + if (!filePath) { + return channel.value([[:], []]) + } + return channel.fromPath(filePath).map { file -> + return [[id: file.simpleName], file] + }.collect() +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END From 35af947231d8b8a7ad3f6a7ac9de6b2f3a54a127 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 16:28:26 +0100 Subject: [PATCH 231/872] add channelFromPathWithMeta --- CHANGELOG.md | 2 +- main.nf | 56 ++++++++++++++++++++++++++++++++++------------------ 2 files changed, 38 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0245d6ea4..9f8fd48b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) - A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) - A helper function channelFromPathOrEmpty to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) -- A helper function channelFromPathWithIdOrDoubleEmpty to create channels in a readable fashion in main.nf [#768](https://github.com/nf-core/raredisease/pull/768) +- A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#768](https://github.com/nf-core/raredisease/pull/768) ### `Changed` diff --git a/main.nf b/main.nf index b276f8600..73b53f5b3 100644 --- a/main.nf +++ b/main.nf @@ -51,6 +51,8 @@ workflow NFCORE_RAREDISEASE { val_fasta val_gens_gnomad_pos val_gens_interval_list + val_gens_pon_female + val_gens_pon_male val_gnomad_af val_gnomad_af_idx val_intervals_wgs @@ -62,11 +64,14 @@ workflow NFCORE_RAREDISEASE { val_mt_aligner val_mt_fasta val_multiqc_samples + val_par_bed + val_ploidy_model val_readcount_intervals val_reduced_penetrance val_rtg_truthvcfs val_run_mt_for_wes val_run_rtgvcfeval + val_sambamba_regions val_score_config_mt val_score_config_snv val_score_config_sv @@ -82,6 +87,8 @@ workflow NFCORE_RAREDISEASE { val_vcfanno_extra_resources val_vcfanno_lua val_vcfanno_toml + val_vep_filters + val_vep_filters_scout_fmt val_verifybamid_svd_bed val_verifybamid_svd_mu val_verifybamid_svd_ud @@ -175,12 +182,23 @@ workflow NFCORE_RAREDISEASE { ch_svdb_bedpedbs = channelFromPathOrEmpty(val_svdb_query_bedpedbs) ch_svdb_dbs = channelFromPathOrEmpty(val_svdb_query_dbs) - // Using channelFromPathWithIdOrDoubleEmpty helper (with simpleName) - ch_call_interval = channelFromPathWithIdOrDoubleEmpty(val_call_interval) - ch_ml_model = channelFromPathWithIdOrDoubleEmpty(val_ml_model) - ch_variant_catalog = channelFromPathWithIdOrDoubleEmpty(val_variant_catalog) - ch_variant_consequences_snv = channelFromPathWithIdOrDoubleEmpty(val_variant_consequences_snv) - ch_variant_consequences_sv = channelFromPathWithIdOrDoubleEmpty(val_variant_consequences_sv) + // Using channelFromPathWithMeta helper (with simpleName). If filepath is null, returns, [[:],[]] + ch_call_interval = channelFromPathWithMeta(val_call_interval, true) + ch_ml_model = channelFromPathWithMeta(val_ml_model, true) + ch_variant_catalog = channelFromPathWithMeta(val_variant_catalog, true) + ch_variant_consequences_snv = channelFromPathWithMeta(val_variant_consequences_snv, true) + ch_variant_consequences_sv = channelFromPathWithMeta(val_variant_consequences_sv, true) + + // Using channelFromPathWithMeta helper (with simpleName). If filepath is null, returns, empty channel + ch_gens_pon_female = channelFromPathWithMeta(val_gens_pon_female) + ch_gens_pon_male = channelFromPathWithMeta(val_gens_pon_male) + ch_ploidy_model = channelFromPathWithMeta(val_ploidy_model) + + // Using channelFromPathWithMeta helper. Returns either an empty channel or [[:],[]] with custom ID. + ch_par_bed = channelFromPathWithMeta(val_par_bed, true, "par_bed") + ch_sambamba_bed = channelFromPathWithMeta(val_sambamba_regions, false, 'sambamba') + ch_vep_filters_std_fmt = channelFromPathWithMeta(val_vep_filters, false, 'standard') + ch_vep_filters_scout_fmt = channelFromPathWithMeta(val_vep_filters_scout_fmt, false, 'scout') ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() @@ -189,18 +207,12 @@ workflow NFCORE_RAREDISEASE { return [[id:file(row.models).simpleName], row.models] } : channel.empty() - ch_gens_pon_female = params.gens_pon_female ? channel.fromPath(params.gens_pon_female).map { it -> [ [id:it.simpleName], it ] }.collect() - : channel.empty() - ch_gens_pon_male = params.gens_pon_male ? channel.fromPath(params.gens_pon_male).map { it -> [ [id:it.simpleName], it ] }.collect() - : channel.empty() ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) : channel.empty() ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() : channel.value([[],[]]) ch_sentieon_pcr_indel_model = channel.value(params.sentieon_dnascope_pcr_indel_model) - ch_ploidy_model = params.ploidy_model ? channel.fromPath(params.ploidy_model).map{ it -> [[id:it.simpleName], it] }.collect() - : channel.empty() ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() : channel.empty() ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) @@ -473,6 +485,8 @@ workflow { params.fasta, params.gens_gnomad_pos, params.gens_interval_list, + params.gens_pon_female, + params.gens_pon_male, params.gnomad_af, params.gnomad_af_idx, params.intervals_wgs, @@ -484,11 +498,14 @@ workflow { params.mt_aligner, params.mt_fasta, params.multiqc_samples, + params.par_bed, + params.ploidy_model, params.readcount_intervals, params.reduced_penetrance, params.rtg_truthvcfs, params.run_mt_for_wes, params.run_rtgvcfeval, + params.sambamba_regions, params.score_config_mt, params.score_config_snv, params.score_config_sv, @@ -504,6 +521,8 @@ workflow { params.vcfanno_extra_resources, params.vcfanno_lua, params.vcfanno_toml, + params.vep_filters, + params.vep_filters_scout_fmt, params.verifybamid_svd_bed, params.verifybamid_svd_mu, params.verifybamid_svd_ud, @@ -547,20 +566,19 @@ def channelFromPathOrValue(filePath) { return filePath ? channel.fromPath(filePath).collect() : channel.value([]) } - /** * Creates a channel from a file path, maps it to [id, file] format, and collects - * Falls back to channel.value([[:], []]) if file path is null * @param filePath The path to the file (can be null) - * @param useSimpleName Whether to use simpleName for the id (default: true) - * @return Channel with [[id:name], file] format or channel.value([[:], []]) + * @param doubleEmpty If true, returns channel.value([[:], []]) when filePath is null; otherwise returns channel.empty() (default: false) + * @return Channel with [[id:name], file] format and collected, or fallback channel */ -def channelFromPathWithIdOrDoubleEmpty(filePath) { +def channelFromPathWithMeta(filePath, doubleEmpty = false, customId = null) { if (!filePath) { - return channel.value([[:], []]) + return doubleEmpty ? channel.value([[:], []]) : channel.empty() } + def meta_id = customId ?: filePath.simplename return channel.fromPath(filePath).map { file -> - return [[id: file.simpleName], file] + return [[id: meta_id], file] }.collect() } /* From 969f77a5df36b4d6758e91301e616a337a1c90d5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 16:35:49 +0100 Subject: [PATCH 232/872] combine functions --- CHANGELOG.md | 3 +-- main.nf | 68 ++++++++++++++++++++++++---------------------------- 2 files changed, 32 insertions(+), 39 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6c3655283..2f8fb3f15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,8 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) -- A helper function channelFromPathOrValue to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) -- A helper function channelFromPathOrEmpty to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) +- A helper function channelFromPath to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) ### `Changed` diff --git a/main.nf b/main.nf index 25451199f..f939b3886 100644 --- a/main.nf +++ b/main.nf @@ -145,30 +145,30 @@ workflow NFCORE_RAREDISEASE { ch_vep_cache = ch_references.vep_resources ch_versions = ch_versions.mix(ch_references.versions) - // Using channelFromPathOrValue helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) - ch_cadd_resources = channelFromPathOrValue(val_cadd_resources) - ch_multiqc_samples = channelFromPathOrValue(val_multiqc_samples) - ch_reduced_penetrance = channelFromPathOrValue(val_reduced_penetrance) - ch_rtg_truthvcfs = channelFromPathOrValue(val_rtg_truthvcfs) - ch_score_config_mt = channelFromPathOrValue(val_score_config_mt) - ch_score_config_snv = channelFromPathOrValue(val_score_config_snv) - ch_score_config_sv = channelFromPathOrValue(val_score_config_sv) - ch_vcf2cytosure_blacklist = channelFromPathOrValue(val_vcf2cytosure_blacklist) - ch_vcfanno_lua = channelFromPathOrValue(val_vcfanno_lua) - ch_vcfanno_toml = channelFromPathOrValue(val_vcfanno_toml) + // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) + ch_cadd_resources = channelFromPath(val_cadd_resources, true) + ch_multiqc_samples = channelFromPath(val_multiqc_samples, true) + ch_reduced_penetrance = channelFromPath(val_reduced_penetrance, true) + ch_rtg_truthvcfs = channelFromPath(val_rtg_truthvcfs, true) + ch_score_config_mt = channelFromPath(val_score_config_mt, true) + ch_score_config_snv = channelFromPath(val_score_config_snv, true) + ch_score_config_sv = channelFromPath(val_score_config_sv, true) + ch_vcf2cytosure_blacklist = channelFromPath(val_vcf2cytosure_blacklist, true) + ch_vcfanno_lua = channelFromPath(val_vcfanno_lua, true) + ch_vcfanno_toml = channelFromPath(val_vcfanno_toml, true) - // Using channelFromPathOrEmpty helper (val_x ? channel.fromPath(val_x).collect() : channel.empty()) - ch_gens_gnomad_pos = channelFromPathOrEmpty(val_gens_gnomad_pos) - ch_gens_interval_list = channelFromPathOrEmpty(val_gens_interval_list) - ch_intervals_wgs = channelFromPathOrEmpty(val_intervals_wgs) - ch_intervals_y = channelFromPathOrEmpty(val_intervals_y) - ch_me_svdb_resources = channelFromPathOrEmpty(val_mobile_element_svdb_annotations) - ch_readcount_intervals = channelFromPathOrEmpty(val_readcount_intervals) - ch_svd_bed = channelFromPathOrEmpty(val_verifybamid_svd_bed) - ch_svd_mu = channelFromPathOrEmpty(val_verifybamid_svd_mu) - ch_svd_ud = channelFromPathOrEmpty(val_verifybamid_svd_ud) - ch_svdb_bedpedbs = channelFromPathOrEmpty(val_svdb_query_bedpedbs) - ch_svdb_dbs = channelFromPathOrEmpty(val_svdb_query_dbs) + // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.empty()) + ch_gens_gnomad_pos = channelFromPath(val_gens_gnomad_pos) + ch_gens_interval_list = channelFromPath(val_gens_interval_list) + ch_intervals_wgs = channelFromPath(val_intervals_wgs) + ch_intervals_y = channelFromPath(val_intervals_y) + ch_me_svdb_resources = channelFromPath(val_mobile_element_svdb_annotations) + ch_readcount_intervals = channelFromPath(val_readcount_intervals) + ch_svd_bed = channelFromPath(val_verifybamid_svd_bed) + ch_svd_mu = channelFromPath(val_verifybamid_svd_mu) + ch_svd_ud = channelFromPath(val_verifybamid_svd_ud) + ch_svdb_bedpedbs = channelFromPath(val_svdb_query_bedpedbs) + ch_svdb_dbs = channelFromPath(val_svdb_query_dbs) ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() @@ -522,23 +522,17 @@ workflow { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - /** - * Creates a channel from a file path if the parameter is provided, otherwise returns an empty channel + * Creates a channel from a file path if provided, otherwise returns a fallback channel * @param filePath The path to the file (can be null) - * @return Channel with collected file path or empty channel + * @param valueFallback If true, returns channel.value([]) when filePath is null; otherwise returns channel.empty() (default: false) + * @return Channel with collected file path or fallback channel */ -def channelFromPathOrEmpty(filePath) { - return filePath ? channel.fromPath(filePath).collect() : channel.empty() -} - -/** - * Creates a channel from a file path if the parameter is provided, otherwise returns a channel with an empty value - * @param filePath The path to the file (can be null) - * @return Channel with collected file path or channel.value([]) - */ -def channelFromPathOrValue(filePath) { - return filePath ? channel.fromPath(filePath).collect() : channel.value([]) +def channelFromPath(filePath, valueFallback = false) { + if (!filePath) { + return valueFallback ? channel.value([]) : channel.empty() + } + return channel.fromPath(filePath).collect() } /* From e20187ebf4f10760fd1c7f8bdeb629368705eb21 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 21 Jan 2026 16:58:27 +0100 Subject: [PATCH 233/872] Fix error --- main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f939b3886..5c8104004 100644 --- a/main.nf +++ b/main.nf @@ -167,8 +167,6 @@ workflow NFCORE_RAREDISEASE { ch_svd_bed = channelFromPath(val_verifybamid_svd_bed) ch_svd_mu = channelFromPath(val_verifybamid_svd_mu) ch_svd_ud = channelFromPath(val_verifybamid_svd_ud) - ch_svdb_bedpedbs = channelFromPath(val_svdb_query_bedpedbs) - ch_svdb_dbs = channelFromPath(val_svdb_query_dbs) ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_call_interval = params.call_interval ? channel.fromPath(params.call_interval).map {it -> [[id:it.simpleName], it]}.collect() @@ -197,6 +195,10 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) : channel.empty() + ch_svdb_bedpedbs = params.svdb_query_bedpedbs ? channel.fromList(samplesheetToList(params.svdb_query_bedpedbs, "assets/svdb_query_bedpe_schema.json")).collect() + : channel.empty() + ch_svdb_dbs = params.svdb_query_dbs ? channel.fromList(samplesheetToList(params.svdb_query_dbs, "assets/svdb_query_vcf_schema.json")).collect() + : channel.empty() ch_variant_catalog = params.variant_catalog ? channel.fromPath(params.variant_catalog).map { it -> [[id:it.simpleName],it]}.collect() : channel.value([[],[]]) ch_variant_consequences_snv = params.variant_consequences_snv ? channel.fromPath(params.variant_consequences_snv).map { it -> [[id:it.simpleName],it]}.collect() From 8a63885575f808240ac0ff23584a10d1e623e8ee Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 22 Jan 2026 11:20:52 +0100 Subject: [PATCH 234/872] fix svdb error --- main.nf | 2 ++ subworkflows/local/annotate_mobile_elements.nf | 13 ++++++------- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index 5c8104004..c33b74ea8 100644 --- a/main.nf +++ b/main.nf @@ -183,6 +183,8 @@ workflow NFCORE_RAREDISEASE { : channel.empty() ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) : channel.empty() + ch_me_svdb_resources = val_mobile_element_svdb_annotations ? channel.fromList(samplesheetToList(val_mobile_element_svdb_annotations, "assets/svdb_query_vcf_schema.json")).collect() + : channel.empty() ch_ml_model = params.variant_caller.equals("sentieon") ? channel.fromPath(params.ml_model).map {it -> [[id:it.simpleName], it]}.collect() : channel.value([[:],[]]) ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index f1064aa91..0a954c0a4 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -25,13 +25,12 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_svdb_dbs = channel.empty() ch_me_svdb_resources - .splitCsv ( header:true ) - .multiMap { row -> - vcf_dbs: row.filename - in_frqs: row.in_freq_info_key - in_occs: row.in_allele_count_info_key - out_frqs: row.out_freq_info_key - out_occs: row.out_allele_count_info_key + .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> + vcf_dbs: file + in_frqs: in_freq_info_key + in_occs: in_allele_count_info_key + out_frqs: out_freq_info_key + out_occs: out_allele_count_info_key } .set { ch_svdb_dbs } From 3a21dc68ba662a7aa2412330aca03ae1e0e2eec9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 22 Jan 2026 12:28:59 +0100 Subject: [PATCH 235/872] move all params to main workflow --- main.nf | 202 +++++++++++++++++++++++++++++++++++--------------------- 1 file changed, 125 insertions(+), 77 deletions(-) diff --git a/main.nf b/main.nf index b5950cb0b..ef43f35ca 100644 --- a/main.nf +++ b/main.nf @@ -47,8 +47,12 @@ workflow NFCORE_RAREDISEASE { val_bwameme val_cadd_resources val_call_interval + val_concatenate_snv_calls + val_extract_alignments val_fai val_fasta + val_gcnvcaller_model + val_genome val_gens_gnomad_pos val_gens_interval_list val_gens_pon_female @@ -59,12 +63,19 @@ workflow NFCORE_RAREDISEASE { val_intervals_y val_known_dbsnp val_known_dbsnp_tbi + val_mbuffer_mem val_ml_model + val_mobile_element_references val_mobile_element_svdb_annotations val_mt_aligner val_mt_fasta + val_mt_subsample_approach + val_mt_subsample_rd + val_mt_subsample_seed val_multiqc_samples + val_ngsbits_samplegender_method val_par_bed + val_platform val_ploidy_model val_readcount_intervals val_reduced_penetrance @@ -72,23 +83,33 @@ workflow NFCORE_RAREDISEASE { val_run_mt_for_wes val_run_rtgvcfeval val_sambamba_regions + val_sample_id_map + val_samtools_sort_threads + val_save_mapped_as_cram val_score_config_mt val_score_config_snv val_score_config_sv val_sdf + val_sentieon_dnascope_pcr_indel_model val_sequence_dictionary + val_skip_tools + val_skip_subworkflows val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed + val_variant_caller val_variant_catalog val_variant_consequences_snv val_variant_consequences_sv val_vcf2cytosure_blacklist val_vcfanno_extra_resources val_vcfanno_lua + val_vcfanno_resources val_vcfanno_toml + val_vep_cache_version val_vep_filters val_vep_filters_scout_fmt + val_vep_plugin_files val_verifybamid_svd_bed val_verifybamid_svd_mu val_verifybamid_svd_ud @@ -192,48 +213,38 @@ workflow NFCORE_RAREDISEASE { ch_gens_pon_male = channelFromPathWithMeta(val_gens_pon_male) ch_ploidy_model = channelFromPathWithMeta(val_ploidy_model) - // Using channelFromPathWithMeta helper. Returns either an empty channel or [[:],[]] with custom ID. + // Using channelFromPathWithMeta helper. Returns either an empty channel or [[:],[]] or a channel with custom ID. ch_par_bed = channelFromPathWithMeta(val_par_bed, true, "par_bed") ch_sambamba_bed = channelFromPathWithMeta(val_sambamba_regions, false, 'sambamba') ch_vep_filters_std_fmt = channelFromPathWithMeta(val_vep_filters, false, 'standard') ch_vep_filters_scout_fmt = channelFromPathWithMeta(val_vep_filters_scout_fmt, false, 'scout') + // Using channelFromSamplesheet helper. Returns either an empty channel or validated channel. + ch_me_references = channelFromSamplesheet(val_mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json", false) + ch_me_svdb_resources = channelFromSamplesheet(val_mobile_element_svdb_annotations, "${projectDir}/assets/svdb_query_vcf_schema.json") + ch_sample_id_map = channelFromSamplesheet(val_sample_id_map, "${projectDir}/assets/sample_id_map.json") + ch_svdb_bedpedbs = channelFromSamplesheet(val_svdb_query_bedpedbs, "${projectDir}/assets/svdb_query_bedpe_schema.json") + ch_svdb_dbs = channelFromSamplesheet(val_svdb_query_dbs, "${projectDir}/assets/svdb_query_vcf_schema.json") + ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() - ch_gcnvcaller_model = params.gcnvcaller_model ? channel.fromPath(params.gcnvcaller_model).splitCsv ( header:true ) - .map { row -> - return [[id:file(row.models).simpleName], row.models] - } - : channel.empty() - ch_me_references = params.mobile_element_references ? channel.fromList(samplesheetToList(params.mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json")) - : channel.empty() - ch_me_svdb_resources = val_mobile_element_svdb_annotations ? channel.fromList(samplesheetToList(val_mobile_element_svdb_annotations, "assets/svdb_query_vcf_schema.json")).collect() - : channel.empty() - ch_ngsbits_method = channel.value(params.ngsbits_samplegender_method) - ch_par_bed = params.par_bed ? channel.fromPath(params.par_bed).map{ it -> [[id:'par_bed'], it] }.collect() - : channel.value([[],[]]) - ch_sentieon_pcr_indel_model = channel.value(params.sentieon_dnascope_pcr_indel_model) - ch_sambamba_bed = params.sambamba_regions ? channel.fromPath(params.sambamba_regions).map{ it -> [[id:'sambamba'], it] }.collect() - : channel.empty() - ch_sample_id_map = params.sample_id_map ? channel.fromList(samplesheetToList(params.sample_id_map, "${projectDir}/assets/sample_id_map.json")) - : channel.empty() - ch_svdb_bedpedbs = params.svdb_query_bedpedbs ? channel.fromList(samplesheetToList(params.svdb_query_bedpedbs, "assets/svdb_query_bedpe_schema.json")).collect() - : channel.empty() - ch_svdb_dbs = params.svdb_query_dbs ? channel.fromList(samplesheetToList(params.svdb_query_dbs, "assets/svdb_query_vcf_schema.json")).collect() - : channel.empty() - ch_vcfanno_resources = params.vcfanno_resources ? channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect() - : channel.value([]) - ch_vep_filters_std_fmt = params.vep_filters ? channel.fromPath(params.vep_filters).map { it -> [[id:'standard'],it]}.collect() - : channel.empty() - ch_vep_filters_scout_fmt = params.vep_filters_scout_fmt ? channel.fromPath(params.vep_filters_scout_fmt).map { it -> [[id:'scout'],it]}.collect() - : channel.empty() + ch_ngsbits_method = channel.value(val_ngsbits_samplegender_method) + ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model) + ch_vcfanno_resources = val_vcfanno_resources ? channel.fromPath(val_vcfanno_resources).splitText().map{it -> it.trim()}.collect() + : channel.value([]) + ch_gcnvcaller_model = val_gcnvcaller_model ? channel.fromPath(val_gcnvcaller_model) + .splitCsv ( header:true ) + .map { row -> + return [[id:file(row.models).simpleName], row.models] + } + : channel.empty() // // Read and store paths in the vep_plugin_files file // ch_vep_extra_files = channel.empty() - if (params.vep_plugin_files) { - channel.fromPath(params.vep_plugin_files) + if (val_vep_plugin_files) { + channel.fromPath(val_vep_plugin_files) .collect() .splitCsv ( header:true ) .map { row -> @@ -266,42 +277,42 @@ workflow NFCORE_RAREDISEASE { ch_versions = ch_versions.mix(CREATE_PEDIGREE_FILE.out.versions) // Tools - skip_eklipse = parseSkipList(params.skip_tools, 'eklipse') - skip_fastp = parseSkipList(params.skip_tools, 'fastp') - skip_fastqc = parseSkipList(params.skip_tools, 'fastqc') - skip_gens = parseSkipList(params.skip_tools, 'gens') - skip_germlinecnvcaller = parseSkipList(params.skip_tools, 'germlinecnvcaller') - skip_haplogrep3 = parseSkipList(params.skip_tools, 'haplogrep3') - skip_ngsbits = parseSkipList(params.skip_tools, 'ngsbits') - skip_peddy = parseSkipList(params.skip_tools, 'peddy') - skip_qualimap = parseSkipList(params.skip_tools, 'qualimap') - skip_smncopynumbercaller = parseSkipList(params.skip_tools, 'smncopynumbercaller') - skip_vcf2cytosure = parseSkipList(params.skip_tools, 'vcf2cytosure') + skip_eklipse = parseSkipList(val_skip_tools, 'eklipse') + skip_fastp = parseSkipList(val_skip_tools, 'fastp') + skip_fastqc = parseSkipList(val_skip_tools, 'fastqc') + skip_gens = parseSkipList(val_skip_tools, 'gens') + skip_germlinecnvcaller = parseSkipList(val_skip_tools, 'germlinecnvcaller') + skip_haplogrep3 = parseSkipList(val_skip_tools, 'haplogrep3') + skip_ngsbits = parseSkipList(val_skip_tools, 'ngsbits') + skip_peddy = parseSkipList(val_skip_tools, 'peddy') + skip_qualimap = parseSkipList(val_skip_tools, 'qualimap') + skip_smncopynumbercaller = parseSkipList(val_skip_tools, 'smncopynumbercaller') + skip_vcf2cytosure = parseSkipList(val_skip_tools, 'vcf2cytosure') // Subworkflows - skip_me_annotation = parseSkipList(params.skip_subworkflows, 'me_annotation') - skip_me_calling = parseSkipList(params.skip_subworkflows, 'me_calling') - skip_mt_annotation = parseSkipList(params.skip_subworkflows, 'mt_annotation') - skip_mt_subsample = parseSkipList(params.skip_subworkflows, 'mt_subsample') - skip_repeat_annotation = parseSkipList(params.skip_subworkflows, 'repeat_annotation') - skip_repeat_calling = parseSkipList(params.skip_subworkflows, 'repeat_calling') - skip_snv_annotation = parseSkipList(params.skip_subworkflows, 'snv_annotation') - skip_snv_calling = parseSkipList(params.skip_subworkflows, 'snv_calling') - skip_sv_annotation = parseSkipList(params.skip_subworkflows, 'sv_annotation') - skip_sv_calling = parseSkipList(params.skip_subworkflows, 'sv_calling') - skip_generate_clinical_set = parseSkipList(params.skip_subworkflows, 'generate_clinical_set') + skip_me_annotation = parseSkipList(val_skip_subworkflows, 'me_annotation') + skip_me_calling = parseSkipList(val_skip_subworkflows, 'me_calling') + skip_mt_annotation = parseSkipList(val_skip_subworkflows, 'mt_annotation') + skip_mt_subsample = parseSkipList(val_skip_subworkflows, 'mt_subsample') + skip_repeat_annotation = parseSkipList(val_skip_subworkflows, 'repeat_annotation') + skip_repeat_calling = parseSkipList(val_skip_subworkflows, 'repeat_calling') + skip_snv_annotation = parseSkipList(val_skip_subworkflows, 'snv_annotation') + skip_snv_calling = parseSkipList(val_skip_subworkflows, 'snv_calling') + skip_sv_annotation = parseSkipList(val_skip_subworkflows, 'sv_annotation') + skip_sv_calling = parseSkipList(val_skip_subworkflows, 'sv_calling') + skip_generate_clinical_set = parseSkipList(val_skip_subworkflows, 'generate_clinical_set') // // SV caller priority // if (skip_germlinecnvcaller) { - if (params.analysis_type.equals("wgs")) { + if (val_analysis_type.equals("wgs")) { ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) } else { ch_svcaller_priority = channel.value([]) } } else { - if (params.analysis_type.equals("wgs")) { + if (val_analysis_type.equals("wgs")) { ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) } else { ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) @@ -422,28 +433,28 @@ workflow NFCORE_RAREDISEASE { skip_qualimap, skip_smncopynumbercaller, skip_vcf2cytosure, - params.aligner, - params.analysis_type, - params.cadd_resources, - params.concatenate_snv_calls, - params.extract_alignments, - params.genome, - params.mbuffer_mem, - params.mt_aligner, - params.mt_subsample_approach, - params.mt_subsample_rd, - params.mt_subsample_seed, - params.platform, - params.run_mt_for_wes, - params.run_rtgvcfeval, - params.sample_id_map, - params.samtools_sort_threads, - params.save_mapped_as_cram, - params.svdb_query_bedpedbs, - params.svdb_query_dbs, - params.target_bed, - params.variant_caller, - params.vep_cache_version + val_aligner, + val_analysis_type, + val_cadd_resources, + val_concatenate_snv_calls, + val_extract_alignments, + val_genome, + val_mbuffer_mem, + val_mt_aligner, + val_mt_subsample_approach, + val_mt_subsample_rd, + val_mt_subsample_seed, + val_platform, + val_run_mt_for_wes, + val_run_rtgvcfeval, + val_sample_id_map, + val_samtools_sort_threads, + val_save_mapped_as_cram, + val_svdb_query_bedpedbs, + val_svdb_query_dbs, + val_target_bed, + val_variant_caller, + val_vep_cache_version ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html @@ -485,8 +496,12 @@ workflow { params.bwameme, params.cadd_resources, params.call_interval, + params.concatenate_snv_calls, + params.extract_alignments, params.fai, params.fasta, + params.gcnvcaller_model, + params.genome, params.gens_gnomad_pos, params.gens_interval_list, params.gens_pon_female, @@ -497,12 +512,19 @@ workflow { params.intervals_y, params.known_dbsnp, params.known_dbsnp_tbi, + params.mbuffer_mem, params.ml_model, + params.mobile_element_references, params.mobile_element_svdb_annotations, params.mt_aligner, params.mt_fasta, + params.mt_subsample_approach, + params.mt_subsample_rd, + params.mt_subsample_seed, params.multiqc_samples, + params.ngsbits_samplegender_method, params.par_bed, + params.platform, params.ploidy_model, params.readcount_intervals, params.reduced_penetrance, @@ -510,23 +532,33 @@ workflow { params.run_mt_for_wes, params.run_rtgvcfeval, params.sambamba_regions, + params.sample_id_map, + params.samtools_sort_threads, + params.save_mapped_as_cram, params.score_config_mt, params.score_config_snv, params.score_config_sv, params.sdf, + params.sentieon_dnascope_pcr_indel_model, params.sequence_dictionary, + params.skip_tools, + params.skip_subworkflows, params.svdb_query_bedpedbs, params.svdb_query_dbs, params.target_bed, + params.variant_caller, params.variant_catalog, params.variant_consequences_snv, params.variant_consequences_sv, params.vcf2cytosure_blacklist, params.vcfanno_extra_resources, params.vcfanno_lua, + params.vcfanno_resources, params.vcfanno_toml, + params.vep_cache_version, params.vep_filters, params.vep_filters_scout_fmt, + params.vep_plugin_files, params.verifybamid_svd_bed, params.verifybamid_svd_mu, params.verifybamid_svd_ud, @@ -569,17 +601,33 @@ def channelFromPath(filePath, valueFallback = false) { * Creates a channel from a file path, maps it to [id, file] format, and collects * @param filePath The path to the file (can be null) * @param doubleEmpty If true, returns channel.value([[:], []]) when filePath is null; otherwise returns channel.empty() (default: false) + * @param customId The custom ID to be used in meta.id (default: null) * @return Channel with [[id:name], file] format and collected, or fallback channel */ def channelFromPathWithMeta(filePath, doubleEmpty = false, customId = null) { if (!filePath) { return doubleEmpty ? channel.value([[:], []]) : channel.empty() } - def meta_id = customId ?: filePath.simplename return channel.fromPath(filePath).map { file -> + def meta_id = customId ?: file.simpleName return [[id: meta_id], file] }.collect() } + +/** + * Creates a channel from a samplesheet file using samplesheetToList, or returns a fallback channel + * @param samplesheetPath The path to the samplesheet file (can be null) + * @param schemaPath The path to the JSON schema file for validation + * @param collect If true, calls .collect() on the channel (default: true) + * @return Channel from samplesheet list or channel.empty() + */ +def channelFromSamplesheet(samplesheetPath, schemaPath, collect = true) { + if (!samplesheetPath) { + return channel.empty() + } + def ch_out = channel.fromList(samplesheetToList(samplesheetPath, schemaPath)) + return collect ? ch_out.collect() : ch_out +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END From db36ff4403823de8305c580fe26ad101205283e3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 22 Jan 2026 13:53:40 +0100 Subject: [PATCH 236/872] add changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b9d31b68..3c5697d6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter to pass a file containing new sample ids to use with multiqc [#764](https://github.com/nf-core/raredisease/pull/764) - A helper function channelFromPath to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) +- A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) ### `Changed` From 38b79b6c46326efabc15b4fc0e4012ebe8a36201 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 22 Jan 2026 15:57:27 +0100 Subject: [PATCH 237/872] move functions to utils --- main.nf | 53 ++----------------- .../utils_nfcore_raredisease_pipeline/main.nf | 46 ++++++++++++++++ 2 files changed, 49 insertions(+), 50 deletions(-) diff --git a/main.nf b/main.nf index ef43f35ca..f50f626f0 100644 --- a/main.nf +++ b/main.nf @@ -17,6 +17,9 @@ include { samplesheetToList } from 'plugin/nf-schema' include { CREATE_HGNCIDS_FILE } from './modules/local/create_hgncids_file' include { CREATE_PEDIGREE_FILE } from './modules/local/create_pedigree_file' +include { channelFromPath } from './subworkflows/local/utils_nfcore_raredisease_pipeline' +include { channelFromPathWithMeta } from './subworkflows/local/utils_nfcore_raredisease_pipeline' +include { channelFromSamplesheet } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { parseSkipList } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_raredisease_pipeline' @@ -578,56 +581,6 @@ workflow { ) } -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - HELPER FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -/** - * Creates a channel from a file path if provided, otherwise returns a fallback channel - * @param filePath The path to the file (can be null) - * @param valueFallback If true, returns channel.value([]) when filePath is null; otherwise returns channel.empty() (default: false) - * @return Channel with collected file path or fallback channel - */ -def channelFromPath(filePath, valueFallback = false) { - if (!filePath) { - return valueFallback ? channel.value([]) : channel.empty() - } - return channel.fromPath(filePath).collect() -} - -/** - * Creates a channel from a file path, maps it to [id, file] format, and collects - * @param filePath The path to the file (can be null) - * @param doubleEmpty If true, returns channel.value([[:], []]) when filePath is null; otherwise returns channel.empty() (default: false) - * @param customId The custom ID to be used in meta.id (default: null) - * @return Channel with [[id:name], file] format and collected, or fallback channel - */ -def channelFromPathWithMeta(filePath, doubleEmpty = false, customId = null) { - if (!filePath) { - return doubleEmpty ? channel.value([[:], []]) : channel.empty() - } - return channel.fromPath(filePath).map { file -> - def meta_id = customId ?: file.simpleName - return [[id: meta_id], file] - }.collect() -} - -/** - * Creates a channel from a samplesheet file using samplesheetToList, or returns a fallback channel - * @param samplesheetPath The path to the samplesheet file (can be null) - * @param schemaPath The path to the JSON schema file for validation - * @param collect If true, calls .collect() on the channel (default: true) - * @return Channel from samplesheet list or channel.empty() - */ -def channelFromSamplesheet(samplesheetPath, schemaPath, collect = true) { - if (!samplesheetPath) { - return channel.empty() - } - def ch_out = channel.fromList(samplesheetToList(samplesheetPath, schemaPath)) - return collect ? ch_out.collect() : ch_out -} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index e711d5c55..a933ee921 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -217,6 +217,52 @@ workflow PIPELINE_COMPLETION { FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ + +/** + * Creates a channel from a file path if provided, otherwise returns a fallback channel + * @param filePath The path to the file (can be null) + * @param valueFallback If true, returns channel.value([]) when filePath is null; otherwise returns channel.empty() (default: false) + * @return Channel with collected file path or fallback channel + */ +def channelFromPath(filePath, valueFallback = false) { + if (!filePath) { + return valueFallback ? channel.value([]) : channel.empty() + } + return channel.fromPath(filePath).collect() +} + +/** + * Creates a channel from a file path, maps it to [id, file] format, and collects + * @param filePath The path to the file (can be null) + * @param doubleEmpty If true, returns channel.value([[:], []]) when filePath is null; otherwise returns channel.empty() (default: false) + * @param customId The custom ID to be used in meta.id (default: null) + * @return Channel with [[id:name], file] format and collected, or fallback channel + */ +def channelFromPathWithMeta(filePath, doubleEmpty = false, customId = null) { + if (!filePath) { + return doubleEmpty ? channel.value([[:], []]) : channel.empty() + } + return channel.fromPath(filePath).map { file -> + def meta_id = customId ?: file.simpleName + return [[id: meta_id], file] + }.collect() +} + +/** + * Creates a channel from a samplesheet file using samplesheetToList, or returns a fallback channel + * @param samplesheetPath The path to the samplesheet file (can be null) + * @param schemaPath The path to the JSON schema file for validation + * @param collect If true, calls .collect() on the channel (default: true) + * @return Channel from samplesheet list or channel.empty() + */ +def channelFromSamplesheet(samplesheetPath, schemaPath, collect = true) { + if (!samplesheetPath) { + return channel.empty() + } + def ch_out = channel.fromList(samplesheetToList(samplesheetPath, schemaPath)) + return collect ? ch_out.collect() : ch_out +} + def generateReadGroupLine(file, meta, params) { return "\'@RG\\tID:" + file.simpleName + "_" + meta.lane + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'" } From e3888fa118f28a5c4c81adfaea0c8fb51b0d08f9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 22 Jan 2026 16:24:06 +0100 Subject: [PATCH 238/872] remove first in versions --- subworkflows/local/align_MT/main.nf | 14 ++++++------- .../local/align_bwa_bwamem2_bwameme/main.nf | 20 +++++++++---------- subworkflows/local/align_sentieon/main.nf | 10 +++++----- subworkflows/local/annotate_cadd/main.nf | 12 +++++------ subworkflows/local/annotate_genome_snvs.nf | 6 +++--- .../local/annotate_rhocallviz/main.nf | 14 ++++++------- subworkflows/local/call_mobile_elements.nf | 14 ++++++------- .../local/call_repeat_expansions/main.nf | 14 ++++++------- subworkflows/local/call_snv_MT/main.nf | 6 +++--- .../local/call_snv_deepvariant/main.nf | 2 +- subworkflows/local/call_snv_sentieon/main.nf | 16 +++++++-------- subworkflows/local/call_sv_MT/main.nf | 4 ++-- subworkflows/local/call_sv_tiddit/main.nf | 2 +- .../local/convert_mt_bam_to_fastq/main.nf | 6 +++--- subworkflows/local/generate_cytosure_files.nf | 8 ++++---- subworkflows/local/gens.nf | 12 +++++------ .../local/postprocess_MT_calls/main.nf | 10 +++++----- subworkflows/local/qc_bam/main.nf | 2 +- subworkflows/local/subsample_mt_frac/main.nf | 6 +++--- workflows/raredisease.nf | 10 +++++----- 20 files changed, 94 insertions(+), 94 deletions(-) diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 334c75f0f..e630b5458 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -27,15 +27,15 @@ workflow ALIGN_MT { if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) ch_align = BWAMEM2_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions.first()) + ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions) } else if (val_mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } - ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions.first()) + ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions) } else if (val_mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) ch_align = BWA_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions.first()) + ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions) } ch_align .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true) @@ -49,10 +49,10 @@ workflow ALIGN_MT { SAMTOOLS_SORT_MT (PICARD_MARKDUPLICATES_MT.out.bam, [[:],[]], 'bai') - ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions.first()) - ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions.first()) - ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions) + ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions) + ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions) emit: marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 9d2d0cd99..ae8440ea2 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -35,15 +35,15 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { if (val_aligner.equals("bwa")) { BWA ( ch_input_reads, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam - ch_versions = ch_versions.mix(BWA.out.versions.first()) + ch_versions = ch_versions.mix(BWA.out.versions) } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions.first()) + ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions) } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions.first()) + ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions) } SAMTOOLS_INDEX_ALIGN ( ch_align ) @@ -76,19 +76,19 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam - ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions.first()) + ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions) } // Marking duplicates MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions.first()) - ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions.first()) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) + ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) emit: marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 92f85563a..5755bde96 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -43,17 +43,17 @@ workflow ALIGN_SENTIEON { if (val_extract_alignments) { EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) - ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions.first()) + ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions) } SENTIEON_DATAMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, false ) SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai ) - ch_versions = ch_versions.mix(SENTIEON_BWAMEM.out.versions.first()) - ch_versions = ch_versions.mix(SENTIEON_DATAMETRICS.out.versions.first()) - ch_versions = ch_versions.mix(SENTIEON_READWRITER.out.versions.first()) - ch_versions = ch_versions.mix(SENTIEON_DEDUP.out.versions.first()) + ch_versions = ch_versions.mix(SENTIEON_BWAMEM.out.versions) + ch_versions = ch_versions.mix(SENTIEON_DATAMETRICS.out.versions) + ch_versions = ch_versions.mix(SENTIEON_READWRITER.out.versions) + ch_versions = ch_versions.mix(SENTIEON_DEDUP.out.versions) emit: marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index f32e36613..7d7884dcd 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -73,12 +73,12 @@ workflow ANNOTATE_CADD { TABIX_ANNOTATE (BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_VIEW.out.versions.first()) - ch_versions = ch_versions.mix(CADD.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_CADD.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions.first()) + ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) + ch_versions = ch_versions.mix(TABIX_VIEW.out.versions) + ch_versions = ch_versions.mix(CADD.out.versions) + ch_versions = ch_versions.mix(TABIX_CADD.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) + ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 4bc6cc3d6..2b690d6d5 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -206,9 +206,9 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) - ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions.first()) - ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_VEP.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) + ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions) + ch_versions = ch_versions.mix(TABIX_VEP.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(TABIX_BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 8596d5fb0..76b45844f 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -54,13 +54,13 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_RHOCALL.out.versions.first()) - ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_UNCOMPRESS.out.versions.first()) - ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions.first()) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions.first()) + ch_versions = ch_versions.mix(BCFTOOLS_VIEW_RHOCALL.out.versions) + ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions) + ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_VIEW_UNCOMPRESS.out.versions) + ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) + ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 2f5fc695b..11c8df587 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -121,13 +121,13 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) - ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions.first()) - ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions.first()) - ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_ME.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_SORT_ME.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_ME.out.versions.first()) + ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions) + ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) + ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_ME.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_SORT_ME.out.versions) + ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_ME.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME.out.versions) diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index a4f1b92fd..d9347d20e 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -58,13 +58,13 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) - ch_versions = ch_versions.mix(EXPANSIONHUNTER.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_EXP.out.versions.first()) - ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions.first() ) - ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions.first()) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_EXP.out.versions.first()) - ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) + ch_versions = ch_versions.mix(EXPANSIONHUNTER.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_EXP.out.versions) + ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) + ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions) + ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_EXP.out.versions) + ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index be84e6538..4456f3585 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -22,7 +22,7 @@ workflow CALL_SNV_MT { GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai, ch_dict, [], [], [],[]) HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf) - ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions.first()) + ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions) // Filter Mutect2 calls ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) @@ -34,8 +34,8 @@ workflow CALL_SNV_MT { GATK4_FILTERMUTECTCALLS_MT (ch_to_filt, ch_fasta, ch_fai, ch_dict) - ch_versions = ch_versions.mix(GATK4_MUTECT2_MT.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_FILTERMUTECTCALLS_MT.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_MUTECT2_MT.out.versions) + ch_versions = ch_versions.mix(GATK4_FILTERMUTECTCALLS_MT.out.versions) emit: filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 896cb78e9..f5e7e3695 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -83,7 +83,7 @@ workflow CALL_SNV_DEEPVARIANT { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(DEEPVARIANT.out.versions.first()) + ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) ch_versions = ch_versions.mix(GLNEXUS.out.versions) ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_GL.out.versions) ch_versions = ch_versions.mix(REMOVE_DUPLICATES_GL.out.versions) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index c8f1afa23..e7feb8be5 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -108,14 +108,14 @@ workflow CALL_SNV_SENTIEON { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(SENTIEON_DNASCOPE.out.versions.first()) - ch_versions = ch_versions.mix(SENTIEON_DNAMODELAPPLY.out.versions.first()) - ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions.first()) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_SEN.out.versions.first()) - ch_versions = ch_versions.mix(REMOVE_DUPLICATES_SEN.out.versions.first()) - ch_versions = ch_versions.mix(TABIX_SEN.out.versions.first()) - ch_versions = ch_versions.mix(BCF_FILTER_ONE.out.versions.first()) - ch_versions = ch_versions.mix(BCF_FILTER_TWO.out.versions.first()) + ch_versions = ch_versions.mix(SENTIEON_DNASCOPE.out.versions) + ch_versions = ch_versions.mix(SENTIEON_DNAMODELAPPLY.out.versions) + ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions) + ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_SEN.out.versions) + ch_versions = ch_versions.mix(REMOVE_DUPLICATES_SEN.out.versions) + ch_versions = ch_versions.mix(TABIX_SEN.out.versions) + ch_versions = ch_versions.mix(BCF_FILTER_ONE.out.versions) + ch_versions = ch_versions.mix(BCF_FILTER_TWO.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 3fa283cea..8fa2d9c52 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -22,11 +22,11 @@ workflow CALL_SV_MT { ch_eklipse_del = EKLIPSE.out.deletions ch_eklipse_genes = EKLIPSE.out.genes ch_eklipse_circos = EKLIPSE.out.circos - ch_versions = ch_versions.mix(EKLIPSE.out.versions.first()) + ch_versions = ch_versions.mix(EKLIPSE.out.versions) } MT_DELETION(ch_bam_bai, ch_fasta) - ch_versions = ch_versions.mix(MT_DELETION.out.versions.first()) + ch_versions = ch_versions.mix(MT_DELETION.out.versions) emit: eklipse_del = ch_eklipse_del // channel: [ val(meta), path(csv) ] diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index 8e58b5ba8..93b80940a 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -29,7 +29,7 @@ workflow CALL_SV_TIDDIT { SVDB_MERGE_TIDDIT ( merge_input_vcfs, [], true ) - ch_versions = TIDDIT_SV.out.versions.first() + ch_versions = TIDDIT_SV.out.versions ch_versions = ch_versions.mix(SVDB_MERGE_TIDDIT.out.versions) ch_versions = ch_versions.mix(INDEX_TIDDIT.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_VIEW_TIDDIT.out.versions) diff --git a/subworkflows/local/convert_mt_bam_to_fastq/main.nf b/subworkflows/local/convert_mt_bam_to_fastq/main.nf index 90167ea82..160e3837a 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/main.nf +++ b/subworkflows/local/convert_mt_bam_to_fastq/main.nf @@ -28,9 +28,9 @@ workflow CONVERT_MT_BAM_TO_FASTQ { // Outputs fastq files GATK4_SAMTOFASTQ_MT ( GATK4_REVERTSAM_MT.out.bam ) - ch_versions = ch_versions.mix(GATK4_PRINTREADS_MT.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_REVERTSAM_MT.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_SAMTOFASTQ_MT.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_PRINTREADS_MT.out.versions) + ch_versions = ch_versions.mix(GATK4_REVERTSAM_MT.out.versions) + ch_versions = ch_versions.mix(GATK4_SAMTOFASTQ_MT.out.versions) emit: bam_bai = ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index d61ca8d27..cb73c3632 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -58,7 +58,7 @@ workflow GENERATE_CYTOSURE_FILES { BCFTOOLS_REHEADER_SV_VCF ( ch_reheader_in, [[:],[]] ).vcf .set {ch_reheader_out} - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_SV_VCF.out.versions.first()) + ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_SV_VCF.out.versions) } SPLIT_AND_FILTER_SV_VCF.out.vcf @@ -89,9 +89,9 @@ workflow GENERATE_CYTOSURE_FILES { ch_blacklist ) - ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions.first()) - ch_versions = ch_versions.mix(SPLIT_AND_FILTER_SV_VCF.out.versions.first()) - ch_versions = ch_versions.mix(VCF2CYTOSURE.out.versions.first()) + ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) + ch_versions = ch_versions.mix(SPLIT_AND_FILTER_SV_VCF.out.versions) + ch_versions = ch_versions.mix(VCF2CYTOSURE.out.versions) emit: versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index 08e302b63..68b8ba99b 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -65,12 +65,12 @@ workflow GENS { GENS_GENERATE_COV_INDEX (GENS_GENERATE.out.cov) - ch_versions = ch_versions.mix(COLLECTREADCOUNTS.out.versions.first()) - ch_versions = ch_versions.mix(DENOISEREADCOUNTS_FEMALE.out.versions.first()) - ch_versions = ch_versions.mix(DENOISEREADCOUNTS_MALE.out.versions.first()) - ch_versions = ch_versions.mix(GENS_GENERATE.out.versions.first()) - ch_versions = ch_versions.mix(GENS_GENERATE_BAF_INDEX.out.versions.first()) - ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions.first()) + ch_versions = ch_versions.mix(COLLECTREADCOUNTS.out.versions) + ch_versions = ch_versions.mix(DENOISEREADCOUNTS_FEMALE.out.versions) + ch_versions = ch_versions.mix(DENOISEREADCOUNTS_MALE.out.versions) + ch_versions = ch_versions.mix(GENS_GENERATE.out.versions) + ch_versions = ch_versions.mix(GENS_GENERATE_BAF_INDEX.out.versions) + ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions) emit: gens_baf_bed_gz = GENS_GENERATE.out.baf // channel: [ val(meta), path(bed) ] diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 1612e9439..859408aba 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -121,11 +121,11 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(PICARD_LIFTOVERVCF.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions.first()) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_MT.out.versions.first()) - ch_versions = ch_versions.mix(REMOVE_DUPLICATES_MT.out.versions.first()) + ch_versions = ch_versions.mix(PICARD_LIFTOVERVCF.out.versions) + ch_versions = ch_versions.mix(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.versions) + ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) + ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_MT.out.versions) + ch_versions = ch_versions.mix(REMOVE_DUPLICATES_MT.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_MERGE_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index bc0373405..3405c19ab 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -108,7 +108,7 @@ workflow QC_BAM { ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) ch_versions = ch_versions.mix(MOSDEPTH.out.versions) ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) - ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions.first()) + ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions) emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 3c8d16f46..67ef02e2d 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -34,9 +34,9 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') - ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first()) - ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions.first()) + ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) + ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 325dd91ed..5dd4d9609 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -216,14 +216,14 @@ workflow RAREDISEASE { // Just one fastq.gz.spring-file with both R1 and R2 ch_one_fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(ch_input_by_sample_type.interleaved_spring, false).fastq - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_FQ_PAIR.out.versions.first()) + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_FQ_PAIR.out.versions) // Two fastq.gz.spring-files - one for R1 and one for R2 ch_r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[0] ]}, true).fastq ch_r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[1] ]}, true).fastq ch_two_fastq_gz_from_spring = ch_r1_fastq_gz_from_spring.join(ch_r2_fastq_gz_from_spring).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]} - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R1_FQ.out.versions.first()) - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R2_FQ.out.versions.first()) + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R1_FQ.out.versions) + ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R2_FQ.out.versions) ch_input_fastqs = ch_input_by_sample_type.fastq_gz.mix(ch_one_fastq_gz_pair_from_spring).mix(ch_two_fastq_gz_from_spring) @@ -234,7 +234,7 @@ workflow RAREDISEASE { if (!skip_fastqc) { FASTQC (ch_input_fastqs) fastqc_report = FASTQC.out.zip - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + ch_versions = ch_versions.mix(FASTQC.out.versions) } /* @@ -743,7 +743,7 @@ workflow RAREDISEASE { CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), ch_pedfile ) - ch_versions = ch_versions.mix(PEDDY.out.versions.first()) + ch_versions = ch_versions.mix(PEDDY.out.versions) } /* From d4fd6aeacd22e60ba4876a8dc9ed3a88e691b4ed Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 Jan 2026 10:48:57 +0100 Subject: [PATCH 239/872] add changes from gms repo --- CHANGELOG.md | 13 +- conf/modules/qc_bam.config | 2 +- .../vcf_filter_bcftools_ensemblvep.config | 9 +- main.nf | 3 + modules.json | 5 + .../bcftools/pluginsetgt/environment.yml | 10 + modules/nf-core/bcftools/pluginsetgt/main.nf | 80 ++++ modules/nf-core/bcftools/pluginsetgt/meta.yml | 133 ++++++ .../bcftools/pluginsetgt/tests/main.nf.test | 298 +++++++++++++ .../pluginsetgt/tests/main.nf.test.snap | 393 ++++++++++++++++++ .../pluginsetgt/tests/nextflow.config | 4 + .../pluginsetgt/tests/vcf_gz_index.config | 5 + .../pluginsetgt/tests/vcf_gz_index_csi.config | 5 + .../pluginsetgt/tests/vcf_gz_index_tbi.config | 5 + nextflow.config | 1 + nextflow_schema.json | 6 + .../vcf_filter_bcftools_ensemblvep/main.nf | 23 +- workflows/raredisease.nf | 15 +- 18 files changed, 992 insertions(+), 18 deletions(-) create mode 100644 modules/nf-core/bcftools/pluginsetgt/environment.yml create mode 100644 modules/nf-core/bcftools/pluginsetgt/main.nf create mode 100644 modules/nf-core/bcftools/pluginsetgt/meta.yml create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c5697d6a..f98eb2f48 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPath to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) +- A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1(homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) ### `Changed` @@ -25,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Call SVs in mitochondria using mitochondrial alignments in the genome alignment files instead of from BAM files generated by the mitochondrial subworkflow. [#742](https://github.com/nf-core/raredisease/pull/742) - Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747) - Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763) +- Sambamba depth now filters on not duplicates and not failed_quality_control [#768](https://github.com/nf-core/raredisease/pull/768) ### `Fixed` @@ -36,11 +38,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| --------------- | ---------------- | -| | sambamba_regions | -| bwa_as_fallback | | -| | multiqc_samples | +| Old parameter | New parameter | +| --------------- | ----------------------- | +| | sambamba_regions | +| bwa_as_fallback | | +| | multiqc_samples | +| | homoplasmy_af_threshold | ### Tool updates diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 08653e936..7415c274d 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -89,7 +89,7 @@ process { "--cov-threshold 50", "--cov-threshold 100", "--min-base-quality 10", - "--filter 'mapping_quality >= 10'", + "--filter 'mapping_quality >= 10 and not duplicate and not failed_quality_control'", ].join(' ') } } diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_ensemblvep.config index c152b5836..69867e0c2 100644 --- a/conf/modules/vcf_filter_bcftools_ensemblvep.config +++ b/conf/modules/vcf_filter_bcftools_ensemblvep.config @@ -46,12 +46,15 @@ process { process { withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW' { ext.prefix = { "${meta.id}_mt_${meta.set}" } - ext.args = { "-Oz -i 'AF>0.05'" } + ext.args = { "-Oz -i 'AF>0.05' --write-index=tbi" } } - withName: '.*:GENERATE_CLINICAL_SET_MT:TABIX_BGZIPTABIX' { - ext.prefix = { "${meta.id}_mt_${meta.set}" } + withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_PLUGINSETGT' { + ext.prefix = { "${meta.id}_mt_${meta.set}_modifiedgt" } + ext.args = "--output-type z --write-index=tbi" + ext.args2 = "-i 'FMT/AF>=0.95 && FMT/DP>=100'" } + } // ME variants diff --git a/main.nf b/main.nf index f50f626f0..bd5b3d73b 100644 --- a/main.nf +++ b/main.nf @@ -62,6 +62,7 @@ workflow NFCORE_RAREDISEASE { val_gens_pon_male val_gnomad_af val_gnomad_af_idx + val_homoplasmy_af_threshold val_intervals_wgs val_intervals_y val_known_dbsnp @@ -442,6 +443,7 @@ workflow NFCORE_RAREDISEASE { val_concatenate_snv_calls, val_extract_alignments, val_genome, + val_homoplasmy_af_threshold, val_mbuffer_mem, val_mt_aligner, val_mt_subsample_approach, @@ -511,6 +513,7 @@ workflow { params.gens_pon_male, params.gnomad_af, params.gnomad_af_idx, + params.homoplasmy_af_threshold, params.intervals_wgs, params.intervals_y, params.known_dbsnp, diff --git a/modules.json b/modules.json index 56535bc9b..2e683df77 100644 --- a/modules.json +++ b/modules.json @@ -30,6 +30,11 @@ "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, + "bcftools/pluginsetgt": { + "branch": "master", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "installed_by": ["modules"] + }, "bcftools/reheader": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", diff --git a/modules/nf-core/bcftools/pluginsetgt/environment.yml b/modules/nf-core/bcftools/pluginsetgt/environment.yml new file mode 100644 index 000000000..ba863b388 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/pluginsetgt/main.nf b/modules/nf-core/bcftools/pluginsetgt/main.nf new file mode 100644 index 000000000..5516d7375 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/main.nf @@ -0,0 +1,80 @@ +process BCFTOOLS_PLUGINSETGT { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" + + input: + tuple val(meta), path(vcf), path(index) + val target_gt + val new_gt + path regions + path targets + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def regions_file = regions ? "--regions-file ${regions}" : "" + def targets_file = targets ? "--targets-file ${targets}" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + """ + bcftools plugin setGT \\ + --output ${prefix}.${extension} \\ + ${regions_file} \\ + ${targets_file} \\ + ${args} \\ + --threads ${task.cpus} \\ + ${vcf} \\ + -- \\ + --target-gt ${target_gt} \\ + --new-gt ${new_gt} \\ + ${args2} + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def stub_index = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && stub_index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${stub_index}" : "" + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + """ +} diff --git a/modules/nf-core/bcftools/pluginsetgt/meta.yml b/modules/nf-core/bcftools/pluginsetgt/meta.yml new file mode 100644 index 000000000..51233bc83 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/meta.yml @@ -0,0 +1,133 @@ +name: "bcftools_pluginsetgt" +description: Sets genotypes according to the specified criteria and filtering expressions. + For example, missing genotypes can be set to ref, but much more than that. +keywords: + - setgt + - bcftools + - genotype + - vcf +tools: + - "bcftools": + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." + homepage: "https://samtools.github.io/bcftools/howtos/index.html" + documentation: "https://samtools.github.io/bcftools/bcftools.html" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args" + identifier: biotools:bcftools + - "bcftools plugin setGT": + description: "Bcftools plugins are tools that can be used with bcftools to manipulate + variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes + according to the specified criteria and filtering expressions. For example, + missing genotypes can be set to ref, but much more than that." + homepage: "https://samtools.github.io/bcftools/howtos/plugins.html" + documentation: "https://samtools.github.io/bcftools/howtos/plugin.setGT.html" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args2" + identifier: biotools:bcftools + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + ontologies: [] + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + ontologies: [] + - target_gt: + type: string + description: | + Genotypes to change + - new_gt: + type: string + description: | + Genotypes to set + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + ontologies: [] + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + ontologies: [] +output: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF output file containing set genotypes + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + ontologies: [] + tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + ontologies: [] + csi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +authors: + - "@eweizy" +maintainers: + - "@eweizy" diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test new file mode 100644 index 000000000..b4f7ffa04 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test @@ -0,0 +1,298 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINSETGT" + script "../main.nf" + process "BCFTOOLS_PLUGINSETGT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginsetgt" + + test("sarscov2 - [vcf, tbi], [], []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + } + + test("sarscov2 - [vcf, tbi], vcf, tsv, []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + } +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap new file mode 100644 index 000000000..b1e83501a --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap @@ -0,0 +1,393 @@ +{ + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:37.442607574" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi" + ] + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:06.297712936" + }, + "sarscov2 - [vcf, tbi], [], []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out.vcf:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:13:42.984688381" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:30.014429156" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:45.443617875" + }, + "sarscov2 - [vcf, tbi], vcf, tsv, []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out.vcf:md5,55e955c359bf9094bb692660f3c1c677" + ] + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:14.614556139" + }, + "sarscov2 - [vcf, tbi], [], [], [] - stub": { + "content": [ + "out.vcf", + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:14:21.981644974" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:13:51.040151596" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_PLUGINSETGT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T12:13:58.936771199" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config b/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config new file mode 100644 index 000000000..eb8000d60 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + ext.args = '--no-version --output-type v' + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config new file mode 100644 index 000000000..9507854d7 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config new file mode 100644 index 000000000..9e53fe259 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config new file mode 100644 index 000000000..38abb7860 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "-s 42" +} diff --git a/nextflow.config b/nextflow.config index 5e969fe74..5597b9d8f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -109,6 +109,7 @@ params { // Variant calling cnvnator_binsize = 1000 variant_caller = 'deepvariant' + homoplasmy_af_threshold = 1.0 // variant annotation vep_cache_version = 112 diff --git a/nextflow_schema.json b/nextflow_schema.json index 8a806a193..baf4ff597 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -542,6 +542,12 @@ "help_text": "Set this to true, and specify the contig(s) using `restrict_to_contigs` parameter", "fa_icon": "fas fa-toggle-on" }, + "homoplasmy_af_threshold": { + "type": "float", + "default": 1.0, + "description": "Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homooplasmic and assigned a 1/1 genotype. Range 0-1.0.", + "fa_icon": "fas fa-less-than" + }, "platform": { "type": "string", "default": "illumina", diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 39b8aafc2..7e453ce6c 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -1,5 +1,6 @@ include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt/main' include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { @@ -9,10 +10,11 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] filter_with_bcftools // bool: should bcftools view be run filter_with_filter_vep // bool: should filter_vep be run + homoplasmy_gt_threshold // float: 0-1 main: - ch_versions = Channel.empty() - ch_tbi = Channel.empty() + ch_versions = channel.empty() + ch_tbi = channel.empty() // Since bcftools is likely much faster than filter_vep, // we run it first to reduce the number of variants that filter_vep has to process. @@ -25,9 +27,22 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { [] ) ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) + ch_vcf = BCFTOOLS_VIEW.out.vcf + ch_tbi = BCFTOOLS_VIEW.out.tbi + + if (homoplasmy_gt_threshold<1) { + BCFTOOLS_PLUGINSETGT ( + BCFTOOLS_VIEW.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, + channel.value('q'), + channel.value("c:'1/1'"), + [], + [] + ) + ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf + ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi + ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSETGT.out.versions) + } - ch_vcf = BCFTOOLS_VIEW.out.vcf - ch_tbi = BCFTOOLS_VIEW.out.tbi } if(filter_with_filter_vep) { diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 325dd91ed..6db789362 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -182,6 +182,7 @@ workflow RAREDISEASE { val_concatenate_snv_calls val_extract_alignments val_genome + val_homoplasmy_af_threshold val_mbuffer_mem val_mt_aligner val_mt_subsample_approach @@ -437,7 +438,8 @@ workflow RAREDISEASE { ch_clin_research_snv_vcf.clinical, ch_hgnc_ids, false, - true + true, + null ) GENERATE_CLINICAL_SET_SNV.out.vcf .set { ch_clinical_snv_vcf } @@ -509,7 +511,8 @@ workflow RAREDISEASE { ch_clin_research_mt_vcf.clinical, ch_hgnc_ids, true, - false + false, + val_homoplasmy_af_threshold ) GENERATE_CLINICAL_SET_MT.out.vcf .set { ch_clinical_mtsnv_vcf } @@ -607,7 +610,8 @@ workflow RAREDISEASE { ch_clin_research_sv_vcf.clinical, ch_hgnc_ids, false, - true + true, + null ) GENERATE_CLINICAL_SET_SV.out.vcf .set { ch_clinical_sv_vcf } @@ -685,7 +689,8 @@ workflow RAREDISEASE { ch_clin_research_me_vcf.clinical, ch_hgnc_ids, false, - true + true, + null ) GENERATE_CLINICAL_SET_ME.out.vcf .set { ch_clinical_me_vcf } @@ -768,7 +773,7 @@ workflow RAREDISEASE { GENS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (!skip_gens && analysis_type.equals("wgs")) { + if (!skip_gens && val_analysis_type.equals("wgs")) { GENS ( ch_mapped.genome_marked_bam_bai, ch_genome_dictionary, From af12581abeb6fbe93f49d42f9d52cf9259b8c496 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 Jan 2026 11:21:31 +0100 Subject: [PATCH 240/872] update snaps --- .../local/align/tests/main.nf.test.snap | 92 +++++- .../local/align_MT/tests/main.nf.test.snap | 44 ++- .../local/qc_bam/tests/main.nf.test.snap | 2 +- tests/test_bam.nf.test.snap | 64 ++++- tests/test_singleton.nf.test.snap | 264 +++++++++++++++++- 5 files changed, 445 insertions(+), 21 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 42f495bb1..e04faf30d 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -239,36 +239,72 @@ ], [ "versions.yml:md5,04cb590a101237e8d8726039ee466819", + "versions.yml:md5,04cb590a101237e8d8726039ee466819", + "versions.yml:md5,04cb590a101237e8d8726039ee466819", + "versions.yml:md5,210790d64830e81c512ff898e8d888db", "versions.yml:md5,210790d64830e81c512ff898e8d888db", + "versions.yml:md5,210790d64830e81c512ff898e8d888db", + "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", + "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", + "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", + "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", 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"versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ], "marked_bai": [ @@ -211,9 +221,19 @@ ], "versions": [ "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ] } @@ -222,7 +242,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-19T17:12:01.590311293" + "timestamp": "2026-01-23T09:23:15.456518407" }, "align mt - bwa": { "content": [ @@ -329,9 +349,19 @@ ], "2": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ], "marked_bai": [ @@ -436,9 +466,19 @@ ], "versions": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", + "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", + "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" ] } @@ -447,6 +487,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-19T17:14:00.976440705" + "timestamp": "2026-01-23T09:26:33.086288065" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index ae47dfe52..3c4cdf24d 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -155,6 +155,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-08T20:32:43.970984019" + "timestamp": "2026-01-23T11:05:48.291219333" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 7ce7c0353..f6dcf4263 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 795, + 817, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -66,6 +66,10 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -143,6 +147,12 @@ "expansionhunter": "5.0.0", "bgzip": 1.18 }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.5.0.0" }, @@ -224,6 +234,9 @@ "MANTA": { "manta": "1.6.0" }, + "MARKDUPLICATES": { + "picard": "3.3.0" + }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, @@ -306,12 +319,21 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, + "SAMTOOLS_INDEX_ALIGN": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX_MARKDUP": { + "samtools": 1.21 + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, @@ -333,6 +355,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -458,10 +483,19 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -532,6 +566,16 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "fastqc", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -834,6 +878,22 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -844,6 +904,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-18T17:30:21.579519047" + "timestamp": "2026-01-22T18:13:02.44209036" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a537d5f6c..2dae49383 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 361, + 817, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -15,6 +15,9 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.2 }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.2 + }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.21 }, @@ -83,6 +86,12 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, "CNVNATOR_CALL": { "CNVnator": "0.4.1" }, @@ -346,6 +355,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -436,6 +448,12 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, + "UPD_REGIONS": { + "upd": 0.1 + }, + "UPD_SITES": { + "upd": 0.1 + }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -463,11 +481,21 @@ }, [ "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -477,6 +505,13 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", + "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", + "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", + "annotate_snv/genome/hugelymodelbat_chromograph_regions", + "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", @@ -485,6 +520,11 @@ "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.csi", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", + "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -514,22 +554,40 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman.png", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman_deletions.csv", + "call_sv/mitochondria/eKLIPse_earlycasualcaiman_genes.csv", "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck.png", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck_deletions.csv", + "call_sv/mitochondria/eKLIPse_slowlycivilbuck_genes.csv", + "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/hugelymodelbat_LNUMBER1", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -542,6 +600,89 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman", + "qc_bam/earlycasualcaiman/css", + "qc_bam/earlycasualcaiman/css/agogo.css", + "qc_bam/earlycasualcaiman/css/ajax-loader.gif", + "qc_bam/earlycasualcaiman/css/basic.css", + "qc_bam/earlycasualcaiman/css/bgfooter.png", + "qc_bam/earlycasualcaiman/css/bgtop.png", + "qc_bam/earlycasualcaiman/css/comment-bright.png", + "qc_bam/earlycasualcaiman/css/comment-close.png", + "qc_bam/earlycasualcaiman/css/comment.png", + "qc_bam/earlycasualcaiman/css/doctools.js", + "qc_bam/earlycasualcaiman/css/down-pressed.png", + "qc_bam/earlycasualcaiman/css/down.png", + "qc_bam/earlycasualcaiman/css/file.png", + "qc_bam/earlycasualcaiman/css/jquery.js", + "qc_bam/earlycasualcaiman/css/minus.png", + "qc_bam/earlycasualcaiman/css/plus.png", + "qc_bam/earlycasualcaiman/css/pygments.css", + "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", + "qc_bam/earlycasualcaiman/css/report.css", + "qc_bam/earlycasualcaiman/css/searchtools.js", + "qc_bam/earlycasualcaiman/css/underscore.js", + "qc_bam/earlycasualcaiman/css/up-pressed.png", + "qc_bam/earlycasualcaiman/css/up.png", + "qc_bam/earlycasualcaiman/css/websupport.js", + "qc_bam/earlycasualcaiman/genome_results.txt", + "qc_bam/earlycasualcaiman/images_qualimapReport", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/earlycasualcaiman/qualimapReport.html", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/earlycasualcaiman_chromographcov", + "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.summary.txt", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/earlycasualcaiman_tidditcov.bed", + "qc_bam/earlycasualcaiman_tidditcov.bw", + "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", "qc_bam/hugelymodelbat/css", "qc_bam/hugelymodelbat/css/agogo.css", @@ -625,6 +766,89 @@ "qc_bam/hugelymodelbat_tidditcov.wig", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck", + "qc_bam/slowlycivilbuck/css", + "qc_bam/slowlycivilbuck/css/agogo.css", + "qc_bam/slowlycivilbuck/css/ajax-loader.gif", + "qc_bam/slowlycivilbuck/css/basic.css", + "qc_bam/slowlycivilbuck/css/bgfooter.png", + "qc_bam/slowlycivilbuck/css/bgtop.png", + "qc_bam/slowlycivilbuck/css/comment-bright.png", + "qc_bam/slowlycivilbuck/css/comment-close.png", + "qc_bam/slowlycivilbuck/css/comment.png", + "qc_bam/slowlycivilbuck/css/doctools.js", + "qc_bam/slowlycivilbuck/css/down-pressed.png", + "qc_bam/slowlycivilbuck/css/down.png", + "qc_bam/slowlycivilbuck/css/file.png", + "qc_bam/slowlycivilbuck/css/jquery.js", + "qc_bam/slowlycivilbuck/css/minus.png", + "qc_bam/slowlycivilbuck/css/plus.png", + "qc_bam/slowlycivilbuck/css/pygments.css", + "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", + "qc_bam/slowlycivilbuck/css/report.css", + "qc_bam/slowlycivilbuck/css/searchtools.js", + "qc_bam/slowlycivilbuck/css/underscore.js", + "qc_bam/slowlycivilbuck/css/up-pressed.png", + "qc_bam/slowlycivilbuck/css/up.png", + "qc_bam/slowlycivilbuck/css/websupport.js", + "qc_bam/slowlycivilbuck/genome_results.txt", + "qc_bam/slowlycivilbuck/images_qualimapReport", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/slowlycivilbuck/qualimapReport.html", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/slowlycivilbuck_chromographcov", + "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.summary.txt", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/slowlycivilbuck_tidditcov.bed", + "qc_bam/slowlycivilbuck_tidditcov.bw", + "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -639,29 +863,47 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "vcf2cytosure/earlycasualcaiman.cgh", + "vcf2cytosure/hugelymodelbat.cgh", + "vcf2cytosure/slowlycivilbuck.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-18T17:37:33.421833397" + "timestamp": "2026-01-22T18:33:49.077521" } } \ No newline at end of file From 9c399722808163c28ea69d797d3684880b109a61 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 Jan 2026 16:07:21 +0100 Subject: [PATCH 241/872] fix? --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c5697d6a..5d147fe09 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) + ### `Changed` - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) From 91a992c8f6204a32b012b484f0463668a5996c0a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 23 Jan 2026 15:10:02 +0000 Subject: [PATCH 242/872] [automated] Fix code linting --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5d147fe09..3c5697d6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - ### `Changed` - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) From e3e35e504ab8442942b7ce86743d73a3e43320fd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 23 Jan 2026 16:48:03 +0100 Subject: [PATCH 243/872] change type --- nextflow.config | 2 +- nextflow_schema.json | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index 5597b9d8f..21bd6e841 100644 --- a/nextflow.config +++ b/nextflow.config @@ -109,7 +109,7 @@ params { // Variant calling cnvnator_binsize = 1000 variant_caller = 'deepvariant' - homoplasmy_af_threshold = 1.0 + homoplasmy_af_threshold = 1 // variant annotation vep_cache_version = 112 diff --git a/nextflow_schema.json b/nextflow_schema.json index baf4ff597..8b6b41a4e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -543,8 +543,8 @@ "fa_icon": "fas fa-toggle-on" }, "homoplasmy_af_threshold": { - "type": "float", - "default": 1.0, + "type": "number", + "default": 1, "description": "Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homooplasmic and assigned a 1/1 genotype. Range 0-1.0.", "fa_icon": "fas fa-less-than" }, From cb61a4f7e843c3c6a6c040a9d0aa47f54dd8f0e0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 24 Jan 2026 00:58:30 +0100 Subject: [PATCH 244/872] update snap --- tests/test_bam.nf.test.snap | 64 +------- tests/test_singleton.nf.test.snap | 264 ++---------------------------- 2 files changed, 13 insertions(+), 315 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index f6dcf4263..50eca51d7 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 817, + 795, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -66,10 +66,6 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -147,12 +143,6 @@ "expansionhunter": "5.0.0", "bgzip": 1.18 }, - "FASTP": { - "fastp": "0.23.4" - }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.5.0.0" }, @@ -234,9 +224,6 @@ "MANTA": { "manta": "1.6.0" }, - "MARKDUPLICATES": { - "picard": "3.3.0" - }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, @@ -319,21 +306,12 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, - "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 - }, - "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_STATS": { - "samtools": 1.21 - }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, @@ -355,9 +333,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -483,19 +458,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -566,16 +532,6 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -878,22 +834,6 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -904,6 +844,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T18:13:02.44209036" + "timestamp": "2026-01-24T00:30:08.403574148" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 2dae49383..5120150da 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 817, + 361, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -15,9 +15,6 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.2 }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.2 - }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.21 }, @@ -86,12 +83,6 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, "CNVNATOR_CALL": { "CNVnator": "0.4.1" }, @@ -355,9 +346,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -448,12 +436,6 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -481,21 +463,11 @@ }, [ "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -505,13 +477,6 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", - "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/hugelymodelbat_chromograph_regions", - "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", @@ -520,11 +485,6 @@ "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.csi", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", - "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -554,40 +514,22 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman.png", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_deletions.csv", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_genes.csv", "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck.png", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_deletions.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_genes.csv", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -600,89 +542,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - "qc_bam/earlycasualcaiman/css/minus.png", - "qc_bam/earlycasualcaiman/css/plus.png", - "qc_bam/earlycasualcaiman/css/pygments.css", - "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", - "qc_bam/earlycasualcaiman/css/report.css", - "qc_bam/earlycasualcaiman/css/searchtools.js", - "qc_bam/earlycasualcaiman/css/underscore.js", - "qc_bam/earlycasualcaiman/css/up-pressed.png", - "qc_bam/earlycasualcaiman/css/up.png", - "qc_bam/earlycasualcaiman/css/websupport.js", - "qc_bam/earlycasualcaiman/genome_results.txt", - "qc_bam/earlycasualcaiman/images_qualimapReport", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/earlycasualcaiman/qualimapReport.html", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/earlycasualcaiman_chromographcov", - "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.summary.txt", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/earlycasualcaiman_tidditcov.bed", - "qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", "qc_bam/hugelymodelbat/css", "qc_bam/hugelymodelbat/css/agogo.css", @@ -766,89 +625,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck", - "qc_bam/slowlycivilbuck/css", - "qc_bam/slowlycivilbuck/css/agogo.css", - "qc_bam/slowlycivilbuck/css/ajax-loader.gif", - "qc_bam/slowlycivilbuck/css/basic.css", - "qc_bam/slowlycivilbuck/css/bgfooter.png", - "qc_bam/slowlycivilbuck/css/bgtop.png", - "qc_bam/slowlycivilbuck/css/comment-bright.png", - "qc_bam/slowlycivilbuck/css/comment-close.png", - "qc_bam/slowlycivilbuck/css/comment.png", - "qc_bam/slowlycivilbuck/css/doctools.js", - "qc_bam/slowlycivilbuck/css/down-pressed.png", - "qc_bam/slowlycivilbuck/css/down.png", - "qc_bam/slowlycivilbuck/css/file.png", - "qc_bam/slowlycivilbuck/css/jquery.js", - "qc_bam/slowlycivilbuck/css/minus.png", - "qc_bam/slowlycivilbuck/css/plus.png", - "qc_bam/slowlycivilbuck/css/pygments.css", - "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", - "qc_bam/slowlycivilbuck/css/report.css", - "qc_bam/slowlycivilbuck/css/searchtools.js", - "qc_bam/slowlycivilbuck/css/underscore.js", - "qc_bam/slowlycivilbuck/css/up-pressed.png", - "qc_bam/slowlycivilbuck/css/up.png", - "qc_bam/slowlycivilbuck/css/websupport.js", - "qc_bam/slowlycivilbuck/genome_results.txt", - "qc_bam/slowlycivilbuck/images_qualimapReport", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/slowlycivilbuck/qualimapReport.html", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/slowlycivilbuck_chromographcov", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -863,47 +639,29 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/earlycasualcaiman.cgh", - "vcf2cytosure/hugelymodelbat.cgh", - "vcf2cytosure/slowlycivilbuck.cgh" + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-22T18:33:49.077521" + "timestamp": "2026-01-24T00:51:35.621202872" } } \ No newline at end of file From 3bd9f2ede749ad4164bea5cf83deeaa59f25988a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 24 Jan 2026 23:46:04 +0100 Subject: [PATCH 245/872] remove versions --- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 7e453ce6c..0a01fadef 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -40,7 +40,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ) ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi - ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSETGT.out.versions) } } From 0e18d370ba9f8d8b5c6d7a8f37c55fe0908aae7a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 24 Jan 2026 23:48:12 +0100 Subject: [PATCH 246/872] rename gt to af --- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 0a01fadef..a51e39191 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -10,7 +10,7 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] filter_with_bcftools // bool: should bcftools view be run filter_with_filter_vep // bool: should filter_vep be run - homoplasmy_gt_threshold // float: 0-1 + homoplasmy_af_threshold // float: 0-1 main: ch_versions = channel.empty() @@ -30,7 +30,7 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi - if (homoplasmy_gt_threshold<1) { + if (homoplasmy_af_threshold<1) { BCFTOOLS_PLUGINSETGT ( BCFTOOLS_VIEW.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, channel.value('q'), From 85f438cf1e488f4cd2c8cc877be7ffc1b58a53b4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 00:46:05 +0100 Subject: [PATCH 247/872] patch --- modules.json | 5 +- .../vcf_filter_bcftools_ensemblvep.diff | 56 +++++++++++++++++++ 2 files changed, 59 insertions(+), 2 deletions(-) create mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff diff --git a/modules.json b/modules.json index 2e683df77..a85d7067d 100644 --- a/modules.json +++ b/modules.json @@ -33,7 +33,7 @@ "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bcftools/reheader": { "branch": "master", @@ -580,7 +580,8 @@ "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"] + "installed_by": ["subworkflows"], + "patch": "subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff" } } } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff new file mode 100644 index 000000000..fc2f472b0 --- /dev/null +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff @@ -0,0 +1,56 @@ +Changes in component 'nf-core/vcf_filter_bcftools_ensemblvep' +'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config' is unchanged +'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml' is unchanged +Changes in 'vcf_filter_bcftools_ensemblvep/main.nf': +--- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf ++++ subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +@@ -1,5 +1,6 @@ + include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' + include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' ++include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt/main' + include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' + // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config + workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { +@@ -9,10 +10,11 @@ + ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] + filter_with_bcftools // bool: should bcftools view be run + filter_with_filter_vep // bool: should filter_vep be run ++ homoplasmy_af_threshold // float: 0-1 + + main: +- ch_versions = Channel.empty() +- ch_tbi = Channel.empty() ++ ch_versions = channel.empty() ++ ch_tbi = channel.empty() + + // Since bcftools is likely much faster than filter_vep, + // we run it first to reduce the number of variants that filter_vep has to process. +@@ -25,9 +27,21 @@ + [] + ) + ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ++ ch_vcf = BCFTOOLS_VIEW.out.vcf ++ ch_tbi = BCFTOOLS_VIEW.out.tbi + +- ch_vcf = BCFTOOLS_VIEW.out.vcf +- ch_tbi = BCFTOOLS_VIEW.out.tbi ++ if (homoplasmy_af_threshold<1) { ++ BCFTOOLS_PLUGINSETGT ( ++ BCFTOOLS_VIEW.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, ++ channel.value('q'), ++ channel.value("c:'1/1'"), ++ [], ++ [] ++ ) ++ ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf ++ ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi ++ } ++ + } + + if(filter_with_filter_vep) { + +'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config' is unchanged +'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test' is unchanged +'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap' is unchanged +************************************************************ From 060b94c8cbbc0f6b08faa793bfd82afb41d52198 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:24:55 +0100 Subject: [PATCH 248/872] update bcftools_annotate --- modules.json | 459 ++++++++--- modules/nf-core/bcftools/annotate/main.nf | 53 +- modules/nf-core/bcftools/annotate/meta.yml | 32 +- .../bcftools/annotate/tests/main.nf.test | 130 +-- .../bcftools/annotate/tests/main.nf.test.snap | 769 +++++------------- subworkflows/local/annotate_cadd/main.nf | 3 - .../local/call_snv_deepvariant/main.nf | 1 - subworkflows/local/call_snv_sentieon/main.nf | 1 - .../local/postprocess_MT_calls/main.nf | 1 - 9 files changed, 648 insertions(+), 801 deletions(-) diff --git a/modules.json b/modules.json index 56535bc9b..57dcf5485 100644 --- a/modules.json +++ b/modules.json @@ -7,551 +7,772 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["modules"] + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -560,25 +781,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 25fef22dc..28964d2a7 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -14,25 +14,28 @@ process BCFTOOLS_ANNOTATE { path rename_chrs output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.${extension}"), emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def annotations_file = annotations ? "--annotations ${annotations}" : '' def columns_file = columns ? "--columns-file ${columns}" : '' def header_file = header_lines ? "--header-lines ${header_lines}" : '' def rename_chrs_file = rename_chrs ? "--rename-chrs ${rename_chrs}" : '' - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" def index_command = !index ? "bcftools index ${input}" : '' if ("${input}" == "${prefix}.${extension}") { @@ -51,24 +54,23 @@ process BCFTOOLS_ANNOTATE { --output ${prefix}.${extension} \\ --threads ${task.cpus} \\ ${input} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) - END_VERSIONS """ stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : "" + prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") ? "csi" : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" @@ -78,10 +80,5 @@ process BCFTOOLS_ANNOTATE { """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 058954d21..af8bcf84d 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -56,7 +56,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.{vcf,vcf.gz,bcf,bcf.gz}": + - "${prefix}.${extension}": type: file description: Compressed annotated VCF file pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" @@ -67,7 +67,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tbi": + - "${prefix}.${extension}.tbi": type: file description: Alternative VCF file index pattern: "*.tbi" @@ -78,18 +78,32 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.csi": + - "${prefix}.${extension}.csi": type: file description: Default VCF file index pattern: "*.csi" ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 79acadcca..39010bdc3 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -31,15 +31,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, - process.out.versions + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output") { @@ -64,15 +65,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, - process.out.versions + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index") { @@ -97,18 +99,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions - ).match() }, - { assert process.out.csi[0][1].endsWith(".csi") } + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi") { @@ -133,18 +133,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions - ).match() }, - { assert process.out.csi[0][1].endsWith(".csi") } + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi") { @@ -169,18 +167,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions - ).match() }, - { assert process.out.tbi[0][1].endsWith(".tbi") } + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name + ":variantsMD5," + path(it).vcf.variantsMD5 }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output") { @@ -208,15 +204,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, - process.out.versions - ).match("bcf-header") } + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output") { @@ -241,15 +238,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, - process.out.versions - ).match("bcf-columns") } + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index") { @@ -277,16 +275,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).LinesGzip.contains("##contig=")}, { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, - process.out.versions + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub") { @@ -312,12 +310,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub") { @@ -343,13 +345,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match()}, - { assert process.out.csi[0][1].endsWith(".csi") } + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub") { @@ -375,13 +380,16 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, - { assert process.out.csi[0][1].endsWith(".csi") } + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub") { @@ -407,13 +415,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() }, - { assert process.out.tbi[0][1].endsWith(".tbi") } + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - } diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index c7f40bf83..4d57dfbb1 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub": { "content": [ [ [ @@ -10,109 +10,35 @@ "test_vcf.vcf.gz" ] ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi" - ] - ], [ ], - [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:55:30.265471036" - }, - "bcf": { - "content": [ [ [ { "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz.csi" ] ], - [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:55:37.270860052" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": { - "content": [ { - "0": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ], - "csi": [ - - ], - "tbi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:47.356548" + "timestamp": "2026-01-15T16:46:28.350541494" }, - "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ [ [ @@ -120,126 +46,38 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] ], [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:55:12.451788461" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tbi": [ - - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T13:56:42.987304" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": { - "content": [ + ], + [ + + ], { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ], - "csi": [ - - ], - "tbi": [ - - ], - "vcf": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "versions": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:34.067026" + "timestamp": "2026-01-15T17:35:23.346991616" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": { "content": [ [ [ @@ -247,41 +85,38 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] ], [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T13:55:52.749146" - }, - "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": { - "content": [ + + ], [ [ { "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_vcf.vcf.gz.csi" ] ], - [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:55:57.699598" + "timestamp": "2026-01-15T17:35:15.126643898" }, - "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": { "content": [ [ [ @@ -292,38 +127,35 @@ "test_vcf.vcf.gz" ] ], - [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T13:56:28.915986" - }, - "bcf-header": { - "content": [ [ [ { "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz.tbi" ] ], [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] + + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:18.654899" + "timestamp": "2026-01-15T16:46:46.844515012" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": { "content": [ [ [ @@ -335,134 +167,34 @@ ] ], [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:55:08.604415962" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ], - "csi": [ - - ], - "tbi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:56:06.054536287" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub": { - "content": [ + ], { - "0": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tbi": [ - - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:38.664942" + "timestamp": "2026-01-15T16:46:37.561478889" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": { "content": [ [ [ @@ -470,8 +202,11 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] + ], + [ + ], [ [ @@ -479,23 +214,26 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.tbi" + "test_vcf.vcf.gz.csi" ] ], - [ - - ], - [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:13.350208" + "timestamp": "2026-01-15T17:35:06.608740206" }, - "bcf-columns": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": { "content": [ [ [ @@ -503,67 +241,32 @@ "id": "test", "single_end": false }, - "test_ann.bcf" + "test_vcf.vcf.gz" ] ], [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T13:56:24.166879" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": { - "content": [ + + ], + [ + + ], { - "0": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ], - "csi": [ - - ], - "tbi": [ - - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T12:55:48.340271359" + "timestamp": "2026-01-15T16:46:18.623176402" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": { + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output": { "content": [ [ [ @@ -571,32 +274,32 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.bcf" ] ], [ ], [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi" - ] + ], - [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-11T13:56:07.974454" + "timestamp": "2026-01-15T16:57:59.109447684" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": { + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ [ [ @@ -604,150 +307,65 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" ] ], [ ], [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi" - ] + ], - [ - "versions.yml:md5,a2d0c0e19854c3fda3386c7757a61171" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-11T13:56:02.490243" - }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub": { - "content": [ { - "0": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tbi": [ - - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T12:55:52.305248991" + "timestamp": "2026-01-15T17:34:58.100296619" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" + ] + ], + [ + + ], + [ + + ], { - "0": [ + "versions_bcftools": [ [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tbi": [ - - ], - "vcf": [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T12:55:59.210314307" + "timestamp": "2026-01-15T17:34:49.49779004" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index": { + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": { "content": [ [ [ @@ -770,38 +388,23 @@ "test_vcf.vcf.gz.csi" ] ], - [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-04-01T12:55:19.532491092" - }, - "sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz" + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] ] - ], - [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T12:55:44.331095545" + "timestamp": "2026-01-15T16:58:16.686295153" }, - "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi": { + "sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output": { "content": [ [ [ @@ -809,29 +412,29 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.bcf" ] ], [ ], [ - [ - { - "id": "test", - "single_end": false - }, - "test_vcf.vcf.gz.csi" - ] + ], - [ - "versions.yml:md5,6f2d10eb553ef65b43a9bd4844c6aa35" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_ANNOTATE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T12:55:23.309288135" + "timestamp": "2026-01-15T16:58:07.908352766" } } \ No newline at end of file diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 7d7884dcd..4d2f9f8e4 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -46,8 +46,6 @@ workflow ANNOTATE_CADD { [], REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt } ) - ch_versions = ch_versions.mix(RENAME_CHRNAMES.out.versions) - RENAME_CHRNAMES.out.vcf .map { meta, vcf -> [ meta, vcf, [] ] } @@ -77,7 +75,6 @@ workflow ANNOTATE_CADD { ch_versions = ch_versions.mix(TABIX_VIEW.out.versions) ch_versions = ch_versions.mix(CADD.out.versions) ch_versions = ch_versions.mix(TABIX_CADD.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index f5e7e3695..aa1a8730e 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -89,7 +89,6 @@ workflow CALL_SNV_DEEPVARIANT { ch_versions = ch_versions.mix(REMOVE_DUPLICATES_GL.out.versions) ch_versions = ch_versions.mix(TABIX_GL.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index e7feb8be5..ec13f2d8b 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -117,7 +117,6 @@ workflow CALL_SNV_SENTIEON { ch_versions = ch_versions.mix(BCF_FILTER_ONE.out.versions) ch_versions = ch_versions.mix(BCF_FILTER_TWO.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 859408aba..2e7ffb3c4 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -128,7 +128,6 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(REMOVE_DUPLICATES_MT.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_MERGE_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_MERGE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_MT.out.versions) From 0e5f073fabd9020f538b5a3d1beb1dbf7fee6744 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:26:21 +0100 Subject: [PATCH 249/872] update bcftools concat --- modules.json | 2 +- .../nf-core/bcftools/concat/environment.yml | 7 +- modules/nf-core/bcftools/concat/main.nf | 80 ++-- modules/nf-core/bcftools/concat/meta.yml | 49 ++- .../bcftools/concat/tests/main.nf.test | 86 ++--- .../bcftools/concat/tests/main.nf.test.snap | 356 +++++++++++------- .../bcftools/concat/tests/nextflow.config | 4 +- .../nf-core/bcftools/concat/tests/tags.yml | 2 - .../bcftools/concat/tests/vcf_gz_index.config | 2 +- .../concat/tests/vcf_gz_index_csi.config | 2 +- .../concat/tests/vcf_gz_index_tbi.config | 2 +- subworkflows/local/annotate_genome_snvs.nf | 1 - subworkflows/local/call_mobile_elements.nf | 1 - subworkflows/local/call_snv.nf | 1 - 14 files changed, 339 insertions(+), 256 deletions(-) delete mode 100644 modules/nf-core/bcftools/concat/tests/tags.yml diff --git a/modules.json b/modules.json index 57dcf5485..fb5d4b98c 100644 --- a/modules.json +++ b/modules.json @@ -14,7 +14,7 @@ }, "bcftools/concat": { "branch": "master", - "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index a94b28d86..269da8e0c 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -1,59 +1,73 @@ process BCFTOOLS_CONCAT { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf - tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.${extension}"), emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name } - def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n ") + def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") || tbi_names.contains(vcf.name + ".csi") ? "" : "tabix ${vcf}" }.join("\n ") + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def input = vcfs.sort { vcf -> vcf.toString() }.join(" ") """ ${create_input_index} bcftools concat \\ - --output ${prefix}.vcf.gz \\ - $args \\ - --threads $task.cpus \\ - ${vcfs} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS + --output ${prefix}.${extension} \\ + ${args} \\ + --threads ${task.cpus} \\ + ${input} """ stub: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" - def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : "" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" + """ - echo "" | gzip > ${prefix}.vcf.gz + ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index d2565b289..1734a8c34 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -31,50 +31,63 @@ input: List containing 2 or more index files (optional) e.g. [ 'file1.tbi', 'file2.tbi' ] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.{vcf.gz}" - - ${prefix}.vcf.gz: + - ${prefix}.${extension}: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.{vcf.gz}" - - tbi: - - meta: + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + tbi: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.tbi" - - ${prefix}.vcf.gz.tbi: + - ${prefix}.${extension}.tbi: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*.tbi" - - csi: - - meta: + csi: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.csi" - - ${prefix}.vcf.gz.csi: + - ${prefix}.${extension}.csi: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@abhi18av" - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index cb4642b29..58e199918 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -9,7 +9,6 @@ nextflow_process { tag "bcftools" tag "bcftools/concat" - test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") { config "./nextflow.config" @@ -20,12 +19,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -38,7 +37,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { @@ -51,12 +49,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -70,12 +68,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { @@ -88,12 +85,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -107,12 +104,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { @@ -125,12 +121,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -144,12 +140,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } @@ -163,8 +158,8 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [] ] @@ -178,7 +173,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { @@ -192,12 +186,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -210,7 +204,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { @@ -224,12 +217,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -243,7 +236,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { @@ -257,12 +249,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -276,7 +268,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { @@ -290,12 +281,12 @@ nextflow_process { input[0] = [ [ id:'test3' ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true) ], [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true) ] ] """ @@ -309,8 +300,7 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 09e87cd3e..5edf5beb6 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,5 +1,42 @@ { - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T11:59:52.705734505" + }, + "homo_sapiens - [[vcf1, vcf2], []]": { "content": [ { "0": [ @@ -7,30 +44,24 @@ { "id": "test3" }, - "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" ] ], "1": [ ], "2": [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ], - "csi": [ [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" ] + ], + "csi": [ + ], "tbi": [ @@ -40,21 +71,25 @@ { "id": "test3" }, - "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:04:11.178539482" + "timestamp": "2026-01-20T12:00:08.498123366" }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ { "0": [ @@ -62,7 +97,7 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -72,7 +107,11 @@ ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ], "csi": [ @@ -85,52 +124,25 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:03:08.765639958" + "timestamp": "2026-01-20T12:00:15.986212097" }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { - "content": [ - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" - ] - ], - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.csi" - ] - ], - [ - - ], - [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-26T11:03:21.607274757" - }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -142,29 +154,33 @@ ] ], "1": [ + + ], + "2": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "2": [ - ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ], "csi": [ - - ], - "tbi": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "tbi": [ + ], "vcf": [ [ @@ -174,49 +190,59 @@ "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:04:27.332133878" + "timestamp": "2026-01-20T12:00:24.007593166" }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { "content": [ [ [ { "id": "test3" }, - "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" ] + ], + [ + ], [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.csi" + "test3_vcf.vcf.gz.tbi" ] ], - [ - - ], - [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:03:36.575719606" + "timestamp": "2026-01-20T12:00:00.937832062" }, - "homo_sapiens - [[vcf1, vcf2], []]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ { "0": [ @@ -224,7 +250,7 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" ] ], "1": [ @@ -234,7 +260,11 @@ ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ], "csi": [ @@ -247,21 +277,62 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:03:54.069826178" + "timestamp": "2026-01-20T11:59:37.378838683" }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + { + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-20T11:59:45.296771646" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -269,73 +340,60 @@ { "id": "test3" }, - "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ - + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ], "csi": [ ], "tbi": [ - + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "vcf": [ [ { "id": "test3" }, - "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:04:02.45346063" - }, - "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { - "content": [ - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" - ] - ], - [ - - ], - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.tbi" - ] - ], - [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-26T11:03:44.618596639" + "timestamp": "2026-01-20T12:00:39.792930532" }, "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { "content": [ @@ -360,7 +418,11 @@ ] ], "3": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -381,15 +443,19 @@ "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + "versions_bcftools": [ + [ + "BCFTOOLS_CONCAT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-26T11:04:19.745768656" + "timestamp": "2026-01-20T12:00:31.985353981" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/nextflow.config b/modules/nf-core/bcftools/concat/tests/nextflow.config index f3e1e98c6..1d5fee9eb 100644 --- a/modules/nf-core/bcftools/concat/tests/nextflow.config +++ b/modules/nf-core/bcftools/concat/tests/nextflow.config @@ -1,3 +1,3 @@ process { - ext.args = "--no-version" -} \ No newline at end of file + ext.args = "--no-version -a" +} diff --git a/modules/nf-core/bcftools/concat/tests/tags.yml b/modules/nf-core/bcftools/concat/tests/tags.yml deleted file mode 100644 index 21710d4eb..000000000 --- a/modules/nf-core/bcftools/concat/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/concat: - - "modules/nf-core/bcftools/concat/**" diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config index 7dd696ee2..b6f9165cf 100644 --- a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config @@ -1,4 +1,4 @@ process { ext.prefix = { "${meta.id}_vcf" } - ext.args = "--output-type z --write-index --no-version" + ext.args = "--output-type z --write-index --no-version --allow-overlaps" } diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config index aebffb6fb..2455b1457 100644 --- a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config @@ -1,4 +1,4 @@ process { ext.prefix = { "${meta.id}_vcf" } - ext.args = "--output-type z --write-index=csi --no-version" + ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps -a" } diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config index b192ae7d1..1ca852310 100644 --- a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config @@ -1,4 +1,4 @@ process { ext.prefix = { "${meta.id}_vcf" } - ext.args = "--output-type z --write-index=tbi --no-version" + ext.args = "--output-type z --write-index=tbi --no-version --allow-overlaps" } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 2b690d6d5..d06ae6849 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -209,7 +209,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions) ch_versions = ch_versions.mix(TABIX_VEP.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(TABIX_BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 11c8df587..adcb84415 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -127,7 +127,6 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_ME.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_SORT_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT_ME.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME.out.versions) diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 3b35da14e..77ee74df0 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -152,7 +152,6 @@ workflow CALL_SNV { BCFTOOLS_CONCAT ( ch_concat_vcf_in ) - ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions) } emit: From 79b50787ae54f6a6ea16289bb2de671913ff4d8c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:27:01 +0100 Subject: [PATCH 250/872] update bcftools filter --- modules.json | 2 +- .../nf-core/bcftools/filter/environment.yml | 7 +- modules/nf-core/bcftools/filter/main.nf | 75 +++---- modules/nf-core/bcftools/filter/meta.yml | 43 +++- .../bcftools/filter/tests/main.nf.test | 19 +- .../bcftools/filter/tests/main.nf.test.snap | 194 ++++++++++++------ .../filter/tests/region_filter.config | 4 + .../nf-core/bcftools/filter/tests/tags.yml | 2 - subworkflows/local/call_snv_sentieon/main.nf | 2 - 9 files changed, 221 insertions(+), 127 deletions(-) create mode 100644 modules/nf-core/bcftools/filter/tests/region_filter.config delete mode 100644 modules/nf-core/bcftools/filter/tests/tags.yml diff --git a/modules.json b/modules.json index fb5d4b98c..4dade6639 100644 --- a/modules.json +++ b/modules.json @@ -21,7 +21,7 @@ }, "bcftools/filter": { "branch": "master", - "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 36cbf8c2b..4b558818a 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -1,20 +1,20 @@ process BCFTOOLS_FILTER { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf), path(tbi) output: tuple val(meta), path("*.${extension}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -23,51 +23,56 @@ process BCFTOOLS_FILTER { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" - if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("${vcf}" == "${prefix}.${extension}") { + error("Input and output names are the same, set prefix in module configuration to disambiguate!") + } """ bcftools filter \\ --output ${prefix}.${extension} \\ --threads ${task.cpus} \\ - $args \\ - $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS + ${args} \\ + ${vcf} """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" - if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + if ("${vcf}" == "${prefix}.${extension}") { + error("Input and output names are the same, set prefix in module configuration to disambiguate!") + } """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index d72f27554..4ab447ff6 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -23,13 +23,15 @@ input: type: file description: VCF input file pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + ontologies: [] - tbi: type: file description: VCF index file pattern: "*.tbi" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -38,8 +40,9 @@ output: type: file description: VCF filtered output file pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -48,8 +51,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -58,11 +62,28 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test b/modules/nf-core/bcftools/filter/tests/main.nf.test index fadff0e30..42cb8ab97 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test @@ -31,7 +31,6 @@ nextflow_process { { assert snapshot(process.out).match("vcf") } ) } - } test("sarscov2 - vcf_gz_index") { @@ -57,12 +56,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_csi") { @@ -88,12 +86,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_tbi") { @@ -119,12 +116,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } test("sarscov2 - vcf - bcf output") { @@ -149,7 +145,6 @@ nextflow_process { { assert snapshot(process.out).match("bcf output") } ) } - } test("sarscov2 - vcf.gz, tbi - region filter") { @@ -174,7 +169,6 @@ nextflow_process { { assert snapshot(process.out).match("region filter") } ) } - } test("sarscov2 - vcf - stub") { @@ -200,7 +194,6 @@ nextflow_process { { assert snapshot(process.out).match("vcf - stub") } ) } - } test("sarscov2 - vcf_gz_index - stub") { @@ -227,7 +220,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_csi - stub") { @@ -254,7 +246,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_tbi - stub") { @@ -281,7 +272,5 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } - -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap index 640907e42..798dade7f 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap @@ -17,7 +17,11 @@ ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ @@ -33,16 +37,20 @@ "bcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-08T09:14:47.394005264" + "timestamp": "2026-01-20T12:02:38.075538496" }, "sarscov2 - vcf_gz_index_tbi - stub": { "content": [ @@ -67,7 +75,11 @@ ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ @@ -88,16 +100,20 @@ "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T13:59:08.235854993" + "timestamp": "2026-01-20T12:03:09.787136694" }, "vcf": { "content": [ @@ -117,7 +133,11 @@ ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ @@ -133,16 +153,20 @@ "vcf_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-04T15:20:28.427974818" + "timestamp": "2026-01-20T12:02:00.400038419" }, "bcf output": { "content": [ @@ -162,7 +186,11 @@ ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ @@ -178,16 +206,20 @@ "bcf_test.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-04T15:20:34.049236749" + "timestamp": "2026-01-20T12:02:30.237925195" }, "sarscov2 - vcf_gz_index": { "content": [ @@ -210,15 +242,21 @@ [ ], - [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T08:09:49.837854646" + "timestamp": "2026-01-20T12:02:07.949745874" }, "sarscov2 - vcf_gz_index_csi": { "content": [ @@ -241,15 +279,21 @@ [ ], - [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T13:57:19.513365022" + "timestamp": "2026-01-20T12:02:15.417109301" }, "vcf - stub": { "content": [ @@ -269,7 +313,11 @@ ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ @@ -285,16 +333,20 @@ "vcf_test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-04T15:29:55.846566153" + "timestamp": "2026-01-20T12:02:46.265722559" }, "sarscov2 - vcf_gz_index - stub": { "content": [ @@ -319,7 +371,11 @@ ] ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -340,16 +396,20 @@ "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-04T15:59:37.636874258" + "timestamp": "2026-01-20T12:02:54.301083152" }, "sarscov2 - vcf_gz_index_csi - stub": { "content": [ @@ -374,7 +434,11 @@ ] ], "3": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -395,16 +459,20 @@ "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T13:58:46.36278584" + "timestamp": "2026-01-20T12:03:02.260111336" }, "sarscov2 - vcf_gz_index_tbi": { "content": [ @@ -427,14 +495,20 @@ "vcf_test_vcf.vcf.gz.tbi" ] ], - [ - "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_FILTER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T13:57:34.748836577" + "timestamp": "2026-01-20T12:02:23.055607519" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/region_filter.config b/modules/nf-core/bcftools/filter/tests/region_filter.config new file mode 100644 index 000000000..b18fb4bf0 --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/region_filter.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z -r MT192765.1 --no-version" +} diff --git a/modules/nf-core/bcftools/filter/tests/tags.yml b/modules/nf-core/bcftools/filter/tests/tags.yml deleted file mode 100644 index d5e010800..000000000 --- a/modules/nf-core/bcftools/filter/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/filter: - - "modules/nf-core/bcftools/filter/**" diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index ec13f2d8b..10e8088fd 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -114,8 +114,6 @@ workflow CALL_SNV_SENTIEON { ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_SEN.out.versions) ch_versions = ch_versions.mix(REMOVE_DUPLICATES_SEN.out.versions) ch_versions = ch_versions.mix(TABIX_SEN.out.versions) - ch_versions = ch_versions.mix(BCF_FILTER_ONE.out.versions) - ch_versions = ch_versions.mix(BCF_FILTER_TWO.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) From 4adb218e7c7c4d2c62651f2184cd2d9afb1738c9 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:30:12 +0100 Subject: [PATCH 251/872] bcftools merge --- modules.json | 2 +- .../nf-core/bcftools/merge/environment.yml | 7 +- modules/nf-core/bcftools/merge/main.nf | 75 ++-- modules/nf-core/bcftools/merge/meta.yml | 41 +- .../nf-core/bcftools/merge/tests/main.nf.test | 44 +- .../bcftools/merge/tests/main.nf.test.snap | 418 ++++++++++++------ modules/nf-core/bcftools/merge/tests/tags.yml | 2 - .../local/postprocess_MT_calls/main.nf | 1 - 8 files changed, 374 insertions(+), 216 deletions(-) delete mode 100644 modules/nf-core/bcftools/merge/tests/tags.yml diff --git a/modules.json b/modules.json index 4dade6639..bf9b0d2f7 100644 --- a/modules.json +++ b/modules.json @@ -28,7 +28,7 @@ }, "bcftools/merge": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index facb14ea1..6c944151b 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -1,11 +1,11 @@ process BCFTOOLS_MERGE { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcfs), path(tbis) @@ -15,8 +15,8 @@ process BCFTOOLS_MERGE { output: tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.{csi,tbi}"), emit: index, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -25,50 +25,51 @@ process BCFTOOLS_MERGE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs - def regions = bed ? "--regions-file $bed" : "" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" + def input = vcfs.collect().size() > 1 ? vcfs.sort { vcf -> vcf.name } : vcfs + def regions = bed ? "--regions-file ${bed}" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" """ bcftools merge \\ - $args \\ - $regions \\ - --threads $task.cpus \\ + ${args} \\ + ${regions} \\ + --threads ${task.cpus} \\ --output ${prefix}.${extension} \\ - $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS + ${input} """ stub: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index 2cf09a1d4..f66b68845 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -24,11 +24,13 @@ input: description: | List containing 2 or more vcf files e.g. [ 'file1.vcf', 'file2.vcf' ] + ontologies: [] - tbis: type: file description: | List containing the tbi index files corresponding to the vcfs input files e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + ontologies: [] - - meta2: type: map description: | @@ -39,6 +41,7 @@ input: description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)" pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -49,6 +52,7 @@ input: description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -58,9 +62,10 @@ input: type: file description: "(Optional) The bed regions to merge on" pattern: "*.bed" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -69,8 +74,9 @@ output: type: file description: merged output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - index: - - meta: + ontologies: [] + index: + - - meta: type: map description: | Groovy Map containing sample information @@ -79,11 +85,28 @@ output: type: file description: index of merged output pattern: "*.{csi,tbi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test index 3995fc1a9..e863f1816 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -40,11 +40,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf output") { @@ -78,11 +77,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).md5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output") { @@ -116,11 +114,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - bcf output") { @@ -154,11 +151,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("bcf") }, { assert snapshot( file(process.out.vcf.get(0).get(1)).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output") { @@ -192,11 +188,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("bcf.gz") }, { assert snapshot( file(process.out.vcf.get(0).get(1)).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index") { @@ -232,11 +227,10 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, file(process.out.index.get(0).get(1)).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index") { @@ -273,11 +267,10 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, file(process.out.index.get(0).get(1)).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index") { @@ -313,11 +306,10 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, file(process.out.index.get(0).get(1)).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], bed") { @@ -354,11 +346,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).md5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { @@ -401,11 +392,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { @@ -436,11 +426,10 @@ nextflow_process { { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, { assert snapshot( path(process.out.vcf.get(0).get(1)).md5, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - stub") { @@ -476,7 +465,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub") { @@ -512,7 +500,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub") { @@ -548,7 +535,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub") { @@ -584,7 +570,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub") { @@ -620,7 +605,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub") { @@ -657,7 +641,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub") { @@ -694,7 +677,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub") { @@ -731,7 +713,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], bed - stub") { @@ -770,7 +751,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub") { @@ -814,7 +794,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") { @@ -848,6 +827,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } } diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap index b3b625563..8f925a8e2 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -3,15 +3,21 @@ "content": [ "e0de448dc8e712956a03ce68d79a0b3a", "test.vcf.gz.tbi", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T12:34:16.977726522" + "timestamp": "2026-01-20T12:05:01.453191274" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub": { "content": [ @@ -28,7 +34,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -41,29 +51,39 @@ "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:17:34.532910365" + "timestamp": "2026-01-20T12:05:43.064165277" }, "sarscov2 - [vcf, tbi], [], [], bed": { "content": [ "febdcfb851dcfc83d8248520830aef10", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:29:48.630057872" + "timestamp": "2026-01-20T12:05:09.906419282" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub": { "content": [ @@ -85,7 +105,11 @@ ] ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -103,29 +127,39 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:17:59.983157569" + "timestamp": "2026-01-20T12:06:17.06290054" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf output": { "content": [ "57bb84274f336465d0a0946b532093b0", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:29:05.528412678" + "timestamp": "2026-01-20T12:04:14.044948834" }, "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub": { "content": [ @@ -142,7 +176,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -155,16 +193,20 @@ "test.bcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:58:46.619657457" + "timestamp": "2026-01-20T12:06:08.633006073" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub": { "content": [ @@ -186,7 +228,11 @@ ] ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -204,16 +250,20 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:18:12.848227353" + "timestamp": "2026-01-20T12:06:33.897407991" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub": { "content": [ @@ -230,7 +280,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -243,43 +297,59 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:23:15.794389239" + "timestamp": "2026-01-20T12:05:51.445673109" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index": { "content": [ "e0de448dc8e712956a03ce68d79a0b3a", "test.vcf.gz.csi", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:57:16.850641473" + "timestamp": "2026-01-20T12:04:53.868676326" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output": { "content": [ "e0de448dc8e712956a03ce68d79a0b3a", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:56:27.949031071" + "timestamp": "2026-01-20T12:04:22.660557224" }, "sarscov2 - [vcf, tbi], [], [], bed - stub": { "content": [ @@ -296,7 +366,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -309,29 +383,39 @@ "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:18:19.273064822" + "timestamp": "2026-01-20T12:06:42.799574825" }, "sarscov2 - [vcf, tbi], [], [], [] - bcf output": { "content": [ "test.bcf", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:56:38.567500859" + "timestamp": "2026-01-20T12:04:30.965022315" }, "sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub": { "content": [ @@ -348,7 +432,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -361,16 +449,20 @@ "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:17:47.356328326" + "timestamp": "2026-01-20T12:05:59.932077434" }, "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": { "content": [ @@ -387,7 +479,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -400,16 +496,20 @@ "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T15:13:18.708495878" + "timestamp": "2026-01-20T12:07:00.260709958" }, "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub": { "content": [ @@ -426,7 +526,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -439,56 +543,78 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:56:45.706125286" + "timestamp": "2026-01-20T12:06:52.181671234" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": { "content": [ "e0de448dc8e712956a03ce68d79a0b3a", "test.vcf.gz.csi", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T12:33:43.639646108" + "timestamp": "2026-01-20T12:04:46.41923299" }, "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output": { "content": [ "645b7f7f9131bfe350a9ec3cf82c17fe", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:55:44.299812124" + "timestamp": "2026-01-20T12:05:18.989455751" }, "sarscov2 - [vcf, tbi], [], [], [] - one sample": { "content": [ "2a374cf02f0c32cf607646167e7f153b", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T15:37:38.491844702" + "timestamp": "2026-01-20T12:05:26.431607458" }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ @@ -505,7 +631,11 @@ ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ @@ -518,16 +648,20 @@ "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:17:28.188178904" + "timestamp": "2026-01-20T12:05:34.692613749" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub": { "content": [ @@ -549,7 +683,11 @@ ] ], "2": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -567,41 +705,57 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T13:18:06.430943593" + "timestamp": "2026-01-20T12:06:25.137261969" }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ "e0de448dc8e712956a03ce68d79a0b3a", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T12:31:03.893007442" + "timestamp": "2026-01-20T12:04:05.637837157" }, "sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output": { "content": [ "test.bcf.gz", - [ - "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_MERGE", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-05T11:56:56.416361069" + "timestamp": "2026-01-20T12:04:38.467108836" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/merge/tests/tags.yml b/modules/nf-core/bcftools/merge/tests/tags.yml deleted file mode 100644 index 1464d0c1c..000000000 --- a/modules/nf-core/bcftools/merge/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/merge: - - "modules/nf-core/bcftools/merge/**" diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 2e7ffb3c4..fadd806af 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -126,7 +126,6 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_MT.out.versions) ch_versions = ch_versions.mix(REMOVE_DUPLICATES_MT.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_MERGE_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_MERGE.out.versions) From 637fca15f37961a2b814e854796495322d62a81c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:31:28 +0100 Subject: [PATCH 252/872] bcftools norm --- modules.json | 2 +- modules/nf-core/bcftools/norm/environment.yml | 5 +- modules/nf-core/bcftools/norm/main.nf | 63 ++-- modules/nf-core/bcftools/norm/meta.yml | 26 +- .../nf-core/bcftools/norm/tests/main.nf.test | 22 +- .../bcftools/norm/tests/main.nf.test.snap | 298 ++++++++++++------ .../local/call_repeat_expansions/main.nf | 1 - .../local/call_snv_deepvariant/main.nf | 2 - subworkflows/local/call_snv_sentieon/main.nf | 3 - .../local/postprocess_MT_calls/main.nf | 2 - 10 files changed, 265 insertions(+), 159 deletions(-) diff --git a/modules.json b/modules.json index bf9b0d2f7..35a987674 100644 --- a/modules.json +++ b/modules.json @@ -35,7 +35,7 @@ }, "bcftools/norm": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 557488607..ba863b388 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 3ad9b35cc..443c8bbbc 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -1,11 +1,11 @@ process BCFTOOLS_NORM { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf), path(tbi) @@ -13,9 +13,9 @@ process BCFTOOLS_NORM { output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -23,52 +23,49 @@ process BCFTOOLS_NORM { script: def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf.gz" - + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf.gz" """ bcftools norm \\ --fasta-ref ${fasta} \\ --output ${prefix}.${extension} \\ - $args \\ - --threads $task.cpus \\ + ${args} \\ + --threads ${task.cpus} \\ ${vcf} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ stub: def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf.gz" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf.gz" def index = '' if (extension in ['vcf.gz', 'bcf', 'bcf.gz']) { - if (['--write-index=tbi', '-W=tbi'].any { args.contains(it) } && extension == 'vcf.gz') { + if (['--write-index=tbi', '-W=tbi'].any { arg -> args.contains(arg) } && extension == 'vcf.gz') { index = 'tbi' - } else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { args.contains(it) }) { + } + else if (['--write-index=tbi', '-W=tbi', '--write-index=csi', '-W=csi', '--write-index', '-W'].any { arg -> args.contains(arg) }) { index = 'csi' } } def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = index ? "touch ${prefix}.${extension}.${index}" : "" - """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index bda91258c..9feecac0d 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -78,13 +78,27 @@ output: description: Default VCF file index pattern: "*.csi" ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test b/modules/nf-core/bcftools/norm/tests/main.nf.test index dbc415023..058517530 100644 --- a/modules/nf-core/bcftools/norm/tests/main.nf.test +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test @@ -35,7 +35,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index") { @@ -68,7 +67,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi") { @@ -101,7 +99,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi") { @@ -134,7 +131,6 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } test("sarscov2 - [ vcf, tbi ], fasta") { @@ -163,7 +159,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - vcf output") { @@ -192,7 +187,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output") { @@ -222,11 +216,10 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - bcf output") { @@ -255,7 +248,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output") { @@ -284,7 +276,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, [] ], fasta - stub") { @@ -314,7 +305,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta -stub") { @@ -344,7 +334,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - vcf output -stub") { @@ -374,7 +363,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output - stub") { @@ -403,7 +391,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - bcf output - stub") { @@ -433,7 +420,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub") { @@ -463,7 +449,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub") { @@ -494,7 +479,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub") { @@ -525,7 +509,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub") { @@ -556,8 +539,7 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap index b71721a73..ee2dadf77 100644 --- a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap @@ -17,7 +17,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -33,16 +37,20 @@ "test_norm.vcf:md5,63e5adbaf3dd94550e9e3d7935dd28db" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:35.039667679" + "timestamp": "2026-01-20T12:09:29.987030961" }, "sarscov2 - [ vcf, [] ], fasta - stub": { "content": [ @@ -62,7 +70,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -78,16 +90,20 @@ "test_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:19.531714933" + "timestamp": "2026-01-20T12:09:06.488086505" }, "sarscov2 - [ vcf, tbi ], fasta - vcf output": { "content": [ @@ -107,7 +123,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -123,16 +143,20 @@ "test_norm.vcf:md5,63e5adbaf3dd94550e9e3d7935dd28db" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:01:53.57043182" + "timestamp": "2026-01-20T12:08:34.863776359" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub": { "content": [ @@ -157,7 +181,11 @@ ] ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -178,16 +206,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:53.457953524" + "timestamp": "2026-01-20T12:09:54.718705045" }, "sarscov2 - [ vcf, tbi ], fasta - vcf_gz output": { "content": [ @@ -205,15 +237,21 @@ [ ], - [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:00.719886153" + "timestamp": "2026-01-20T12:08:43.007377633" }, "sarscov2 - [ vcf, [] ], fasta": { "content": [ @@ -233,7 +271,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -249,16 +291,20 @@ "test_norm.vcf.gz:md5,63e5adbaf3dd94550e9e3d7935dd28db" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:01:23.75323253" + "timestamp": "2026-01-20T12:07:54.877084219" }, "sarscov2 - [ vcf, tbi ], fasta - vcf output -stub": { "content": [ @@ -278,7 +324,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -294,16 +344,20 @@ "test_norm.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:30.863210572" + "timestamp": "2026-01-20T12:09:22.220435939" }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output": { "content": [ @@ -323,7 +377,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -339,16 +397,20 @@ "test_norm.bcf:md5,bf88706ef69c44ca9e287bc953ba3593" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:12.325415263" + "timestamp": "2026-01-20T12:08:58.483532889" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub": { "content": [ @@ -373,7 +435,11 @@ ] ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -394,16 +460,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:03:00.652023677" + "timestamp": "2026-01-20T12:10:03.22576704" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi": { "content": [ @@ -443,7 +513,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -459,16 +533,20 @@ "test_norm.vcf.gz:md5,63e5adbaf3dd94550e9e3d7935dd28db" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:01:46.207313323" + "timestamp": "2026-01-20T12:08:27.281315407" }, "sarscov2 - [ vcf, tbi ], fasta -stub": { "content": [ @@ -488,7 +566,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -504,16 +586,20 @@ "test_norm.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:26.686137644" + "timestamp": "2026-01-20T12:09:14.249715835" }, "sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub": { "content": [ @@ -533,7 +619,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -549,16 +639,20 @@ "test_norm.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:46.406125297" + "timestamp": "2026-01-20T12:09:46.665932019" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index": { "content": [ @@ -603,7 +697,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -619,16 +717,20 @@ "test_norm.bcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:39.213092385" + "timestamp": "2026-01-20T12:09:38.144449162" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub": { "content": [ @@ -653,7 +755,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -674,16 +780,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:03:07.888046412" + "timestamp": "2026-01-20T12:10:10.602984345" }, "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi": { "content": [ @@ -728,7 +838,11 @@ ], "3": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ], "csi": [ @@ -744,15 +858,19 @@ "test_norm.bcf.gz:md5,638c3c25bdd495c90ecbccb69ee77f07" ] ], - "versions": [ - "versions.yml:md5,cb38669b7069800497b0706a09932aec" + "versions_bcftools": [ + [ + "BCFTOOLS_NORM", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:02:04.993236789" + "timestamp": "2026-01-20T12:08:51.053195842" } } \ No newline at end of file diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index d9347d20e..b61d1d791 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -62,7 +62,6 @@ workflow CALL_REPEAT_EXPANSIONS { ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_EXP.out.versions) ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_EXP.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index aa1a8730e..74306f690 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -85,8 +85,6 @@ workflow CALL_SNV_DEEPVARIANT { ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) ch_versions = ch_versions.mix(GLNEXUS.out.versions) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_GL.out.versions) - ch_versions = ch_versions.mix(REMOVE_DUPLICATES_GL.out.versions) ch_versions = ch_versions.mix(TABIX_GL.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 10e8088fd..a9a3e0bea 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -110,9 +110,6 @@ workflow CALL_SNV_SENTIEON { ch_versions = ch_versions.mix(SENTIEON_DNASCOPE.out.versions) ch_versions = ch_versions.mix(SENTIEON_DNAMODELAPPLY.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_SEN.out.versions) - ch_versions = ch_versions.mix(REMOVE_DUPLICATES_SEN.out.versions) ch_versions = ch_versions.mix(TABIX_SEN.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index fadd806af..59d77a645 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -124,8 +124,6 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(PICARD_LIFTOVERVCF.out.versions) ch_versions = ch_versions.mix(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.versions) ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) - ch_versions = ch_versions.mix(SPLIT_MULTIALLELICS_MT.out.versions) - ch_versions = ch_versions.mix(REMOVE_DUPLICATES_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_MERGE.out.versions) From 9c638eeae5b4b01b664922be63beeb893d6c5bbd Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:32:53 +0100 Subject: [PATCH 253/872] reheader --- modules.json | 2 +- .../nf-core/bcftools/reheader/environment.yml | 5 +- modules/nf-core/bcftools/reheader/main.nf | 81 +++--- modules/nf-core/bcftools/reheader/meta.yml | 26 +- .../bcftools/reheader/tests/bcf.config | 2 +- .../bcftools/reheader/tests/main.nf.test | 21 +- .../bcftools/reheader/tests/main.nf.test.snap | 232 ++++++++++++------ .../bcftools/reheader/tests/vcf.config | 2 +- .../bcftools/reheader/tests/vcf.gz.config | 2 +- subworkflows/local/call_mobile_elements.nf | 1 - .../local/call_repeat_expansions/main.nf | 1 - subworkflows/local/generate_cytosure_files.nf | 1 - subworkflows/local/variant_evaluation.nf | 1 - 13 files changed, 233 insertions(+), 144 deletions(-) diff --git a/modules.json b/modules.json index 35a987674..3761f1a95 100644 --- a/modules.json +++ b/modules.json @@ -42,7 +42,7 @@ }, "bcftools/reheader": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 557488607..ba863b388 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 37062ab14..443cb4756 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -1,11 +1,11 @@ process BCFTOOLS_REHEADER { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data': - 'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf), path(header), path(samples) @@ -13,8 +13,8 @@ process BCFTOOLS_REHEADER { output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.{csi,tbi}"), emit: index, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -22,58 +22,59 @@ process BCFTOOLS_REHEADER { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def fai_argument = fai ? "--fai $fai" : "" - def header_argument = header ? "--header $header" : "" - def samples_argument = samples ? "--samples $samples" : "" + def fai_argument = fai ? "--fai ${fai}" : "" + def header_argument = header ? "--header ${header}" : "" + def samples_argument = samples ? "--samples ${samples}" : "" def args2 = task.ext.args2 ?: '--output-type z' - def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" : - args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" : - args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" : - args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : - "vcf" + def extension = args2.contains("--output-type b") || args2.contains("-Ob") + ? "bcf.gz" + : args2.contains("--output-type u") || args2.contains("-Ou") + ? "bcf" + : args2.contains("--output-type z") || args2.contains("-Oz") + ? "vcf.gz" + : args2.contains("--output-type v") || args2.contains("-Ov") + ? "vcf" + : "vcf" """ bcftools \\ reheader \\ - $fai_argument \\ - $header_argument \\ - $samples_argument \\ - $args \\ - --threads $task.cpus \\ - $vcf \\ + ${fai_argument} \\ + ${header_argument} \\ + ${samples_argument} \\ + ${args} \\ + --threads ${task.cpus} \\ + ${vcf} \\ | bcftools view \\ - $args2 \\ + ${args2} \\ --output ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ stub: def args2 = task.ext.args2 ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" : - args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" : - args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" : - args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : - "vcf" - def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" : - args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" : - args2.contains("--write-index") || args2.contains("-W") ? "csi" : - "" + def extension = args2.contains("--output-type b") || args2.contains("-Ob") + ? "bcf.gz" + : args2.contains("--output-type u") || args2.contains("-Ou") + ? "bcf" + : args2.contains("--output-type z") || args2.contains("-Oz") + ? "vcf.gz" + : args2.contains("--output-type v") || args2.contains("-Ov") + ? "vcf" + : "vcf" + def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") + ? "tbi" + : args2.contains("--write-index=csi") || args2.contains("-W=csi") + ? "csi" + : args2.contains("--write-index") || args2.contains("-W") + ? "csi" + : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index 4bc15ad65..77d3e96b1 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -67,13 +67,27 @@ output: description: Index of VCF with updated header pattern: "*.{csi,tbi}" ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/reheader/tests/bcf.config b/modules/nf-core/bcftools/reheader/tests/bcf.config index 2b7dff551..05ef8990f 100644 --- a/modules/nf-core/bcftools/reheader/tests/bcf.config +++ b/modules/nf-core/bcftools/reheader/tests/bcf.config @@ -1,4 +1,4 @@ process { ext.args2 = { "--no-version --output-type b" } ext.prefix = "tested" -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test b/modules/nf-core/bcftools/reheader/tests/main.nf.test index 96c1b7b0e..6d557bdbe 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test @@ -35,7 +35,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output") { @@ -65,7 +64,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index") { @@ -95,12 +93,11 @@ nextflow_process { { assert snapshot( process.out.vcf, process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.index[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index") { @@ -130,12 +127,11 @@ nextflow_process { { assert snapshot( process.out.vcf, process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.index[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index") { @@ -165,12 +161,11 @@ nextflow_process { { assert snapshot( process.out.vcf, process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.index[0][1].endsWith(".tbi") } ) } - } test("sarscov2 - [vcf, [], []], fai - bcf output") { @@ -200,7 +195,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, header, []], []") { @@ -230,7 +224,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], samples], fai") { @@ -262,7 +255,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - stub") { @@ -292,11 +284,10 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.vcf[0][1]).name, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, ).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub") { @@ -326,7 +317,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub") { @@ -357,7 +347,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub") { @@ -388,7 +377,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap index fc8dfd58b..ccfd36cad 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap @@ -19,15 +19,21 @@ "test_vcf.vcf.gz.tbi" ] ], - [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:50.163995386" + "timestamp": "2026-01-20T12:17:33.223574431" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": { "content": [ @@ -51,7 +57,11 @@ ] ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -71,16 +81,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:22.786980419" + "timestamp": "2026-01-20T12:18:06.228305957" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": { "content": [ @@ -104,7 +118,11 @@ ] ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -124,16 +142,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:30.908145496" + "timestamp": "2026-01-20T12:18:19.515117697" }, "sarscov2 - [vcf, [], []], fai - vcf output": { "content": [ @@ -151,7 +173,11 @@ ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ @@ -165,16 +191,20 @@ "tested.vcf:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:27.878225575" + "timestamp": "2026-01-20T12:17:07.237153461" }, "sarscov2 - [vcf, [], []], fai - bcf output": { "content": [ @@ -192,7 +222,11 @@ ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ @@ -206,16 +240,20 @@ "tested.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:57.340213283" + "timestamp": "2026-01-20T12:17:39.607699561" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output": { "content": [ @@ -233,7 +271,11 @@ ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ @@ -247,16 +289,20 @@ "tested.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:32.00582809" + "timestamp": "2026-01-20T12:17:13.971326724" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": { "content": [ @@ -278,15 +324,21 @@ "test_vcf.vcf.gz.csi" ] ], - [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:38.993337881" + "timestamp": "2026-01-20T12:17:20.34202516" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": { "content": [ @@ -310,7 +362,11 @@ ] ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ [ @@ -330,29 +386,39 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:26.882028182" + "timestamp": "2026-01-20T12:18:12.675831882" }, "sarscov2 - [vcf, [], []], fai - stub": { "content": [ "tested.vcf", - [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:15.695515447" + "timestamp": "2026-01-20T12:17:59.535920415" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": { "content": [ @@ -374,15 +440,21 @@ "test_vcf.vcf.gz.csi" ] ], - [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:09:43.054413402" + "timestamp": "2026-01-20T12:17:26.832291904" }, "sarscov2 - [vcf, [], samples], fai": { "content": [ @@ -400,7 +472,11 @@ ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ @@ -414,16 +490,20 @@ "tested.vcf:md5,c64c373c10b0be24b29d6f18708ec1e8" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:11.620196263" + "timestamp": "2026-01-20T12:17:52.840234682" }, "sarscov2 - [vcf, header, []], []": { "content": [ @@ -441,7 +521,11 @@ ], "2": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ], "index": [ @@ -455,15 +539,19 @@ "tested.vcf:md5,3189bc9a720d5d5d3006bf72d91300cb" ] ], - "versions": [ - "versions.yml:md5,61e09a272da74ae6a9ddb0195cfd491a" + "versions_bcftools": [ + [ + "BCFTOOLS_REHEADER", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-04-01T14:10:04.588597619" + "timestamp": "2026-01-20T12:17:46.214653984" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/tests/vcf.config b/modules/nf-core/bcftools/reheader/tests/vcf.config index 820f2ae66..3fed69282 100644 --- a/modules/nf-core/bcftools/reheader/tests/vcf.config +++ b/modules/nf-core/bcftools/reheader/tests/vcf.config @@ -1,4 +1,4 @@ process { ext.args2 = { "--no-version" } ext.prefix = "tested" -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/reheader/tests/vcf.gz.config b/modules/nf-core/bcftools/reheader/tests/vcf.gz.config index c3031c317..abc12ca36 100644 --- a/modules/nf-core/bcftools/reheader/tests/vcf.gz.config +++ b/modules/nf-core/bcftools/reheader/tests/vcf.gz.config @@ -1,4 +1,4 @@ process { ext.args2 = { "--no-version --output-type z" } ext.prefix = "tested" -} \ No newline at end of file +} diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index adcb84415..0ad815245 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -124,7 +124,6 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions) ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_ME.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_SORT_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index b61d1d791..5acce86c7 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -59,7 +59,6 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) ch_versions = ch_versions.mix(EXPANSIONHUNTER.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_EXP.out.versions) ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index cb73c3632..29cb5cc37 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -58,7 +58,6 @@ workflow GENERATE_CYTOSURE_FILES { BCFTOOLS_REHEADER_SV_VCF ( ch_reheader_in, [[:],[]] ).vcf .set {ch_reheader_out} - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER_SV_VCF.out.versions) } SPLIT_AND_FILTER_SV_VCF.out.vcf diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index 0debbdd0c..f4f0e4027 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -42,7 +42,6 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) - ch_versions = ch_versions.mix(BCFTOOLS_REHEADER.out.versions) ch_versions = ch_versions.mix(TABIX_TRUTHVCF.out.versions) ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions) From bdf81374a92b5e320c5d209673a649b100ef2958 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:33:24 +0100 Subject: [PATCH 254/872] roh --- modules.json | 2 +- modules/nf-core/bcftools/roh/environment.yml | 7 +- modules/nf-core/bcftools/roh/main.nf | 50 ++++++-------- modules/nf-core/bcftools/roh/meta.yml | 67 +++++++++++++------ .../nf-core/bcftools/roh/tests/main.nf.test | 1 - .../bcftools/roh/tests/main.nf.test.snap | 44 ++++++++---- subworkflows/local/annotate_genome_snvs.nf | 1 - .../local/annotate_rhocallviz/main.nf | 1 - 8 files changed, 103 insertions(+), 70 deletions(-) diff --git a/modules.json b/modules.json index 3761f1a95..0fec9d9dd 100644 --- a/modules.json +++ b/modules.json @@ -49,7 +49,7 @@ }, "bcftools/roh": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/roh/environment.yml b/modules/nf-core/bcftools/roh/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/roh/environment.yml +++ b/modules/nf-core/bcftools/roh/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/roh/main.nf b/modules/nf-core/bcftools/roh/main.nf index ac96eef54..e275d64d5 100644 --- a/modules/nf-core/bcftools/roh/main.nf +++ b/modules/nf-core/bcftools/roh/main.nf @@ -1,11 +1,11 @@ process BCFTOOLS_ROH { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf), path(tbi) @@ -17,45 +17,35 @@ process BCFTOOLS_ROH { output: tuple val(meta), path("*.roh"), emit: roh - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def af_read = af_file ? "--AF-file ${af_file}" : '' - def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : '' - def reg_file = regions_file ? "--regions-file ${regions_file}" : '' - def samp_file = samples_file ? "--samples-file ${samples_file}" : '' - def targ_file = targets_file ? "--targets-file ${targets_file}" : '' + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def af_read = af_file ? "--AF-file ${af_file}" : '' + def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : '' + def reg_file = regions_file ? "--regions-file ${regions_file}" : '' + def samp_file = samples_file ? "--samples-file ${samples_file}" : '' + def targ_file = targets_file ? "--targets-file ${targets_file}" : '' """ bcftools \\ roh \\ - $args \\ - $af_read \\ - $gen_map \\ - $reg_file \\ - $samp_file \\ - $targ_file \\ + ${args} \\ + ${af_read} \\ + ${gen_map} \\ + ${reg_file} \\ + ${samp_file} \\ + ${targ_file} \\ -o ${prefix}.roh \\ - $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS + ${vcf} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.roh - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/roh/meta.yml b/modules/nf-core/bcftools/roh/meta.yml index 032148fa4..aada879c9 100644 --- a/modules/nf-core/bcftools/roh/meta.yml +++ b/modules/nf-core/bcftools/roh/meta.yml @@ -25,34 +25,42 @@ input: type: file description: VCF file pattern: "*.{vcf,.vcf.gz}" + ontologies: [] - tbi: type: file description: TBI file patthern: "*.tbi" + ontologies: [] - - af_file: type: file description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." + ontologies: [] - af_file_tbi: type: file description: "tbi index of af_file." - - - genetic_map: - type: file - description: "Genetic map in the format required also by IMPUTE2." - - - regions_file: - type: file - description: "Regions can be specified either on command line or in a VCF, BED, - or tab-delimited file (the default)." - - - samples_file: - type: file - description: "File of sample names to include or exclude if prefixed with '^'." - - - targets_file: - type: file - description: "Targets can be specified either on command line or in a VCF, BED, - or tab-delimited file (the default)." + ontologies: [] + - genetic_map: + type: file + description: "Genetic map in the format required also by IMPUTE2." + ontologies: [] + - regions_file: + type: file + description: "Regions can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." + ontologies: [] + - samples_file: + type: file + description: "File of sample names to include or exclude if prefixed with '^'." + ontologies: [] + - targets_file: + type: file + description: "Targets can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." + ontologies: [] output: - - roh: - - meta: + roh: + - - meta: type: map description: | Groovy Map containing sample information @@ -62,11 +70,28 @@ output: description: Contains site-specific and/or per-region runs of homo/autozygosity calls. pattern: "*.{roh}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test b/modules/nf-core/bcftools/roh/tests/main.nf.test index bb73b80c0..67cd98e53 100644 --- a/modules/nf-core/bcftools/roh/tests/main.nf.test +++ b/modules/nf-core/bcftools/roh/tests/main.nf.test @@ -63,5 +63,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap index 3b008a01e..281d96630 100644 --- a/modules/nf-core/bcftools/roh/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/roh/tests/main.nf.test.snap @@ -7,30 +7,38 @@ { "id": "test" }, - "test.roh:md5,853de778be3030754be40e11be0aa557" + "test.roh:md5,a75b347243c2e955ad4203a6be6dc616" ] ], "1": [ - "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + [ + "BCFTOOLS_ROH", + "bcftools", + "1.22" + ] ], "roh": [ [ { "id": "test" }, - "test.roh:md5,853de778be3030754be40e11be0aa557" + "test.roh:md5,a75b347243c2e955ad4203a6be6dc616" ] ], - "versions": [ - "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + "versions_bcftools": [ + [ + "BCFTOOLS_ROH", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T14:19:06.961553" + "timestamp": "2026-01-20T12:18:25.872864592" }, "test-bcftools-roh-stub": { "content": [ @@ -44,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + [ + "BCFTOOLS_ROH", + "bcftools", + "1.22" + ] ], "roh": [ [ @@ -54,15 +66,19 @@ "test.roh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,684b9cddcfaf57299e6e245b12b7d710" + "versions_bcftools": [ + [ + "BCFTOOLS_ROH", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T14:19:11.161719" + "timestamp": "2026-01-20T12:18:32.403407806" } } \ No newline at end of file diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index d06ae6849..42d686f60 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -196,7 +196,6 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) - ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions) ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_ROHCALL.out.versions) ch_versions = ch_versions.mix(VCFANNO.out.versions) diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 76b45844f..08770b84b 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -57,7 +57,6 @@ workflow ANNOTATE_RHOCALLVIZ { ch_versions = ch_versions.mix(BCFTOOLS_VIEW_RHOCALL.out.versions) ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_ROH.out.versions) ch_versions = ch_versions.mix(BCFTOOLS_VIEW_UNCOMPRESS.out.versions) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) From a6f789d9b124566823fb45db9ce2d1b4549cae4b Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:34:10 +0100 Subject: [PATCH 255/872] view --- modules.json | 2 +- modules/nf-core/bcftools/sort/environment.yml | 7 +- modules/nf-core/bcftools/sort/main.nf | 70 ++++---- modules/nf-core/bcftools/sort/meta.yml | 42 +++-- .../nf-core/bcftools/sort/tests/main.nf.test | 16 +- .../bcftools/sort/tests/main.nf.test.snap | 154 ++++++++++++------ modules/nf-core/bcftools/sort/tests/tags.yml | 2 - subworkflows/local/call_mobile_elements.nf | 1 - subworkflows/local/rank_variants.nf | 1 - 9 files changed, 184 insertions(+), 111 deletions(-) delete mode 100644 modules/nf-core/bcftools/sort/tests/tags.yml diff --git a/modules.json b/modules.json index 0fec9d9dd..ad1142751 100644 --- a/modules.json +++ b/modules.json @@ -56,7 +56,7 @@ }, "bcftools/sort": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules" ] diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 7d4c9b8e9..e0dfad2df 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -1,20 +1,20 @@ process BCFTOOLS_SORT { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -22,49 +22,51 @@ process BCFTOOLS_SORT { script: def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def max_memory = task.memory ? "--max-mem ${task.memory.toUnit('MB') * 0.9}M" : "" """ bcftools \\ sort \\ --output ${prefix}.${extension} \\ --temp-dir . \\ - $args \\ - $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS + ${max_memory} \\ + ${args} \\ + ${vcf} """ stub: def args = task.ext.args ?: '--output-type z' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index f7a6eff17..1c3f2a540 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -23,9 +23,10 @@ input: type: file description: The VCF/BCF file to be sorted pattern: "*.{vcf.gz,vcf,bcf}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,8 +35,9 @@ output: type: file description: Sorted VCF file pattern: "*.{vcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -44,8 +46,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -54,11 +57,28 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test index b9bdd76a0..bda7bacee 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -27,7 +27,6 @@ nextflow_process { { assert snapshot(process.out).match("vcf") } ) } - } test("sarscov2 - vcf_gz_index") { @@ -52,12 +51,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_csi") { @@ -82,12 +80,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_tbi") { @@ -112,12 +109,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } test("sarscov2 - vcf - stub") { @@ -139,7 +135,6 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - vcf_gz_index - stub") { @@ -165,7 +160,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_csi - stub") { @@ -191,7 +185,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - vcf_gz_index_tbi - stub") { @@ -217,6 +210,5 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap index f38272cb2..9b9e4dc7c 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -22,7 +22,11 @@ ], "3": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ], "csi": [ @@ -43,16 +47,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:06:05.201680777" + "timestamp": "2026-01-20T12:19:24.286732272" }, "vcf": { "content": [ @@ -72,7 +80,11 @@ ], "3": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ], "csi": [ @@ -88,16 +100,20 @@ "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:04:43.889971134" + "timestamp": "2026-01-20T12:18:38.783455397" }, "sarscov2 - vcf_gz_index": { "content": [ @@ -120,15 +136,21 @@ [ ], - [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:04:55.385964497" + "timestamp": "2026-01-20T12:18:45.081447395" }, "sarscov2 - vcf_gz_index_csi": { "content": [ @@ -151,15 +173,21 @@ [ ], - [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:05:06.662818922" + "timestamp": "2026-01-20T12:18:51.194304667" }, "sarscov2 - vcf_gz_index - stub": { "content": [ @@ -184,7 +212,11 @@ ] ], "3": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -205,16 +237,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:05:40.012912381" + "timestamp": "2026-01-20T12:19:11.413154111" }, "sarscov2 - vcf_gz_index_csi - stub": { "content": [ @@ -239,7 +275,11 @@ ] ], "3": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -260,16 +300,20 @@ "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:05:52.405673587" + "timestamp": "2026-01-20T12:19:17.770087535" }, "sarscov2 - vcf - stub": { "content": [ @@ -289,7 +333,11 @@ ], "3": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ], "csi": [ @@ -305,16 +353,20 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:05:29.117946461" + "timestamp": "2026-01-20T12:19:04.409593559" }, "sarscov2 - vcf_gz_index_tbi": { "content": [ @@ -337,14 +389,20 @@ "test_vcf.vcf.gz.tbi" ] ], - [ - "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_SORT", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:05:17.217274984" + "timestamp": "2026-01-20T12:18:57.536633502" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/tags.yml b/modules/nf-core/bcftools/sort/tests/tags.yml deleted file mode 100644 index 6e9520dd3..000000000 --- a/modules/nf-core/bcftools/sort/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/sort: - - "modules/nf-core/bcftools/sort/**" diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 0ad815245..be7ba8ee9 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -124,7 +124,6 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions) ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_SORT_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) ch_versions = ch_versions.mix(TABIX_ME.out.versions) diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 2a425cf87..126c51b91 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -35,7 +35,6 @@ workflow RANK_VARIANTS { if (process_with_sort) { ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf).vcf // SV file needs to be sorted before indexing - ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions) } else { ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_tbi.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) From 043f9967d73fdbb839a2688f7ed6c71119a616a2 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:38:25 +0100 Subject: [PATCH 256/872] bcftools view --- modules.json | 2 +- modules/nf-core/bcftools/view/environment.yml | 7 +- modules/nf-core/bcftools/view/main.nf | 80 ++++----- modules/nf-core/bcftools/view/meta.yml | 76 +++++--- .../nf-core/bcftools/view/tests/main.nf.test | 24 +-- .../bcftools/view/tests/main.nf.test.snap | 168 ++++++++++++------ modules/nf-core/bcftools/view/tests/tags.yml | 2 - subworkflows/local/annotate_cadd/main.nf | 1 - subworkflows/local/annotate_genome_snvs.nf | 1 - .../local/annotate_mobile_elements.nf | 1 - .../local/annotate_rhocallviz/main.nf | 2 - .../local/annotate_structural_variants.nf | 1 - subworkflows/local/call_sv_cnvnator/main.nf | 1 - .../local/call_sv_germlinecnvcaller/main.nf | 1 - subworkflows/local/call_sv_manta/main.nf | 1 - subworkflows/local/call_sv_tiddit/main.nf | 1 - subworkflows/local/generate_cytosure_files.nf | 1 - 17 files changed, 218 insertions(+), 152 deletions(-) delete mode 100644 modules/nf-core/bcftools/view/tests/tags.yml diff --git a/modules.json b/modules.json index ad1142751..b0a11bb54 100644 --- a/modules.json +++ b/modules.json @@ -63,7 +63,7 @@ }, "bcftools/view": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": [ "modules", "vcf_filter_bcftools_ensemblvep" diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml index 5c00b116a..ba863b388 100644 --- a/modules/nf-core/bcftools/view/environment.yml +++ b/modules/nf-core/bcftools/view/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::bcftools=1.20 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/bcftools + - bioconda::bcftools=1.22 diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf index 7fe4303c0..b3fd7b733 100644 --- a/modules/nf-core/bcftools/view/main.nf +++ b/modules/nf-core/bcftools/view/main.nf @@ -1,23 +1,23 @@ process BCFTOOLS_VIEW { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': - 'biocontainers/bcftools:1.20--h8b25389_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data' + : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: tuple val(meta), path(vcf), path(index) - path(regions) - path(targets) - path(samples) + path regions + path targets + path samples output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi, optional: true - tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools when: task.ext.when == null || task.ext.when @@ -25,52 +25,52 @@ process BCFTOOLS_VIEW { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def regions_file = regions ? "--regions-file ${regions}" : "" + def regions_file = regions ? "--regions-file ${regions}" : "" def targets_file = targets ? "--targets-file ${targets}" : "" - def samples_file = samples ? "--samples-file ${samples}" : "" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" + def samples_file = samples ? "--samples-file ${samples}" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" """ bcftools view \\ --output ${prefix}.${extension} \\ ${regions_file} \\ ${targets_file} \\ ${samples_file} \\ - $args \\ - --threads $task.cpus \\ + ${args} \\ + --threads ${task.cpus} \\ ${vcf} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : - args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : - args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : - args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : - "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def extension = args.contains("--output-type b") || args.contains("-Ob") + ? "bcf.gz" + : args.contains("--output-type u") || args.contains("-Ou") + ? "bcf" + : args.contains("--output-type z") || args.contains("-Oz") + ? "vcf.gz" + : args.contains("--output-type v") || args.contains("-Ov") + ? "vcf" + : "vcf" + def stub_index = args.contains("--write-index=tbi") || args.contains("-W=tbi") + ? "tbi" + : args.contains("--write-index=csi") || args.contains("-W=csi") + ? "csi" + : args.contains("--write-index") || args.contains("-W") + ? "csi" + : "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" - def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" - + def create_index = extension.endsWith(".gz") && stub_index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${stub_index}" : "" """ ${create_cmd} ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml index aa7785f12..46761894d 100644 --- a/modules/nf-core/bcftools/view/meta.yml +++ b/modules/nf-core/bcftools/view/meta.yml @@ -26,29 +26,34 @@ input: description: | The vcf file to be inspected. e.g. 'file.vcf' + ontologies: [] - index: type: file description: | The tab index for the VCF file to be inspected. e.g. 'file.tbi' - - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + ontologies: [] + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + ontologies: [] + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + ontologies: [] + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -57,8 +62,9 @@ output: type: file description: VCF normalized output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +73,9 @@ output: type: file description: Alternative VCF file index pattern: "*.tbi" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,11 +84,28 @@ output: type: file description: Default VCF file index pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bcftools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bcftools: + type: string + description: The tool name + - "bcftools --version | sed '1!d; s/^.*bcftools //'": + type: string + description: The command used to generate the version of the tool authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test index 1e60c50d5..3ed2b90c1 100644 --- a/modules/nf-core/bcftools/view/tests/main.nf.test +++ b/modules/nf-core/bcftools/view/tests/main.nf.test @@ -33,11 +33,10 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index") { @@ -66,12 +65,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi") { @@ -100,12 +98,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi") { @@ -134,12 +131,11 @@ nextflow_process { process.out.vcf, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } test("sarscov2 - [vcf, tbi], vcf, tsv, []") { @@ -166,11 +162,10 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - stub") { @@ -198,11 +193,10 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.vcf[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub") { @@ -232,7 +226,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub") { @@ -262,7 +255,6 @@ nextflow_process { { assert process.out.csi[0][1].endsWith(".csi") } ) } - } test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub") { @@ -292,7 +284,5 @@ nextflow_process { { assert process.out.tbi[0][1].endsWith(".tbi") } ) } - } - -} \ No newline at end of file +} diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test.snap b/modules/nf-core/bcftools/view/tests/main.nf.test.snap index fec22e366..92972d192 100644 --- a/modules/nf-core/bcftools/view/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/view/tests/main.nf.test.snap @@ -24,7 +24,11 @@ ] ], "3": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -47,16 +51,20 @@ "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:14:38.717458272" + "timestamp": "2026-01-20T12:21:02.710815567" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ @@ -81,15 +89,21 @@ "out_vcf.vcf.gz.tbi" ] ], - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:13:44.760671384" + "timestamp": "2026-01-20T12:20:36.071823323" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": { "content": [ @@ -116,7 +130,11 @@ ] ], "3": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ], "csi": [ [ @@ -139,16 +157,20 @@ "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-04T16:06:21.669668533" + "timestamp": "2026-01-20T12:20:56.054811979" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": { "content": [ @@ -175,7 +197,11 @@ ], "3": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ], "csi": [ @@ -198,16 +224,20 @@ "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:14:53.026083914" + "timestamp": "2026-01-20T12:21:09.229049434" }, "sarscov2 - [vcf, tbi], vcf, tsv, []": { "content": [ @@ -220,28 +250,40 @@ "out.vcf:md5,1bcbd0eff25d316ba915d06463aab17b" ] ], - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-31T15:15:14.663512924" + "timestamp": "2026-01-20T12:20:42.68820706" }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ "out.vcf", - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-31T15:15:19.723448323" + "timestamp": "2026-01-20T12:20:49.538986405" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": { "content": [ @@ -266,15 +308,21 @@ [ ], - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T08:24:36.358469315" + "timestamp": "2026-01-20T12:20:22.451426124" }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -287,15 +335,21 @@ "out.vcf:md5,8e722884ffb75155212a3fc053918766" ] ], - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-31T15:15:09.588867653" + "timestamp": "2026-01-20T12:20:16.040611233" }, "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": { "content": [ @@ -320,14 +374,20 @@ [ ], - [ - "versions.yml:md5,241125d00357804552689c37bbabe1f5" - ] + { + "versions_bcftools": [ + [ + "BCFTOOLS_VIEW", + "bcftools", + "1.22" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-06-05T12:13:33.834986869" + "timestamp": "2026-01-20T12:20:29.512063514" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/view/tests/tags.yml b/modules/nf-core/bcftools/view/tests/tags.yml deleted file mode 100644 index 43b1f0aa0..000000000 --- a/modules/nf-core/bcftools/view/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bcftools/view: - - "modules/nf-core/bcftools/view/**" diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 4d2f9f8e4..fb7828b92 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -71,7 +71,6 @@ workflow ANNOTATE_CADD { TABIX_ANNOTATE (BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(TABIX_VIEW.out.versions) ch_versions = ch_versions.mix(CADD.out.versions) ch_versions = ch_versions.mix(TABIX_CADD.out.versions) diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 42d686f60..b43311123 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -204,7 +204,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(CHROMOGRAPH_SITES.out.versions) ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions) ch_versions = ch_versions.mix(TABIX_VEP.out.versions) diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index 0a954c0a4..6b276d5d3 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -74,7 +74,6 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_versions = ch_versions.mix( SVDB_QUERY_DB.out.versions ) ch_versions = ch_versions.mix( PICARD_SORTVCF.out.versions ) ch_versions = ch_versions.mix( ENSEMBLVEP_ME.out.versions ) - ch_versions = ch_versions.mix( BCFTOOLS_VIEW_FILTER.out.versions ) emit: vcf_ann = BCFTOOLS_VIEW_FILTER.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 08770b84b..f80fb7129 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -54,10 +54,8 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_RHOCALL.out.versions) ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_UNCOMPRESS.out.versions) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 9bca4d2fe..aa67c0066 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -101,7 +101,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) ch_versions = ch_versions.mix(PICARD_SORTVCF.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(ENSEMBLVEP_SV.out.versions) ch_versions = ch_versions.mix(TABIX_VEP.out.versions) diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 51c90ad28..153928c94 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -48,7 +48,6 @@ workflow CALL_SV_CNVNATOR { ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions) ch_versions = ch_versions.mix(INDEX_CNVNATOR.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_CNVNATOR.out.versions) emit: vcf = SVDB_MERGE_CNVNATOR.out.vcf // channel: [ val(meta), path(*.tar.gz) ] diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index 129ec0caf..aaae54735 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -81,7 +81,6 @@ workflow CALL_SV_GERMLINECNVCALLER { ch_versions = ch_versions.mix(GATK4_GERMLINECNVCALLER.out.versions) ch_versions = ch_versions.mix(GATK4_POSTPROCESSGERMLINECNVCALLS.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_GCNVCALLER.out.versions) emit: diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 02499e999..c7c4ae6f9 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -49,7 +49,6 @@ workflow CALL_SV_MANTA { BCFTOOLS_VIEW_MANTA (ch_filter_in, [], [], []) ch_versions = MANTA.out.versions - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_MANTA.out.versions) emit: candidate_small_indels_vcf = MANTA.out.candidate_small_indels_vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index 93b80940a..d368a8049 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -32,7 +32,6 @@ workflow CALL_SV_TIDDIT { ch_versions = TIDDIT_SV.out.versions ch_versions = ch_versions.mix(SVDB_MERGE_TIDDIT.out.versions) ch_versions = ch_versions.mix(INDEX_TIDDIT.out.versions) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW_TIDDIT.out.versions) emit: vcf = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 29cb5cc37..fd8600298 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -89,7 +89,6 @@ workflow GENERATE_CYTOSURE_FILES { ) ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) - ch_versions = ch_versions.mix(SPLIT_AND_FILTER_SV_VCF.out.versions) ch_versions = ch_versions.mix(VCF2CYTOSURE.out.versions) emit: From 7b19491f2bc780deb3b965b93446277dddbec4eb Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:39:14 +0100 Subject: [PATCH 257/872] update modules.json --- modules.json | 457 +++++++++++++-------------------------------------- 1 file changed, 114 insertions(+), 343 deletions(-) diff --git a/modules.json b/modules.json index b0a11bb54..83f116992 100644 --- a/modules.json +++ b/modules.json @@ -8,771 +8,550 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/slop": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwameme/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwameme/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "chromograph": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/addmostseverepli": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "eklipse": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/filtervep": { "branch": "master", "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "expansionhunter": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/denoisereadcounts": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/germlinecnvcaller": { "branch": "master", "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mergebamalignment": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/postprocessgermlinecnvcalls": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/printreads": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/revertsam": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/samtofastq": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/selectvariants": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/shiftfasta": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/splitintervals": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/annotate": { "branch": "master", "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", - "installed_by": [ - 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"installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "qualimap/bamqc": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rhocall/annotate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rhocall/viz": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": [ - 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"installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/datametrics": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/readwriter": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stranger": { "branch": "master", "git_sha": "ffe458cbd1208b82e33e607fa43fbe80df191047", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -781,33 +560,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 41377c9fc291a8971ea0d874427c86ce4b782b2c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 15:42:40 +0100 Subject: [PATCH 258/872] update bedtools --- modules.json | 4 +- .../bedtools/genomecov/environment.yml | 2 + modules/nf-core/bedtools/genomecov/main.nf | 56 +++----- modules/nf-core/bedtools/genomecov/meta.yml | 57 ++++++--- .../genomecov/tests/main.nf.test.snap | 120 ++++++++++++------ .../bedtools/genomecov/tests/nextflow.config | 2 +- modules/nf-core/bedtools/slop/environment.yml | 2 + modules/nf-core/bedtools/slop/main.nf | 32 ++--- modules/nf-core/bedtools/slop/meta.yml | 39 ++++-- .../bedtools/slop/tests/main.nf.test.snap | 20 ++- subworkflows/local/prepare_references/main.nf | 3 +- subworkflows/local/subsample_mt_frac/main.nf | 1 - 12 files changed, 206 insertions(+), 132 deletions(-) diff --git a/modules.json b/modules.json index 83f116992..c33f401f5 100644 --- a/modules.json +++ b/modules.json @@ -52,12 +52,12 @@ }, "bedtools/genomecov": { "branch": "master", - "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", + "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", "installed_by": ["modules"] }, "bedtools/slop": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", "installed_by": ["modules"] }, "bwa/index": { diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 5683bc05f..45c307b0e 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 35e2ab14b..710da5b47 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -1,66 +1,57 @@ process BEDTOOLS_GENOMECOV { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data' + : 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b'}" input: tuple val(meta), path(intervals), val(scale) - path sizes - val extension - val sort + path sizes + val extension + val sort output: tuple val(meta), path("*.${extension}"), emit: genomecov - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bedtools'), eval("bedtools --version | sed -e 's/bedtools v//g'"), topic: versions, emit: versions_bedtools when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args_list = args.tokenize() - args += (scale > 0 && scale != 1) ? " -scale $scale" : "" + args += scale > 0 && scale != 1 ? " -scale ${scale}" : "" if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) { args += " -bg" } // Sorts output file by chromosome and position using additional options for performance and consistency // See https://www.biostars.org/p/66927/ for further details - def buffer = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : '' - def sort_cmd = sort ? "| LC_ALL=C sort --parallel=$task.cpus $buffer -k1,1 -k2,2n" : '' + def buffer = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : '' + def sort_cmd = sort ? "| LC_ALL=C sort --parallel=${task.cpus} ${buffer} -k1,1 -k2,2n" : '' def prefix = task.ext.prefix ?: "${meta.id}" if (intervals.name =~ /\.bam/) { """ bedtools \\ genomecov \\ - -ibam $intervals \\ - $args \\ - $sort_cmd \\ + -ibam ${intervals} \\ + ${args} \\ + ${sort_cmd} \\ > ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS """ - } else { + } + else { """ bedtools \\ genomecov \\ - -i $intervals \\ - -g $sizes \\ - $args \\ - $sort_cmd \\ + -i ${intervals} \\ + -g ${sizes} \\ + ${args} \\ + ${sort_cmd} \\ > ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS """ } @@ -68,10 +59,5 @@ process BEDTOOLS_GENOMECOV { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS """ } diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml index 41b1f8f49..69b911c23 100644 --- a/modules/nf-core/bedtools/genomecov/meta.yml +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -24,26 +24,28 @@ input: type: file description: BAM/BED/GFF/VCF pattern: "*.{bam|bed|gff|vcf}" + ontologies: [] - scale: type: integer description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and - chromosome sizes in the second column - - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", - ".tab", etc.) It is set arbitrarily by the user and corresponds to the file - format which depends on arguments. - - - sort: - type: boolean - description: Sort the output + - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and chromosome + sizes in the second column + ontologies: [] + - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", + ".tab", etc.) It is set arbitrarily by the user and corresponds to the file + format which depends on arguments. + - sort: + type: boolean + description: Sort the output output: - - genomecov: - - meta: + genomecov: + - - meta: type: map description: | Groovy Map containing sample information @@ -52,11 +54,28 @@ output: type: file description: Computed genome coverage file pattern: "*.${extension}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bedtools: + - - ${task.process}: + type: string + description: The name of the process + - bedtools: + type: string + description: The name of the tool + - "bedtools --version | sed -e 's/bedtools v//g'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bedtools: + type: string + description: The name of the tool + - "bedtools --version | sed -e 's/bedtools v//g'": + type: eval + description: The expression to obtain the version of the tool authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap index da6dbe875..4175ae7c9 100644 --- a/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap +++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -21,16 +25,20 @@ "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T11:59:33.898146" + "timestamp": "2026-01-21T11:30:01.187722797" }, "sarscov2 - no scale - stub": { "content": [ @@ -44,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -54,16 +66,20 @@ "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T11:59:52.483371" + "timestamp": "2026-01-21T11:30:16.248235814" }, "sarscov2 - scale": { "content": [ @@ -77,7 +93,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -87,16 +107,20 @@ "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T11:59:43.69501" + "timestamp": "2026-01-21T11:30:08.76325362" }, "sarscov2 - scale - stub": { "content": [ @@ -110,7 +134,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -120,16 +148,20 @@ "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T12:00:09.930036" + "timestamp": "2026-01-21T11:30:32.324649338" }, "sarscov2 - no scale": { "content": [ @@ -143,7 +175,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -153,16 +189,20 @@ "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T11:59:25.448817" + "timestamp": "2026-01-21T11:29:54.109132031" }, "sarscov2 - dummy sizes - stub": { "content": [ @@ -176,7 +216,11 @@ ] ], "1": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ], "genomecov": [ [ @@ -186,15 +230,19 @@ "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2" + "versions_bedtools": [ + [ + "BEDTOOLS_GENOMECOV", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T12:00:01.086433" + "timestamp": "2026-01-21T11:30:23.839839194" } } \ No newline at end of file diff --git a/modules/nf-core/bedtools/genomecov/tests/nextflow.config b/modules/nf-core/bedtools/genomecov/tests/nextflow.config index bdb74ae5a..670ef7fd5 100644 --- a/modules/nf-core/bedtools/genomecov/tests/nextflow.config +++ b/modules/nf-core/bedtools/genomecov/tests/nextflow.config @@ -3,5 +3,5 @@ process { withName: BEDTOOLS_GENOMECOV { ext.prefix = { "${meta.id}.coverage" } } - + } diff --git a/modules/nf-core/bedtools/slop/environment.yml b/modules/nf-core/bedtools/slop/environment.yml index 5683bc05f..45c307b0e 100644 --- a/modules/nf-core/bedtools/slop/environment.yml +++ b/modules/nf-core/bedtools/slop/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/bedtools/slop/main.nf b/modules/nf-core/bedtools/slop/main.nf index e5b8e1ef0..b0e636bf7 100644 --- a/modules/nf-core/bedtools/slop/main.nf +++ b/modules/nf-core/bedtools/slop/main.nf @@ -1,19 +1,19 @@ process BEDTOOLS_SLOP { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : - 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' + : 'biocontainers/bedtools:2.31.1--hf5e1c6e_0'}" input: tuple val(meta), path(bed) - path sizes + path sizes output: tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bedtools'), eval("bedtools --version | sed -e 's/bedtools v//g'"), topic: versions, emit: versions_bedtools when: task.ext.when == null || task.ext.when @@ -21,29 +21,21 @@ process BEDTOOLS_SLOP { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + if ("${bed}" == "${prefix}.bed") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ bedtools \\ slop \\ - -i $bed \\ - -g $sizes \\ - $args \\ + -i ${bed} \\ + -g ${sizes} \\ + ${args} \\ > ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - END_VERSIONS """ } diff --git a/modules/nf-core/bedtools/slop/meta.yml b/modules/nf-core/bedtools/slop/meta.yml index 762db534a..681ee3164 100644 --- a/modules/nf-core/bedtools/slop/meta.yml +++ b/modules/nf-core/bedtools/slop/meta.yml @@ -22,12 +22,14 @@ input: type: file description: Input BED file pattern: "*.{bed}" - - - sizes: - type: file - description: Chromosome sizes file + ontologies: [] + - sizes: + type: file + description: Chromosome sizes file + ontologies: [] output: - - bed: - - meta: + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -36,11 +38,28 @@ output: type: file description: Slopped BED file pattern: "*.{bed}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bedtools: + - - ${task.process}: + type: string + description: The name of the process + - bedtools: + type: string + description: The name of the tool + - "bedtools --version | sed -e 's/bedtools v//g'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bedtools: + type: string + description: The name of the tool + - "bedtools --version | sed -e 's/bedtools v//g'": + type: eval + description: The expression to obtain the version of the tool authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap index 899ac21ba..1da1814d7 100644 --- a/modules/nf-core/bedtools/slop/tests/main.nf.test.snap +++ b/modules/nf-core/bedtools/slop/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf" + [ + "BEDTOOLS_SLOP", + "bedtools", + "2.31.1" + ] ], "bed": [ [ @@ -21,15 +25,19 @@ "test_out.bed:md5,4f1d8924925fe5d205c9e1981fe290a4" ] ], - "versions": [ - "versions.yml:md5,ee6210f0a2c4a60d9cad324bfe18e0cf" + "versions_bedtools": [ + [ + "BEDTOOLS_SLOP", + "bedtools", + "2.31.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T13:52:04.945029" + "timestamp": "2026-01-21T11:43:36.722281618" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 76ff9391b..088840d16 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -234,8 +234,7 @@ workflow PREPARE_REFERENCES { ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) - ch_versions = ch_versions.mix(BEDTOOLS_PAD_TARGET_BED.out.versions, - TABIX_BGZIPINDEX_PADDED_BED.out.versions, + ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions, GATK_BILT.out.versions, GATK_ILT.out.versions, CAT_CAT_BAIT.out.versions) diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 67ef02e2d..fe9a1e19b 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -34,7 +34,6 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') - ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions) ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) From 551ee6cd2321c2dc8b0430b9dc3b68f1f5736962 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:00:45 +0100 Subject: [PATCH 259/872] update cat --- modules.json | 459 +++++++++++++----- modules/nf-core/cat/cat/environment.yml | 4 +- modules/nf-core/cat/cat/main.nf | 6 +- modules/nf-core/cat/cat/meta.yml | 42 +- modules/nf-core/cat/cat/tests/main.nf.test | 85 ++-- .../nf-core/cat/cat/tests/main.nf.test.snap | 282 ++++++++--- modules/nf-core/cat/cat/tests/nextflow.config | 6 + .../cat/tests/nextflow_unzipped_zipped.config | 6 - .../cat/tests/nextflow_zipped_unzipped.config | 8 - modules/nf-core/cat/cat/tests/tags.yml | 2 - subworkflows/local/prepare_references/main.nf | 3 +- 11 files changed, 640 insertions(+), 263 deletions(-) create mode 100644 modules/nf-core/cat/cat/tests/nextflow.config delete mode 100644 modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config delete mode 100644 modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config delete mode 100644 modules/nf-core/cat/cat/tests/tags.yml diff --git a/modules.json b/modules.json index c33f401f5..68285a861 100644 --- a/modules.json +++ b/modules.json @@ -8,550 +8,771 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "git_sha": "69614d4579a6bd9b8a2ecffb35959809d9c36559", + "installed_by": [ + "modules" + ] }, "chromograph": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/annotate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/viz": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/format": { "branch": "master", "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sambamba/depth": { "branch": "master", "git_sha": "b093f74ddc3ada57a84a209f0e4fb3871bacf2ad", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/collate": { "branch": "master", "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwamem": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/datametrics": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dedup": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnascope": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/readwriter": { "branch": "master", "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "ffe458cbd1208b82e33e607fa43fbe80df191047", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -560,25 +781,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index 9b01c865a..985117698 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - conda-forge::pigz=2.3.4 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 2862c64cd..aa72fc4d9 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -4,15 +4,15 @@ process CAT_CAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - 'biocontainers/pigz:2.3.4' }" + 'https://depot.galaxyproject.org/singularity/pigz:2.8' : + 'biocontainers/pigz:2.8' }" input: tuple val(meta), path(files_in) output: tuple val(meta), path("${prefix}"), emit: file_out - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("pigz"), eval("pigz --version 2>&1 | sed 's/pigz //g'"), topic: versions, emit: versions_cat when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 81778a067..36a7359bb 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -20,21 +20,41 @@ input: type: file description: List of compressed / uncompressed files pattern: "*" + ontologies: [] output: - - file_out: - - meta: - type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" - pattern: "${file_out}" + file_out: + - - meta: + type: map + description: Groovy Map containing sample information - ${prefix}: type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" + description: Concatenated file. Will be gzipped if file_out ends with + ".gz" pattern: "${file_out}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_cat: + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - "pigz --version 2>&1 | sed 's/pigz //g'": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - "pigz --version 2>&1 | sed 's/pigz //g'": + type: eval + description: The expression to obtain the version of the tool + authors: - "@erikrikarddaniel" - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index 9cb161788..030c6649d 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -3,16 +3,14 @@ nextflow_process { name "Test Process CAT_CAT" script "../main.nf" process "CAT_CAT" + tag "modules" tag "modules_nfcore" tag "cat" tag "cat/cat" - test("test_cat_name_conflict") { + test("sarscov2 - genome - error: name conflict") { when { - params { - outdir = "${outputDir}" - } process { """ input[0] = @@ -30,16 +28,13 @@ nextflow_process { assertAll( { assert !process.success }, { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(process.out).match() } ) } } - test("test_cat_unzipped_unzipped") { + test("sarscov2 - [ fasta, sizes ] - unzipped") { when { - params { - outdir = "${outputDir}" - } process { """ input[0] = @@ -62,11 +57,8 @@ nextflow_process { } - test("test_cat_zipped_zipped") { + test("sarscov2 - [ gff3_gz, maf_gz ] - zipped") { when { - params { - outdir = "${outputDir}" - } process { """ input[0] = @@ -81,25 +73,20 @@ nextflow_process { } } then { - def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() + { assert snapshot(process.out).match() } ) } } - test("test_cat_zipped_unzipped") { - config './nextflow_zipped_unzipped.config' + test("sarscov2 - [ gff3_gz, maf_gz ] - unzipped") { + config './nextflow.config' when { params { - outdir = "${outputDir}" + cat_prefix = "cat.txt" } process { """ @@ -124,11 +111,12 @@ nextflow_process { } - test("test_cat_unzipped_zipped") { - config './nextflow_unzipped_zipped.config' + test("sarscov2 - [ fasta, sizes ] - zipped") { + config './nextflow.config' + when { params { - outdir = "${outputDir}" + cat_prefix = "cat.txt.gz" } process { """ @@ -144,24 +132,19 @@ nextflow_process { } } then { - def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } ) } } - test("test_cat_one_file_unzipped_zipped") { - config './nextflow_unzipped_zipped.config' + test("sarscov2 - fasta - zipped") { + config './nextflow.config' + when { params { - outdir = "${outputDir}" + cat_prefix = "cat.txt.gz" } process { """ @@ -176,15 +159,33 @@ nextflow_process { } } then { - def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - fasta - unzipped - stub") { + options "-stub" + + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap index b7623ee65..5b4e4cc3d 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test.snap +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_cat_unzipped_unzipped": { + "sarscov2 - [ gff3_gz, maf_gz ] - unzipped": { "content": [ { "0": [ @@ -8,11 +8,15 @@ "id": "test", "single_end": true }, - "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" ] ], "1": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + [ + "CAT_CAT", + "pigz", + "2.8" + ] ], "file_out": [ [ @@ -20,21 +24,25 @@ "id": "test", "single_end": true }, - "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" ] ], - "versions": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2023-10-16T14:32:18.500464399" + "timestamp": "2025-12-10T09:08:31.479828" }, - "test_cat_zipped_unzipped": { + "sarscov2 - fasta - unzipped - stub": { "content": [ { "0": [ @@ -43,11 +51,15 @@ "id": "test", "single_end": true }, - "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + [ + "CAT_CAT", + "pigz", + "2.8" + ] ], "file_out": [ [ @@ -55,93 +67,217 @@ "id": "test", "single_end": true }, - "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2023-10-16T14:32:49.642741302" + "timestamp": "2025-12-10T16:16:28.118094" }, - "test_cat_zipped_zipped": { + "sarscov2 - [ fasta, sizes ] - zipped": { "content": [ - [ - "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", - "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", - "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", - "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", - "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", - "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" - ], - 78, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T16:15:56.529595" + }, + "sarscov2 - genome - error: name conflict": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "file_out": [ + + ], + "versions_cat": [ + + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-22T11:51:46.802978" + "timestamp": "2025-12-10T16:14:54.496538" }, - "test_cat_name_conflict": { + "sarscov2 - [ fasta, sizes ] - unzipped": { "content": [ - [ - - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-22T11:51:29.45394" + "timestamp": "2025-12-10T11:26:29.942203" }, - "test_cat_one_file_unzipped_zipped": { + "sarscov2 - [ gff3_gz, maf_gz ] - zipped": { "content": [ - [ - ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", - "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", - "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", - "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", - "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", - "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" - ], - 374, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-22T11:52:02.774016" + "timestamp": "2025-12-10T11:26:45.679401" }, - "test_cat_unzipped_zipped": { + "sarscov2 - fasta - zipped": { "content": [ - [ - ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", - "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", - "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", - "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", - "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", - "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" - ], - 375, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,6e9fe4042a72f2345f644f239272b7e6" + ] + ], + "1": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,6e9fe4042a72f2345f644f239272b7e6" + ] + ], + "versions_cat": [ + [ + "CAT_CAT", + "pigz", + "2.8" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-22T11:51:57.581523" + "timestamp": "2025-12-10T16:16:12.439911" } } \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow.config b/modules/nf-core/cat/cat/tests/nextflow.config new file mode 100644 index 000000000..5bc9bf50e --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = "${params.cat_prefix}" + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config deleted file mode 100644 index ec26b0fdc..000000000 --- a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config +++ /dev/null @@ -1,6 +0,0 @@ - -process { - withName: CAT_CAT { - ext.prefix = 'cat.txt.gz' - } -} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config deleted file mode 100644 index fbc79783d..000000000 --- a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config +++ /dev/null @@ -1,8 +0,0 @@ - -process { - - withName: CAT_CAT { - ext.prefix = 'cat.txt' - } - -} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml deleted file mode 100644 index 37b578f52..000000000 --- a/modules/nf-core/cat/cat/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -cat/cat: - - modules/nf-core/cat/cat/** diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 088840d16..ef781e070 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -236,8 +236,7 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions, GATK_BILT.out.versions, - GATK_ILT.out.versions, - CAT_CAT_BAIT.out.versions) + GATK_ILT.out.versions) } // // Prepare vcfanno extra files From 8e05fad4557745e6a3d740c46f1589fdeba6cbc5 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:05:03 +0100 Subject: [PATCH 260/872] update ensemblvep --- modules.json | 4 +- .../ensemblvep/filtervep/environment.yml | 5 +- modules/nf-core/ensemblvep/filtervep/main.nf | 32 +-- modules/nf-core/ensemblvep/filtervep/meta.yml | 43 +++- .../ensemblvep/filtervep/tests/main.nf.test | 49 +---- .../filtervep/tests/main.nf.test.snap | 36 ++- .../filtervep/tests/nextflow.config | 2 +- .../ensemblvep/filtervep/tests/tab.gz.config | 6 - .../ensemblvep/filtervep/tests/tags.yml | 2 - .../ensemblvep/filtervep/tests/vcf.config | 6 - .../nf-core/ensemblvep/vep/environment.yml | 8 + modules/nf-core/ensemblvep/vep/main.nf | 77 +++---- modules/nf-core/ensemblvep/vep/meta.yml | 206 +++++++++++++----- .../nf-core/ensemblvep/vep/tests/main.nf.test | 89 ++++++++ .../ensemblvep/vep/tests/main.nf.test.snap | 55 +++++ .../ensemblvep/vep/tests/nextflow.config | 5 + .../ensemblvep/vep/tests/tab.gz.config | 5 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + subworkflows/local/annotate_genome_snvs.nf | 1 - .../local/annotate_mobile_elements.nf | 1 - subworkflows/local/annotate_mt_snvs.nf | 1 - .../local/annotate_structural_variants.nf | 1 - .../vcf_filter_bcftools_ensemblvep/main.nf | 1 - 23 files changed, 445 insertions(+), 195 deletions(-) delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/tags.yml create mode 100644 modules/nf-core/ensemblvep/vep/environment.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config diff --git a/modules.json b/modules.json index 68285a861..77a373beb 100644 --- a/modules.json +++ b/modules.json @@ -191,7 +191,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", + "git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2", "installed_by": [ "modules", "vcf_filter_bcftools_ensemblvep" @@ -199,7 +199,7 @@ }, "ensemblvep/vep": { "branch": "master", - "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", + "git_sha": "51d2d20973eca80048a9490339e8b421db122908", "installed_by": [ "modules" ], diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 3d36eb17c..d9ed9b6bd 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::ensembl-vep=113.0 + # renovate: datasource=conda depName=bioconda/ensembl-vep + - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index 69245df0e..dcf0148ef 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -1,49 +1,39 @@ process ENSEMBLVEP_FILTERVEP { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' + : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" input: tuple val(meta), path(input) - path (feature_file) + path feature_file output: tuple val(meta), path("*.${extension}"), emit: output - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ filter_vep \\ - $args \\ - --input_file $input \\ + ${args} \\ + --input_file ${input} \\ --output_file ${prefix}.${extension} \\ --only_matched - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ touch ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index a73e3b7a7..68928cfc8 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -24,13 +24,16 @@ input: type: file description: VCF/TAB file annotated with vep pattern: "*.{vcf,tab,tsv,txt}" - - - feature_file: - type: file - description: File containing features on separate lines. To be used with --filter - option. + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - feature_file: + type: file + description: File containing features on separate lines. To be used with --filter + option. + ontologies: [] output: - - output: - - meta: + output: + - - meta: type: map description: | Groovy Map containing sample information @@ -39,11 +42,29 @@ output: type: file description: VCF/TAB file pattern: "*.{vcf,tab,txt,tsv}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_ensemblvep: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test index 7147792f7..044934579 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test @@ -10,32 +10,18 @@ nextflow_process { tag "ensemblvep" tag "ensemblvep/vep" tag "ensemblvep/filtervep" - tag "ensemblvep/download" - // Test for filtering VCF file test("test_ensemblvep_filtervep_vcf") { config "./vcf.config" setup { - run("ENSEMBLVEP_DOWNLOAD") { - script "../../download/main.nf" - - process { - """ - input[0] = Channel.of([ - [id:"113_WBcel235"], - params.vep_genome, - params.vep_species, - params.vep_cache_version - ]) - """ - } - } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -44,7 +30,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[4] = vep_cache input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -65,38 +51,25 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match() }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, { assert path(process.out.output.get(0).get(1)).readLines().first().contains("##fileformat=VCFv4.2") } ) } } - // Test for filtering TAB file test("test_ensemblvep_filtervep_tab_gz") { config "./tab.gz.config" setup { - run("ENSEMBLVEP_DOWNLOAD") { - script "../../download/main.nf" - - process { - """ - input[0] = Channel.of([ - [id:"113_WBcel235"], - params.vep_genome, - params.vep_species, - params.vep_cache_version - ]) - """ - } - } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -105,7 +78,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[4] = vep_cache input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -126,10 +99,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, + { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } ) } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 065d747ba..1559d7e79 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -1,26 +1,38 @@ { "test_ensemblvep_filtervep_vcf": { "content": [ - [ - "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" - ] + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_FILTERVEP", + "ensemblvep", + "115.2" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-21T09:10:47.874831491" + "timestamp": "2026-01-07T17:41:53.157363596" }, "test_ensemblvep_filtervep_tab_gz": { "content": [ - [ - "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" - ] + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_FILTERVEP", + "ensemblvep", + "115.2" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-21T09:11:18.765461163" + "timestamp": "2026-01-07T17:42:10.309756999" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config index 40b3a3bd6..32ff2cb6f 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params { - vep_cache_version = "113" + vep_cache_version = "115" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index cdad2d94d..f1eb11d65 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -6,12 +6,6 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ENSEMBLVEP_DOWNLOAD { - ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' - } - withName: ENSEMBLVEP_VEP { ext.args = '--tab' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml deleted file mode 100644 index b43bf40d6..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -ensemblvep/filtervep: - - "modules/nf-core/ensemblvep/filtervep/**" diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index ee2aef574..a737274ef 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -6,12 +6,6 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ENSEMBLVEP_DOWNLOAD { - ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' - } - withName: ENSEMBLVEP_VEP { ext.args = '--vcf' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml new file mode 100644 index 000000000..d9ed9b6bd --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/ensembl-vep + - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 4886b05e6..dd656a787 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,71 +1,66 @@ process ENSEMBLVEP_VEP { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' - conda "bioconda::ensembl-vep=110.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' + : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" input: tuple val(meta), path(vcf), path(custom_extra_files) - val genome - val species - val cache_version - path cache + val genome + val species + val cache_version + path cache tuple val(meta2), path(fasta) - path extra_files + path extra_files output: - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , optional:true, emit: report - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.tab.gz"), emit: tab, optional: true + tuple val(meta), path("*.json.gz"), emit: json, optional: true + tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true + tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' + def args2 = task.ext.args2 ?: '' + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip' def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" - def reference = fasta ? "--fasta $fasta" : "" + def reference = fasta ? "--fasta ${fasta}" : "" + def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : "" """ vep \\ - -i $vcf \\ + -i ${vcf} \\ -o ${prefix}.${file_extension}.gz \\ - $args \\ - $compress_cmd \\ - $reference \\ - --assembly $genome \\ - --species $species \\ + ${args} \\ + ${compress_cmd} \\ + ${reference} \\ + --assembly ${genome} \\ + --species ${species} \\ --cache \\ - --cache_version $cache_version \\ - --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --cache_version ${cache_version} \\ + --dir_cache ${dir_cache} \\ + --fork ${task.cpus} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS + ${create_index} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' + def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : "" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz - touch ${prefix}.summary.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS + echo "" | gzip > ${prefix}.${file_extension}.gz + ${create_index} + touch ${prefix}_summary.html """ } diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847dc..921a34127 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ -name: ENSEMBLVEP_VEP -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +name: ensemblvep_vep +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled + through `task.ext.args`. keywords: - annotation - vcf @@ -13,21 +14,24 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + ontologies: [] + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + ontologies: [] - genome: type: string description: | @@ -44,45 +48,149 @@ input: type: file description: | path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + ontologies: [] - extra_files: type: file description: | path to file(s) needed for plugins (optional) + ontologies: [] output: - - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" - - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" - - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" - - report: - type: file - description: VEP report file - pattern: "*.html" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + vcf: + - - meta: + type: map + description: | + Map with sample information + - "*.vcf.gz": + type: file + description: | + annotated vcf (optional) + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: + type: map + description: | + Map with sample information + - "*.vcf.gz.tbi": + type: file + description: | + annotated vcf index (optional) + pattern: "*.vcf.gz.tbi" + ontologies: [] + tab: + - - meta: + type: map + description: | + Map with sample information + - "*.tab.gz": + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + json: + - - meta: + type: map + description: | + Map with sample information + - "*.json.gz": + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + report: + - - meta: + type: map + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions_ensemblvep: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool + versions_tabix: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + +topics: + multiqc_files: + - - meta: + type: map + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 000000000..374f840cf --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + + test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") { + config "./vcf.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.vcf[0][1]).name + ",variantsMD5:" + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.tab[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") + }).match() }, + { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 000000000..00a27d57b --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + "test.tab.gz", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-16T13:49:54.784347273" + }, + "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { + "content": [ + "test.vcf.gz,variantsMD5:d41d8cd98f00b204e9800998ecf8427e", + "test.vcf.gz.tbi", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-16T13:49:36.798576341" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 000000000..8e68fe24a --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,5 @@ +params { + vep_cache_version = "115" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 000000000..40eb03e59 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 000000000..ad8955a37 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index b43311123..d80dda6ff 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -205,7 +205,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO.out.versions) ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) - ch_versions = ch_versions.mix(ENSEMBLVEP_SNV.out.versions) ch_versions = ch_versions.mix(TABIX_VEP.out.versions) ch_versions = ch_versions.mix(TABIX_BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index 6b276d5d3..80e0594f5 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -73,7 +73,6 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_versions = ch_versions.mix( SVDB_QUERY_DB.out.versions ) ch_versions = ch_versions.mix( PICARD_SORTVCF.out.versions ) - ch_versions = ch_versions.mix( ENSEMBLVEP_ME.out.versions ) emit: vcf_ann = BCFTOOLS_VIEW_FILTER.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 6c327c1c0..70697435b 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -106,7 +106,6 @@ workflow ANNOTATE_MT_SNVS { ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt } - ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions) ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index aa67c0066..34982ea4c 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -101,7 +101,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) ch_versions = ch_versions.mix(PICARD_SORTVCF.out.versions) - ch_versions = ch_versions.mix(ENSEMBLVEP_SV.out.versions) ch_versions = ch_versions.mix(TABIX_VEP.out.versions) emit: diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 39b8aafc2..c02e9a2bd 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -36,7 +36,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_vcf, ch_filter_vep_feature_file.map { _meta, file -> file } ) - ch_versions = ch_versions.mix(ENSEMBLVEP_FILTERVEP.out.versions) TABIX_BGZIPTABIX ( ENSEMBLVEP_FILTERVEP.out.output From b5dba023d38a60aa4b1bc5eb88d5a787db0f5abc Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:10:49 +0100 Subject: [PATCH 261/872] fastp --- modules/nf-core/fastp/environment.yml | 5 +- modules/nf-core/fastp/main.nf | 53 +- modules/nf-core/fastp/meta.yml | 89 ++-- modules/nf-core/fastp/tests/main.nf.test | 329 +++++++----- modules/nf-core/fastp/tests/main.nf.test.snap | 479 ++++++++++-------- modules/nf-core/fastp/tests/tags.yml | 2 - 6 files changed, 549 insertions(+), 408 deletions(-) delete mode 100644 modules/nf-core/fastp/tests/tags.yml diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 26d4aca5d..0c36eed25 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::fastp=0.23.4 + # renovate: datasource=conda depName=bioconda/fastp + - bioconda::fastp=1.0.1 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index e1b9f5656..e13509ca2 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -4,12 +4,11 @@ process FASTP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : - 'biocontainers/fastp:0.23.4--h5f740d0_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/527b18847a97451091dba07a886b24f17f742a861f9f6c9a6bfb79d4f1f3bf9d/data' : + 'community.wave.seqera.io/library/fastp:1.0.1--c8b87fe62dcc103c' }" input: - tuple val(meta), path(reads) - path adapter_fasta + tuple val(meta), path(reads), path(adapter_fasta) val discard_trimmed_pass val save_trimmed_fail val save_merged @@ -21,7 +20,7 @@ process FASTP { tuple val(meta), path('*.log') , emit: log tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | sed -e "s/fastp //g"'), emit: versions_fastp, topic: versions when: task.ext.when == null || task.ext.when @@ -30,9 +29,9 @@ process FASTP { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : "" - def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--failed_out ${prefix}.paired.fail.fastq.gz --unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' - def out_fq1 = discard_trimmed_pass ?: ( meta.single_end ? "--out1 ${prefix}.fastp.fastq.gz" : "--out1 ${prefix}_1.fastp.fastq.gz" ) - def out_fq2 = discard_trimmed_pass ?: "--out2 ${prefix}_2.fastp.fastq.gz" + def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--failed_out ${prefix}.paired.fail.fastq.gz --unpaired1 ${prefix}_R1.fail.fastq.gz --unpaired2 ${prefix}_R2.fail.fastq.gz" : '' + def out_fq1 = discard_trimmed_pass ?: ( meta.single_end ? "--out1 ${prefix}.fastp.fastq.gz" : "--out1 ${prefix}_R1.fastp.fastq.gz" ) + def out_fq2 = discard_trimmed_pass ?: "--out2 ${prefix}_R2.fastp.fastq.gz" // Added soft-links to original fastqs for consistent naming in MultiQC // Use single ended for interleaved. Add --interleaved_in in config. if ( task.ext.args?.contains('--interleaved_in') ) { @@ -48,13 +47,8 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) \\ + 2>| >(tee ${prefix}.fastp.log >&2) \\ | gzip -c > ${prefix}.fastp.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") - END_VERSIONS """ } else if (meta.single_end) { """ @@ -69,21 +63,16 @@ process FASTP { $adapter_list \\ $fail_fastq \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") - END_VERSIONS + 2>| >(tee ${prefix}.fastp.log >&2) """ } else { def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : '' """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz + [ ! -f ${prefix}_R1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_R1.fastq.gz + [ ! -f ${prefix}_R2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_R2.fastq.gz fastp \\ - --in1 ${prefix}_1.fastq.gz \\ - --in2 ${prefix}_2.fastq.gz \\ + --in1 ${prefix}_R1.fastq.gz \\ + --in2 ${prefix}_R2.fastq.gz \\ $out_fq1 \\ $out_fq2 \\ --json ${prefix}.fastp.json \\ @@ -94,21 +83,16 @@ process FASTP { --thread $task.cpus \\ --detect_adapter_for_pe \\ $args \\ - 2> >(tee ${prefix}.fastp.log >&2) - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") - END_VERSIONS + 2>| >(tee ${prefix}.fastp.log >&2) """ } stub: def prefix = task.ext.prefix ?: "${meta.id}" def is_single_output = task.ext.args?.contains('--interleaved_in') || meta.single_end - def touch_reads = (discard_trimmed_pass) ? "" : (is_single_output) ? "echo '' | gzip > ${prefix}.fastp.fastq.gz" : "echo '' | gzip > ${prefix}_1.fastp.fastq.gz ; echo '' | gzip > ${prefix}_2.fastp.fastq.gz" + def touch_reads = (discard_trimmed_pass) ? "" : (is_single_output) ? "echo '' | gzip > ${prefix}.fastp.fastq.gz" : "echo '' | gzip > ${prefix}_R1.fastp.fastq.gz ; echo '' | gzip > ${prefix}_R2.fastp.fastq.gz" def touch_merged = (!is_single_output && save_merged) ? "echo '' | gzip > ${prefix}.merged.fastq.gz" : "" - def touch_fail_fastq = (!save_trimmed_fail) ? "" : meta.single_end ? "echo '' | gzip > ${prefix}.fail.fastq.gz" : "echo '' | gzip > ${prefix}.paired.fail.fastq.gz ; echo '' | gzip > ${prefix}_1.fail.fastq.gz ; echo '' | gzip > ${prefix}_2.fail.fastq.gz" + def touch_fail_fastq = (!save_trimmed_fail) ? "" : meta.single_end ? "echo '' | gzip > ${prefix}.fail.fastq.gz" : "echo '' | gzip > ${prefix}.paired.fail.fastq.gz ; echo '' | gzip > ${prefix}_R1.fail.fastq.gz ; echo '' | gzip > ${prefix}_R2.fail.fastq.gz" """ $touch_reads $touch_fail_fastq @@ -116,10 +100,5 @@ process FASTP { touch "${prefix}.fastp.json" touch "${prefix}.fastp.html" touch "${prefix}.fastp.log" - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g") - END_VERSIONS """ } diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 159404d08..a67be395b 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -24,24 +24,27 @@ input: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. If you wish to run interleaved paired-end data, supply as single-end data but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - - adapter_fasta: + ontologies: [] + - adapter_fasta: type: file description: File in FASTA format containing possible adapters to remove. pattern: "*.{fasta,fna,fas,fa}" - - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. - | This can be used to use fastp for the output report only. - - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds - ending in `*.fail.fastq.gz` - - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + ontologies: [] + - discard_trimmed_pass: + type: boolean + description: | + Specify true to not write any reads that pass trimming thresholds. + This can be used to use fastp for the output report only. + - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - reads: - - meta: + reads: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,8 +53,11 @@ output: type: file description: The trimmed/modified/unmerged fastq reads pattern: "*fastp.fastq.gz" - - json: - - meta: + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_3989 # GZIP format + json: + - - meta: type: map description: | Groovy Map containing sample information @@ -60,8 +66,10 @@ output: type: file description: Results in JSON format pattern: "*.json" - - html: - - meta: + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + html: + - - meta: type: map description: | Groovy Map containing sample information @@ -70,8 +78,9 @@ output: type: file description: Results in HTML format pattern: "*.html" - - log: - - meta: + ontologies: [] + log: + - - meta: type: map description: | Groovy Map containing sample information @@ -80,8 +89,9 @@ output: type: file description: fastq log file pattern: "*.log" - - reads_fail: - - meta: + ontologies: [] + reads_fail: + - - meta: type: map description: | Groovy Map containing sample information @@ -90,8 +100,11 @@ output: type: file description: Reads the failed the preprocessing pattern: "*fail.fastq.gz" - - reads_merged: - - meta: + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + - edam: http://edamontology.org/format_3989 # GZIP format + reads_merged: + - - meta: type: map description: | Groovy Map containing sample information @@ -100,14 +113,32 @@ output: type: file description: Reads that were successfully merged pattern: "*.{merged.fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_fastp: + - - "${task.process}": + type: string + description: The name of the process + - fastp: + type: string + description: The name of the tool + - 'fastp --version 2>&1 | sed -e "s/fastp //g"': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - "${task.process}": + type: string + description: The name of the process + - fastp: + type: string + description: The name of the tool + - 'fastp --version 2>&1 | sed -e "s/fastp //g"': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@kevinmenden" + - "@eit-maxlcummins" maintainers: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 30dbb8aab..b79015781 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -13,14 +13,19 @@ nextflow_process { process { """ + adapter_fasta = [] // empty list for no adapter file! + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -31,11 +36,11 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") }, { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() + } ) } } @@ -46,20 +51,22 @@ nextflow_process { process { """ - adapter_fasta = [] - save_trimmed_pass = true - save_trimmed_fail = false - save_merged = false + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -70,11 +77,10 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -85,14 +91,19 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -106,8 +117,7 @@ nextflow_process { { assert process.out.reads_merged == [] }, { assert snapshot( process.out.reads, - process.out.json, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -118,14 +128,19 @@ nextflow_process { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = true + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -136,11 +151,10 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") }, { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -151,15 +165,22 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = true + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -173,8 +194,7 @@ nextflow_process { process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.json, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -184,15 +204,22 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = true + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = true + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -203,11 +230,10 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, { assert path(process.out.log.get(0).get(1)).getText().contains("total reads: 75") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.versions).match() }, + process.out.findAll { key, val -> key.startsWith('versions') }).match() }, ) } } @@ -217,15 +243,22 @@ nextflow_process { when { process { """ + adapter_fasta = file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = true + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) + input[1] = false input[2] = false - input[3] = false - input[4] = true + input[3] = true """ } } @@ -236,11 +269,10 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("
    ") }, { assert path(process.out.log.get(0).get(1)).getText().contains("total bases: 13683") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads_fail, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -250,14 +282,20 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = true + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false + + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -268,14 +306,13 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") }, { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads, process.out.reads_fail, process.out.reads_fail, process.out.reads_merged, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -285,15 +322,22 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = true + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -304,14 +348,13 @@ nextflow_process { { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") }, { assert snapshot( - process.out.json, process.out.reads, process.out.reads, process.out.reads_fail, process.out.reads_fail, process.out.reads_merged, process.out.reads_merged, - process.out.versions).match() } + process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } } @@ -324,14 +367,19 @@ nextflow_process { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -352,20 +400,20 @@ nextflow_process { process { """ - adapter_fasta = [] - save_trimmed_pass = true - save_trimmed_fail = false - save_merged = false + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -386,14 +434,19 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -414,14 +467,19 @@ nextflow_process { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = true + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -442,15 +500,20 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = true + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -470,15 +533,20 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = true + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = true + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -498,15 +566,22 @@ nextflow_process { when { process { """ + adapter_fasta = file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) + discard_trimmed_pass = false + save_trimmed_fail = false + save_merged = true + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ], + adapter_fasta ]) - input[1] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) - input[2] = false - input[3] = false - input[4] = true + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -526,14 +601,19 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = true + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -553,15 +633,20 @@ nextflow_process { when { process { """ + adapter_fasta = [] + discard_trimmed_pass = true + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ], + adapter_fasta ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false + input[1] = discard_trimmed_pass + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -573,4 +658,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index 54be7e45f..567723589 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -39,7 +39,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -77,28 +81,23 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T14:31:10.841098" + "timestamp": "2026-01-22T13:00:52.14535813" }, "test_fastp_paired_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" - ] - ], [ [ { @@ -106,8 +105,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", - "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" + "test_R1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", + "test_R2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" ] ] ], @@ -117,27 +116,24 @@ [ ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:43:28.665779" + "timestamp": "2026-01-23T09:46:26.421773402" }, "test_fastp_paired_end_merged_adapterlist": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,5914ca3f21ce162123a824e33e8564f6" - ] - ], [ [ { @@ -145,8 +141,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", - "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" + "test_R1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", + "test_R2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" ] ] ], @@ -162,27 +158,24 @@ "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5" ] ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:44:18.210375" + "timestamp": "2026-01-23T09:46:59.832295907" }, "test_fastp_single_end_qc_only": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,5cc5f01e449309e0e689ed6f51a2294a" - ] - ], [ ], @@ -201,15 +194,21 @@ [ ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:44:27.380974" + "timestamp": "2026-01-23T09:47:06.486959565" }, "test_fastp_paired_end_trim_fail": { "content": [ @@ -220,8 +219,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7", - "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a" + "test_R1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7", + "test_R2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a" ] ] ], @@ -233,32 +232,29 @@ }, [ "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366", - "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6", - "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995" + "test_R1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6", + "test_R2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995" ] ] ], [ ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519" + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] - ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:43:58.749589" + "timestamp": "2026-01-23T09:46:46.736511024" }, "fastp - stub test_fastp_interleaved": { "content": [ @@ -306,7 +302,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -350,16 +350,20 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:50:00.270029" + "timestamp": "2026-01-22T13:00:16.097071654" }, "test_fastp_single_end - stub": { "content": [ @@ -407,7 +411,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -451,16 +459,20 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:49:42.502789" + "timestamp": "2026-01-22T13:00:03.317192706" }, "test_fastp_paired_end_merged_adapterlist - stub": { "content": [ @@ -472,8 +484,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -517,7 +529,11 @@ ] ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -553,8 +569,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -570,16 +586,20 @@ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:54:53.458252" + "timestamp": "2026-01-22T13:00:44.851708205" }, "test_fastp_paired_end_merged - stub": { "content": [ @@ -591,8 +611,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -636,7 +656,11 @@ ] ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -672,8 +696,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -689,28 +713,23 @@ "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:50:27.689379" + "timestamp": "2026-01-22T13:00:37.581047713" }, "test_fastp_paired_end_merged": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" - ] - ], [ [ { @@ -718,8 +737,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", - "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" + "test_R1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", + "test_R2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" ] ] ], @@ -735,15 +754,21 @@ "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5" ] ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:44:08.68476" + "timestamp": "2026-01-23T09:46:53.190202914" }, "test_fastp_paired_end - stub": { "content": [ @@ -755,8 +780,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -794,7 +819,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -830,8 +859,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -841,28 +870,23 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:49:51.679221" + "timestamp": "2026-01-22T13:00:09.585957282" }, "test_fastp_single_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" - ] - ], [ [ { @@ -878,15 +902,21 @@ [ ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:43:18.834322" + "timestamp": "2026-01-23T09:46:19.624824985" }, "test_fastp_single_end_trim_fail - stub": { "content": [ @@ -940,7 +970,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -990,16 +1024,20 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T14:05:36.898142" + "timestamp": "2026-01-22T13:00:22.800659826" }, "test_fastp_paired_end_trim_fail - stub": { "content": [ @@ -1011,8 +1049,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1051,8 +1089,8 @@ }, [ "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1060,7 +1098,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -1096,8 +1138,8 @@ "single_end": false }, [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1109,24 +1151,28 @@ }, [ "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_R1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T14:05:49.212847" + "timestamp": "2026-01-22T13:00:30.271734068" }, "fastp test_fastp_interleaved": { "content": [ @@ -1139,36 +1185,24 @@ "test.fastp.fastq.gz:md5,217d62dc13a23e92513a1bd8e1bcea39" ] ], - [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,b24e0624df5cc0b11cd5ba21b726fb22" + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] - ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:43:38.910832" + "timestamp": "2026-01-23T09:46:33.4628687" }, "test_fastp_single_end_trim_fail": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" - ] - ], [ [ { @@ -1190,27 +1224,24 @@ [ ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:43:48.22378" + "timestamp": "2026-01-23T09:46:39.895973372" }, "test_fastp_paired_end_qc_only": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,623064a45912dac6f2b64e3f2e9901df" - ] - ], [ ], @@ -1229,15 +1260,21 @@ [ ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] + { + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T13:44:36.334938" + "timestamp": "2026-01-23T09:47:13.015833707" }, "test_fastp_paired_end_qc_only - stub": { "content": [ @@ -1279,7 +1316,11 @@ ], "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + "FASTP", + "fastp", + "1.0.1" + ] ], "html": [ [ @@ -1317,15 +1358,19 @@ "reads_merged": [ ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "versions_fastp": [ + [ + "FASTP", + "fastp", + "1.0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-05T14:31:27.096468" + "timestamp": "2026-01-22T13:00:59.670106791" } } \ No newline at end of file diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml deleted file mode 100644 index c1afcce75..000000000 --- a/modules/nf-core/fastp/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastp: - - modules/nf-core/fastp/** From 3b95f05c68ca7890bbff2edf4cb72b72ad0e55a3 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:10:59 +0100 Subject: [PATCH 262/872] fastqc --- modules/nf-core/fastqc/main.nf | 16 +- modules/nf-core/fastqc/meta.yml | 51 +++- modules/nf-core/fastqc/tests/main.nf.test | 12 +- .../nf-core/fastqc/tests/main.nf.test.snap | 228 ++++++++++++------ 4 files changed, 210 insertions(+), 97 deletions(-) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 23e16634c..4b3041dc5 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -11,9 +11,9 @@ process FASTQC { tuple val(meta), path(reads) output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions + tuple val(meta) , path("*.html") , emit: html + tuple val(meta) , path("*.zip") , emit: zip + tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions when: task.ext.when == null || task.ext.when @@ -43,11 +43,6 @@ process FASTQC { --threads ${task.cpus} \\ --memory ${fastqc_memory} \\ ${renamed_files} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ stub: @@ -55,10 +50,5 @@ process FASTQC { """ touch ${prefix}.html touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index c8d9d025a..49164c88f 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -53,13 +53,28 @@ output: description: FastQC report archive pattern: "*_{fastqc.zip}" ontologies: [] + versions_fastqc: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//": + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@grst" @@ -70,3 +85,27 @@ maintainers: - "@grst" - "@ewels" - "@FelixKrueger" +containers: + conda: + linux_amd64: + lock_file: https://wave.seqera.io/v1alpha1/builds/bd-af7a5314d5015c29_1/condalock + linux_arm64: + lock_file: https://wave.seqera.io/v1alpha1/builds/bd-df99cb252670875a_2/condalock + docker: + linux_amd64: + build_id: bd-af7a5314d5015c29_1 + name: community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29 + scanId: sc-a618548acbee5a8a_30 + linux_arm64: + build_id: bd-df99cb252670875a_2 + name: community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a + scanId: sc-b5913ed5d42b22d2_18 + singularity: + linux_amd64: + build_id: bd-104d26ddd9519960_1 + name: oras://community.wave.seqera.io/library/fastqc:0.12.1--104d26ddd9519960 + https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:e0c976cb2eca5fee72618a581537a4f8ea42fcae24c9b201e2e0f764fd28648a + linux_arm64: + build_id: bd-d56b505a93aef38a_1 + name: oras://community.wave.seqera.io/library/fastqc:0.12.1--d56b505a93aef38a + https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:fd39534bf298698cbe3ee4d4a6f1e73330ec4bca44c38dd9a4d06cb5ea838017 diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a074..66c44da9b 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -58,7 +58,7 @@ nextflow_process { { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -82,7 +82,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -106,7 +106,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -142,7 +142,7 @@ nextflow_process { { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db3092f..c8ee120f5 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,15 +1,21 @@ { "sarscov2 custom_prefix": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2025-10-28T16:39:14.518503" }, "sarscov2 single-end [fastq] - stub": { "content": [ @@ -33,7 +39,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -44,8 +54,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -59,10 +73,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:24.993809" + "timestamp": "2025-10-28T16:39:19.309008" }, "sarscov2 custom_prefix - stub": { "content": [ @@ -86,7 +100,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -97,8 +115,12 @@ "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -112,58 +134,82 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:03:10.93942" + "timestamp": "2025-10-28T16:39:44.94888" }, "sarscov2 interleaved [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:42.355718" + "timestamp": "2025-10-28T16:38:45.168496" }, "sarscov2 paired-end [bam]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:53.276274" + "timestamp": "2025-10-28T16:38:53.268919" }, "sarscov2 multiple [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:05.527626" + "timestamp": "2025-10-28T16:39:05.050305" }, "sarscov2 paired-end [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:31.188871" + "timestamp": "2025-10-28T16:38:37.2373" }, "sarscov2 paired-end [fastq] - stub": { "content": [ @@ -187,7 +233,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -198,8 +248,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -213,10 +267,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:34.273566" + "timestamp": "2025-10-28T16:39:24.450398" }, "sarscov2 multiple [fastq] - stub": { "content": [ @@ -240,7 +294,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -251,8 +309,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -266,22 +328,28 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:03:02.304411" + "timestamp": "2025-10-28T16:39:39.758762" }, "sarscov2 single-end [fastq]": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:01:19.095607" + "timestamp": "2025-10-28T16:38:29.555068" }, "sarscov2 interleaved [fastq] - stub": { "content": [ @@ -305,7 +373,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -316,8 +388,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -331,10 +407,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:44.640184" + "timestamp": "2025-10-28T16:39:29.193136" }, "sarscov2 paired-end [bam] - stub": { "content": [ @@ -358,7 +434,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -369,8 +449,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -384,9 +468,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:53.550742" + "timestamp": "2025-10-28T16:39:34.144919" } } \ No newline at end of file From 06c6c59f9a52afd3f05c6abc2a7be5bcdee9210c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:11:21 +0100 Subject: [PATCH 263/872] genmod --- modules.json | 12 ++-- .../nf-core/genmod/annotate/environment.yml | 5 +- modules/nf-core/genmod/annotate/main.nf | 16 +---- modules/nf-core/genmod/annotate/meta.yml | 32 +++++++-- .../genmod/annotate/tests/main.nf.test | 5 +- .../genmod/annotate/tests/main.nf.test.snap | 65 +++++++++++++++++++ .../nf-core/genmod/annotate/tests/tags.yml | 2 - .../nf-core/genmod/compound/environment.yml | 5 +- modules/nf-core/genmod/compound/main.nf | 16 +---- modules/nf-core/genmod/compound/meta.yml | 32 +++++++-- .../genmod/compound/tests/main.nf.test | 4 +- .../genmod/compound/tests/main.nf.test.snap | 64 ++++++++++++++++++ .../nf-core/genmod/compound/tests/tags.yml | 2 - modules/nf-core/genmod/models/environment.yml | 5 +- modules/nf-core/genmod/models/main.nf | 16 +---- modules/nf-core/genmod/models/meta.yml | 43 ++++++++---- .../nf-core/genmod/models/tests/main.nf.test | 4 +- .../genmod/models/tests/main.nf.test.snap | 64 ++++++++++++++++++ modules/nf-core/genmod/models/tests/tags.yml | 2 - modules/nf-core/genmod/score/environment.yml | 5 +- modules/nf-core/genmod/score/main.nf | 16 +---- modules/nf-core/genmod/score/meta.yml | 42 ++++++++---- .../nf-core/genmod/score/tests/main.nf.test | 5 +- .../genmod/score/tests/main.nf.test.snap | 65 +++++++++++++++++++ modules/nf-core/genmod/score/tests/tags.yml | 2 - subworkflows/local/align/main.nf | 1 - subworkflows/local/rank_variants.nf | 5 -- workflows/raredisease.nf | 1 - 28 files changed, 415 insertions(+), 121 deletions(-) create mode 100644 modules/nf-core/genmod/annotate/tests/main.nf.test.snap delete mode 100644 modules/nf-core/genmod/annotate/tests/tags.yml create mode 100644 modules/nf-core/genmod/compound/tests/main.nf.test.snap delete mode 100644 modules/nf-core/genmod/compound/tests/tags.yml create mode 100644 modules/nf-core/genmod/models/tests/main.nf.test.snap delete mode 100644 modules/nf-core/genmod/models/tests/tags.yml create mode 100644 modules/nf-core/genmod/score/tests/main.nf.test.snap delete mode 100644 modules/nf-core/genmod/score/tests/tags.yml diff --git a/modules.json b/modules.json index 77a373beb..509fd3164 100644 --- a/modules.json +++ b/modules.json @@ -214,14 +214,14 @@ }, "fastp": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a331ecfd1aa48b2b2298aab23bb4516c800e410b", "installed_by": [ "modules" ] }, "fastqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "5bdb098216aaf5df9c3b6343e6204cd932503c16", "installed_by": [ "modules" ] @@ -368,28 +368,28 @@ }, "genmod/annotate": { "branch": "master", - "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", + "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", "installed_by": [ "modules" ] }, "genmod/compound": { "branch": "master", - "git_sha": "91a84f951358143e93dc9e03470db4e6a4a7105c", + "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", "installed_by": [ "modules" ] }, "genmod/models": { "branch": "master", - "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6", + "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", "installed_by": [ "modules" ] }, "genmod/score": { "branch": "master", - "git_sha": "f888300c726e1f817a9f93a680866ff7e6c669f6", + "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", "installed_by": [ "modules" ] diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml index 227ee8920..6b91c71a0 100644 --- a/modules/nf-core/genmod/annotate/environment.yml +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.9 + - bioconda::genmod=3.10.2 + - conda-forge::python=3.11.14 diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index 0b8b232de..6236e8566 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -4,15 +4,15 @@ process GENMOD_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0': - 'biocontainers/genmod:3.9--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31b331bee43c7ff070bdde5460a4102ba31c3bfb0ee0d70197001ff011036555/data' : + 'community.wave.seqera.io/library/genmod_python:31b2fba4d3b7ba6f' }" input: tuple val(meta), path(input_vcf) output: tuple val(meta), path("*_annotate.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions when: task.ext.when == null || task.ext.when @@ -26,21 +26,11 @@ process GENMOD_ANNOTATE { $args \\ --outfile ${prefix}_annotate.vcf \\ $input_vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_annotate.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml index bb4afb6b4..65f8fda0c 100644 --- a/modules/nf-core/genmod/annotate/meta.yml +++ b/modules/nf-core/genmod/annotate/meta.yml @@ -22,9 +22,10 @@ input: type: file description: VCF file pattern: "*.{vcf}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -33,11 +34,28 @@ output: type: file description: Annotated VCF file pattern: "*.{vcf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_genmod: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test index a4b3fccba..7b053b2ee 100644 --- a/modules/nf-core/genmod/annotate/tests/main.nf.test +++ b/modules/nf-core/genmod/annotate/tests/main.nf.test @@ -26,9 +26,10 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, path(process.out.vcf.get(0).get(1)).vcf.summary, - ).match() } + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.findAll { key, val -> key.startsWith("versions") }, + ).match() } ) } diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap new file mode 100644 index 000000000..23618cce2 --- /dev/null +++ b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "genmod_annotate": { + "content": [ + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]", + "ec9b1d7d21c9f6c0a6e0dffb56732fc3", + { + "versions_genmod": [ + [ + "GENMOD_ANNOTATE", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:45:39.879885252" + }, + "genmod_annotate - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GENMOD_ANNOTATE", + "genmod", + "3.10.2" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_genmod": [ + [ + "GENMOD_ANNOTATE", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:14:43.571171183" + } +} \ No newline at end of file diff --git a/modules/nf-core/genmod/annotate/tests/tags.yml b/modules/nf-core/genmod/annotate/tests/tags.yml deleted file mode 100644 index 88bb35a18..000000000 --- a/modules/nf-core/genmod/annotate/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -genmod/annotate: - - modules/nf-core/genmod/annotate/** diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml index 227ee8920..6b91c71a0 100644 --- a/modules/nf-core/genmod/compound/environment.yml +++ b/modules/nf-core/genmod/compound/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.9 + - bioconda::genmod=3.10.2 + - conda-forge::python=3.11.14 diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index ca6a22a19..d28bda9be 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -4,15 +4,15 @@ process GENMOD_COMPOUND { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0': - 'biocontainers/genmod:3.9--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31b331bee43c7ff070bdde5460a4102ba31c3bfb0ee0d70197001ff011036555/data' : + 'community.wave.seqera.io/library/genmod_python:31b2fba4d3b7ba6f' }" input: tuple val(meta), path(input_vcf) output: tuple val(meta), path("*_compound.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions when: task.ext.when == null || task.ext.when @@ -27,21 +27,11 @@ process GENMOD_COMPOUND { --processes ${task.cpus} \\ --outfile ${prefix}_compound.vcf \\ $input_vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_compound.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml index ebd6a110c..87b33921b 100644 --- a/modules/nf-core/genmod/compound/meta.yml +++ b/modules/nf-core/genmod/compound/meta.yml @@ -22,9 +22,10 @@ input: type: file description: VCF file pattern: "*.{vcf}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -33,11 +34,28 @@ output: type: file description: Output VCF file pattern: "*.{vcf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_genmod: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test index 4c667c173..760126600 100644 --- a/modules/nf-core/genmod/compound/tests/main.nf.test +++ b/modules/nf-core/genmod/compound/tests/main.nf.test @@ -25,9 +25,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, path(process.out.vcf.get(0).get(1)).vcf.summary, - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") }, + ).match() } ) } diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test.snap b/modules/nf-core/genmod/compound/tests/main.nf.test.snap new file mode 100644 index 000000000..15d10bc06 --- /dev/null +++ b/modules/nf-core/genmod/compound/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "genmod_compound": { + "content": [ + "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]", + { + "versions_genmod": [ + [ + "GENMOD_COMPOUND", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:47:53.481557902" + }, + "genmod_compound - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GENMOD_COMPOUND", + "genmod", + "3.10.2" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_genmod": [ + [ + "GENMOD_COMPOUND", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:14:51.229110934" + } +} \ No newline at end of file diff --git a/modules/nf-core/genmod/compound/tests/tags.yml b/modules/nf-core/genmod/compound/tests/tags.yml deleted file mode 100644 index 870b35e8b..000000000 --- a/modules/nf-core/genmod/compound/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -genmod/compound: - - modules/nf-core/genmod/compound/** diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml index 227ee8920..6b91c71a0 100644 --- a/modules/nf-core/genmod/models/environment.yml +++ b/modules/nf-core/genmod/models/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.9 + - bioconda::genmod=3.10.2 + - conda-forge::python=3.11.14 diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index a869221e9..39a1c1a16 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -4,8 +4,8 @@ process GENMOD_MODELS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0': - 'biocontainers/genmod:3.9--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31b331bee43c7ff070bdde5460a4102ba31c3bfb0ee0d70197001ff011036555/data' : + 'community.wave.seqera.io/library/genmod_python:31b2fba4d3b7ba6f' }" input: tuple val(meta), path(input_vcf), path (fam) @@ -13,7 +13,7 @@ process GENMOD_MODELS { output: tuple val(meta), path("*_models.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions when: task.ext.when == null || task.ext.when @@ -32,21 +32,11 @@ process GENMOD_MODELS { --processes ${task.cpus} \\ --outfile ${prefix}_models.vcf \\ $input_vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_models.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml index a6249114a..5754d011b 100644 --- a/modules/nf-core/genmod/models/meta.yml +++ b/modules/nf-core/genmod/models/meta.yml @@ -22,16 +22,20 @@ input: type: file description: vcf file pattern: "*.{vcf}" + ontologies: [] - fam: type: file description: PED file with family information - - - reduced_penetrance: - type: file - description: file with gene ids that have reduced penetrance - pattern: "*.{tsv}" + ontologies: [] + - reduced_penetrance: + type: file + description: file with gene ids that have reduced penetrance + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,11 +44,28 @@ output: type: file description: Output VCF file pattern: "*.{vcf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_genmod: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test index 0b9a3ebd0..83fbd4093 100644 --- a/modules/nf-core/genmod/models/tests/main.nf.test +++ b/modules/nf-core/genmod/models/tests/main.nf.test @@ -27,9 +27,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, path(process.out.vcf.get(0).get(1)).vcf.summary, - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") }, + ).match() } ) } diff --git a/modules/nf-core/genmod/models/tests/main.nf.test.snap b/modules/nf-core/genmod/models/tests/main.nf.test.snap new file mode 100644 index 000000000..2184f631b --- /dev/null +++ b/modules/nf-core/genmod/models/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "genmod_models - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GENMOD_MODELS", + "genmod", + "3.10.2" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_genmod": [ + [ + "GENMOD_MODELS", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:14:58.376387801" + }, + "genmod_models": { + "content": [ + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]", + { + "versions_genmod": [ + [ + "GENMOD_MODELS", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:47:59.960270364" + } +} \ No newline at end of file diff --git a/modules/nf-core/genmod/models/tests/tags.yml b/modules/nf-core/genmod/models/tests/tags.yml deleted file mode 100644 index 72b3b6bbd..000000000 --- a/modules/nf-core/genmod/models/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -genmod/models: - - modules/nf-core/genmod/models/** diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml index 227ee8920..6b91c71a0 100644 --- a/modules/nf-core/genmod/score/environment.yml +++ b/modules/nf-core/genmod/score/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.9 + - bioconda::genmod=3.10.2 + - conda-forge::python=3.11.14 diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 756fc7313..f5db31eab 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -4,8 +4,8 @@ process GENMOD_SCORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.9--pyhdfd78af_0': - 'biocontainers/genmod:3.9--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31b331bee43c7ff070bdde5460a4102ba31c3bfb0ee0d70197001ff011036555/data' : + 'community.wave.seqera.io/library/genmod_python:31b2fba4d3b7ba6f' }" input: tuple val(meta), path(input_vcf), path (fam) @@ -13,7 +13,7 @@ process GENMOD_SCORE { output: tuple val(meta), path("*_score.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions when: task.ext.when == null || task.ext.when @@ -31,21 +31,11 @@ process GENMOD_SCORE { $config_file \\ --outfile ${prefix}_score.vcf \\ $input_vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_score.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml index c5fe2e2ac..893b620d6 100644 --- a/modules/nf-core/genmod/score/meta.yml +++ b/modules/nf-core/genmod/score/meta.yml @@ -22,16 +22,19 @@ input: type: file description: vcf file pattern: "*.{vcf}" + ontologies: [] - fam: type: file description: PED file with family information - - - score_config: - type: file - description: rank model config file - pattern: "*.{ini}" + ontologies: [] + - score_config: + type: file + description: rank model config file + pattern: "*.{ini}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,11 +43,28 @@ output: type: file description: Output VCF file pattern: "*.{vcf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_genmod: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: Name of the process + - genmod: + type: string + description: Name of the tool + - "genmod --version | sed 's/^.*genmod version: //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test index 6181f63ae..710176292 100644 --- a/modules/nf-core/genmod/score/tests/main.nf.test +++ b/modules/nf-core/genmod/score/tests/main.nf.test @@ -27,9 +27,10 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, path(process.out.vcf.get(0).get(1)).vcf.summary, - ).match() } + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.findAll { key, val -> key.startsWith("versions") }, + ).match() } ) } diff --git a/modules/nf-core/genmod/score/tests/main.nf.test.snap b/modules/nf-core/genmod/score/tests/main.nf.test.snap new file mode 100644 index 000000000..9923b99c4 --- /dev/null +++ b/modules/nf-core/genmod/score/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "genmod_score": { + "content": [ + "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]", + "50a04b1524fe1e21e49ebd9afdd0d91e", + { + "versions_genmod": [ + [ + "GENMOD_SCORE", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:46:03.729403607" + }, + "genmod_score - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_score.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GENMOD_SCORE", + "genmod", + "3.10.2" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_score.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_genmod": [ + [ + "GENMOD_SCORE", + "genmod", + "3.10.2" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.2" + }, + "timestamp": "2025-12-22T14:08:59.88453697" + } +} \ No newline at end of file diff --git a/modules/nf-core/genmod/score/tests/tags.yml b/modules/nf-core/genmod/score/tests/tags.yml deleted file mode 100644 index cef831ed3..000000000 --- a/modules/nf-core/genmod/score/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -genmod/score: - - modules/nf-core/genmod/score/** diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index d5f96741a..b3fb0e940 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -56,7 +56,6 @@ workflow ALIGN { if (!skip_fastp) { FASTP (ch_input_reads, [], false, false, false) ch_input_reads = FASTP.out.reads - ch_versions = ch_versions.mix(FASTP.out.versions) ch_fastp_json = FASTP.out.json } diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 126c51b91..2d297a1b7 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -40,11 +40,6 @@ workflow RANK_VARIANTS { ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) } - ch_versions = ch_versions.mix(GENMOD_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(GENMOD_MODELS.out.versions) - ch_versions = ch_versions.mix(GENMOD_SCORE.out.versions) - ch_versions = ch_versions.mix(GENMOD_COMPOUND.out.versions) - emit: vcf = ch_vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 5dd4d9609..9a0ea23fb 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -234,7 +234,6 @@ workflow RAREDISEASE { if (!skip_fastqc) { FASTQC (ch_input_fastqs) fastqc_report = FASTQC.out.zip - ch_versions = ch_versions.mix(FASTQC.out.versions) } /* From e0e1d636f671425a49e385144a573bc52ab4b613 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:13:48 +0100 Subject: [PATCH 264/872] manta --- modules.json | 2 +- .../nf-core/manta/germline/environment.yml | 3 + modules/nf-core/manta/germline/main.nf | 30 +++---- modules/nf-core/manta/germline/meta.yml | 73 ++++++++++----- .../nf-core/manta/germline/tests/main.nf.test | 30 ++++--- .../manta/germline/tests/main.nf.test.snap | 89 ++++++++++++++----- modules/nf-core/manta/germline/tests/tags.yml | 2 - subworkflows/local/call_sv_manta/main.nf | 3 - 8 files changed, 152 insertions(+), 80 deletions(-) delete mode 100644 modules/nf-core/manta/germline/tests/tags.yml diff --git a/modules.json b/modules.json index 509fd3164..0e3244731 100644 --- a/modules.json +++ b/modules.json @@ -425,7 +425,7 @@ }, "manta/germline": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "3485512d3930df1fcb66b5f92af639179bdfe4be", "installed_by": [ "modules" ] diff --git a/modules/nf-core/manta/germline/environment.yml b/modules/nf-core/manta/germline/environment.yml index fe5ade506..697c36d1c 100644 --- a/modules/nf-core/manta/germline/environment.yml +++ b/modules/nf-core/manta/germline/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - bioconda::manta=1.6.0 + - conda-forge::python=2.7.15 diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf index c1b339a95..c1550f5c6 100644 --- a/modules/nf-core/manta/germline/main.nf +++ b/modules/nf-core/manta/germline/main.nf @@ -5,8 +5,8 @@ process MANTA_GERMLINE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : - 'biocontainers/manta:1.6.0--h9ee0642_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f6/f696c93e6209e33ac0d15f1ecfa799bc67329eec07b0569e065ea8b220b53953/data' : + 'community.wave.seqera.io/library/manta_python:0eb71149179b3920' }" input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file @@ -16,13 +16,13 @@ process MANTA_GERMLINE { path(config) output: - tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf - tuple val(meta), path("*candidate_small_indels.vcf.gz.tbi"), emit: candidate_small_indels_vcf_tbi - tuple val(meta), path("*candidate_sv.vcf.gz") , emit: candidate_sv_vcf - tuple val(meta), path("*candidate_sv.vcf.gz.tbi") , emit: candidate_sv_vcf_tbi - tuple val(meta), path("*diploid_sv.vcf.gz") , emit: diploid_sv_vcf - tuple val(meta), path("*diploid_sv.vcf.gz.tbi") , emit: diploid_sv_vcf_tbi - path "versions.yml" , emit: versions + tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf + tuple val(meta), path("*candidate_small_indels.vcf.gz.tbi") , emit: candidate_small_indels_vcf_tbi + tuple val(meta), path("*candidate_sv.vcf.gz") , emit: candidate_sv_vcf + tuple val(meta), path("*candidate_sv.vcf.gz.tbi") , emit: candidate_sv_vcf_tbi + tuple val(meta), path("*diploid_sv.vcf.gz") , emit: diploid_sv_vcf + tuple val(meta), path("*diploid_sv.vcf.gz.tbi") , emit: diploid_sv_vcf_tbi + tuple val("${task.process}"), val("manta"), eval("configManta.py --version"), topic: versions, emit: versions_manta when: task.ext.when == null || task.ext.when @@ -30,7 +30,7 @@ process MANTA_GERMLINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input_files = input.collect{"--bam ${it}"}.join(' ') + def input_files = input.collect{ bam -> "--bam ${bam}"}.join(' ') def options_manta = target_bed ? "--callRegions $target_bed" : "" def config_option = config ? "--config ${config}" : "" """ @@ -56,11 +56,6 @@ process MANTA_GERMLINE { ${prefix}.diploid_sv.vcf.gz mv manta/results/variants/diploidSV.vcf.gz.tbi \\ ${prefix}.diploid_sv.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - manta: \$( configManta.py --version ) - END_VERSIONS """ stub: @@ -72,10 +67,5 @@ process MANTA_GERMLINE { touch ${prefix}.candidate_sv.vcf.gz.tbi echo "" | gzip > ${prefix}.diploid_sv.vcf.gz touch ${prefix}.diploid_sv.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - manta: \$( configManta.py --version ) - END_VERSIONS """ } diff --git a/modules/nf-core/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml index 4072ab8e5..83ff420b8 100644 --- a/modules/nf-core/manta/germline/meta.yml +++ b/modules/nf-core/manta/germline/meta.yml @@ -29,18 +29,22 @@ input: type: file description: BAM/CRAM/SAM file. For joint calling use a list of files. pattern: "*.{bam,cram,sam}" + ontologies: [] - index: type: file description: BAM/CRAM/SAM index file. For joint calling use a list of files. pattern: "*.{bai,crai,sai}" + ontologies: [] - target_bed: type: file description: BED file containing target regions for variant calling pattern: "*.{bed}" + ontologies: [] - target_bed_tbi: type: file description: Index for BED file containing target regions for variant calling pattern: "*.{bed.tbi}" + ontologies: [] - - meta2: type: map description: | @@ -50,6 +54,7 @@ input: type: file description: Genome reference FASTA file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -59,13 +64,15 @@ input: type: file description: Genome reference FASTA index file pattern: "*.{fa.fai,fasta.fai}" - - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + ontologies: [] + - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" + ontologies: [] output: - - candidate_small_indels_vcf: - - meta: + candidate_small_indels_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -74,8 +81,9 @@ output: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - - candidate_small_indels_vcf_tbi: - - meta: + ontologies: [] + candidate_small_indels_vcf_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -84,8 +92,9 @@ output: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - - candidate_sv_vcf: - - meta: + ontologies: [] + candidate_sv_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -94,8 +103,9 @@ output: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - - candidate_sv_vcf_tbi: - - meta: + ontologies: [] + candidate_sv_vcf_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -104,8 +114,9 @@ output: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - - diploid_sv_vcf: - - meta: + ontologies: [] + diploid_sv_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -114,8 +125,9 @@ output: type: file description: Gzipped VCF file containing variants pattern: "*.{vcf.gz}" - - diploid_sv_vcf_tbi: - - meta: + ontologies: [] + diploid_sv_vcf_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -124,11 +136,30 @@ output: type: file description: Index for gzipped VCF file containing variants pattern: "*.{vcf.gz.tbi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_manta: + - - ${task.process}: + type: string + description: The name of the process + - manta: + type: string + description: The name of the tool + - configManta.py --version: + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - manta: + type: string + description: The name of the tool + - configManta.py --version: + type: eval + description: The expression to obtain the version of the tool + authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/manta/germline/tests/main.nf.test b/modules/nf-core/manta/germline/tests/main.nf.test index 1d49ad23a..cfae4b3d6 100644 --- a/modules/nf-core/manta/germline/tests/main.nf.test +++ b/modules/nf-core/manta/germline/tests/main.nf.test @@ -38,10 +38,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert snapshot(process.out.version).match("version") } + { assert snapshot ( + path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + process.out.findAll { key, val -> key.startsWith("versions_") } + ).match() } ) } @@ -75,10 +77,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert snapshot(process.out.version).match("bed_version") } + { assert snapshot ( + path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + process.out.findAll { key, val -> key.startsWith("versions_") } + ).match() } ) } @@ -116,10 +120,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") }, - { assert snapshot(process.out.version).match("joint_version") } + { assert snapshot ( + path(process.out.candidate_small_indels_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.candidate_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + path(process.out.diploid_sv_vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1"), + process.out.findAll { key, val -> key.startsWith("versions_") } + ).match() } ) } diff --git a/modules/nf-core/manta/germline/tests/main.nf.test.snap b/modules/nf-core/manta/germline/tests/main.nf.test.snap index 79d5541e3..1b23abf61 100644 --- a/modules/nf-core/manta/germline/tests/main.nf.test.snap +++ b/modules/nf-core/manta/germline/tests/main.nf.test.snap @@ -51,7 +51,11 @@ ] ], "6": [ - "versions.yml:md5,18070b443a26855ef64dafa179dfba01" + [ + "MANTA_GERMLINE", + "manta", + "1.6.0" + ] ], "candidate_small_indels_vcf": [ [ @@ -101,39 +105,82 @@ "test.diploid_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,18070b443a26855ef64dafa179dfba01" + "versions_manta": [ + [ + "MANTA_GERMLINE", + "manta", + "1.6.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-21T17:54:09.788372" + "timestamp": "2025-12-11T16:30:33.370543407" }, - "joint_version": { - "content": null, + "human - cram": { + "content": [ + true, + true, + true, + { + "versions_manta": [ + [ + "MANTA_GERMLINE", + "manta", + "1.6.0" + ] + ] + } + ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-21T15:03:07.745972" + "timestamp": "2025-12-11T16:43:35.235895962" }, - "bed_version": { - "content": null, + "human - cram - bed": { + "content": [ + true, + true, + true, + { + "versions_manta": [ + [ + "MANTA_GERMLINE", + "manta", + "1.6.0" + ] + ] + } + ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-21T13:49:38.745653" + "timestamp": "2025-12-11T16:43:45.131664257" }, - "version": { - "content": null, + "human - cram - bed - jointcalling": { + "content": [ + true, + true, + true, + { + "versions_manta": [ + [ + "MANTA_GERMLINE", + "manta", + "1.6.0" + ] + ] + } + ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-03-21T13:49:14.885769" + "timestamp": "2025-12-11T16:43:55.610167195" } } \ No newline at end of file diff --git a/modules/nf-core/manta/germline/tests/tags.yml b/modules/nf-core/manta/germline/tests/tags.yml deleted file mode 100644 index 99d1a73ca..000000000 --- a/modules/nf-core/manta/germline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -manta/germline: - - "modules/nf-core/manta/germline/**" diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index c7c4ae6f9..5cef7a157 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -48,8 +48,6 @@ workflow CALL_SV_MANTA { .set {ch_filter_in} BCFTOOLS_VIEW_MANTA (ch_filter_in, [], [], []) - ch_versions = MANTA.out.versions - emit: candidate_small_indels_vcf = MANTA.out.candidate_small_indels_vcf // channel: [ val(meta), path(vcf) ] candidate_small_indels_vcf_tbi = MANTA.out.candidate_small_indels_vcf_tbi // channel: [ val(meta), path(tbi) ] @@ -58,5 +56,4 @@ workflow CALL_SV_MANTA { diploid_sv_vcf = MANTA.out.diploid_sv_vcf // channel: [ val(meta), path(vcf) ] diploid_sv_vcf_tbi = MANTA.out.diploid_sv_vcf_tbi // channel: [ val(meta), path(tbi) ] filtered_diploid_sv_vcf = BCFTOOLS_VIEW_MANTA.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions } From 9514a210e144b99b36e4290d3fa15fb5b4a0dd63 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:15:21 +0100 Subject: [PATCH 265/872] mosdepth --- modules.json | 4 +- modules/nf-core/mosdepth/environment.yml | 3 +- modules/nf-core/mosdepth/main.nf | 29 ++- modules/nf-core/mosdepth/meta.yml | 28 ++- modules/nf-core/mosdepth/tests/main.nf.test | 68 ++++-- .../nf-core/mosdepth/tests/main.nf.test.snap | 196 ++++++++++++------ .../nf-core/mosdepth/tests/nextflow.config | 5 + .../nf-core/mosdepth/tests/quantized.config | 3 - .../nf-core/mosdepth/tests/threshold.config | 3 - modules/nf-core/mosdepth/tests/window.config | 3 - modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 44 ++-- modules/nf-core/multiqc/meta.yml | 43 +++- .../multiqc/tests/custom_prefix.config | 5 + modules/nf-core/multiqc/tests/main.nf.test | 32 ++- .../nf-core/multiqc/tests/main.nf.test.snap | 52 +++-- subworkflows/local/qc_bam/main.nf | 1 - 17 files changed, 342 insertions(+), 179 deletions(-) create mode 100644 modules/nf-core/mosdepth/tests/nextflow.config delete mode 100644 modules/nf-core/mosdepth/tests/quantized.config delete mode 100644 modules/nf-core/mosdepth/tests/threshold.config delete mode 100644 modules/nf-core/mosdepth/tests/window.config create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config diff --git a/modules.json b/modules.json index 0e3244731..e329580b6 100644 --- a/modules.json +++ b/modules.json @@ -432,14 +432,14 @@ }, "mosdepth": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "6832b69ef7f98c54876d6436360b6b945370c615", "installed_by": [ "modules" ] }, "multiqc": { "branch": "master", - "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", + "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2", "installed_by": [ "modules" ] diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index f871e054e..1c7f3ee84 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,5 @@ channels: - bioconda dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.10 + - htslib=1.22.1 + - mosdepth=0.3.11=h0ec343a_1 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 3bf945f90..63739bfae 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.10--h4e814b3_1' : - 'biocontainers/mosdepth:0.3.10--h4e814b3_1'}" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/00/00d32b53160c26794959da7303ee6e2107afd4d292060c9f287b0af1fddbd847/data' : + 'community.wave.seqera.io/library/mosdepth_htslib:0f58993cb6d93294'}" input: tuple val(meta), path(bam), path(bai), path(bed) @@ -24,7 +24,7 @@ process MOSDEPTH { tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('mosdepth'), eval("mosdepth --version | sed 's/mosdepth //g'"), topic: versions, emit: versions_mosdepth when: task.ext.when == null || task.ext.when @@ -34,11 +34,11 @@ process MOSDEPTH { def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--fasta ${fasta}" : "" def interval = bed ? "--by ${bed}" : "" - if (bed && args.contains("--by")) { + if (bed && (args.contains("--by") || args.contains("-b "))) { error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" } - if (!bed && args.contains("--thresholds")) { - error "'--thresholds' can only be specified in conjunction with '--by'" + if (args.contains("--thresholds") && !(bed || args.contains("--by") || args.contains("-b "))) { + error "'--thresholds' can only be specified in conjunction with '--by' or an input bed file" } """ @@ -49,15 +49,17 @@ process MOSDEPTH { $args \\ $prefix \\ $bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') - END_VERSIONS """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + if (bed && (args.contains("--by") || args.contains("-b "))) { + error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" + } + if (args.contains("--thresholds") && !(bed || args.contains("--by") || args.contains("-b "))) { + error "'--thresholds' can only be specified in conjunction with '--by' or an input bed file" + } """ touch ${prefix}.global.dist.txt touch ${prefix}.region.dist.txt @@ -71,10 +73,5 @@ process MOSDEPTH { touch ${prefix}.quantized.bed.gz.csi echo "" | gzip > ${prefix}.thresholds.bed.gz touch ${prefix}.thresholds.bed.gz.csi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index af1ea44ad..04c8bfe1e 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -178,13 +178,28 @@ output: description: Index file for BED file with threshold coverage pattern: "*.{thresholds.bed.gz.csi}" ontologies: [] + versions_mosdepth: + - - ${task.process}: + type: string + description: The process the versions were collected from + - mosdepth: + type: string + description: The tool name + - "mosdepth --version | sed 's/mosdepth //g'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - mosdepth: + type: string + description: The tool name + - "mosdepth --version | sed 's/mosdepth //g'": + type: string + description: The command used to generate the version of the tool authors: - "@joseespinosa" - "@drpatelh" @@ -192,6 +207,5 @@ authors: - "@matthdsm" maintainers: - "@joseespinosa" - - "@drpatelh" - "@ramprasadn" - "@matthdsm" diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index 0b3c860d3..b05dde5be 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -7,10 +7,14 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "mosdepth" + config "./nextflow.config" test("homo_sapiens - bam, bai, []") { when { + params { + module_args = "" + } process { """ input[0] = [ @@ -25,9 +29,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -36,6 +40,9 @@ nextflow_process { test("homo_sapiens - bam, bai, bed") { when { + params { + module_args = "" + } process { """ input[0] = [ @@ -50,9 +57,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -61,6 +68,9 @@ nextflow_process { test("homo_sapiens - cram, crai, []") { when { + params { + module_args = "" + } process { """ input[0] = [ @@ -78,9 +88,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -89,6 +99,9 @@ nextflow_process { test("homo_sapiens - cram, crai, bed") { when { + params { + module_args = "" + } process { """ input[0] = [ @@ -106,9 +119,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -116,8 +129,10 @@ nextflow_process { test("homo_sapiens - bam, bai, [] - window") { - config "./window.config" when { + params { + module_args = "--by 100" + } process { """ input[0] = [ @@ -132,9 +147,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -142,8 +157,10 @@ nextflow_process { test("homo_sapiens - bam, bai, [] - quantized") { - config "./quantized.config" when { + params { + module_args = "--quantize 0:1:4:100:200" + } process { """ input[0] = [ @@ -158,9 +175,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -168,8 +185,10 @@ nextflow_process { test("homo_sapiens - bam, bai, bed - thresholds") { - config "./threshold.config" when { + params { + module_args = "--thresholds 1,10,20,30" + } process { """ input[0] = [ @@ -184,9 +203,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } @@ -194,8 +213,10 @@ nextflow_process { test("homo_sapiens - bam, bai, bed - fail") { - config "./window.config" when { + params { + module_args = "--by 100" + } process { """ input[0] = [ @@ -210,9 +231,7 @@ nextflow_process { } then { - assertAll( - { assert process.failed } - ) + assert process.failed } } @@ -221,6 +240,9 @@ nextflow_process { options "-stub" when { + params { + module_args = "" + } process { """ input[0] = [ @@ -235,9 +257,9 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index 67e16562b..c27fcc791 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -39,7 +39,11 @@ ] ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ [ @@ -221,16 +225,20 @@ "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:57:12.350279421" + "timestamp": "2025-09-23T13:06:13.219131" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -260,7 +268,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ [ @@ -289,7 +301,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -307,7 +319,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "8": [ @@ -340,7 +352,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -367,7 +379,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "regions_txt": [ @@ -394,16 +406,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:56:12.528228123" + "timestamp": "2025-09-23T13:22:14.011309" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -433,7 +449,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ @@ -456,7 +476,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -480,7 +500,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,c0a3176a59010639455a4aefb3f247ef" ] ], "global_txt": [ @@ -507,7 +527,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -528,7 +548,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,c0a3176a59010639455a4aefb3f247ef" ] ], "regions_bed": [ @@ -555,16 +575,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:56:38.422491251" + "timestamp": "2025-09-23T13:22:22.818082" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -594,7 +618,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ [ @@ -623,7 +651,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -641,7 +669,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "8": [ @@ -674,7 +702,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -701,7 +729,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "regions_txt": [ @@ -728,16 +756,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:55:43.01015749" + "timestamp": "2025-09-23T13:22:04.449943" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -767,7 +799,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ [ @@ -796,7 +832,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -814,7 +850,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,17a2cbe22a948d7c004b90a1f28347a1" ] ], "8": [ @@ -847,7 +883,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -874,7 +910,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,17a2cbe22a948d7c004b90a1f28347a1" ] ], "regions_txt": [ @@ -901,16 +937,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:56:27.10647246" + "timestamp": "2025-09-23T13:22:18.435089" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -940,7 +980,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ @@ -963,7 +1007,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -1002,7 +1046,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -1038,16 +1082,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:55:30.449110281" + "timestamp": "2025-09-23T13:21:59.785829" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -1077,7 +1125,11 @@ ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ @@ -1100,7 +1152,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -1139,7 +1191,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -1175,16 +1227,20 @@ "thresholds_csi": [ ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:55:55.244274402" + "timestamp": "2025-09-23T13:22:09.294766" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -1222,11 +1278,15 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,2c52ab89e7496af475de3cb2ca04c7b3" ] ], "12": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ], "2": [ [ @@ -1255,7 +1315,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "6": [ @@ -1273,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "8": [ @@ -1306,7 +1366,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6adccf94ed775c9f53422e3e9c7af27f" ] ], "per_base_d4": [ @@ -1333,7 +1393,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,c33ac5c86370039463796f01434fc0e4" ] ], "regions_txt": [ @@ -1369,18 +1429,22 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,2c52ab89e7496af475de3cb2ca04c7b3" ] ], - "versions": [ - "versions.yml:md5,333368078626c18a32eeb12299080cc9" + "versions_mosdepth": [ + [ + "MOSDEPTH", + "mosdepth", + "0.3.11" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "25.04.7" }, - "timestamp": "2025-01-17T14:56:49.888375978" + "timestamp": "2025-09-23T13:22:27.300204" } } \ No newline at end of file diff --git a/modules/nf-core/mosdepth/tests/nextflow.config b/modules/nf-core/mosdepth/tests/nextflow.config new file mode 100644 index 000000000..b21c05b56 --- /dev/null +++ b/modules/nf-core/mosdepth/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: "MOSDEPTH" { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/mosdepth/tests/quantized.config b/modules/nf-core/mosdepth/tests/quantized.config deleted file mode 100644 index 63c553506..000000000 --- a/modules/nf-core/mosdepth/tests/quantized.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--quantize 0:1:4:100:200" -} \ No newline at end of file diff --git a/modules/nf-core/mosdepth/tests/threshold.config b/modules/nf-core/mosdepth/tests/threshold.config deleted file mode 100644 index 9b014ddf5..000000000 --- a/modules/nf-core/mosdepth/tests/threshold.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--thresholds 1,10,20,30" -} \ No newline at end of file diff --git a/modules/nf-core/mosdepth/tests/window.config b/modules/nf-core/mosdepth/tests/window.config deleted file mode 100644 index 7a0f755ce..000000000 --- a/modules/nf-core/mosdepth/tests/window.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--by 100" -} \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index d02016a00..009874d4c 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.32 + - bioconda::multiqc=1.33 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index c1158fb08..3b0e975be 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,11 +3,11 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : - 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' : + 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' }" input: - path multiqc_files, stageAs: "?/*" + path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) @@ -15,10 +15,11 @@ process MULTIQC { path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + path "*.html" , emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever when: task.ext.when == null || task.ext.when @@ -26,38 +27,29 @@ process MULTIQC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def config = multiqc_config ? "--config ${multiqc_config}" : '' + def extra_config = extra_multiqc_config ? "--config ${extra_multiqc_config}" : '' def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${extra_config} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data + touch multiqc_data/.stub mkdir multiqc_plots touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ce30eb732..861cd7f76 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -57,10 +57,10 @@ input: - edam: http://edamontology.org/format_3475 # TSV output: report: - - "*multiqc_report.html": + - "*.html": type: file description: MultiQC report file - pattern: "multiqc_report.html" + pattern: ".html" ontologies: [] data: - "*_data": @@ -74,12 +74,15 @@ output: pattern: "*_data" ontologies: [] versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -90,3 +93,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock + linux/arm64: + lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock + docker: + linux/amd64: + build_id: bd-ee7739d47738383b_1 + name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b + scanId: sc-6ddec592dcadd583_4 + linux/arm64: + build_id: bd-58d7dee710ab3aa8_1 + name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8 + scanId: sc-a04c42273e34c55c_2 + singularity: + linux/amd64: + build_id: bd-e3576ddf588fa00d_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data + name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d + linux/arm64: + build_id: bd-2537ca5f8445e3c2_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data + name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2 diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 000000000..b30b1358b --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7dd..d1ae8b06c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -30,7 +30,33 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() } + ) + } + + } + + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/custom_prefix.html" }, + { assert process.out.data[0] ==~ ".*/custom_prefix_data" } ) } @@ -56,7 +82,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() } ) } } @@ -84,7 +110,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index a88bafd67..d72d35b74 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,61 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.33" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-27T13:33:24.356715" + "timestamp": "2025-12-09T10:10:43.020315838" }, - "multiqc_stub": { + "sarscov2 single-end [fastqc] - stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" + { + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.33" + ] + ] + } ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-27T13:34:11.103619" + "timestamp": "2025-12-09T10:11:14.131950776" }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] [config]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.33" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "24.10.4" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-27T13:34:04.615233" + "timestamp": "2025-12-09T10:11:07.15692209" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 3405c19ab..995afc287 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -106,7 +106,6 @@ workflow QC_BAM { ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions) ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) - ch_versions = ch_versions.mix(MOSDEPTH.out.versions) ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions) From 522d05d1422c6f181f9e9c45ee77a8a7443b945e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:17:08 +0100 Subject: [PATCH 266/872] collecthsmetrics --- modules.json | 2 +- .../picard/collecthsmetrics/environment.yml | 3 +- .../nf-core/picard/collecthsmetrics/main.nf | 29 +-- .../nf-core/picard/collecthsmetrics/meta.yml | 47 +++- .../collecthsmetrics/tests/main.nf.test | 55 +++- .../collecthsmetrics/tests/main.nf.test.snap | 237 +++++++++++++++--- subworkflows/local/qc_bam/main.nf | 1 - 7 files changed, 305 insertions(+), 69 deletions(-) diff --git a/modules.json b/modules.json index e329580b6..e93a6de93 100644 --- a/modules.json +++ b/modules.json @@ -467,7 +467,7 @@ }, "picard/collecthsmetrics": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "976ed20e328a92cb24ab6c63a8983ed31bf48469", "installed_by": [ "modules" ] diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index 8f34e975c..b4ac4fe08 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index 1d017ef8d..b13871f8c 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,18 +4,19 @@ process PICARD_COLLECTHSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(dict) + tuple val(meta2), path(ref) + tuple val(meta3), path(ref_fai) + tuple val(meta4), path(ref_dict) + tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped output: tuple val(meta), path("*_metrics") , emit: metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -23,7 +24,7 @@ process PICARD_COLLECTHSMETRICS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" + def reference = ref ? "--REFERENCE_SEQUENCE ${ref}" : "" def avail_mem = 3072 if (!task.memory) { @@ -36,14 +37,14 @@ process PICARD_COLLECTHSMETRICS { def bait_intervallist_cmd = "" if (bait_intervals =~ /.(bed|bed.gz)$/){ bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." + bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } def target_interval_list = target_intervals def target_intervallist_cmd = "" if (target_intervals =~ /.(bed|bed.gz)$/){ target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") - target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${dict} --TMP_DIR ." + target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } @@ -62,21 +63,11 @@ process PICARD_COLLECTHSMETRICS { --INPUT $bam \\ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.CollectHsMetrics.coverage_metrics - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index 68549f7a0..a21aa6ecd 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -49,21 +49,21 @@ input: description: | Groovy Map containing reference information e.g. [ id:'genome' ] - - fasta: + - ref: type: file description: | A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input. - pattern: "*.{fa,fasta,fna}" + pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" ontologies: [] - - meta3: type: map description: | Groovy Map containing reference information e.g. [ id:'genome' ] - - fai: + - ref_fai: type: file - description: Index of FASTA file. Only needed when fasta is supplied. + description: Index of reference file. Only needed when reference is supplied. pattern: "*.fai" ontologies: [] - - meta4: @@ -71,12 +71,22 @@ input: description: | Groovy Map containing reference information e.g. [ id:'genome' ] - - dict: + - ref_dict: type: file description: Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied. pattern: "*.dict" ontologies: [] + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - ref_gzi: + type: file + description: Index of reference file. Only needed when gzipped reference is supplied. + pattern: "*.gzi" + ontologies: [] output: metrics: - - meta: @@ -89,13 +99,28 @@ output: description: Alignment metrics files generated by picard pattern: "*_{metrics}" ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 3bbbd8cf5..07a9ccf42 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + input[4] = [[:],[]] """ } } @@ -38,7 +39,45 @@ nextflow_process { file(process.out.metrics[0][1]).name, size, lines, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } + ) + } + + } + + test("sarscov2 - bam - gzippedfa") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/targets.interval_list', checkIfExists: true) + ] + input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.fai', checkIfExists: true)] + input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + input[4] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz.gzi', checkIfExists: true)] + """ + } + } + + then { + def size = path(process.out.metrics[0][1]).size() + def lines = path(process.out.metrics[0][1]).readLines()[0..100] + lines.remove(3) // remove timestamp + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.metrics[0][1]).name, + size, + lines, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -63,6 +102,7 @@ nextflow_process { input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + input[4] = [[:],[]] """ } } @@ -70,7 +110,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } @@ -91,6 +131,7 @@ nextflow_process { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = [[:],[]] """ } } @@ -105,7 +146,7 @@ nextflow_process { file(process.out.metrics[0][1]).name, size, lines, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -129,6 +170,7 @@ nextflow_process { input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + input[4] = [[:],[]] """ } } @@ -143,7 +185,7 @@ nextflow_process { file(process.out.metrics[0][1]).name, size, lines, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -167,6 +209,7 @@ nextflow_process { input[1] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + input[4] = [[:],[]] """ } } @@ -181,11 +224,11 @@ nextflow_process { file(process.out.metrics[0][1]).name, size, lines, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 4d21710a0..74d9441fa 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -105,27 +105,186 @@ "88\t0\t0", "89\t0\t0" ], - [ - "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:51:55.291163084" + "timestamp": "2026-01-05T17:03:29.566021877" }, - "versions": { + "sarscov2 - bam - stub": { "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-05T17:03:13.333276975" + }, + "sarscov2 - bam - gzippedfa": { + "content": [ + "test.CollectHsMetrics.coverage_metrics", + 3601, [ - "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" - ] + "## htsjdk.samtools.metrics.StringHeader", + "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta.gz --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader", + "", + "## METRICS CLASS\tpicard.analysis.directed.HsMetrics", + "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP", + "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t", + "", + "## HISTOGRAM\tjava.lang.Integer", + "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count", + "0\t89\t0", + "1\t5\t0", + "2\t0\t0", + "3\t0\t0", + "4\t0\t0", + "5\t0\t0", + "6\t0\t0", + "7\t0\t0", + "8\t0\t0", + "9\t0\t0", + "10\t0\t0", + "11\t0\t0", + "12\t0\t0", + "13\t0\t0", + "14\t0\t5", + "15\t0\t0", + "16\t0\t0", + "17\t0\t0", + "18\t0\t0", + "19\t0\t0", + "20\t0\t0", + "21\t0\t1", + "22\t0\t0", + "23\t0\t0", + "24\t0\t0", + "25\t0\t0", + "26\t0\t0", + "27\t0\t0", + "28\t0\t0", + "29\t0\t0", + "30\t0\t0", + "31\t0\t0", + "32\t0\t1", + "33\t0\t0", + "34\t0\t0", + "35\t0\t0", + "36\t0\t3", + "37\t0\t0", + "38\t0\t0", + "39\t0\t0", + "40\t0\t0", + "41\t0\t0", + "42\t0\t0", + "43\t0\t0", + "44\t0\t0", + "45\t0\t0", + "46\t0\t0", + "47\t0\t0", + "48\t0\t0", + "49\t0\t0", + "50\t0\t0", + "51\t0\t0", + "52\t0\t0", + "53\t0\t0", + "54\t0\t0", + "55\t0\t0", + "56\t0\t0", + "57\t0\t0", + "58\t0\t0", + "59\t0\t0", + "60\t0\t0", + "61\t0\t0", + "62\t0\t0", + "63\t0\t0", + "64\t0\t0", + "65\t0\t0", + "66\t0\t0", + "67\t0\t0", + "68\t0\t0", + "69\t0\t0", + "70\t0\t0", + "71\t0\t0", + "72\t0\t0", + "73\t0\t0", + "74\t0\t0", + "75\t0\t0", + "76\t0\t0", + "77\t0\t0", + "78\t0\t0", + "79\t0\t0", + "80\t0\t0", + "81\t0\t0", + "82\t0\t0", + "83\t0\t0", + "84\t0\t0", + "85\t0\t0", + "86\t0\t0", + "87\t0\t0", + "88\t0\t0", + "89\t0\t0" + ], + { + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:51:30.748857589" + "timestamp": "2026-01-05T17:03:04.382110367" }, "sarscov2 - bam - samebed": { "content": [ @@ -233,15 +392,21 @@ "88\t0\t0", "89\t0\t0" ], - [ - "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:52:43.803456585" + "timestamp": "2026-01-05T17:13:22.872920293" }, "sarscov2 - bam": { "content": [ @@ -349,15 +514,21 @@ "88\t0\t0", "89\t0\t0" ], - [ - "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:51:01.881343611" + "timestamp": "2026-01-05T17:02:47.615784738" }, "sarscov2 - bam - bed": { "content": [ @@ -465,14 +636,20 @@ "88\t0\t0", "89\t0\t0" ], - [ - "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTHSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:52:22.830749735" + "timestamp": "2026-01-05T17:13:02.812282052" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 995afc287..d98774e6d 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -57,7 +57,6 @@ workflow QC_BAM { if (val_target_bed) { ch_hsmetrics = PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]).metrics - ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions) } if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results From b02c02b6df0cd80bedf5436807206014e94357dd Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:21:04 +0100 Subject: [PATCH 267/872] samtools faidx --- modules.json | 2 +- .../nf-core/samtools/faidx/environment.yml | 6 +- modules/nf-core/samtools/faidx/main.nf | 26 +- modules/nf-core/samtools/faidx/meta.yml | 65 ++- .../nf-core/samtools/faidx/tests/main.nf.test | 161 ++++++- .../samtools/faidx/tests/main.nf.test.snap | 446 ++++++++++++++++-- .../samtools/faidx/tests/nextflow.config | 2 +- .../samtools/faidx/tests/nextflow2.config | 6 - modules/nf-core/samtools/faidx/tests/tags.yml | 2 - subworkflows/local/prepare_references/main.nf | 4 +- 10 files changed, 619 insertions(+), 101 deletions(-) delete mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config delete mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml diff --git a/modules.json b/modules.json index e93a6de93..371d13895 100644 --- a/modules.json +++ b/modules.json @@ -565,7 +565,7 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", "installed_by": [ "modules" ] diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 28c0a81cf..57a03497f 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,47 +4,47 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(fasta) tuple val(meta2), path(fai) + val get_sizes output: - tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true + tuple val(meta), path ("*.sizes") , emit: sizes, optional: true tuple val(meta), path ("*.fai") , emit: fai, optional: true tuple val(meta), path ("*.gzi") , emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + def get_sizes_command = get_sizes ? "cut -f 1,2 ${fasta}.fai > ${fasta}.sizes" : '' """ samtools \\ faidx \\ $fasta \\ $args - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + ${get_sizes_command} """ stub: def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() def fastacmd = match[0] ? "touch ${match[0][1]}" : '' + def get_sizes_command = get_sizes ? "touch ${fasta}.sizes" : '' """ ${fastacmd} touch ${fasta}.fai + if [[ "${fasta.extension}" == "gz" ]]; then + touch ${fasta}.gzi + fi - cat <<-END_VERSIONS > versions.yml - - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS + ${get_sizes_command} """ } diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 6721b2cb8..163c30151 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -1,9 +1,10 @@ name: samtools_faidx -description: Index FASTA file +description: Index FASTA file, and optionally generate a file of chromosome sizes keywords: - index - fasta - faidx + - chromosome tools: - samtools: description: | @@ -25,6 +26,7 @@ input: type: file description: FASTA file pattern: "*.{fa,fasta}" + ontologies: [] - - meta2: type: map description: | @@ -34,9 +36,14 @@ input: type: file description: FASTA index file pattern: "*.{fai}" + ontologies: [] + - get_sizes: + type: boolean + description: use cut to get the sizes of the index (true) or not (false) + output: - - fa: - - meta: + fa: + - - meta: type: map description: | Groovy Map containing sample information @@ -45,8 +52,20 @@ output: type: file description: FASTA file pattern: "*.{fa}" - - fai: - - meta: + ontologies: [] + sizes: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" + ontologies: [] + fai: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,8 +74,9 @@ output: type: file description: FASTA index file pattern: "*.{fai}" - - gzi: - - meta: + ontologies: [] + gzi: + - - meta: type: map description: | Groovy Map containing sample information @@ -65,16 +85,33 @@ output: type: file description: Optional gzip index file for compressed inputs pattern: "*.gzi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@ewels" - "@phue" maintainers: - - "@drpatelh" - - "@ewels" + - "@maxulysse" - "@phue" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 17244ef2e..02ba5040c 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -8,24 +8,28 @@ nextflow_process { tag "modules_nfcore" tag "samtools" tag "samtools/faidx" + config "./nextflow.config" test("test_samtools_faidx") { when { + params { + module_args = '' + } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [[],[]] + input[2] = false """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } } @@ -33,90 +37,209 @@ nextflow_process { test("test_samtools_faidx_bgzip") { when { + params { + module_args = '' + } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] - input[1] = [[],[]] + input[2] = false """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } } test("test_samtools_faidx_fasta") { - config "./nextflow.config" - when { + params { + module_args = 'MT192765.1 -o extract.fa' + } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[2] = false """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } } test("test_samtools_faidx_stub_fasta") { - config "./nextflow2.config" - + options "-stub" when { + params { + module_args = '-o extract.fa' + } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[2] = false """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } } test("test_samtools_faidx_stub_fai") { + options "-stub" when { + params { + module_args = '' + } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[1] = [[],[]] + input[2] = false + """ + } + } + then { + assert process.success + assertAll( + { assert snapshot(process.out).match()} + ) + } + } + + test("test_samtools_faidx_get_sizes") { + + when { + params { + module_args = '' + } + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[1] = [[],[]] + input[2] = true """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match()} ) } } -} \ No newline at end of file + + test("test_samtools_faidx_get_sizes_bgzip") { + + when { + params { + module_args = '' + } + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ]) + input[1] = [[],[]] + input[2] = true + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match()} + ) + } + } + + test("test_samtools_faidx_get_sizes - stub") { + + options "-stub" + + when { + params { + module_args = '' + } + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = [[],[]] + input[2] = true + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match()} + ) + } + } + + test("test_samtools_faidx_get_sizes_bgzip - stub") { + + options "-stub" + + when { + params { + module_args = '' + } + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ]) + input[1] = [[],[]] + input[2] = true + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match()} + ) + } + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 1bbb3ec2b..565d20e71 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -6,6 +6,9 @@ ], "1": [ + + ], + "2": [ [ { "id": "test", @@ -14,11 +17,15 @@ "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] ], - "2": [ + "3": [ ], - "3": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ], "fa": [ @@ -35,16 +42,171 @@ "gzi": [ ], - "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-23T14:02:40.159309157" + }, + "test_samtools_faidx_get_sizes_bgzip - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gzi": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-23T14:03:39.550619177" + }, + "test_samtools_faidx_get_sizes": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "3": [ + + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T07:57:47.450887871" + "timestamp": "2025-12-23T14:03:16.844965756" }, "test_samtools_faidx_bgzip": { "content": [ @@ -53,6 +215,9 @@ ], "1": [ + + ], + "2": [ [ { "id": "test", @@ -61,7 +226,7 @@ "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] ], - "2": [ + "3": [ [ { "id": "test", @@ -70,8 +235,12 @@ "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" ] ], - "3": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ], "fa": [ @@ -94,16 +263,23 @@ "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" ] ], - "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T07:58:04.804905659" + "timestamp": "2025-12-23T14:02:47.301476131" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +300,14 @@ ], "3": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ], "fa": [ [ @@ -141,16 +324,92 @@ "gzi": [ ], - "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-23T09:44:40.559583279" + }, + "test_samtools_faidx_get_sizes - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gzi": [ + + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T07:58:23.831268154" + "timestamp": "2025-12-23T14:03:31.989929281" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -161,7 +420,7 @@ "id": "test", "single_end": false }, - "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -171,7 +430,14 @@ ], "3": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ], "fa": [ [ @@ -179,7 +445,7 @@ "id": "test", "single_end": false }, - "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "fai": [ @@ -188,16 +454,23 @@ "gzi": [ ], - "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T07:58:35.600243706" + "timestamp": "2025-12-23T09:44:48.295693103" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -206,19 +479,26 @@ ], "1": [ + + ], + "2": [ [ { "id": "test", "single_end": false }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ + "3": [ ], - "3": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ], "fa": [ @@ -229,21 +509,107 @@ "id": "test", "single_end": false }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "gzi": [ ], - "versions": [ - "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + "sizes": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-23T14:03:09.784289542" + }, + "test_samtools_faidx_get_sizes_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "4": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "sizes": [ + [ + { + "id": "test" + }, + "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_FAIDX", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T07:58:54.705460167" + "timestamp": "2025-12-23T14:03:24.814967939" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config index f76a3ba09..202c036ed 100644 --- a/modules/nf-core/samtools/faidx/tests/nextflow.config +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -1,7 +1,7 @@ process { withName: SAMTOOLS_FAIDX { - ext.args = 'MT192765.1 -o extract.fa' + ext.args = params.module_args } } diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config deleted file mode 100644 index 33ebbd5df..000000000 --- a/modules/nf-core/samtools/faidx/tests/nextflow2.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - withName: SAMTOOLS_FAIDX { - ext.args = '-o extract.fa' - } -} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml deleted file mode 100644 index e4a839481..000000000 --- a/modules/nf-core/samtools/faidx/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/faidx: - - modules/nf-core/samtools/faidx/** diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index ef781e070..d5dc769fb 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -89,7 +89,6 @@ workflow PREPARE_REFERENCES { // if (!val_fai) { ch_genome_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]).fai.collect() - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions) } else { ch_genome_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() } @@ -163,8 +162,7 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions, - GATK_SD_MT.out.versions, + ch_versions = ch_versions.mix(GATK_SD_MT.out.versions, GATK_SHIFTFASTA.out.versions) } // From abdda3606981424466606baec5f825c34a7f66c5 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:22:36 +0100 Subject: [PATCH 268/872] samtools merge and sort --- modules.json | 4 +- .../nf-core/samtools/merge/environment.yml | 6 +- modules/nf-core/samtools/merge/main.nf | 19 +- modules/nf-core/samtools/merge/meta.yml | 67 ++- .../nf-core/samtools/merge/tests/index.config | 3 - .../nf-core/samtools/merge/tests/main.nf.test | 197 ++++++--- .../samtools/merge/tests/main.nf.test.snap | 392 +++++++++--------- .../samtools/merge/tests/nextflow.config | 5 + modules/nf-core/samtools/merge/tests/tags.yml | 2 - modules/nf-core/samtools/sort/main.nf | 10 +- modules/nf-core/samtools/sort/meta.yml | 29 +- .../nf-core/samtools/sort/tests/main.nf.test | 20 +- .../samtools/sort/tests/main.nf.test.snap | 349 +++++----------- subworkflows/local/align_MT/main.nf | 1 - .../local/align_bwa_bwamem2_bwameme/main.nf | 1 - .../local/call_repeat_expansions/main.nf | 1 - subworkflows/local/subsample_mt_reads/main.nf | 1 - 17 files changed, 550 insertions(+), 557 deletions(-) delete mode 100644 modules/nf-core/samtools/merge/tests/index.config create mode 100644 modules/nf-core/samtools/merge/tests/nextflow.config delete mode 100644 modules/nf-core/samtools/merge/tests/tags.yml diff --git a/modules.json b/modules.json index 371d13895..f2dcd44bc 100644 --- a/modules.json +++ b/modules.json @@ -579,14 +579,14 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", "installed_by": [ "modules" ] }, "samtools/sort": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", "installed_by": [ "modules" ] diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 34da4c7c8..6785f22e8 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,21 +4,21 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") tuple val(meta2), path(fasta) tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) output: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai") , optional:true, emit: crai - path "versions.yml" , emit: versions - + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -29,6 +29,7 @@ process SAMTOOLS_MERGE { def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() def reference = fasta ? "--reference ${fasta}" : "" """ + # Note: --threads value represents *additional* CPUs to allocate (total CPUs = 1 + --threads). samtools \\ merge \\ --threads ${task.cpus-1} \\ @@ -36,11 +37,6 @@ process SAMTOOLS_MERGE { ${reference} \\ ${prefix}.${file_type} \\ $input_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -52,10 +48,5 @@ process SAMTOOLS_MERGE { """ touch ${prefix}.${file_type} ${index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 235aa2194..4237ce74e 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -26,6 +26,7 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +36,7 @@ input: type: file description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -44,9 +46,21 @@ input: type: file description: Index of the reference file the CRAM was created with (optional) pattern: "*.fai" + ontologies: [] + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: Index of the compressed reference file the CRAM was created with + (optional) + pattern: "*.gzi" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,8 +69,9 @@ output: type: file description: BAM file pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -65,8 +80,9 @@ output: type: file description: CRAM file pattern: "*.{cram}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -75,8 +91,9 @@ output: type: file description: BAM index file (optional) pattern: "*.csi" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -85,20 +102,36 @@ output: type: file description: CRAM index file (optional) pattern: "*.crai" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool authors: - - "@drpatelh" - - "@yuukiiwa " + - "@yuukiiwa" - "@maxulysse" - "@FriederikeHanssen" - "@ramprasadn" maintainers: - - "@drpatelh" - - "@yuukiiwa " + - "@yuukiiwa" - "@maxulysse" - "@FriederikeHanssen" - "@ramprasadn" diff --git a/modules/nf-core/samtools/merge/tests/index.config b/modules/nf-core/samtools/merge/tests/index.config deleted file mode 100644 index 8c5668cf3..000000000 --- a/modules/nf-core/samtools/merge/tests/index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--write-index" -} \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index 40b36e82b..08ef26945 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -8,70 +8,127 @@ nextflow_process { tag "modules_nfcore" tag "samtools" tag "samtools/merge" + config "./nextflow.config" test("bams") { - config "./index.config" - when { + params { + module_args = '--write-index' + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] - ]) + ] input[1] = [[],[]] input[2] = [[],[]] + input[3] = [[],[]] """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bams_bam") }, - { assert snapshot(process.out.cram).match("bams_cram") }, - { assert snapshot(file(process.out.csi[0][1]).name).match("bams_csi") }, - { assert snapshot(process.out.crai).match("bams_crai") }, - { assert snapshot(process.out.versions).match("bams_versions") } + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + file(process.out.csi[0][1]).name, + process.out.cram, + process.out.crai, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } ) } } - test("crams") { - - config "./index.config" + test("crams_fastq") { when { + params { + module_args = '--write-index --output-fmt cram,version=3.0' + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ] + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) - input[2] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[2] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ]) + ] + input[3] = [[],[]] + """ + } + } + + then { + def fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta' + assert process.success + assertAll( + { assert snapshot( + cram(process.out.cram[0][1], fasta).getReadsMD5(), + process.out.csi, + process.out.bam, + file(process.out.crai[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } + ) + } + } + + test("crams_fastq_gz") { + + when { + params { + module_args = '--write-index' + } + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) + ] """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(file(process.out.cram[0][1]).name).match("crams_cram") }, - { assert snapshot(process.out.bam).match("crams_bam") }, - { assert snapshot(file(process.out.crai[0][1]).name).match("crams_crai") }, - { assert snapshot(process.out.csi).match("crams_csi") }, - { assert snapshot(process.out.versions).match("crams_versions") } + { assert snapshot( + //nft-bam doesn't like the fasta.gz + file(process.out.cram[0][1]).name, + process.out.csi, + process.out.bam, + file(process.out.crai[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } ) } } @@ -79,59 +136,97 @@ nextflow_process { test("bam") { when { + params { + module_args = '' + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] - ]) + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.csi, + process.out.cram, + process.out.crai, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } + ) + } + } + + test("bams - stub") { + + options "-stub" + + when { + params { + module_args = '' + } + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + ] input[1] = [[],[]] input[2] = [[],[]] + input[3] = [[],[]] """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, - { assert snapshot(process.out.cram).match("bam_cram") }, - { assert snapshot(process.out.crai).match("bam_crai") }, - { assert snapshot(process.out.csi).match("bam_csi") }, - { assert snapshot(process.out.versions).match("bam_versions") } + { assert snapshot(process.out).match()} ) } } - test("bams_stub") { + test("bams_no_index - stub") { - config "./index.config" options "-stub" when { + params { + module_args = '' + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] - ]) + ] input[1] = [[],[]] input[2] = [[],[]] + input[3] = [[],[]] """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bams_stub_bam") }, - { assert snapshot(process.out.cram).match("bams_stub_cram") }, - { assert snapshot(file(process.out.csi[0][1]).name).match("bams_stub_csi") }, - { assert snapshot(process.out.crai).match("bams_stub_crai") }, - { assert snapshot(process.out.versions).match("bams_stub_versions") } + { assert snapshot(process.out).match()} ) } } + } diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 0a41e01af..e8d4d18a0 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -1,228 +1,226 @@ { - "crams_cram": { - "content": [ - "test.cram" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:00.647389" - }, - "bams_stub_cram": { - "content": [ + "bams_no_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-22T09:07:54.643129787" + }, + "crams_fastq": { + "content": [ + "c4525b95f05075208347295e6a1fb232", [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:19.937013" - }, - "bams_crai": { - "content": [ + ], [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:49:24.928616" - }, - "bams_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:49:24.923289" - }, - "bams_cram": { - "content": [ + ], + "test.cram.crai", + { + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-21T15:47:17.739468093" + }, + "bams - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-22T09:07:47.303781531" + }, + "bams": { + "content": [ + "47c9f174d8c8afc1a13c75ee4b5e5d43", + "test.bam.csi", [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:49:24.925716" - }, - "crams_csi": { - "content": [ + ], [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:00.655959" - }, - "bam_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:10.319539" - }, - "bam_versions": { - "content": [ - [ - "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-16T09:16:30.476887194" - }, - "bams_csi": { - "content": [ - "test.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:49:24.92719" - }, - "bams_stub_csi": { - "content": [ - "test.csi" + ], + { + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-02-12T18:50:19.940498" + "timestamp": "2025-12-21T15:47:07.586929894" }, - "bam_crai": { + "crams_fastq_gz": { "content": [ + "test.cram", [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:10.328852" - }, - "bams_stub_versions": { - "content": [ - [ - "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-16T09:16:52.203823961" - }, - "bam_cram": { - "content": [ + ], [ - ] + ], + "test.cram.crai", + { + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-02-12T18:50:10.324219" + "timestamp": "2025-12-21T15:47:26.095542073" }, - "bams_stub_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:19.933153" - }, - "bams_versions": { - "content": [ - [ - "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-16T08:29:57.524363148" - }, - "crams_bam": { + "bam": { "content": [ + "8da8fc1099a955e3ceb198665350e766", [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:00.650652" - }, - "crams_versions": { - "content": [ - [ - "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-16T09:16:06.977096207" - }, - "bam_csi": { - "content": [ + ], [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:10.33292" - }, - "crams_crai": { - "content": [ - "test.cram.crai" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:00.653512" - }, - "bams_stub_crai": { - "content": [ + ], [ - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T18:50:19.943839" + ], + { + "versions_samtools": [ + [ + "SAMTOOLS_MERGE", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-21T15:47:33.563513564" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/tests/nextflow.config b/modules/nf-core/samtools/merge/tests/nextflow.config new file mode 100644 index 000000000..2b2a46100 --- /dev/null +++ b/modules/nf-core/samtools/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: "SAMTOOLS_MERGE" { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/samtools/merge/tests/tags.yml b/modules/nf-core/samtools/merge/tests/tags.yml deleted file mode 100644 index b869abcb8..000000000 --- a/modules/nf-core/samtools/merge/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/merge: - - "modules/nf-core/samtools/merge/**" diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index d4bd5a327..6b5aa31dd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -19,7 +19,7 @@ process SAMTOOLS_SORT { tuple val(meta), path("${prefix}.${extension}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true tuple val(meta), path("${prefix}.${extension}.bai"), emit: bai, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -53,10 +53,6 @@ process SAMTOOLS_SORT { -o ${output_file} \\ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -78,9 +74,5 @@ process SAMTOOLS_SORT { touch ${prefix}.${extension} ${index} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 4c4010bbb..699683047 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -76,7 +76,6 @@ output: description: Sorted SAM file pattern: "*.{sam}" ontologies: [] - crai: - - meta: type: map @@ -110,13 +109,29 @@ output: description: BAM index file (optional) pattern: "*.bai" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - samtools: + type: string + description: The tool name + - "samtools version | sed '1!d;s/.* //'": + type: string + description: The command used to generate the version of the tool + authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index ff0691906..df47bb25c 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -34,7 +34,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -66,7 +66,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -98,7 +98,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -133,7 +133,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -168,7 +168,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.bai.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -203,7 +203,7 @@ nextflow_process { { assert snapshot( process.out.bam, process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -235,7 +235,7 @@ nextflow_process { { assert snapshot( process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match()} ) } @@ -265,7 +265,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } @@ -296,7 +296,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } @@ -325,7 +325,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 473e17450..4e618fa3f 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -19,80 +19,21 @@ "test.sorted.cram.crai" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T14:43:31.395604" - }, - "bam - stub": { - "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:37.387063" + "timestamp": "2025-10-29T12:47:01.171084" }, "bam_csi_index": { "content": [ @@ -114,15 +55,39 @@ "test.sorted.bam.csi:md5,01394e702c729cb478df914ffaf9f7f8" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:06.976036" + "timestamp": "2025-10-29T12:46:00.961675" + }, + "bam - stub": { + "content": [ + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.0" + }, + "timestamp": "2025-10-29T12:47:12.154354" }, "multiple bam bai index": { "content": [ @@ -144,80 +109,39 @@ "test.sorted.bam.bai" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:18.72271" + "timestamp": "2025-10-29T12:46:25.488622" }, "cram - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ - - ], - "crai": [ - - ], - "cram": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:48.734367" + "timestamp": "2025-10-29T12:47:28.485045" }, "multiple bam": { "content": [ @@ -233,80 +157,39 @@ [ ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:12.989244" + "timestamp": "2025-10-29T12:46:13.168476" }, "multiple bam - stub": { "content": [ { - "0": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" + "SAMTOOLS_SORT", + "samtools", + "1.22.1" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ], - "bai": [ - - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,cd4eb0077f25e9cff395366b8883dd1f" - ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - - ], - "sam": [ - - ], - "versions": [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:43.196638" + "timestamp": "2025-10-29T12:47:21.628088" }, "bam_no_index": { "content": [ @@ -322,15 +205,21 @@ [ ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:42:54.926504" + "timestamp": "2025-10-29T12:45:47.139418" }, "multiple bam csi index": { "content": [ @@ -352,45 +241,21 @@ "test.sorted.bam.csi" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T14:43:25.059178" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi" + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] ] - ], - [ - "versions.yml:md5,2659b187d681241451539d4c53500b9f" - ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-10-08T11:59:46.372244" + "timestamp": "2025-10-29T12:46:51.5531" }, "bam_bai_index": { "content": [ @@ -412,14 +277,20 @@ "test.sorted.bam.bai:md5,50dd467c169545a4d5d1f709f7e986e0" ] ], - [ - "versions.yml:md5,18e8b3709b62aa2ba61966672eee91b2" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_SORT", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2025-09-10T14:43:00.82974" + "timestamp": "2025-10-29T12:45:52.796936" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index e630b5458..e429e8ff2 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -52,7 +52,6 @@ workflow ALIGN_MT { ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions) ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions) ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_SORT_MT.out.versions) emit: marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index ae8440ea2..d100d3bbf 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -86,7 +86,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 5acce86c7..8a6fcfa25 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -62,7 +62,6 @@ workflow CALL_REPEAT_EXPANSIONS { ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 347603379..f30a3caa1 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -32,7 +32,6 @@ workflow SUBSAMPLE_MT_READS { ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) ch_versions = ch_versions.mix(GAWK.out.versions) ch_versions = ch_versions.mix(SAM_TO_BAM.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] From f0f1de6871414e50fdf49b1cced3693b23e316e4 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:25:06 +0100 Subject: [PATCH 269/872] samtools sort & view --- modules.json | 4 +- .../nf-core/samtools/stats/environment.yml | 6 +- modules/nf-core/samtools/stats/main.nf | 21 +- modules/nf-core/samtools/stats/meta.yml | 36 +- .../samtools/stats/tests/main.nf.test.snap | 88 +- modules/nf-core/samtools/stats/tests/tags.yml | 2 - modules/nf-core/samtools/view/main.nf | 12 +- modules/nf-core/samtools/view/meta.yml | 28 +- .../nf-core/samtools/view/tests/main.nf.test | 77 +- .../samtools/view/tests/main.nf.test.snap | 1276 +++++++++-------- subworkflows/local/align/main.nf | 1 - .../local/align_bwa_bwamem2_bwameme/main.nf | 2 - subworkflows/local/align_sentieon/main.nf | 1 - subworkflows/local/call_mobile_elements.nf | 1 - subworkflows/local/subsample_mt_frac/main.nf | 1 - subworkflows/local/subsample_mt_reads/main.nf | 2 - 16 files changed, 784 insertions(+), 774 deletions(-) delete mode 100644 modules/nf-core/samtools/stats/tests/tags.yml diff --git a/modules.json b/modules.json index f2dcd44bc..aed10d264 100644 --- a/modules.json +++ b/modules.json @@ -593,14 +593,14 @@ }, "samtools/stats": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df", "installed_by": [ "modules" ] }, "samtools/view": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", "installed_by": [ "modules" ] diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 493525a9e..57d246806 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input), path(input_index) @@ -13,37 +13,28 @@ process SAMTOOLS_STATS { output: tuple val(meta), path("*.stats"), emit: stats - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" """ samtools \\ stats \\ + ${args} \\ --threads ${task.cpus} \\ ${reference} \\ ${input} \\ > ${prefix}.stats - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.stats - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 77b020f76..5c59cce43 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -27,10 +27,12 @@ input: type: file description: BAM/CRAM file from alignment pattern: "*.{bam,cram}" + ontologies: [] - input_index: type: file description: BAI/CRAI file from alignment pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -40,9 +42,10 @@ input: type: file description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" + ontologies: [] output: - - stats: - - meta: + stats: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,11 +54,30 @@ output: type: file description: File containing samtools stats output pattern: "*.{stats}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool + authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index df507be7a..94d981b2a 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba" ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -20,19 +24,23 @@ "id": "test", "single_end": false }, - "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba" ] ], - "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-09-16T09:29:16.767396182" + "timestamp": "2025-11-01T02:27:18.460724" }, "bam - stub": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -58,16 +70,20 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-09-16T09:29:29.721580274" + "timestamp": "2025-11-01T02:27:30.245839" }, "cram - stub": { "content": [ @@ -82,7 +98,11 @@ ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -93,16 +113,20 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-09-16T09:29:53.567964304" + "timestamp": "2025-11-01T02:27:39.041649" }, "bam": { "content": [ @@ -113,11 +137,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,d53a2584376d78942839e9933a34d11b" + "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9" ] ], "1": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ], "stats": [ [ @@ -125,18 +153,22 @@ "id": "test", "single_end": false }, - "test.stats:md5,d53a2584376d78942839e9933a34d11b" + "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9" ] ], - "versions": [ - "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + "versions_samtools": [ + [ + "SAMTOOLS_STATS", + "samtools", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.0" }, - "timestamp": "2024-09-16T09:28:50.73610604" + "timestamp": "2025-11-01T02:26:55.988241" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml deleted file mode 100644 index 7c28e30f3..000000000 --- a/modules/nf-core/samtools/stats/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -samtools/stats: - - modules/nf-core/samtools/stats/** diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 02d9b0f99..aab585ac4 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -22,7 +22,7 @@ process SAMTOOLS_VIEW { tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -60,11 +60,6 @@ process SAMTOOLS_VIEW { -o ${output_file} \\ $input \\ $args2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -95,10 +90,5 @@ process SAMTOOLS_VIEW { ${index} ${unselected} ${unselected_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 3ebbdb891..167206773 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -140,13 +140,29 @@ output: description: index for the "unselected" file pattern: "*.unselected.{csi,crai}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools --version | head -1 | sed -e "s/samtools //": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools --version | head -1 | sed -e "s/samtools //": + type: eval + description: The expression to obtain the version of the tool + authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index d8551dd8c..de57b8e36 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -29,13 +29,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, - { assert snapshot(process.out.bai).match("bam_bai") }, - { assert snapshot(process.out.crai).match("bam_crai") }, - { assert snapshot(process.out.cram).match("bam_cram") }, - { assert snapshot(process.out.csi).match("bam_csi") }, - { assert snapshot(process.out.sam).match("bam_sam") }, - { assert snapshot(process.out.versions).match("bam_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()} ) } } @@ -62,11 +56,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.csi[0][1]).name, - process.out.versions).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()} ) } } @@ -93,10 +83,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.bai[0][1]).name, - process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai"])).match()} ) } } @@ -124,13 +111,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.bai[0][1]).name, - file(process.out.unselected[0][1]).name, - file(process.out.unselected_index[0][1]).name, - process.out.versions).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()} ) } } @@ -158,13 +139,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.cram[0][1]).name, - file(process.out.crai[0][1]).name, - file(process.out.unselected[0][1]).name, - file(process.out.unselected_index[0][1]).name, - process.out.versions).match() - } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index", "crai"])).match()} ) } } @@ -192,13 +167,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") }, - { assert snapshot(process.out.bai).match("cram_bai") }, - { assert snapshot(process.out.bam).match("cram_bam") }, - { assert snapshot(process.out.crai).match("cram_crai") }, - { assert snapshot(process.out.csi).match("cram_csi") }, - { assert snapshot(process.out.sam).match("cram_sam") }, - { assert snapshot(process.out.versions).match("cram_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cram"])).match()} ) } } @@ -228,13 +197,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") }, - { assert snapshot(process.out.bai).match("cram_to_bam_bai") }, - { assert snapshot(process.out.crai).match("cram_to_bam_crai") }, - { assert snapshot(process.out.cram).match("cram_to_bam_cram") }, - { assert snapshot(process.out.csi).match("cram_to_bam_csi") }, - { assert snapshot(process.out.sam).match("cram_to_bam_sam") }, - { assert snapshot(process.out.versions).match("cram_to_bam_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()} ) } } @@ -264,13 +227,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") }, - { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") }, - { assert snapshot(process.out.bai).match("cram_to_bam_index_bai") }, - { assert snapshot(process.out.crai).match("cram_to_bam_index_crai") }, - { assert snapshot(process.out.cram).match("cram_to_bam_index_cram") }, - { assert snapshot(process.out.sam).match("cram_to_bam_index_sam") }, - { assert snapshot(process.out.versions).match("cram_to_bam_index_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()} ) } } @@ -300,15 +257,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") }, - { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") }, - { assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") }, - { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, - { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, - { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, - { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") }, - { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") }, - { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "bai", "unselected", "unselected_index"])).match()} ) } } @@ -336,13 +285,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, - { assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") }, - { assert snapshot(process.out.bai).match("bam_stub_bai") }, - { assert snapshot(process.out.crai).match("bam_stub_crai") }, - { assert snapshot(process.out.cram).match("bam_stub_cram") }, - { assert snapshot(process.out.sam).match("bam_stub_sam") }, - { assert snapshot(process.out.versions).match("bam_stub_versions") } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["bam", "csi"])).match()} ) } } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 5ec65d62b..6ee160cd4 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -1,244 +1,49 @@ { - "bam_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:51.256068" - }, - "bam_stub_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:32.065301" - }, - "bam_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:51.258578" - }, - "bam_stub_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:32.071284" - }, - "bam_stub_versions": { - "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:20:28.366024" - }, - "cram_to_bam_index_qname_csi": { - "content": [ - "test.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.325496" - }, - "cram_to_bam_index_qname_unselected_csi": { - "content": [ - "test.unselected.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.328458" - }, - "bam_csi": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:51.262882" - }, - "cram_to_bam_index_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.95456" - }, - "cram_to_bam_index_versions": { - "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:20:20.3853" - }, - "bam_csi_index": { - "content": [ - "test.bam", - "test.bam.csi", - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:19:54.889079" - }, - "bam_versions": { - "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:19:51.017781" - }, - "cram_crai_index_unselected - stub": { + "cram_to_bam_index": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ + "bai": [ ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ + "bam": [ [ { "id": "test", "single_end": false }, - "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam" ] ], - "8": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ], - "bai": [ + "crai": [ ], - "bam": [ + "cram": [ ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "cram": [ + "csi": [ [ { "id": "test", "single_end": false }, - "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.csi" ] - ], - "csi": [ - ], "sam": [ ], "unselected": [ - [ - { - "id": "test", - "single_end": false - }, - "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "unselected_index": [ + + ], + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" ] - ], - "versions": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" ] } ], @@ -246,79 +51,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:44.809515" - }, - "bam_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:51.259774" - }, - "bam_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:51.261287" - }, - "cram_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.502625" - }, - "cram_versions": { - "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:20:12.471005" - }, - "cram_to_bam_index_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.962863" - }, - "cram_to_bam_index_qname_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.337634" + "timestamp": "2025-10-29T15:41:48.952660444" }, "bam_csi_index - stub": { "content": [ @@ -360,7 +93,11 @@ ], "8": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] ], "bai": [ @@ -398,8 +135,12 @@ "unselected_index": [ ], - "versions": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] ] } ], @@ -407,94 +148,67 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:32.118817" - }, - "cram_to_bam_index_csi": { - "content": [ - "test.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.958617" - }, - "bam_bai_index": { - "content": [ - "test.bam", - "test.bam.bai", - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T15:19:58.85102" - }, - "cram_to_bam_index_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.972288" + "timestamp": "2025-10-29T15:42:14.881335093" }, - "bam_bai_index - stub": { + "bam_csi_index": { "content": [ { - "0": [ + "bai": [ + + ], + "bam": [ [ { "id": "test", "single_end": false }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam" ] ], - "1": [ + "crai": [ ], - "2": [ + "cram": [ ], - "3": [ + "csi": [ [ { "id": "test", "single_end": false }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam.csi" ] ], - "4": [ - - ], - "5": [ + "sam": [ ], - "6": [ + "unselected": [ ], - "7": [ + "unselected_index": [ ], - "8": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ], - "bai": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" ] + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-10-29T15:40:50.701779393" + }, + "cram_to_bam_index_qname": { + "content": [ + { + "bai": [ + ], "bam": [ [ @@ -502,7 +216,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam" ] ], "crai": [ @@ -512,19 +226,41 @@ ], "csi": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.bam.csi:md5,15d725bced7ececd45b4312b2af99a6b" + ] ], "sam": [ ], "unselected": [ - - ], + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam" + ] + ], "unselected_index": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam.csi" + ] ], - "versions": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] ] } ], @@ -532,297 +268,489 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:35.787886" - }, - "cram_to_bam_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:04.999247" - }, - "cram_to_bam_index_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.976457" - }, - "cram_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.497581" - }, - "cram_csi": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.50038" - }, - "cram_to_bam_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:04.992239" - }, - "bam_stub_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:32.079529" + "timestamp": "2025-10-29T15:41:58.085628072" }, - "cram_cram": { - "content": [ - "test.cram" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.490286" - }, - "cram_to_bam_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:04.989247" - }, - "cram_to_bam_index_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:12.967681" - }, - "cram_crai_index_unselected": { + "bam_bai_index_unselected": { "content": [ - "test.cram", - "test.cram.crai", - "test.unselected.cram", - "test.unselected.cram.crai", - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] + { + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam" + ] + ], + "unselected_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.bam.csi" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:07.026136" + "timestamp": "2025-10-29T15:41:10.249194373" }, - "cram_to_bam_index_qname_versions": { + "cram_crai_index_unselected - stub": { "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ], + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "unselected_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:24.609054" + "timestamp": "2025-10-29T15:42:39.3240134" }, - "cram_to_bam_bam": { + "bam": { "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:04.982361" - }, - "cram_to_bam_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:04.98601" - }, - "cram_to_bam_versions": { - "content": [ - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:16.51014" - }, - "cram_bam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.495512" - }, - "bam_stub_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:32.076908" - }, - "cram_to_bam_index_qname_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.328458" + "timestamp": "2025-10-29T15:40:42.829284764" }, - "cram_to_bam_index_qname_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.330789" - }, - "cram_bai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:37:56.493129" - }, - "bam_stub_crai": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:32.074313" - }, - "cram_to_bam_index_qname_bam": { + "bam_bai_index": { "content": [ - "test.bam" + { + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:38:23.322874" + "timestamp": "2025-10-29T15:41:00.734899949" }, - "bam_bai_index_unselected": { + "cram_to_bam": { "content": [ - "test.bam", - "test.bam.bai", - "test.unselected.bam", - "test.unselected.bam.csi", - [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" - ] + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:03.049076" + "timestamp": "2025-10-29T15:41:40.148480065" }, - "cram_to_bam_index_qname_cram": { + "bam_bai_index - stub": { "content": [ - [ - - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:38:23.333248" + "timestamp": "2025-10-29T15:42:22.748940869" }, - "cram_to_bam_csi": { + "cram": { "content": [ - [ - - ] + { + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram" + ] + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:38:04.995454" + "timestamp": "2025-10-29T15:41:30.602610389" }, "bam_bai_index_uselected - stub": { "content": [ @@ -876,7 +804,11 @@ ] ], "8": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] ], "bai": [ [ @@ -926,8 +858,12 @@ "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,376bd183239f91c807210bfeb299d306" + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] ] } ], @@ -935,38 +871,126 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-10T15:20:39.633146" - }, - "cram_to_bam_index_qname_unselected": { - "content": [ - "test.unselected.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.322874" + "timestamp": "2025-10-29T15:42:31.1133801" }, - "bam_sam": { + "cram_crai_index_unselected": { "content": [ - [ - - ] + { + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram.crai" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,9b6eeca8f6b4b744297ae7cc87c031a4" + ] + ], + "csi": [ + + ], + "sam": [ + + ], + "unselected": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram" + ] + ], + "unselected_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.unselected.cram.crai" + ] + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:37:51.264651" + "timestamp": "2025-10-29T15:49:09.738258028" }, - "bam_stub_csi": { + "bam_stub": { "content": [ - "test.bam.csi" + { + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.csi" + ] + ], + "sam": [ + + ], + "unselected": [ + + ], + "unselected_index": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_VIEW", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-02-12T19:38:32.068596" + "timestamp": "2025-10-29T15:42:06.108061867" } } \ No newline at end of file diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index b3fb0e940..224149535 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -157,7 +157,6 @@ workflow ALIGN { if (val_save_mapped_as_cram) { SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) } emit: diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index d100d3bbf..2e6539e20 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -76,7 +76,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam - ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions) } @@ -85,7 +84,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 5755bde96..6ace66bc2 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -43,7 +43,6 @@ workflow ALIGN_SENTIEON { if (val_extract_alignments) { EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) - ch_versions = ch_versions.mix(EXTRACT_ALIGNMENTS.out.versions) } SENTIEON_DATAMETRICS ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, false ) diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index be7ba8ee9..088246a63 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -121,7 +121,6 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) - ch_versions = ch_versions.mix(ME_SPLIT_ALIGNMENT.out.versions) ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index fe9a1e19b..25b64d2b3 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -35,7 +35,6 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index f30a3caa1..e7663da39 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -28,10 +28,8 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') - ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) ch_versions = ch_versions.mix(GAWK.out.versions) - ch_versions = ch_versions.mix(SAM_TO_BAM.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] From 2e97c8f88696c517d2f0905242b2bc559dd6427e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:32:24 +0100 Subject: [PATCH 270/872] update sentieon --- modules.json | 16 +- .../nf-core/sentieon/bwaindex/environment.yml | 2 +- modules/nf-core/sentieon/bwaindex/main.nf | 32 +-- modules/nf-core/sentieon/bwaindex/meta.yml | 36 ++- .../sentieon/bwaindex/tests/main.nf.test | 7 +- .../sentieon/bwaindex/tests/main.nf.test.snap | 40 ++- .../sentieon/bwaindex/tests/nextflow.config | 12 +- .../nf-core/sentieon/bwamem/environment.yml | 2 +- modules/nf-core/sentieon/bwamem/main.nf | 42 +-- modules/nf-core/sentieon/bwamem/meta.yml | 57 +++- .../sentieon/bwamem/tests/main.nf.test | 92 +++--- .../sentieon/bwamem/tests/main.nf.test.snap | 176 ++++++------ .../sentieon/bwamem/tests/nextflow.config | 11 +- .../bwamem/tests/nextflow_out_cram.config | 16 -- .../sentieon/datametrics/environment.yml | 3 +- modules/nf-core/sentieon/datametrics/main.nf | 62 ++-- modules/nf-core/sentieon/datametrics/meta.yml | 96 ++++--- .../sentieon/datametrics/tests/main.nf.test | 36 +-- .../datametrics/tests/main.nf.test.snap | 250 +++-------------- .../datametrics/tests/nextflow.config | 15 +- .../nf-core/sentieon/dedup/environment.yml | 2 +- modules/nf-core/sentieon/dedup/main.nf | 46 ++- modules/nf-core/sentieon/dedup/meta.yml | 71 +++-- .../nf-core/sentieon/dedup/tests/main.nf.test | 58 +++- .../sentieon/dedup/tests/main.nf.test.snap | 264 +++--------------- .../sentieon/dedup/tests/nextflow.config | 18 +- .../dedup/tests/nextflow_rmdup.config | 15 - .../sentieon/dnamodelapply/environment.yml | 2 +- .../nf-core/sentieon/dnamodelapply/main.nf | 43 ++- .../nf-core/sentieon/dnamodelapply/meta.yml | 41 ++- .../sentieon/dnamodelapply/tests/main.nf.test | 25 +- .../dnamodelapply/tests/main.nf.test.snap | 46 ++- .../dnamodelapply/tests/nextflow.config | 8 +- .../nf-core/sentieon/dnascope/environment.yml | 2 +- modules/nf-core/sentieon/dnascope/main.nf | 88 +++--- modules/nf-core/sentieon/dnascope/meta.yml | 87 ++++-- .../sentieon/dnascope/tests/main.nf.test | 63 +++-- .../sentieon/dnascope/tests/main.nf.test.snap | 84 +++--- .../sentieon/dnascope/tests/nextflow.config | 17 +- .../sentieon/readwriter/environment.yml | 2 +- modules/nf-core/sentieon/readwriter/main.nf | 52 ++-- modules/nf-core/sentieon/readwriter/meta.yml | 53 +++- .../sentieon/readwriter/tests/main.nf.test | 72 ++--- .../readwriter/tests/main.nf.test.snap | 92 ++++-- .../sentieon/readwriter/tests/nextflow.config | 14 +- .../tests/nextflow_outputcram.config | 16 -- .../sentieon/wgsmetrics/environment.yml | 2 +- modules/nf-core/sentieon/wgsmetrics/main.nf | 48 ++-- modules/nf-core/sentieon/wgsmetrics/meta.yml | 29 +- .../sentieon/wgsmetrics/tests/main.nf.test | 23 +- .../wgsmetrics/tests/main.nf.test.snap | 44 +-- .../sentieon/wgsmetrics/tests/nextflow.config | 8 +- subworkflows/local/align_MT/main.nf | 1 - subworkflows/local/align_sentieon/main.nf | 7 - subworkflows/local/call_snv_sentieon/main.nf | 2 - subworkflows/local/prepare_references/main.nf | 2 - subworkflows/local/qc_bam/main.nf | 1 - 57 files changed, 1184 insertions(+), 1267 deletions(-) delete mode 100644 modules/nf-core/sentieon/bwamem/tests/nextflow_out_cram.config delete mode 100644 modules/nf-core/sentieon/dedup/tests/nextflow_rmdup.config delete mode 100644 modules/nf-core/sentieon/readwriter/tests/nextflow_outputcram.config diff --git a/modules.json b/modules.json index aed10d264..fceed0050 100644 --- a/modules.json +++ b/modules.json @@ -607,56 +607,56 @@ }, "sentieon/bwaindex": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", "installed_by": [ "modules" ] }, "sentieon/bwamem": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", "installed_by": [ "modules" ] }, "sentieon/datametrics": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", "installed_by": [ "modules" ] }, "sentieon/dedup": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", "installed_by": [ "modules" ] }, "sentieon/dnamodelapply": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", "installed_by": [ "modules" ] }, "sentieon/dnascope": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", "installed_by": [ "modules" ] }, "sentieon/readwriter": { "branch": "master", - "git_sha": "6b36f8e5427ec38911565398de57656ca3a2606a", + "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", "installed_by": [ "modules" ] }, "sentieon/wgsmetrics": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", "installed_by": [ "modules" ] diff --git a/modules/nf-core/sentieon/bwaindex/environment.yml b/modules/nf-core/sentieon/bwaindex/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/bwaindex/environment.yml +++ b/modules/nf-core/sentieon/bwaindex/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/bwaindex/main.nf b/modules/nf-core/sentieon/bwaindex/main.nf index 010165e47..1b36961a1 100644 --- a/modules/nf-core/sentieon/bwaindex/main.nf +++ b/modules/nf-core/sentieon/bwaindex/main.nf @@ -1,19 +1,19 @@ process SENTIEON_BWAINDEX { - tag "$fasta" + tag "${fasta}" label 'process_high' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(fasta) output: tuple val(meta), path("bwa"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when @@ -21,20 +21,18 @@ process SENTIEON_BWAINDEX { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ? "bwa/${task.ext.prefix}" : "bwa/${fasta.baseName}" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ + ${sentieonLicense} mkdir bwa sentieon \\ bwa index \\ - $args \\ - -p $prefix \\ - $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS + ${args} \\ + -p ${prefix} \\ + ${fasta} """ stub: @@ -46,11 +44,5 @@ process SENTIEON_BWAINDEX { touch bwa/genome.bwt touch bwa/genome.pac touch bwa/genome.sa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/bwaindex/meta.yml b/modules/nf-core/sentieon/bwaindex/meta.yml index f265049d1..165247da8 100644 --- a/modules/nf-core/sentieon/bwaindex/meta.yml +++ b/modules/nf-core/sentieon/bwaindex/meta.yml @@ -23,25 +23,41 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: [] output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - - "bwa": + - bwa: type: file description: BWA genome index files pattern: "*.{amb,ann,bwt,pac,sa}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool authors: - - "@drpatelh" - "@maxulysse" maintainers: - - "@drpatelh" - "@maxulysse" diff --git a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test index 7df044019..57526c705 100644 --- a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test +++ b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test @@ -23,12 +23,11 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("build index - fasta - stub") { @@ -47,12 +46,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap index a4672d557..98d1984ac 100644 --- a/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/bwaindex/tests/main.nf.test.snap @@ -17,7 +17,11 @@ ] ], "1": [ - "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + [ + "SENTIEON_BWAINDEX", + "sentieon", + "202503.02" + ] ], "index": [ [ @@ -33,16 +37,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + "versions_sentieon": [ + [ + "SENTIEON_BWAINDEX", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:00:00.130499875" + "timestamp": "2026-01-19T18:27:10.208416609" }, "build index - fasta": { "content": [ @@ -62,7 +70,11 @@ ] ], "1": [ - "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + [ + "SENTIEON_BWAINDEX", + "sentieon", + "202503.02" + ] ], "index": [ [ @@ -78,15 +90,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,10660ecce12c1124349e0d69e2bcfcb7" + "versions_sentieon": [ + [ + "SENTIEON_BWAINDEX", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T07:59:32.96587875" + "timestamp": "2026-01-19T18:27:03.694090374" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/bwaindex/tests/nextflow.config b/modules/nf-core/sentieon/bwaindex/tests/nextflow.config index 47f5ec002..9a93f5007 100644 --- a/modules/nf-core/sentieon/bwaindex/tests/nextflow.config +++ b/modules/nf-core/sentieon/bwaindex/tests/nextflow.config @@ -1,11 +1,11 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = $SENTIEON_LICSRVR_IP + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = $SENTIEON_AUTH_MECH + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat | base64 -w 0) -} -process { + // NOTE This is how users will test out Sentieon in Sarek with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf index 2f014d064..ca37c2c59 100644 --- a/modules/nf-core/sentieon/bwamem/main.nf +++ b/modules/nf-core/sentieon/bwamem/main.nf @@ -1,12 +1,12 @@ process SENTIEON_BWAMEM { - tag "$meta.id" + tag "${meta.id}" label 'process_high' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(reads) @@ -16,7 +16,8 @@ process SENTIEON_BWAMEM { output: tuple val(meta), path("${prefix}"), path("${prefix}.{bai,crai}"), emit: bam_and_bai - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwa'), eval('sentieon bwa 2>&1 | sed -n "s/^Version: *//p"'), topic: versions, emit: versions_bwa + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when @@ -24,47 +25,34 @@ process SENTIEON_BWAMEM { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}.bam" - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} export bwt_max_mem="${(task.memory * 0.9).toGiga()}G" INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'` sentieon bwa mem \\ - $args \\ - -t $task.cpus \\ + ${args} \\ + -t ${task.cpus} \\ \$INDEX \\ - $reads \\ - | sentieon util sort -r $fasta -t $task.cpus -o ${prefix} --sam2bam - + ${reads} \\ + | sentieon util sort -r ${fasta} -t ${task.cpus} -o ${prefix} --sam2bam - # Delete *.bai file if prefix ends with .cram if [[ "${prefix}" == *.cram ]]; then rm -f "${prefix}.bai" fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${meta.id}.bam" - index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" - + index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" """ touch ${prefix} touch ${prefix}.${index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml index b27dd4877..a36fb5f5e 100644 --- a/modules/nf-core/sentieon/bwamem/meta.yml +++ b/modules/nf-core/sentieon/bwamem/meta.yml @@ -25,6 +25,7 @@ input: - reads: type: file description: Genome fastq files (single-end or paired-end) + ontologies: [] - - meta2: type: map description: | @@ -34,6 +35,7 @@ input: type: file description: BWA genome index files pattern: "*.{amb,ann,bwt,pac,sa}" + ontologies: [] - - meta3: type: map description: | @@ -43,6 +45,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta4: type: map description: | @@ -52,9 +55,10 @@ input: type: file description: The index of the FASTA reference. pattern: "*.fai" + ontologies: [] output: - - bam_and_bai: - - meta: + bam_and_bai: + - - meta: type: map description: | Groovy Map containing reference information. @@ -63,15 +67,54 @@ output: type: file description: BAM file with corresponding index. pattern: "*.{bam,bai}" + ontologies: [] - ${prefix}.{bai,crai}: type: file description: BAM file with corresponding index. pattern: "*.{bam,bai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwa: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'sentieon bwa 2>&1 | sed -n "s/^Version: *//p"': + type: string + description: The command used to generate the version of the tool + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'sentieon bwa 2>&1 | sed -n "s/^Version: *//p"': + type: string + description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool + authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test b/modules/nf-core/sentieon/bwamem/tests/main.nf.test index 074722882..676ec10b8 100644 --- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test +++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test @@ -11,9 +11,9 @@ nextflow_process { script "../main.nf" process "SENTIEON_BWAMEM" + config "./nextflow.config" test("Single-End") { - config "./nextflow.config" setup { run("SENTIEON_BWAINDEX") { @@ -30,6 +30,10 @@ nextflow_process { } when { + params { + module_args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + module_out_cram = false + } process { """ input[0] = [ @@ -46,16 +50,18 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + bam(process.out.bam_and_bai[0][1]).getReadsMD5(), + file(process.out.bam_and_bai[0][2]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("Single-End Output CRAM") { - config "./nextflow_out_cram.config" setup { run("SENTIEON_BWAINDEX") { @@ -72,6 +78,10 @@ nextflow_process { } when { + params { + module_args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + module_out_cram = true + } process { """ input[0] = [ @@ -88,16 +98,19 @@ nextflow_process { } then { + def fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/sarscov2/genome/genome.fasta" + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + cram(process.out.bam_and_bai[0][1], fasta).getReadsMD5(), + file(process.out.bam_and_bai[0][2]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("Paired-End") { - config "./nextflow.config" setup { run("SENTIEON_BWAINDEX") { @@ -114,23 +127,10 @@ nextflow_process { } when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = SENTIEON_BWAINDEX.out.index - input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[3] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - """ + params { + module_args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + module_out_cram = false } - } - - when { process { """ input[0] = [ @@ -147,16 +147,20 @@ nextflow_process { } } + then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + bam(process.out.bam_and_bai[0][1]).getReadsMD5(), + file(process.out.bam_and_bai[0][2]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } test("Single-End - stub") { - config "./nextflow.config" options "-stub" setup { @@ -174,6 +178,10 @@ nextflow_process { } when { + params { + module_args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + module_out_cram = false + } process { """ input[0] = [ @@ -190,16 +198,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("Paired-End - stub") { - config "./nextflow.config" options "-stub" setup { @@ -217,23 +223,10 @@ nextflow_process { } when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = SENTIEON_BWAINDEX.out.index - input[2] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] - input[3] = [[id: 'test'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)] - """ + params { + module_args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + module_out_cram = false } - } - - when { process { """ input[0] = [ @@ -250,13 +243,12 @@ nextflow_process { } } + then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - - } diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap index 88b8f5e0d..5a0fa2006 100644 --- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap @@ -1,40 +1,30 @@ { "Single-End": { "content": [ + "30c325e1e032eb1782a280d34c0fb1c7", + "test.bam.bai", { - "0": [ + "versions_bwa": [ [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,dea3fc9d19388fefd3fca90f07b0a1f8", - "test.bam.bai:md5,0cdb1f6a29cf060612b607d9166e4c36" + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" ] ], - "1": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" - ], - "bam_and_bai": [ + "versions_sentieon": [ [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,dea3fc9d19388fefd3fca90f07b0a1f8", - "test.bam.bai:md5,0cdb1f6a29cf060612b607d9166e4c36" + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" ] - ], - "versions": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:00:37.715936422" + "timestamp": "2026-01-20T13:36:45.282690704" }, "Paired-End - stub": { "content": [ @@ -50,7 +40,18 @@ ] ], "1": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" + [ + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" + ] + ], + "2": [ + [ + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" + ] ], "bam_and_bai": [ [ @@ -62,53 +63,54 @@ "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" + "versions_bwa": [ + [ + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" + ] + ], + "versions_sentieon": [ + [ + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:03:07.521348975" + "timestamp": "2026-01-19T16:27:57.975551525" }, "Paired-End": { "content": [ + "2d64e4363d9f3c0e2167fce49d5087cf", + "test.bam.bai", { - "0": [ + "versions_bwa": [ [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,ee68f972e594b3d1751696eef91f183b", - "test.bam.bai:md5,b22cbbc501adedc7433d2334f631f754" + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" ] ], - "1": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" - ], - "bam_and_bai": [ + "versions_sentieon": [ [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,ee68f972e594b3d1751696eef91f183b", - "test.bam.bai:md5,b22cbbc501adedc7433d2334f631f754" + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" ] - ], - "versions": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:01:52.416216804" + "timestamp": "2026-01-20T13:37:06.816187615" }, "Single-End - stub": { "content": [ @@ -124,7 +126,18 @@ ] ], "1": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" + [ + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" + ] + ], + "2": [ + [ + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" + ] ], "bam_and_bai": [ [ @@ -136,52 +149,53 @@ "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" + "versions_bwa": [ + [ + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" + ] + ], + "versions_sentieon": [ + [ + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:02:30.011453766" + "timestamp": "2026-01-19T16:27:48.308820347" }, "Single-End Output CRAM": { "content": [ + "30c325e1e032eb1782a280d34c0fb1c7", + "test.cram.crai", { - "0": [ + "versions_bwa": [ [ - { - "id": "test", - "single_end": true - }, - "test.cram:md5,0922ee1600c3a9bb77547bde94dbe846", - "test.cram.crai:md5,554d760554ce52d5ec269c8949eb3ab2" + "SENTIEON_BWAMEM", + "bwa", + "0.7.17-r1188" ] ], - "1": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" - ], - "bam_and_bai": [ + "versions_sentieon": [ [ - { - "id": "test", - "single_end": true - }, - "test.cram:md5,0922ee1600c3a9bb77547bde94dbe846", - "test.cram.crai:md5,554d760554ce52d5ec269c8949eb3ab2" + "SENTIEON_BWAMEM", + "sentieon", + "202503.02" ] - ], - "versions": [ - "versions.yml:md5,1c6ad703a3f032bd4293054ce5081d8b" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:01:15.037591768" + "timestamp": "2026-01-20T13:36:56.563978907" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/bwamem/tests/nextflow.config b/modules/nf-core/sentieon/bwamem/tests/nextflow.config index 717fb52c7..e3d56f721 100644 --- a/modules/nf-core/sentieon/bwamem/tests/nextflow.config +++ b/modules/nf-core/sentieon/bwamem/tests/nextflow.config @@ -1,15 +1,18 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } process { withName: 'SENTIEON_BWAMEM' { - ext.args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" + ext.args = params.module_args + ext.prefix = { "${meta.id}." + (params.module_out_cram ? 'cram' : 'bam') } } } diff --git a/modules/nf-core/sentieon/bwamem/tests/nextflow_out_cram.config b/modules/nf-core/sentieon/bwamem/tests/nextflow_out_cram.config deleted file mode 100644 index 07ae63d98..000000000 --- a/modules/nf-core/sentieon/bwamem/tests/nextflow_out_cram.config +++ /dev/null @@ -1,16 +0,0 @@ -env { - // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} - -process { - withName: 'SENTIEON_BWAMEM' { - ext.args = "-R \"@RG\\tID:sample_lane\\tPU:lane\\tSM:patient_sample\\tLB:sample\\tDS:fasta\\tPL:seqplatform\"" - ext.prefix = { "${meta.id}.cram" } - } -} diff --git a/modules/nf-core/sentieon/datametrics/environment.yml b/modules/nf-core/sentieon/datametrics/environment.yml index ec48106f3..2986b7b43 100644 --- a/modules/nf-core/sentieon/datametrics/environment.yml +++ b/modules/nf-core/sentieon/datametrics/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 + - conda-forge::gnuplot=5.4.10 diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf index 3a4fce755..9c1b8dd65 100644 --- a/modules/nf-core/sentieon/datametrics/main.nf +++ b/modules/nf-core/sentieon/datametrics/main.nf @@ -1,12 +1,12 @@ process SENTIEON_DATAMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/68/68b1ed28e610d30e71f2941062dd1dddc5ccaa59496442761d0a3579e0ab9d69/data' : - 'community.wave.seqera.io/library/sentieon_gnuplot:be1a7a35856e97bb' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ae/ae67a134620c3af22c8563a2913c4639caa0d75ce25764e7b10c996b242aa023/data' + : 'community.wave.seqera.io/library/sentieon_gnuplot:41931fca35668c97'}" input: tuple val(meta), path(bam), path(bai) @@ -15,55 +15,50 @@ process SENTIEON_DATAMETRICS { val plot_results output: - tuple val(meta), path('*mq_metrics.txt') , emit: mq_metrics - tuple val(meta), path('*qd_metrics.txt') , emit: qd_metrics - tuple val(meta), path('*gc_summary.txt') , emit: gc_summary - tuple val(meta), path('*gc_metrics.txt') , emit: gc_metrics + tuple val(meta), path('*mq_metrics.txt'), emit: mq_metrics + tuple val(meta), path('*qd_metrics.txt'), emit: qd_metrics + tuple val(meta), path('*gc_summary.txt'), emit: gc_summary + tuple val(meta), path('*gc_metrics.txt'), emit: gc_metrics tuple val(meta), path('*aln_metrics.txt'), emit: aln_metrics - tuple val(meta), path('*is_metrics.txt') , emit: is_metrics - tuple val(meta), path('*mq_metrics.pdf') , emit: mq_plot, optional: true - tuple val(meta), path('*qd_metrics.pdf') , emit: qd_plot, optional: true - tuple val(meta), path('*is_metrics.pdf') , emit: is_plot, optional: true - tuple val(meta), path('*gc_metrics.pdf') , emit: gc_plot, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path('*is_metrics.txt'), emit: is_metrics + tuple val(meta), path('*mq_metrics.pdf'), emit: mq_plot, optional: true + tuple val(meta), path('*qd_metrics.pdf'), emit: qd_plot, optional: true + tuple val(meta), path('*is_metrics.pdf'), emit: is_plot, optional: true + tuple val(meta), path('*gc_metrics.pdf'), emit: gc_plot, optional: true + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = bam.sort().collect{"-i $it"}.join(' ') - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def input = bam.sort().collect {in -> "-i ${in}" }.join(' ') + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} sentieon \\ driver \\ - -t $task.cpus \\ - -r $fasta \\ - $input \\ - $args \\ + -t ${task.cpus} \\ + -r ${fasta} \\ + ${input} \\ + ${args} \\ --algo GCBias --summary ${prefix}_gc_summary.txt ${prefix}_gc_metrics.txt \\ --algo MeanQualityByCycle ${prefix}_mq_metrics.txt \\ --algo QualDistribution ${prefix}_qd_metrics.txt \\ --algo InsertSizeMetricAlgo ${prefix}_is_metrics.txt \\ --algo AlignmentStat ${prefix}_aln_metrics.txt - if $plot_results + if ${plot_results} then sentieon plot GCBias -o ${prefix}_gc_metrics.pdf ${prefix}_gc_metrics.txt sentieon plot MeanQualityByCycle -o ${prefix}_mq_metrics.pdf ${prefix}_mq_metrics.txt sentieon plot QualDistribution -o ${prefix}_qd_metrics.pdf ${prefix}_qd_metrics.txt sentieon plot InsertSizeMetricAlgo -o ${prefix}_is_metrics.pdf ${prefix}_is_metrics.txt fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ stub: @@ -76,17 +71,12 @@ process SENTIEON_DATAMETRICS { touch ${prefix}_aln_metrics.txt touch ${prefix}_is_metrics.txt - if $plot_results + if ${plot_results} then touch ${prefix}_gc_metrics.pdf touch ${prefix}_mq_metrics.pdf touch ${prefix}_qd_metrics.pdf touch ${prefix}_is_metrics.pdf fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/datametrics/meta.yml b/modules/nf-core/sentieon/datametrics/meta.yml index 91c60b756..ad5e18d93 100644 --- a/modules/nf-core/sentieon/datametrics/meta.yml +++ b/modules/nf-core/sentieon/datametrics/meta.yml @@ -22,10 +22,12 @@ input: type: file description: Sorted BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - bai: type: file description: Index of th sorted BAM/CRAM/SAM file pattern: "*.{bai,crai,sai}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +37,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -44,35 +47,38 @@ input: type: file description: Index of the genome fasta file pattern: "*.fai" - - - plot_results: - type: boolean - description: Boolean to determine whether plots should be generated - pattern: "true or false" + ontologies: [] + - plot_results: + type: boolean + description: Boolean to determine whether plots should be generated + pattern: "true or false" output: - - mq_metrics: - - meta: + mq_metrics: + - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - "*mq_metrics.txt": type: file - description: File containing the information about mean base quality score for - each sequencing cycle + description: File containing the information about mean base quality score + for each sequencing cycle pattern: "*.txt" - - qd_metrics: - - meta: + ontologies: [] + qd_metrics: + - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - "*qd_metrics.txt": type: file - description: File containing the information about number of bases with a specific - base quality score + description: File containing the information about number of bases with a + specific base quality score pattern: "*.txt" - - gc_summary: - - meta: + ontologies: [] + gc_summary: + - - meta: type: map description: | Groovy Map containing sample information @@ -82,8 +88,9 @@ output: description: File containing the information about GC bias in the reference and the sample pattern: "*.txt" - - gc_metrics: - - meta: + ontologies: [] + gc_metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -93,8 +100,9 @@ output: description: File containing the information about GC bias in the reference and the sample pattern: "*.txt" - - aln_metrics: - - meta: + ontologies: [] + aln_metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -103,8 +111,9 @@ output: type: file description: File containing the statistics about the alignment of the reads pattern: "*.txt" - - is_metrics: - - meta: + ontologies: [] + is_metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -114,8 +123,9 @@ output: description: File containing the information about statistical distribution of insert sizes pattern: "*.txt" - - mq_plot: - - meta: + ontologies: [] + mq_plot: + - - meta: type: map description: | Groovy Map containing sample information @@ -124,8 +134,9 @@ output: type: file description: "PDF containing plot of mean base quality scores" pattern: "*.pdf" - - qd_plot: - - meta: + ontologies: [] + qd_plot: + - - meta: type: map description: | Groovy Map containing sample information @@ -134,8 +145,9 @@ output: type: file description: "PDF containing plot of specific base quality score" pattern: "*.pdf" - - is_plot: - - meta: + ontologies: [] + is_plot: + - - meta: type: map description: | Groovy Map containing sample information @@ -144,8 +156,9 @@ output: type: file description: "PDF containing plot of insert sizes" pattern: "*.pdf" - - gc_plot: - - meta: + ontologies: [] + gc_plot: + - - meta: type: map description: | Groovy Map containing sample information @@ -154,11 +167,28 @@ output: type: file description: "PDF containing plot of GC bias" pattern: "*.pdf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test b/modules/nf-core/sentieon/datametrics/tests/main.nf.test index 44f631a61..87b193ca3 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test @@ -33,12 +33,20 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + path(process.out.mq_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.qd_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.gc_summary[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.gc_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.aln_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.is_metrics[0][1]).readLines()[1..3].join("\n").md5(), + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } ) } - } test("metrics - with plots") { @@ -67,23 +75,21 @@ nextflow_process { assert process.success assertAll( { assert snapshot( - process.out.mq_metrics, - process.out.qd_metrics, - process.out.gc_summary, - process.out.gc_metrics, - process.out.aln_metrics, - process.out.is_metrics, + path(process.out.mq_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.qd_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.gc_summary[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.gc_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.aln_metrics[0][1]).readLines()[1..3].join("\n").md5(), + path(process.out.is_metrics[0][1]).readLines()[1..3].join("\n").md5(), file(process.out.mq_plot[0][1]).name, file(process.out.qd_plot[0][1]).name, file(process.out.is_plot[0][1]).name, file(process.out.gc_plot[0][1]).name, - process.out.versions, - path(process.out.versions[0]).yaml - ).match() + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sarscov2 - stub") { @@ -112,12 +118,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap index b5180833d..5683e7ecb 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap @@ -21,7 +21,11 @@ ] ], "10": [ - "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" + [ + "SENTIEON_DATAMETRICS", + "sentieon", + "202503.02" + ] ], "2": [ [ @@ -185,239 +189,71 @@ "test_qd_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" + "versions_sentieon": [ + [ + "SENTIEON_DATAMETRICS", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:08:55.410924336" + "timestamp": "2026-01-22T07:24:06.675145986" }, "metrics - with plots": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" - ] - ], + "8fdd2f19b222aa3a8f1d4f82d3792809", + "a5b70394b8ab8ab26fad4a0b819df96c", + "1e40f4ebb6098e8f7e07f51d873cc26b", + "547b7f29acc4efc43462d4df3f34b774", + "8d28671f4ef0d56ed1704cf236bf0952", + "186761dcce9ac40f25ae4bdaa0153544", "test_mq_metrics.pdf", "test_qd_metrics.pdf", "test_is_metrics.pdf", "test_gc_metrics.pdf", - [ - "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" - ], { - "SENTIEON_DATAMETRICS": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DATAMETRICS", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T09:59:14.060728182" + "timestamp": "2026-01-22T20:37:45.530044821" }, "metrics - no plots": { "content": [ + "8fdd2f19b222aa3a8f1d4f82d3792809", + "a5b70394b8ab8ab26fad4a0b819df96c", + "1e40f4ebb6098e8f7e07f51d873cc26b", + "547b7f29acc4efc43462d4df3f34b774", + "8d28671f4ef0d56ed1704cf236bf0952", + "186761dcce9ac40f25ae4bdaa0153544", { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" - ] - ], - "1": [ + "versions_sentieon": [ [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" + "SENTIEON_DATAMETRICS", + "sentieon", + "202503.02" ] - ], - "10": [ - "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" - ] - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - - ], - "aln_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_aln_metrics.txt:md5,6654ad1befe3414df846ca3035770264" - ] - ], - "gc_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_metrics.txt:md5,79633d7d4c20e1ea498e631b4ae628e7" - ] - ], - "gc_plot": [ - - ], - "gc_summary": [ - [ - { - "id": "test", - "single_end": false - }, - "test_gc_summary.txt:md5,b7d161fcbde35e4c1a392f870a468880" - ] - ], - "is_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_is_metrics.txt:md5,dd605dc5e3298bfd4f898dc915df466e" - ] - ], - "is_plot": [ - - ], - "mq_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_mq_metrics.txt:md5,57b7e9c495f628b633522a7763b197d5" - ] - ], - "mq_plot": [ - - ], - "qd_metrics": [ - [ - { - "id": "test", - "single_end": false - }, - "test_qd_metrics.txt:md5,b86ede9fe091e20176509ebe1d828893" - ] - ], - "qd_plot": [ - - ], - "versions": [ - "versions.yml:md5,f812a63180adf66d8221361d7b330fe2" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:07:40.668772808" + "timestamp": "2026-01-22T20:39:54.583316564" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/datametrics/tests/nextflow.config b/modules/nf-core/sentieon/datametrics/tests/nextflow.config index dead4e323..5ea3ffb66 100644 --- a/modules/nf-core/sentieon/datametrics/tests/nextflow.config +++ b/modules/nf-core/sentieon/datametrics/tests/nextflow.config @@ -1,16 +1,11 @@ env { // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how pipeline users will test out Sentieon with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } - -process { - withLabel: 'sentieon' { - ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 - ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 - } -} diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf index 976d0baa1..321c0712f 100644 --- a/modules/nf-core/sentieon/dedup/main.nf +++ b/modules/nf-core/sentieon/dedup/main.nf @@ -1,12 +1,12 @@ process SENTIEON_DEDUP { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(bam), path(bai) @@ -14,14 +14,14 @@ process SENTIEON_DEDUP { tuple val(meta3), path(fasta_fai) output: - tuple val(meta), path("*.cram") , emit: cram, optional: true - tuple val(meta), path("*.crai") , emit: crai, optional: true - tuple val(meta), path("*.bam") , emit: bam , optional: true - tuple val(meta), path("*.bai") , emit: bai - tuple val(meta), path("*.score") , emit: score - tuple val(meta), path("*.metrics") , emit: metrics + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.bai"), emit: bai + tuple val(meta), path("*.score"), emit: score + tuple val(meta), path("*.metrics"), emit: metrics tuple val(meta), path("*.metrics.multiqc.tsv"), emit: metrics_multiqc_tsv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when @@ -33,25 +33,20 @@ process SENTIEON_DEDUP { def args4 = task.ext.args4 ?: '' def prefix = task.ext.prefix ?: "${meta.id}.cram" def metrics = task.ext.metrics ?: "${prefix}.metrics" - def input_list = bam.collect{"-i $it"}.join(' ') + def input_list = bam.collect {input -> "-i ${input}" }.join(' ') def prefix_basename = prefix.substring(0, prefix.lastIndexOf(".")) - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} - sentieon driver $args -t $task.cpus $input_list -r ${fasta} --algo LocusCollector $args2 --fun score_info ${prefix_basename}.score - sentieon driver $args3 -t $task.cpus $input_list -r ${fasta} --algo Dedup $args4 --score_info ${prefix_basename}.score --metrics ${metrics} ${prefix} + sentieon driver ${args} -t ${task.cpus} ${input_list} -r ${fasta} --algo LocusCollector ${args2} --fun score_info ${prefix_basename}.score + sentieon driver ${args3} -t ${task.cpus} ${input_list} -r ${fasta} --algo Dedup ${args4} --score_info ${prefix_basename}.score --metrics ${metrics} ${prefix} # This following tsv-file is produced in order to get a proper tsv-file with Dedup-metrics for importing in MultiQC as "custom content". # It should be removed once MultiQC has a module for displaying Dedup-metrics. head -3 ${metrics} > ${metrics}.multiqc.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ stub: @@ -66,10 +61,5 @@ process SENTIEON_DEDUP { touch "${metrics}" touch "${metrics}.multiqc.tsv" touch "${prefix_basename}.score" - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml index 003d74bef..af4541ce7 100644 --- a/modules/nf-core/sentieon/dedup/meta.yml +++ b/modules/nf-core/sentieon/dedup/meta.yml @@ -27,10 +27,12 @@ input: type: file description: BAM file. pattern: "*.bam" + ontologies: [] - bai: type: file description: BAI file pattern: "*.bai" + ontologies: [] - - meta2: type: map description: | @@ -40,6 +42,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -49,9 +52,10 @@ input: type: file description: The index of the FASTA reference. pattern: "*.fai" + ontologies: [] output: - - cram: - - meta: + cram: + - - meta: type: map description: | Groovy Map containing reference information. @@ -60,8 +64,9 @@ output: type: file description: CRAM file pattern: "*.cram" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing reference information. @@ -70,8 +75,9 @@ output: type: file description: CRAM index file pattern: "*.crai" - - bam: - - meta: + ontologies: [] + bam: + - - meta: type: map description: | Groovy Map containing reference information. @@ -80,8 +86,9 @@ output: type: file description: BAM file. pattern: "*.bam" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing reference information. @@ -90,19 +97,21 @@ output: type: file description: BAI file pattern: "*.bai" - - score: - - meta: + ontologies: [] + score: + - - meta: type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - "*.score": type: file - description: The score file indicates which reads LocusCollector finds are likely - duplicates. + description: The score file indicates which reads LocusCollector finds are + likely duplicates. pattern: "*.score" - - metrics: - - meta: + ontologies: [] + metrics: + - - meta: type: map description: | Groovy Map containing reference information. @@ -111,8 +120,9 @@ output: type: file description: Output file containing Dedup metrics incl. histogram data. pattern: "*.metrics" - - metrics_multiqc_tsv: - - meta: + ontologies: [] + metrics_multiqc_tsv: + - - meta: type: map description: | Groovy Map containing reference information. @@ -121,11 +131,30 @@ output: type: file description: Output tsv-file containing Dedup metrics excl. histogram data. pattern: "*.metrics.multiqc.tsv" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test b/modules/nf-core/sentieon/dedup/tests/main.nf.test index c842a4a00..9e5179d61 100644 --- a/modules/nf-core/sentieon/dedup/tests/main.nf.test +++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test @@ -10,10 +10,18 @@ nextflow_process { script "../main.nf" process "SENTIEON_DEDUP" - test("Test marking duplicates") { - config "./nextflow.config" + config "./nextflow.config" + + test("Test marking duplicates, bam") { when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_args4 = '' + module_prefix = "test.dedup.bam" + } process { """ input[0] = [ @@ -28,18 +36,30 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + file(process.out.bai[0][1]).name, + path(process.out.score[0][1]).contains("SentieonCommandLine"), + path(process.out.metrics[0][1]).contains("SentieonCommandLine"), + path(process.out.metrics_multiqc_tsv[0][1]).contains("SentieonCommandLine"), + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - test("Test removing duplicates") { - config "./nextflow_rmdup.config" + test("Test removing duplicates, cram") { when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_args4 = '--rmdup' + module_prefix = "test.dedup.cram" + } process { """ input[0] = [ @@ -54,18 +74,31 @@ nextflow_process { } then { + def fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/sarscov2/genome/genome.fasta' + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + cram(process.out.cram[0][1], fasta).getReadsMD5(), + file(process.out.crai[0][1]).name, + path(process.out.score[0][1]).contains("SentieonCommandLine"), + path(process.out.metrics[0][1]).contains("SentieonCommandLine"), + path(process.out.metrics_multiqc_tsv[0][1]).contains("SentieonCommandLine"), + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("Test stub") { - config "./nextflow.config" options "-stub" when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_args4 = '' + module_prefix = '' + } process { """ input[0] = [ @@ -80,11 +113,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } } diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap index a0c84a503..1cf940dcc 100644 --- a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap @@ -1,241 +1,49 @@ { - "Test marking duplicates": { + "Test removing duplicates, cram": { "content": [ + "894549ee3ced6b5ca2eed2563a985217", + "test.dedup.cram.crai", + false, + false, + false, { - "0": [ - [ - { - "id": "test" - }, - "test.cram:md5,4e01d75d8942343a339f05b71b09c9d3" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.cram.crai:md5,b9ea073c563afd5a7c3239e3051a7a15" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test" - }, - "test.cram.bai:md5,827bf9e62729b7760290fc27750821c2" - ] - ], - "4": [ - [ - { - "id": "test" - }, - "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" - ] - ], - "5": [ - [ - { - "id": "test" - }, - "test.cram.metrics:md5,a082690dac37c795965e86387a7d610f" - ] - ], - "6": [ - [ - { - "id": "test" - }, - "test.cram.metrics.multiqc.tsv:md5,a082690dac37c795965e86387a7d610f" - ] - ], - "7": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" - ], - "bai": [ - [ - { - "id": "test" - }, - "test.cram.bai:md5,827bf9e62729b7760290fc27750821c2" - ] - ], - "bam": [ - - ], - "crai": [ - [ - { - "id": "test" - }, - "test.cram.crai:md5,b9ea073c563afd5a7c3239e3051a7a15" - ] - ], - "cram": [ - [ - { - "id": "test" - }, - "test.cram:md5,4e01d75d8942343a339f05b71b09c9d3" - ] - ], - "metrics": [ + "versions_sentieon": [ [ - { - "id": "test" - }, - "test.cram.metrics:md5,a082690dac37c795965e86387a7d610f" + "SENTIEON_DEDUP", + "sentieon", + "202503.02" ] - ], - "metrics_multiqc_tsv": [ - [ - { - "id": "test" - }, - "test.cram.metrics.multiqc.tsv:md5,a082690dac37c795965e86387a7d610f" - ] - ], - "score": [ - [ - { - "id": "test" - }, - "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" - ] - ], - "versions": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:09:22.353050455" + "timestamp": "2026-01-21T11:42:11.871897434" }, - "Test removing duplicates": { + "Test marking duplicates, bam": { "content": [ + "894549ee3ced6b5ca2eed2563a985217", + "test.dedup.bam.bai", + false, + false, + false, { - "0": [ - [ - { - "id": "test" - }, - "test.cram:md5,0c75659393aefbe720f7d351beae67d6" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.cram.crai:md5,00eaec21ddce36812f449c0fc36d13e1" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test" - }, - "test.cram.bai:md5,86d206b627fe39eb667b72dee25ad849" - ] - ], - "4": [ - [ - { - "id": "test" - }, - "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" - ] - ], - "5": [ - [ - { - "id": "test" - }, - "test.cram.metrics:md5,ce60af7e91a325b6c720009ac9a68d74" - ] - ], - "6": [ - [ - { - "id": "test" - }, - "test.cram.metrics.multiqc.tsv:md5,ce60af7e91a325b6c720009ac9a68d74" - ] - ], - "7": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" - ], - "bai": [ + "versions_sentieon": [ [ - { - "id": "test" - }, - "test.cram.bai:md5,86d206b627fe39eb667b72dee25ad849" - ] - ], - "bam": [ - - ], - "crai": [ - [ - { - "id": "test" - }, - "test.cram.crai:md5,00eaec21ddce36812f449c0fc36d13e1" - ] - ], - "cram": [ - [ - { - "id": "test" - }, - "test.cram:md5,0c75659393aefbe720f7d351beae67d6" - ] - ], - "metrics": [ - [ - { - "id": "test" - }, - "test.cram.metrics:md5,ce60af7e91a325b6c720009ac9a68d74" - ] - ], - "metrics_multiqc_tsv": [ - [ - { - "id": "test" - }, - "test.cram.metrics.multiqc.tsv:md5,ce60af7e91a325b6c720009ac9a68d74" + "SENTIEON_DEDUP", + "sentieon", + "202503.02" ] - ], - "score": [ - [ - { - "id": "test" - }, - "test.score:md5,f0ca06cebab41a9c52ad4b5630574446" - ] - ], - "versions": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:09:49.954445693" + "timestamp": "2026-01-21T11:41:33.04379133" }, "Test stub": { "content": [ @@ -292,7 +100,11 @@ ] ], "7": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" + [ + "SENTIEON_DEDUP", + "sentieon", + "202503.02" + ] ], "bai": [ [ @@ -345,15 +157,19 @@ "test.score:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,c9d8da8678d05dbf2368fe7002de48b5" + "versions_sentieon": [ + [ + "SENTIEON_DEDUP", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:10:17.139642524" + "timestamp": "2026-01-19T18:07:52.331783324" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dedup/tests/nextflow.config b/modules/nf-core/sentieon/dedup/tests/nextflow.config index 09a068ee6..a4f002090 100644 --- a/modules/nf-core/sentieon/dedup/tests/nextflow.config +++ b/modules/nf-core/sentieon/dedup/tests/nextflow.config @@ -1,9 +1,21 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } + +process { + withName: 'SENTIEON_DEDUP' { + ext.args = params.module_args + ext.args2 = params.module_args2 + ext.args3 = params.module_args3 + ext.args4 = params.module_args4 + ext.prefix = params.module_prefix + } +} diff --git a/modules/nf-core/sentieon/dedup/tests/nextflow_rmdup.config b/modules/nf-core/sentieon/dedup/tests/nextflow_rmdup.config deleted file mode 100644 index 21e7b945d..000000000 --- a/modules/nf-core/sentieon/dedup/tests/nextflow_rmdup.config +++ /dev/null @@ -1,15 +0,0 @@ -env { - // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} - -process { - withName: 'SENTIEON_DEDUP' { - ext.args4 = '--rmdup' - } -} diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf index acc7edd47..eed1a0fe8 100644 --- a/modules/nf-core/sentieon/dnamodelapply/main.nf +++ b/modules/nf-core/sentieon/dnamodelapply/main.nf @@ -1,12 +1,12 @@ process SENTIEON_DNAMODELAPPLY { - tag "$meta.id" + tag "${meta.id}" label 'process_high' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(vcf), path(idx) @@ -15,35 +15,31 @@ process SENTIEON_DNAMODELAPPLY { tuple val(meta4), path(ml_model) output: - tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}_applied" - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}_applied" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} sentieon driver \\ - -t $task.cpus \\ - -r $fasta \\ - $args \\ + -t ${task.cpus} \\ + -r ${fasta} \\ + ${args} \\ --algo DNAModelApply \\ - --model $ml_model \\ - -v $vcf \\ + --model ${ml_model} \\ + -v ${vcf} \\ ${prefix}.vcf.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ stub: @@ -51,10 +47,5 @@ process SENTIEON_DNAMODELAPPLY { """ echo | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index b73064111..ab1d6e0fe 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -23,10 +23,12 @@ input: type: file description: INPUT VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] - idx: type: file description: Index of the input VCF file pattern: "*.{tbi}" + ontologies: [] - - meta2: type: map description: | @@ -36,6 +38,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -45,6 +48,7 @@ input: type: file description: Index of the genome fasta file pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -54,9 +58,10 @@ input: type: file description: machine learning model file pattern: "*.model" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -65,8 +70,9 @@ output: type: file description: INPUT VCF file pattern: "*.{vcf,vcf.gz}" - - tbi: - - meta: + ontologies: [] + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -75,11 +81,28 @@ output: type: file description: Index of the input VCF file pattern: "*.{tbi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test index 6d4384168..4dbb8776e 100644 --- a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test +++ b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test @@ -4,17 +4,17 @@ nextflow_process { config "./nextflow.config" script "../main.nf" process "SENTIEON_DNAMODELAPPLY" - + tag "modules" tag "modules_nfcore" tag "sentieon" tag "sentieon/dnascope" tag "sentieon/dnamodelapply" - + setup { run("SENTIEON_DNASCOPE") { script "../../dnascope/main.nf" - + process { """ input[0] = [ @@ -35,9 +35,9 @@ nextflow_process { } } } - + test("apply model") { - + when { process { """ @@ -54,13 +54,13 @@ nextflow_process { { assert snapshot( path(process.out.vcf[0][1]).vcf.summary, file(process.out.tbi[0][1]).name, - path(process.out.versions[0]).yaml - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - - + + test("apply model -- stub") { options '-stub' when { @@ -78,10 +78,9 @@ nextflow_process { assertAll( { assert snapshot( process.out, - path(process.out.versions[0]).yaml - ).match() - } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap index 9d5dd67f9..884357723 100644 --- a/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/dnamodelapply/tests/main.nf.test.snap @@ -4,16 +4,20 @@ "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", "test_applied.vcf.gz.tbi", { - "SENTIEON_DNAMODELAPPLY": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNAMODELAPPLY", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:11:55.349533849" + "timestamp": "2026-01-21T16:33:14.121445833" }, "apply model -- stub": { "content": [ @@ -37,7 +41,11 @@ ] ], "2": [ - "versions.yml:md5,b14db672791c6252e540cb6404148c5d" + [ + "SENTIEON_DNAMODELAPPLY", + "sentieon", + "202503.02" + ] ], "tbi": [ [ @@ -57,20 +65,28 @@ "test_applied.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,b14db672791c6252e540cb6404148c5d" + "versions_sentieon": [ + [ + "SENTIEON_DNAMODELAPPLY", + "sentieon", + "202503.02" + ] ] }, { - "SENTIEON_DNAMODELAPPLY": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNAMODELAPPLY", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:12:33.395536554" + "timestamp": "2026-01-21T16:33:27.190638415" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config b/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config index 09a068ee6..9a93f5007 100644 --- a/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config +++ b/modules/nf-core/sentieon/dnamodelapply/tests/nextflow.config @@ -1,9 +1,11 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf index f027783c2..341264ec2 100644 --- a/modules/nf-core/sentieon/dnascope/main.nf +++ b/modules/nf-core/sentieon/dnascope/main.nf @@ -1,12 +1,12 @@ process SENTIEON_DNASCOPE { - tag "$meta.id" + tag "${meta.id}" label 'process_high' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(bam), path(bai), path(intervals) @@ -15,67 +15,71 @@ process SENTIEON_DNASCOPE { tuple val(meta4), path(dbsnp) tuple val(meta5), path(dbsnp_tbi) tuple val(meta6), path(ml_model) - val(pcr_indel_model) - val(emit_vcf) - val(emit_gvcf) + val pcr_indel_model + val emit_vcf + val emit_gvcf output: - tuple val(meta), path("*.unfiltered.vcf.gz") , optional:true, emit: vcf // added the substring ".unfiltered" in the filename of the vcf-files since without that the g.vcf.gz-files were ending up in the vcf-channel - tuple val(meta), path("*.unfiltered.vcf.gz.tbi"), optional:true, emit: vcf_tbi - tuple val(meta), path("*.g.vcf.gz") , optional:true, emit: gvcf // these output-files have to have the extension ".vcf.gz", otherwise the subsequent GATK-MergeVCFs will fail. - tuple val(meta), path("*.g.vcf.gz.tbi") , optional:true, emit: gvcf_tbi - path "versions.yml" , emit: versions + // added the substring ".unfiltered" in the filename of the vcf-files since without that the g.vcf.gz-files were ending up in the vcf-channel + tuple val(meta), path("*.unfiltered.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("*.unfiltered.vcf.gz.tbi"), emit: vcf_tbi, optional: true + // these output-files have to have the extension ".vcf.gz", otherwise the subsequent GATK-MergeVCFs will fail. + tuple val(meta), path("*.g.vcf.gz"), emit: gvcf, optional: true + tuple val(meta), path("*.g.vcf.gz.tbi"), emit: gvcf_tbi, optional: true + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' // options for the driver - def args2 = task.ext.args2 ?: '' // options for the vcf generation - def args3 = task.ext.args3 ?: '' // options for the gvcf generation - def interval = intervals ? "--interval ${intervals}" : '' - def dbsnp_cmd = dbsnp ? "-d ${dbsnp}" : '' - def model_cmd = ml_model ? " --model ${ml_model}" : '' + def args = task.ext.args ?: '' + // options for the driver + def args2 = task.ext.args2 ?: '' + // options for the vcf generation + def args3 = task.ext.args3 ?: '' + // options for the gvcf generation + def interval = intervals ? "--interval ${intervals}" : '' + def dbsnp_cmd = dbsnp ? "-d ${dbsnp}" : '' + def model_cmd = ml_model ? " --model ${ml_model}" : '' def pcr_indel_model_cmd = pcr_indel_model ? " --pcr_indel_model ${pcr_indel_model}" : '' - def prefix = task.ext.prefix ?: "${meta.id}" - def vcf_cmd = "" - def gvcf_cmd = "" - def base_cmd = '--algo DNAscope ' + dbsnp_cmd + ' ' + def prefix = task.ext.prefix ?: "${meta.id}" + def vcf_cmd = "" + def gvcf_cmd = "" + def base_cmd = '--algo DNAscope ' + dbsnp_cmd + ' ' - if (emit_vcf) { // emit_vcf can be the empty string, 'variant', 'confident' or 'all' but NOT 'gvcf' + if (emit_vcf) { + // emit_vcf can be the empty string, 'variant', 'confident' or 'all' but NOT 'gvcf' vcf_cmd = base_cmd + args2 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode ' + emit_vcf + ' ' + prefix + '.unfiltered.vcf.gz' } - if (emit_gvcf) { // emit_gvcf can be either true or false + if (emit_gvcf) { + // emit_gvcf can be either true or false gvcf_cmd = base_cmd + args3 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode gvcf ' + prefix + '.g.vcf.gz' } - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} - sentieon driver $args -r $fasta -t $task.cpus -i $bam $interval $vcf_cmd $gvcf_cmd - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS + sentieon driver \\ + ${args} \\ + -r ${fasta} \\ + -t ${task.cpus} \\ + -i ${bam} \\ + ${interval} \\ + ${vcf_cmd} \\ + ${gvcf_cmd} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def gvcf_cmd = emit_gvcf ? "echo | gzip > ${prefix}.g.vcf.gz; touch ${prefix}.g.vcf.gz.tbi": "" + def prefix = task.ext.prefix ?: "${meta.id}" + def gvcf_cmd = emit_gvcf ? "echo | gzip > ${prefix}.g.vcf.gz; touch ${prefix}.g.vcf.gz.tbi" : "" """ echo | gzip > ${prefix}.unfiltered.vcf.gz touch ${prefix}.unfiltered.vcf.gz.tbi - $gvcf_cmd - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" ) - END_VERSIONS + ${gvcf_cmd} """ } diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml index e3e0eba8c..e499927da 100644 --- a/modules/nf-core/sentieon/dnascope/meta.yml +++ b/modules/nf-core/sentieon/dnascope/meta.yml @@ -23,15 +23,18 @@ input: type: file description: BAM file. pattern: "*.bam" + ontologies: [] - bai: type: file description: BAI file pattern: "*.bai" + ontologies: [] - intervals: type: file description: bed or interval_list file containing interval in the reference that will be used in the analysis pattern: "*.{bed,interval_list}" + ontologies: [] - - meta2: type: map description: | @@ -40,6 +43,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -48,6 +52,7 @@ input: type: file description: Index of the genome fasta file pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -56,6 +61,8 @@ input: type: file description: Single Nucleotide Polymorphism database (dbSNP) file pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - - meta5: type: map description: | @@ -64,6 +71,7 @@ input: type: file description: Index of the Single Nucleotide Polymorphism database (dbSNP) file pattern: "*.vcf.gz.tbi" + ontologies: [] - - meta6: type: map description: | @@ -72,24 +80,25 @@ input: type: file description: machine learning model file pattern: "*.model" - - - pcr_indel_model: - type: string - description: | - Controls the option pcr_indel_model for Dnascope. - The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". - See Sentieons documentation for further explanation. - - - emit_vcf: - type: string - description: | - Controls the vcf output from Dnascope. - Possible options are "all", "confident" and "variant". - See Sentieons documentation for further explanation. - - - emit_gvcf: - type: boolean - description: If true, the haplotyper will output a gvcf + ontologies: [] + - pcr_indel_model: + type: string + description: | + Controls the option pcr_indel_model for Dnascope. + The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". + See Sentieons documentation for further explanation. + - emit_vcf: + type: string + description: | + Controls the vcf output from Dnascope. + Possible options are "all", "confident" and "variant". + See Sentieons documentation for further explanation. + - emit_gvcf: + type: boolean + description: If true, the haplotyper will output a gvcf output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing reference information. @@ -98,8 +107,10 @@ output: type: file description: Compressed VCF file pattern: "*.unfiltered.vcf.gz" - - vcf_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + vcf_tbi: + - - meta: type: map description: | Groovy Map containing reference information. @@ -108,8 +119,9 @@ output: type: file description: Index of VCF file pattern: "*.unfiltered.vcf.gz.tbi" - - gvcf: - - meta: + ontologies: [] + gvcf: + - - meta: type: map description: | Groovy Map containing reference information. @@ -118,8 +130,10 @@ output: type: file description: Compressed GVCF file pattern: "*.g.vcf.gz" - - gvcf_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + gvcf_tbi: + - - meta: type: map description: | Groovy Map containing reference information. @@ -128,11 +142,28 @@ output: type: file description: Index of GVCF file pattern: "*.g.vcf.gz.tbi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dnascope/tests/main.nf.test b/modules/nf-core/sentieon/dnascope/tests/main.nf.test index 010266471..0d4dc14b5 100644 --- a/modules/nf-core/sentieon/dnascope/tests/main.nf.test +++ b/modules/nf-core/sentieon/dnascope/tests/main.nf.test @@ -4,7 +4,7 @@ nextflow_process { config "./nextflow.config" script "../main.nf" process "SENTIEON_DNASCOPE" - + tag "modules" tag "modules_nfcore" tag "sentieon" @@ -12,8 +12,14 @@ nextflow_process { config './nextflow.config' test("conservative indel model - variant") { - + when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_prefix = '' + } process { """ input[0] = [ @@ -39,16 +45,22 @@ nextflow_process { { assert snapshot( path(process.out.vcf[0][1]).vcf.summary, file(process.out.vcf_tbi[0][1]).name, - path(process.out.versions[0]).yaml - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - - + + test("conservative indel model - all") { - + when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_prefix = '' + } process { """ input[0] = [ @@ -74,17 +86,22 @@ nextflow_process { { assert snapshot( path(process.out.vcf[0][1]).vcf.summary, file(process.out.vcf_tbi[0][1]).name, - process.out.versions, - path(process.out.versions[0]).yaml - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - - + + test("hostile indel model - confident") { - + when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_prefix = '' + } process { """ input[0] = [ @@ -110,17 +127,22 @@ nextflow_process { { assert snapshot( path(process.out.vcf[0][1]).vcf.summary, file(process.out.vcf_tbi[0][1]).name, - process.out.versions, - path(process.out.versions[0]).yaml - ).match() } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - - + + test("conversative indel model - variant - stub") { options '-stub' when { + params { + module_args = '' + module_args2 = '' + module_args3 = '' + module_prefix = '' + } process { """ input[0] = [ @@ -145,11 +167,10 @@ nextflow_process { assertAll( { assert snapshot( process.out, - path(process.out.versions[0]).yaml + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - -} \ No newline at end of file +} diff --git a/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap b/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap index 0720c00e2..c3522735b 100644 --- a/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/dnascope/tests/main.nf.test.snap @@ -3,36 +3,41 @@ "content": [ "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", "test.unfiltered.vcf.gz.tbi", - [ - "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" - ], { - "SENTIEON_DNASCOPE": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:13:57.370693339" + "timestamp": "2026-01-22T06:46:27.438392862" }, "conservative indel model - variant": { "content": [ "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=5, phased=false, phasedAutodetect=false]", "test.unfiltered.vcf.gz.tbi", { - "SENTIEON_DNASCOPE": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:13:01.800860635" + "timestamp": "2026-01-22T06:46:06.432231055" }, "conversative indel model - variant - stub": { "content": [ @@ -60,7 +65,11 @@ ], "4": [ - "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] ], "gvcf": [ @@ -84,39 +93,48 @@ "test.unfiltered.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" + "versions_sentieon": [ + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] ] }, { - "SENTIEON_DNASCOPE": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:14:24.965334187" + "timestamp": "2026-01-22T06:46:35.277276222" }, "conservative indel model - all": { "content": [ "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=8, phased=false, phasedAutodetect=false]", "test.unfiltered.vcf.gz.tbi", - [ - "versions.yml:md5,6f99846a52d1baaae01b4799da38896d" - ], { - "SENTIEON_DNASCOPE": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_DNASCOPE", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:13:30.044864434" + "timestamp": "2026-01-22T06:46:18.796510157" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnascope/tests/nextflow.config b/modules/nf-core/sentieon/dnascope/tests/nextflow.config index 09a068ee6..582cf60ff 100644 --- a/modules/nf-core/sentieon/dnascope/tests/nextflow.config +++ b/modules/nf-core/sentieon/dnascope/tests/nextflow.config @@ -1,9 +1,20 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } + +process { + withName: 'SENTIEON_DNASCOPE' { + ext.args = params.module_args + ext.args2 = params.module_args2 + ext.args3 = params.module_args3 + ext.prefix = params.module_prefix ?: null + } +} diff --git a/modules/nf-core/sentieon/readwriter/environment.yml b/modules/nf-core/sentieon/readwriter/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/readwriter/environment.yml +++ b/modules/nf-core/sentieon/readwriter/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/readwriter/main.nf b/modules/nf-core/sentieon/readwriter/main.nf index a785e593d..1a59eba88 100644 --- a/modules/nf-core/sentieon/readwriter/main.nf +++ b/modules/nf-core/sentieon/readwriter/main.nf @@ -1,12 +1,12 @@ process SENTIEON_READWRITER { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: tuple val(meta), path(input), path(index) @@ -17,7 +17,7 @@ process SENTIEON_READWRITER { tuple val(meta), path("${prefix}"), emit: output tuple val(meta), path("${prefix}.${index}"), emit: index tuple val(meta), path("${prefix}"), path("${prefix}.${index}"), emit: output_index - path "versions.yml", emit: versions + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when @@ -25,50 +25,42 @@ process SENTIEON_READWRITER { script: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' - def input_str = input.sort{ it.getName() }.collect{"-i $it"}.join(' ') - def reference = fasta ? "-r $fasta" : '' + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def input_str = input.sort {in -> in.getName() }.collect {in -> "-i ${in}" }.join(' ') + def reference = fasta ? "-r ${fasta}" : '' // bam -> bam: prefix = ".bam" // bam -> cram: prefix = ".cram" // cram -> cram: prefix = ".cram" - prefix = task.ext.prefix ?: "${meta.id}.bam" - index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" + prefix = task.ext.prefix ?: "${meta.id}.bam" + index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} sentieon \\ driver \\ - -t $task.cpus \\ - $reference \\ - $args \\ - $input_str \\ + -t ${task.cpus} \\ + ${reference} \\ + ${args} \\ + ${input_str} \\ --algo ReadWriter \\ - $args2 \\ + ${args2} \\ ${prefix} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ stub: - prefix = task.ext.prefix ?: "${meta.id}.cram" - index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" + prefix = task.ext.prefix ?: "${meta.id}.cram" + index = prefix.tokenize('.')[-1] == "bam" ? "bai" : "crai" """ touch ${prefix} touch ${prefix}.${index} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/readwriter/meta.yml b/modules/nf-core/sentieon/readwriter/meta.yml index 6e79ea190..42373bdd9 100644 --- a/modules/nf-core/sentieon/readwriter/meta.yml +++ b/modules/nf-core/sentieon/readwriter/meta.yml @@ -24,10 +24,12 @@ input: type: file description: BAM/CRAM file. pattern: "*.{bam,cram}" + ontologies: [] - index: type: file description: BAI/CRAI file. pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -37,6 +39,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -46,9 +49,10 @@ input: type: file description: The index of the FASTA reference. pattern: "*.fai" + ontologies: [] output: - - output: - - meta: + output: + - - meta: type: map description: | Groovy Map containing reference information. @@ -58,8 +62,9 @@ output: description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = .bam", CRAM "ext.prefix = .cram". Defaults to cram pattern: "*.{bam,cram}" - - index: - - meta: + ontologies: [] + index: + - - meta: type: map description: | Groovy Map containing reference information. @@ -68,23 +73,45 @@ output: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" - - output_index: - - meta: + ontologies: [] + output_index: + - - meta: type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - ${prefix}: type: file - description: BAM/CRAM alignment and the corresponding index file + description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix + = .bam", CRAM "ext.prefix = .cram". Defaults to cram + pattern: "*.{bam,cram}" + ontologies: [] - ${prefix}.${index}: type: file - description: BAM/CRAM alignment and the corresponding index file - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + ontologies: [] + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - sentieon driver --version | sed "s/.*-//g": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/readwriter/tests/main.nf.test b/modules/nf-core/sentieon/readwriter/tests/main.nf.test index 9a787b44c..ec341879d 100644 --- a/modules/nf-core/sentieon/readwriter/tests/main.nf.test +++ b/modules/nf-core/sentieon/readwriter/tests/main.nf.test @@ -4,15 +4,18 @@ nextflow_process { script "../main.nf" process "SENTIEON_READWRITER" + config "./nextflow.config" tag "modules" tag "modules_nfcore" tag "sentieon" tag "sentieon/readwriter" test("merge bam") { - config "./nextflow.config" when { + params { + module_prefix = '' + } process { """ input[0] = [ [id: 'test' ], @@ -26,22 +29,22 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(), - file(process.out.index.get(0).get(1)).name, - process.out.versions - ).match() } - + bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(), + file(process.out.index.get(0).get(1)).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("cram") { - config "./nextflow_outputcram.config" when { + params { + module_prefix = 'test.cram' + } process { """ input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta' ], @@ -55,22 +58,23 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(), - file(process.out.index.get(0).get(1)).name, - process.out.versions - ).match() } - + bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(), + file(process.out.index.get(0).get(1)).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } test("merging - output bam") { - config "./nextflow.config" when { + params { + module_prefix = '' + } process { """ input[0] = [ [id: 'test' ], @@ -90,23 +94,23 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(), - file(process.out.index.get(0).get(1)).name, - process.out.versions - ).match() } - + bam(process.out.output[0][1], stringency: "lenient").getReadsMD5(), + file(process.out.index.get(0).get(1)).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("merging - output bam to cram") { - config "./nextflow_outputcram.config" when { + params { + module_prefix = 'test.cram' + } process { """ input[0] = [ [id: 'test', fasta: params.modules_testdata_base_path + '/genomics/sarscov2/genome/genome.fasta' ], @@ -126,24 +130,24 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(), - file(process.out.index.get(0).get(1)).name, - process.out.versions - ).match() } - + bam(process.out.output[0][1], process.out.output[0][0].fasta).getReadsMD5(), + file(process.out.index.get(0).get(1)).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("sentieon readwriter - stub") { options "-stub" - config "./nextflow.config" when { + params { + module_prefix = '' + } process { """ input[0] = [ [id: 'test' ], @@ -157,12 +161,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap index f56e17cb9..ba6695c00 100644 --- a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap @@ -3,57 +3,81 @@ "content": [ "2f11e4fe3390b8ad0a1852616fd1da04", "test.bam.bai", - [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" - ] + { + "versions_sentieon": [ + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:25:19.723258714" + "timestamp": "2026-01-22T06:50:06.653644023" }, "cram": { "content": [ "2f11e4fe3390b8ad0a1852616fd1da04", "test.cram.crai", - [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" - ] + { + "versions_sentieon": [ + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:25:47.849309508" + "timestamp": "2026-01-22T06:50:15.682983539" }, "merging - output bam": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.bam.bai", - [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" - ] + { + "versions_sentieon": [ + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:26:15.337826518" + "timestamp": "2026-01-22T06:50:24.255987992" }, "merging - output bam to cram": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.cram.crai", - [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" - ] + { + "versions_sentieon": [ + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:26:44.414501574" + "timestamp": "2026-01-22T06:50:34.625552047" }, "sentieon readwriter - stub": { "content": [ @@ -84,7 +108,11 @@ ] ], "3": [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] ], "index": [ [ @@ -111,15 +139,19 @@ "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,31bdefaee518a851ad15f8d5b96c7c8b" + "versions_sentieon": [ + [ + "SENTIEON_READWRITER", + "sentieon", + "202503.02" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T08:27:11.322150361" + "timestamp": "2026-01-22T06:50:41.960295919" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/readwriter/tests/nextflow.config b/modules/nf-core/sentieon/readwriter/tests/nextflow.config index c1e9e4864..bb68b37fe 100644 --- a/modules/nf-core/sentieon/readwriter/tests/nextflow.config +++ b/modules/nf-core/sentieon/readwriter/tests/nextflow.config @@ -1,9 +1,17 @@ env { // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how pipeline users will test out Sentieon with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } + +process { + withName: 'SENTIEON_READWRITER' { + ext.prefix = params.module_prefix + } +} diff --git a/modules/nf-core/sentieon/readwriter/tests/nextflow_outputcram.config b/modules/nf-core/sentieon/readwriter/tests/nextflow_outputcram.config deleted file mode 100644 index 56c30c265..000000000 --- a/modules/nf-core/sentieon/readwriter/tests/nextflow_outputcram.config +++ /dev/null @@ -1,16 +0,0 @@ -env { - // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how pipeline users will test out Sentieon with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} - - -process { - withName: "SENTIEON_READWRITER" { - ext.prefix = { "${meta.id}.cram" } - } -} diff --git a/modules/nf-core/sentieon/wgsmetrics/environment.yml b/modules/nf-core/sentieon/wgsmetrics/environment.yml index ec48106f3..6b8bb5232 100644 --- a/modules/nf-core/sentieon/wgsmetrics/environment.yml +++ b/modules/nf-core/sentieon/wgsmetrics/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202503 + - bioconda::sentieon=202503.02 diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf index 8ccdbe8f4..d0a641c13 100644 --- a/modules/nf-core/sentieon/wgsmetrics/main.nf +++ b/modules/nf-core/sentieon/wgsmetrics/main.nf @@ -1,61 +1,51 @@ process SENTIEON_WGSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' label 'sentieon' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/80ccb05eb4f1a193a3bd99c4da90f55f74ea6556c25f154e53e1ff5a6caa372d/data' : - 'community.wave.seqera.io/library/sentieon:202503--5e378058d837c58c' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73e9111552beb76e2ad3ad89eb75bed162d7c5b85b2433723ecb4fc96a02674a/data' + : 'community.wave.seqera.io/library/sentieon:202503.02--def60555294d04fa'}" input: - tuple val(meta) , path(bam), path(bai) + tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(intervals_list) output: tuple val(meta), path('*.txt'), emit: wgs_metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('sentieon'), eval('sentieon driver --version | sed "s/.*-//g"'), topic: versions, emit: versions_sentieon when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def interval = intervals_list ? "--interval ${intervals_list}" : "" - def input = bam.sort().collect{"-i $it"}.join(' ') - def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ? - "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " : - "" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def interval = intervals_list ? "--interval ${intervals_list}" : "" + def input = bam.sort().collect {in -> "-i ${in}" }.join(' ') + def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 + ? "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " + : "" """ - $sentieonLicense + ${sentieonLicense} sentieon \\ driver \\ - -t $task.cpus \\ - -r $fasta \\ - $input \\ - $interval \\ - $args \\ + -t ${task.cpus} \\ + -r ${fasta} \\ + ${input} \\ + ${interval} \\ + ${args} \\ --algo WgsMetricsAlgo \\ ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") - END_VERSIONS """ } diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml index 7e04bfd8f..588246fab 100644 --- a/modules/nf-core/sentieon/wgsmetrics/meta.yml +++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml @@ -70,14 +70,29 @@ output: for each sequencing cycle pattern: "*.txt" ontologies: [] - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + versions_sentieon: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: - "@ramprasadn" + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - sentieon: + type: string + description: The tool name + - 'sentieon driver --version | sed "s/.*-//g"': + type: string + description: The command used to generate the version of the tool diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test index ee431a8e9..08179fb21 100644 --- a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test +++ b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test @@ -4,14 +4,14 @@ nextflow_process { config "./nextflow.config" script "../main.nf" process "SENTIEON_WGSMETRICS" - + tag "modules" tag "modules_nfcore" tag "sentieon" tag "sentieon/wgsmetrics" - + test("sarscov2 - bam") { - + when { process { """ @@ -37,15 +37,12 @@ nextflow_process { assertAll( { assert snapshot( file(process.out.wgs_metrics[0][1]).readLines()[1..5], - process.out.versions, - path(process.out.versions[0]).yaml - ).match() - } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - - + test("sarscov2 - bam -- stub") { options '-stub' when { @@ -74,12 +71,8 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot( - process.out, - path(process.out.versions[0]).yaml - ).match() - } + { assert snapshot(process.out).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap index dae6dfaeb..0c10cc9d0 100644 --- a/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/wgsmetrics/tests/main.nf.test.snap @@ -12,10 +12,18 @@ ] ], "1": [ - "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" + [ + "SENTIEON_WGSMETRICS", + "sentieon", + "202503.02" + ] ], - "versions": [ - "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" + "versions_sentieon": [ + [ + "SENTIEON_WGSMETRICS", + "sentieon", + "202503.02" + ] ], "wgs_metrics": [ [ @@ -26,18 +34,13 @@ "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] - }, - { - "SENTIEON_WGSMETRICS": { - "sentieon": 202503 - } } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T09:20:45.201824519" + "timestamp": "2026-01-21T09:28:12.500084203" }, "sarscov2 - bam": { "content": [ @@ -48,19 +51,20 @@ "coverage\thigh_quality_coverage_count\t", "0\t17554" ], - [ - "versions.yml:md5,45a8778b2661743a5e6583e6fec08f70" - ], { - "SENTIEON_WGSMETRICS": { - "sentieon": 202503 - } + "versions_sentieon": [ + [ + "SENTIEON_WGSMETRICS", + "sentieon", + "202503.02" + ] + ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-05-09T09:20:17.64441942" + "timestamp": "2026-01-21T09:37:25.493486027" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config b/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config index 09a068ee6..9a93f5007 100644 --- a/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config +++ b/modules/nf-core/sentieon/wgsmetrics/tests/nextflow.config @@ -1,9 +1,11 @@ env { // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // TODO: Update to `env('SENTIEON_LICSRVR_IP')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + // TODO: Update to `env('SENTIEON_AUTH_MECH')` when minimum Nextflow version is >= 26.04.0 + SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file + // NOTE This is how users will test out Sentieon in Sarek with a license file // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) } diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index e429e8ff2..4030d370c 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -31,7 +31,6 @@ workflow ALIGN_MT { } else if (val_mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } - ch_versions = ch_versions.mix(SENTIEON_BWAMEM_MT.out.versions) } else if (val_mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) ch_align = BWA_MEM_MT.out.bam diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 6ace66bc2..498c1b64f 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -18,7 +18,6 @@ workflow ALIGN_SENTIEON { val_platform // string: [mandatory] default: illumina main: - ch_versions = channel.empty() SENTIEON_BWAMEM ( ch_input_reads, ch_bwa_index, ch_genome_fasta, ch_genome_fai ) @@ -49,11 +48,6 @@ workflow ALIGN_SENTIEON { SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai ) - ch_versions = ch_versions.mix(SENTIEON_BWAMEM.out.versions) - ch_versions = ch_versions.mix(SENTIEON_DATAMETRICS.out.versions) - ch_versions = ch_versions.mix(SENTIEON_READWRITER.out.versions) - ch_versions = ch_versions.mix(SENTIEON_DEDUP.out.versions) - emit: marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] marked_bai = SENTIEON_DEDUP.out.bai // channel: [ val(meta), path(bai) ] @@ -63,5 +57,4 @@ workflow ALIGN_SENTIEON { gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index a9a3e0bea..f280f5176 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -108,8 +108,6 @@ workflow CALL_SNV_SENTIEON { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(SENTIEON_DNASCOPE.out.versions) - ch_versions = ch_versions.mix(SENTIEON_DNAMODELAPPLY.out.versions) ch_versions = ch_versions.mix(TABIX_SEN.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index d5dc769fb..4f2e2473d 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -111,7 +111,6 @@ workflow PREPARE_REFERENCES { } if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { ch_bwa = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions) } } else if (val_bwa) { ch_bwa = channel.fromPath(val_bwa).map {it -> [[id:it.simpleName], it]}.collect() @@ -181,7 +180,6 @@ workflow PREPARE_REFERENCES { if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("sentieon")) { ch_mt_bwa_index = SENTIEON_BWAINDEX_MT(ch_mt_fasta).index.collect() ch_mtshift_bwa_index = SENTIEON_BWAINDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() - ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_MT.out.versions, SENTIEON_BWAINDEX_MT_SHIFT.out.versions) } // // Vcf, tab and bed indices diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index d98774e6d..162c9d459 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -88,7 +88,6 @@ workflow QC_BAM { SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} ) ch_cov = SENTIEON_WGSMETRICS_WG.out.wgs_metrics ch_cov_y = SENTIEON_WGSMETRICS_Y.out.wgs_metrics - ch_versions = ch_versions.mix(SENTIEON_WGSMETRICS_WG.out.versions, SENTIEON_WGSMETRICS_Y.out.versions) } } // Check sex From 9c25dcd9e8f6232c31c826c46a254a6c8946a0d5 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:38:10 +0100 Subject: [PATCH 271/872] stranger and tabix/tabix --- modules.json | 4 +- modules/nf-core/stranger/environment.yml | 5 +- modules/nf-core/stranger/main.nf | 19 +-- modules/nf-core/stranger/meta.yml | 68 ++++++-- .../nf-core/stranger/tests/main.nf.test.snap | 76 +++++++-- modules/nf-core/tabix/tabix/environment.yml | 1 - modules/nf-core/tabix/tabix/main.nf | 20 +-- modules/nf-core/tabix/tabix/meta.yml | 47 +++--- .../nf-core/tabix/tabix/tests/main.nf.test | 47 +++--- .../tabix/tabix/tests/main.nf.test.snap | 159 +++++++++--------- .../{tabix_vcf_csi.config => nextflow.config} | 2 +- .../tabix/tabix/tests/tabix_bed.config | 5 - .../tabix/tabix/tests/tabix_gff.config | 5 - .../tabix/tabix/tests/tabix_vcf_tbi.config | 5 - .../local/annotate_consequence_pli.nf | 1 - subworkflows/local/annotate_mt_snvs.nf | 1 - .../local/annotate_rhocallviz/main.nf | 1 - .../local/call_repeat_expansions/main.nf | 1 - .../local/call_snv_deepvariant/main.nf | 2 - subworkflows/local/call_snv_sentieon/main.nf | 2 - .../local/call_structural_variants.nf | 1 - .../local/call_sv_germlinecnvcaller/main.nf | 1 - .../local/postprocess_MT_calls/main.nf | 3 - subworkflows/local/prepare_references/main.nf | 3 - workflows/raredisease.nf | 1 - 25 files changed, 256 insertions(+), 224 deletions(-) rename modules/nf-core/tabix/tabix/tests/{tabix_vcf_csi.config => nextflow.config} (54%) delete mode 100644 modules/nf-core/tabix/tabix/tests/tabix_bed.config delete mode 100644 modules/nf-core/tabix/tabix/tests/tabix_gff.config delete mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config diff --git a/modules.json b/modules.json index fceed0050..38ccecaf7 100644 --- a/modules.json +++ b/modules.json @@ -677,7 +677,7 @@ }, "stranger": { "branch": "master", - "git_sha": "ffe458cbd1208b82e33e607fa43fbe80df191047", + "git_sha": "72717e1f3feabaa57a6a71ba5a85d9c4ceeba514", "installed_by": [ "modules" ] @@ -713,7 +713,7 @@ }, "tabix/tabix": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", "installed_by": [ "modules" ] diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml index 3a7f17717..788dd06ef 100644 --- a/modules/nf-core/stranger/environment.yml +++ b/modules/nf-core/stranger/environment.yml @@ -4,5 +4,8 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stranger=0.9.4 - bioconda::tabix=1.11 + - conda-forge::pip=25.3 + - conda-forge::python=3.14.2 + - pip: + - stranger==0.10.0 diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index 314051fca..a793f4375 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -4,8 +4,8 @@ process STRANGER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/19/19f14a7c1b0ec9cbdeb6d32e3692208d559e9186b210e9a0a6922e001cb6ad32/data': - 'community.wave.seqera.io/library/stranger_tabix:847b205e87ed124b' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bc/bc075f106c93d3bb9c786c73f897c8cb005962e4c31c08226bd55eef742e9025/data': + 'community.wave.seqera.io/library/tabix_pip_stranger:9685bd298256c94b' }" input: tuple val(meta), path(vcf) @@ -14,7 +14,8 @@ process STRANGER { output: tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('stranger'), eval("stranger --version | sed 's/stranger, version //g'"), topic: versions, emit: versions_stranger + tuple val("${task.process}"), val('tabix'), eval("tabix --version | sed -n 's/^.*htslib) //p'"), topic: versions, emit: versions_tabix when: task.ext.when == null || task.ext.when @@ -37,12 +38,6 @@ process STRANGER { $args3 \\ --threads ${task.cpus} \\ ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - stranger: \$( stranger --version | sed 's/stranger, version //g' ) - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -52,11 +47,5 @@ process STRANGER { """ echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - stranger: \$( stranger --version | sed 's/stranger, version //g' ) - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml index 0cec73af1..15e513e60 100644 --- a/modules/nf-core/stranger/meta.yml +++ b/modules/nf-core/stranger/meta.yml @@ -1,6 +1,6 @@ name: stranger -description: Annotates output files from ExpansionHunter with the pathologic implications - of the repeat sizes. +description: Annotates output files from ExpansionHunter with the pathologic + implications of the repeat sizes. keywords: - STR - repeat_expansions @@ -25,6 +25,7 @@ input: type: file description: VCF with repeat expansions pattern: "*.{vcf.gz,vcf}" + ontologies: [] - - meta2: type: map description: | @@ -34,9 +35,11 @@ input: type: file description: json file with repeat expansion sites to genotype pattern: "*.{json}" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON output: - - vcf: - - meta: + vcf: + - - meta: type: map description: Annotated VCF file pattern: "*.{vcf.gz}" @@ -44,20 +47,59 @@ output: type: map description: Annotated VCF file pattern: "*.{vcf.gz}" - - tbi: - - meta: + tbi: + - - meta: type: map - description: Index of the annotated VCF file - pattern: "*.{vcf.gz.tbi}" + description: Annotated VCF file + pattern: "*.{vcf.gz}" - "*.vcf.gz.tbi": type: map description: Index of the annotated VCF file pattern: "*.{vcf.gz.tbi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_stranger: + - - ${task.process}: + type: string + description: The name of the process + - stranger: + type: string + description: The name of the tool + - '"stranger --version | sed ''s/stranger': + type: eval + description: The expression to obtain the version of the tool + + versions_tabix: + - - ${task.process}: + type: string + description: The name of the process + - tabix: + type: string + description: The name of the tool + - tabix --version | sed -n 's/^.*htslib) //p': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - stranger: + type: string + description: The name of the tool + - '"stranger --version | sed ''s/stranger': + type: eval + description: The expression to obtain the version of the tool + + - - ${task.process}: + type: string + description: The name of the process + - tabix: + type: string + description: The name of the tool + - tabix --version | sed -n 's/^.*htslib) //p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@ljmesi" maintainers: diff --git a/modules/nf-core/stranger/tests/main.nf.test.snap b/modules/nf-core/stranger/tests/main.nf.test.snap index bb688bade..50a0a98e6 100644 --- a/modules/nf-core/stranger/tests/main.nf.test.snap +++ b/modules/nf-core/stranger/tests/main.nf.test.snap @@ -19,7 +19,18 @@ ] ], "2": [ - "versions.yml:md5,85a7b3c900c0e406e2bc25e9c7d42bd5" + [ + "STRANGER", + "stranger", + "0.10.0" + ] + ], + "3": [ + [ + "STRANGER", + "tabix", + "1.22.1" + ] ], "tbi": [ [ @@ -37,16 +48,27 @@ "stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,85a7b3c900c0e406e2bc25e9c7d42bd5" + "versions_stranger": [ + [ + "STRANGER", + "stranger", + "0.10.0" + ] + ], + "versions_tabix": [ + [ + "STRANGER", + "tabix", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.04.2" }, - "timestamp": "2025-05-19T16:22:00.38081072" + "timestamp": "2025-12-16T09:36:05.482418969" }, "homo_sapiens - vcf, repeat_catalogue": { "content": [ @@ -56,7 +78,7 @@ { "id": "test" }, - "stranger.vcf.gz:md5,e933cd71d9f9f146265b8e8dd90b712c" + "stranger.vcf.gz:md5,5c55cbc7404f2d03b8cac82733175783" ] ], "1": [ @@ -64,18 +86,29 @@ { "id": "test" }, - "stranger.vcf.gz.tbi:md5,2445c81019fb4fa8d9c861c8e4b37196" + "stranger.vcf.gz.tbi:md5,9ac34e9ea9d9e3eee971b542629259c3" ] ], "2": [ - "versions.yml:md5,85a7b3c900c0e406e2bc25e9c7d42bd5" + [ + "STRANGER", + "stranger", + "0.10.0" + ] + ], + "3": [ + [ + "STRANGER", + "tabix", + "1.22.1" + ] ], "tbi": [ [ { "id": "test" }, - "stranger.vcf.gz.tbi:md5,2445c81019fb4fa8d9c861c8e4b37196" + "stranger.vcf.gz.tbi:md5,9ac34e9ea9d9e3eee971b542629259c3" ] ], "vcf": [ @@ -83,18 +116,29 @@ { "id": "test" }, - "stranger.vcf.gz:md5,e933cd71d9f9f146265b8e8dd90b712c" + "stranger.vcf.gz:md5,5c55cbc7404f2d03b8cac82733175783" ] ], - "versions": [ - "versions.yml:md5,85a7b3c900c0e406e2bc25e9c7d42bd5" + "versions_stranger": [ + [ + "STRANGER", + "stranger", + "0.10.0" + ] + ], + "versions_tabix": [ + [ + "STRANGER", + "tabix", + "1.22.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.04.2" }, - "timestamp": "2025-05-19T16:21:56.946267992" + "timestamp": "2025-12-16T09:36:01.200222427" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 6221bb53a..771b13870 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -6,4 +6,3 @@ channels: dependencies: - bioconda::htslib=1.21 - - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 325b8bbff..c8bcef64e 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -11,9 +11,8 @@ process TABIX_TABIX { tuple val(meta), path(tab) output: - tuple val(meta), path("*.tbi"), optional:true, emit: tbi - tuple val(meta), path("*.csi"), optional:true, emit: csi - path "versions.yml" , emit: versions + tuple val(meta), path("*.{tbi,csi}"), emit: index + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix when: task.ext.when == null || task.ext.when @@ -26,20 +25,11 @@ process TABIX_TABIX { $args \\ $tab - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ - stub: + def args = task.ext.args ?: '' + def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi" """ - touch ${tab}.tbi - touch ${tab}.csi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS + touch ${tab}.${index} """ } diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index c172968d8..f5b6b3c16 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -24,35 +24,40 @@ input: pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" ontologies: [] output: - tbi: + index: - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tbi": + - "*.{tbi,csi}": type: file - description: tabix index file - pattern: "*.{tbi}" - ontologies: [] - csi: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.csi": - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + description: Tabix index file (either tbi or csi) + pattern: "*.{tbi,csi}" ontologies: [] + versions_tabix: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index e74afd926..19eefab87 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -9,9 +9,13 @@ nextflow_process { tag "tabix" tag "tabix/tabix" + config "./nextflow.config" + test("sarscov2_bedgz_tbi") { - config "./tabix_bed.config" when { + params { + module_args = '-p bed' + } process { """ input[0] = [ @@ -25,17 +29,16 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - process.out, - file(process.out.tbi[0][1]).name - ).match() } + { assert snapshot(process.out).match() } ) } } test("sarscov2_gff_tbi") { - config "./tabix_gff.config" when { + params { + module_args = '-p gff' + } process { """ input[0] = [ @@ -49,17 +52,17 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - process.out, - file(process.out.tbi[0][1]).name).match() } + { assert snapshot(process.out).match() } ) } } test("sarscov2_vcf_tbi") { - config "./tabix_vcf_tbi.config" when { + params { + module_args = '-p vcf' + } process { """ input[0] = [ @@ -73,18 +76,17 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - process.out, - file(process.out.tbi[0][1]).name - ).match() } + { assert snapshot(process.out).match() } ) } } test("sarscov2_vcf_csi") { - config "./tabix_vcf_csi.config" when { + params { + module_args = '-p vcf --csi' + } process { """ input[0] = [ @@ -98,19 +100,18 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - process.out, - file(process.out.csi[0][1]).name - ).match() } + { assert snapshot(process.out).match() } ) } } test("sarscov2_vcf_csi_stub") { - config "./tabix_vcf_csi.config" options "-stub" when { + params { + module_args = '-p vcf --csi' + } process { """ input[0] = [ @@ -124,13 +125,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - process.out, - file(process.out.csi[0][1]).name - ).match() } + { assert snapshot(process.out).match() } ) } - } } diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index 67b8e3c2f..91a3a66de 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -11,15 +11,13 @@ ] ], "1": [ - - ], - "2": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" - ], - "csi": [ - + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ], - "tbi": [ + "index": [ [ { "id": "tbi_gff" @@ -27,17 +25,20 @@ "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" ] ], - "versions": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" + "versions_tabix": [ + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ] - }, - "genome.gff3.gz.tbi" + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-03-26T13:52:48.638506004" + "timestamp": "2025-11-20T13:47:34.055936" }, "sarscov2_bedgz_tbi": { "content": [ @@ -51,15 +52,13 @@ ] ], "1": [ - - ], - "2": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" - ], - "csi": [ - + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ], - "tbi": [ + "index": [ [ { "id": "tbi_bed" @@ -67,17 +66,20 @@ "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" ] ], - "versions": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" + "versions_tabix": [ + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ] - }, - "test.bed.gz.tbi" + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-03-26T13:52:44.910707349" + "timestamp": "2025-11-20T13:47:29.90469" }, "sarscov2_vcf_tbi": { "content": [ @@ -91,15 +93,13 @@ ] ], "1": [ - - ], - "2": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" - ], - "csi": [ - + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ], - "tbi": [ + "index": [ [ { "id": "tbi_vcf" @@ -107,17 +107,20 @@ "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" ] ], - "versions": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" + "versions_tabix": [ + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ] - }, - "test.vcf.gz.tbi" + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-03-26T13:52:52.405662623" + "timestamp": "2025-11-20T13:47:38.044307" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -127,21 +130,17 @@ { "id": "vcf_csi_stub" }, - "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ - { - "id": "vcf_csi_stub" - }, - "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "TABIX_TABIX", + "tabix", + "1.21" ] ], - "2": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" - ], - "csi": [ + "index": [ [ { "id": "vcf_csi_stub" @@ -149,33 +148,25 @@ "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "tbi": [ + "versions_tabix": [ [ - { - "id": "vcf_csi_stub" - }, - "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "TABIX_TABIX", + "tabix", + "1.21" ] - ], - "versions": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" ] - }, - "test.vcf.gz.csi" + } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-26T13:52:59.633992323" + "timestamp": "2025-12-10T14:31:29.90297082" }, "sarscov2_vcf_csi": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "vcf_csi" @@ -183,10 +174,14 @@ "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], - "2": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" + "1": [ + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ], - "csi": [ + "index": [ [ { "id": "vcf_csi" @@ -194,19 +189,19 @@ "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], - "tbi": [ - - ], - "versions": [ - "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5" + "versions_tabix": [ + [ + "TABIX_TABIX", + "tabix", + "1.21" + ] ] - }, - "test.vcf.gz.csi" + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.04.7" }, - "timestamp": "2025-03-26T13:52:56.083553332" + "timestamp": "2025-11-20T13:47:42.013054" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/nextflow.config similarity index 54% rename from modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config rename to modules/nf-core/tabix/tabix/tests/nextflow.config index eb4f2d7e2..96685ef28 100644 --- a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config +++ b/modules/nf-core/tabix/tabix/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: TABIX_TABIX { - ext.args = '-p vcf --csi' + ext.args = params.module_args } } diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config deleted file mode 100644 index 7ff059056..000000000 --- a/modules/nf-core/tabix/tabix/tests/tabix_bed.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: TABIX_TABIX { - ext.args = '-p bed' - } -} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config deleted file mode 100644 index 20c0a1e34..000000000 --- a/modules/nf-core/tabix/tabix/tests/tabix_gff.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: TABIX_TABIX { - ext.args = '-p gff' - } -} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config deleted file mode 100644 index 2774c8a90..000000000 --- a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: TABIX_TABIX { - ext.args = '-p vcf' - } -} \ No newline at end of file diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index c6aa34511..af57747d9 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -21,7 +21,6 @@ workflow ANNOTATE_CSQ_PLI { if (val_index) { TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) } ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.versions) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 70697435b..6707ab11b 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -106,7 +106,6 @@ workflow ANNOTATE_MT_SNVS { ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt } - ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions) ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO_MT.out.versions) diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index f80fb7129..9ff4f0882 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -55,7 +55,6 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 8a6fcfa25..64a7d5589 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -60,7 +60,6 @@ workflow CALL_REPEAT_EXPANSIONS { ch_versions = ch_versions.mix(EXPANSIONHUNTER.out.versions) ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) - ch_versions = ch_versions.mix(TABIX_EXP_RENAME.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) emit: diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 74306f690..80d73cbb0 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -85,9 +85,7 @@ workflow CALL_SNV_DEEPVARIANT { ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) ch_versions = ch_versions.mix(GLNEXUS.out.versions) - ch_versions = ch_versions.mix(TABIX_GL.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index f280f5176..f14f15413 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -108,9 +108,7 @@ workflow CALL_SNV_SENTIEON { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(TABIX_SEN.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: gvcf = SENTIEON_DNASCOPE.out.gvcf // channel: [ val(meta), path(gvcf) ] diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index b3f3f8bc5..04394f7fc 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -110,7 +110,6 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.tbi - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) } diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index aaae54735..1687c7079 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -80,7 +80,6 @@ workflow CALL_SV_GERMLINECNVCALLER { ch_versions = ch_versions.mix(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.versions) ch_versions = ch_versions.mix(GATK4_GERMLINECNVCALLER.out.versions) ch_versions = ch_versions.mix(GATK4_POSTPROCESSGERMLINECNVCALLS.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_GCNVCALLER.out.versions) emit: diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 59d77a645..4729955be 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -126,9 +126,6 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX_MERGE.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX_MT.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX_MT2.out.versions) emit: tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 4f2e2473d..f29fb4258 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -190,7 +190,6 @@ workflow PREPARE_REFERENCES { ch_dbsnp_tbi = channel.fromPath(val_known_dbsnp_tbi).map{ it -> [[id:it.simpleName], it] }.collect() } else { ch_dbsnp_tbi = TABIX_DBSNP(ch_dbsnp).tbi.collect() - ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) } } @@ -200,7 +199,6 @@ workflow PREPARE_REFERENCES { ch_gnomad_idx = channel.fromPath(val_gnomad_af_idx).map{ it -> [[id:it.simpleName], it] }.collect() } else { ch_gnomad_idx = TABIX_GNOMAD_AF(ch_gnomad_af).tbi.collect() - ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions) } ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() } @@ -245,7 +243,6 @@ workflow PREPARE_REFERENCES { .join(ch_vcfanno_tabix_in) .map { _meta, tbi, vcf -> return [[vcf,tbi]]} .set {ch_vcfanno_extra} - ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions) } else { TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in) channel.empty() diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 9a0ea23fb..530873679 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -351,7 +351,6 @@ workflow RAREDISEASE { CALL_REPEAT_EXPANSIONS.out.vcf, ch_variant_catalog ) - ch_versions = ch_versions.mix(STRANGER.out.versions) } } From d3aaebf5aab2b0491df359fc7a6d7b823427909d Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 25 Jan 2026 16:39:36 +0100 Subject: [PATCH 272/872] prettier --- modules.json | 457 +++++++++++++-------------------------------------- 1 file changed, 114 insertions(+), 343 deletions(-) diff --git a/modules.json b/modules.json index 38ccecaf7..c114f1cb9 100644 --- a/modules.json +++ b/modules.json @@ -8,771 +8,550 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - 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"modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -781,33 +560,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From fafc63156a0994b7cac91469e30e464a9aa00106 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 11:45:45 +0100 Subject: [PATCH 273/872] fix errors --- conf/modules/annotate_genome_snvs.config | 1 + conf/modules/qc_bam.config | 1 - modules.json | 461 ++++++--- .../ensemblvep/filtervep/environment.yml | 5 +- modules/nf-core/ensemblvep/filtervep/main.nf | 32 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 43 +- .../ensemblvep/filtervep/tests/main.nf.test | 49 +- .../filtervep/tests/main.nf.test.snap | 36 +- .../filtervep/tests/nextflow.config | 2 +- .../ensemblvep/filtervep/tests/tab.gz.config | 6 + .../ensemblvep/filtervep/tests/tags.yml | 2 + .../ensemblvep/filtervep/tests/vcf.config | 6 + .../ensemblvep/vep/ensemblvep-vep.diff | 2 +- .../nf-core/ensemblvep/vep/environment.yml | 8 - modules/nf-core/ensemblvep/vep/main.nf | 77 +- modules/nf-core/ensemblvep/vep/meta.yml | 206 +--- .../nf-core/ensemblvep/vep/tests/main.nf.test | 89 -- .../ensemblvep/vep/tests/main.nf.test.snap | 55 -- .../ensemblvep/vep/tests/nextflow.config | 5 - .../ensemblvep/vep/tests/tab.gz.config | 5 - .../nf-core/ensemblvep/vep/tests/vcf.config | 5 - .../local/align_MT/tests/main.nf.test.snap | 16 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- subworkflows/local/annotate_genome_snvs.nf | 12 +- subworkflows/local/annotate_mt_snvs.nf | 10 +- .../local/annotate_rhocallviz/main.nf | 2 +- .../local/annotate_structural_variants.nf | 3 +- subworkflows/local/call_mobile_elements.nf | 14 +- .../local/call_repeat_expansions/main.nf | 2 +- .../local/call_snv_deepvariant/main.nf | 4 +- .../local/call_structural_variants.nf | 3 +- .../local/postprocess_MT_calls/main.nf | 9 +- subworkflows/local/prepare_references/main.nf | 13 +- subworkflows/local/qc_bam/main.nf | 2 +- .../local/qc_bam/tests/main.nf.test.snap | 132 +-- .../vcf_filter_bcftools_ensemblvep/main.nf | 1 - tests/default.nf.test.snap | 899 +----------------- tests/test_bam.nf.test.snap | 841 +--------------- tests/test_singleton.nf.test.snap | 659 +------------ 39 files changed, 598 insertions(+), 3122 deletions(-) create mode 100644 modules/nf-core/ensemblvep/filtervep/tests/tags.yml delete mode 100644 modules/nf-core/ensemblvep/vep/environment.yml delete mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test delete mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap delete mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config delete mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config delete mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index 6ec08c8b7..454690487 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -101,6 +101,7 @@ process { } withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT' { + ext.args = { "-Oz" } ext.prefix = { "${meta.prefix}_vep" } publishDir = [ path: { "${params.outdir}/annotate_snv/genome" }, diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 08653e936..5253a9ba7 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -54,7 +54,6 @@ process { } withName: '.*QC_BAM:MOSDEPTH' { - ext.args = "--d4" ext.prefix = { "${meta.id}_mosdepth" } } diff --git a/modules.json b/modules.json index c114f1cb9..b407cfec4 100644 --- a/modules.json +++ b/modules.json @@ -8,550 +8,771 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "69614d4579a6bd9b8a2ecffb35959809d9c36559", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "chromograph": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostseverepli": { "branch": "master", "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/annotate": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/viz": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/format": { "branch": "master", "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sambamba/depth": { "branch": "master", "git_sha": "b093f74ddc3ada57a84a209f0e4fb3871bacf2ad", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/collate": { "branch": "master", "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwamem": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/datametrics": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dedup": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnascope": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/readwriter": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "72717e1f3feabaa57a6a71ba5a85d9c4ceeba514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -560,25 +781,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index d9ed9b6bd..3d36eb17c 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -1,8 +1,5 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/ensembl-vep - - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 + - bioconda::ensembl-vep=113.0 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index dcf0148ef..69245df0e 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -1,39 +1,49 @@ process ENSEMBLVEP_FILTERVEP { - tag "${meta.id}" + tag "$meta.id" label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' - : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(input) - path feature_file + path (feature_file) output: tuple val(meta), path("*.${extension}"), emit: output - tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ filter_vep \\ - ${args} \\ - --input_file ${input} \\ + $args \\ + --input_file $input \\ --output_file ${prefix}.${extension} \\ --only_matched + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index 68928cfc8..a73e3b7a7 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -24,16 +24,13 @@ input: type: file description: VCF/TAB file annotated with vep pattern: "*.{vcf,tab,tsv,txt}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - - feature_file: - type: file - description: File containing features on separate lines. To be used with --filter - option. - ontologies: [] + - - feature_file: + type: file + description: File containing features on separate lines. To be used with --filter + option. output: - output: - - - meta: + - output: + - meta: type: map description: | Groovy Map containing sample information @@ -42,29 +39,11 @@ output: type: file description: VCF/TAB file pattern: "*.{vcf,tab,txt,tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - versions_ensemblvep: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string - description: The command used to generate the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string - description: The command used to generate the version of the tool + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test index 044934579..7147792f7 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test @@ -10,18 +10,32 @@ nextflow_process { tag "ensemblvep" tag "ensemblvep/vep" tag "ensemblvep/filtervep" + tag "ensemblvep/download" + // Test for filtering VCF file test("test_ensemblvep_filtervep_vcf") { config "./vcf.config" setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"113_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -30,7 +44,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = vep_cache + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -51,25 +65,38 @@ nextflow_process { } then { - assert process.success assertAll( - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, + { assert process.success }, + { assert snapshot(process.out.versions).match() }, { assert path(process.out.output.get(0).get(1)).readLines().first().contains("##fileformat=VCFv4.2") } ) } } + // Test for filtering TAB file test("test_ensemblvep_filtervep_tab_gz") { config "./tab.gz.config" setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"113_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -78,7 +105,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = vep_cache + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -99,10 +126,10 @@ nextflow_process { } then { - assert process.success assertAll( - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } ) } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 1559d7e79..065d747ba 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -1,38 +1,26 @@ { "test_ensemblvep_filtervep_vcf": { "content": [ - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_FILTERVEP", - "ensemblvep", - "115.2" - ] - ] - } + [ + "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2026-01-07T17:41:53.157363596" + "timestamp": "2024-10-21T09:10:47.874831491" }, "test_ensemblvep_filtervep_tab_gz": { "content": [ - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_FILTERVEP", - "ensemblvep", - "115.2" - ] - ] - } + [ + "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2026-01-07T17:42:10.309756999" + "timestamp": "2024-10-21T09:11:18.765461163" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config index 32ff2cb6f..40b3a3bd6 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params { - vep_cache_version = "115" + vep_cache_version = "113" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index f1eb11d65..cdad2d94d 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -6,6 +6,12 @@ process { + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + } + withName: ENSEMBLVEP_VEP { ext.args = '--tab' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml new file mode 100644 index 000000000..b43bf40d6 --- /dev/null +++ b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/filtervep: + - "modules/nf-core/ensemblvep/filtervep/**" diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index a737274ef..ee2aef574 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -6,6 +6,12 @@ process { + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + } + withName: ENSEMBLVEP_VEP { ext.args = '--vcf' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index c5a7d13d7..ef4a555c1 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -1,4 +1,4 @@ -Changes in module 'nf-core/ensemblvep/vep' +Changes in component 'nf-core/ensemblvep/vep' 'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml deleted file mode 100644 index d9ed9b6bd..000000000 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - # renovate: datasource=conda depName=bioconda/ensembl-vep - - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index dd656a787..4886b05e6 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,66 +1,71 @@ process ENSEMBLVEP_VEP { - tag "${meta.id}" + tag "$meta.id" label 'process_medium' - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' - : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" + conda "bioconda::ensembl-vep=110.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) - val genome - val species - val cache_version - path cache + val genome + val species + val cache_version + path cache tuple val(meta2), path(fasta) - path extra_files + path extra_files output: - tuple val(meta), path("*.vcf.gz"), emit: vcf, optional: true - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.tab.gz"), emit: tab, optional: true - tuple val(meta), path("*.json.gz"), emit: json, optional: true - tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true - tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix + tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf + tuple val(meta), path("*.tab.gz") , optional:true, emit: tab + tuple val(meta), path("*.json.gz") , optional:true, emit: json + path "*.summary.html" , optional:true, emit: report + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' - def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip' def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" - def reference = fasta ? "--fasta ${fasta}" : "" - def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : "" + def reference = fasta ? "--fasta $fasta" : "" """ vep \\ - -i ${vcf} \\ + -i $vcf \\ -o ${prefix}.${file_extension}.gz \\ - ${args} \\ - ${compress_cmd} \\ - ${reference} \\ - --assembly ${genome} \\ - --species ${species} \\ + $args \\ + $compress_cmd \\ + $reference \\ + --assembly $genome \\ + --species $species \\ --cache \\ - --cache_version ${cache_version} \\ - --dir_cache ${dir_cache} \\ - --fork ${task.cpus} + --cache_version $cache_version \\ + --dir_cache $dir_cache \\ + --fork $task.cpus \\ + --stats_file ${prefix}.summary.html \\ - ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' - def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : "" """ - echo "" | gzip > ${prefix}.${file_extension}.gz - ${create_index} - touch ${prefix}_summary.html + touch ${prefix}.vcf.gz + touch ${prefix}.tab.gz + touch ${prefix}.json.gz + touch ${prefix}.summary.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + END_VERSIONS """ } diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 921a34127..7783847dc 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,6 +1,5 @@ -name: ensemblvep_vep -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled - through `task.ext.args`. +name: ENSEMBLVEP_VEP +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation - vcf @@ -14,24 +13,21 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] - identifier: "" input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - ontologies: [] - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) - ontologies: [] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) - genome: type: string description: | @@ -48,149 +44,45 @@ input: type: file description: | path to VEP cache (optional) - ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" - ontologies: [] + - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" - extra_files: type: file description: | path to file(s) needed for plugins (optional) - ontologies: [] output: - vcf: - - - meta: - type: map - description: | - Map with sample information - - "*.vcf.gz": - type: file - description: | - annotated vcf (optional) - pattern: "*.vcf.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format - tbi: - - - meta: - type: map - description: | - Map with sample information - - "*.vcf.gz.tbi": - type: file - description: | - annotated vcf index (optional) - pattern: "*.vcf.gz.tbi" - ontologies: [] - tab: - - - meta: - type: map - description: | - Map with sample information - - "*.tab.gz": - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format - json: - - - meta: - type: map - description: | - Map with sample information - - "*.json.gz": - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format - report: - - - meta: - type: map - description: | - Map with sample information - - ${task.process}: - type: string - description: The process - - ensemblvep: - type: string - description: The tool name - - "*.html": - type: file - description: VEP report file - pattern: "*.html" - ontologies: [] - versions_ensemblvep: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string - description: The command used to generate the version of the tool - versions_tabix: - - - ${task.process}: - type: string - description: The process the versions were collected from - - tabix: - type: string - description: The tool name - - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': - type: eval - description: The expression to obtain the version of the tool - -topics: - multiqc_files: - - - meta: - type: map - description: | - Map with sample information - - ${task.process}: - type: string - description: The process - - ensemblvep: - type: string - description: The tool name - - "*.html": - type: file - description: VEP report file - pattern: "*.html" - ontologies: [] - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string - description: The command used to generate the version of the tool - - - ${task.process}: - type: string - description: The process the versions were collected from - - tabix: - type: string - description: The tool name - - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': - type: eval - description: The expression to obtain the version of the tool + - vcf: + type: file + description: | + annotated vcf (optional) + pattern: "*.ann.vcf.gz" + - tab: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + - json: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + - report: + type: file + description: VEP report file + pattern: "*.html" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" -maintainers: - - "@maxulysse" - - "@matthdsm" - - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test deleted file mode 100644 index 374f840cf..000000000 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test +++ /dev/null @@ -1,89 +0,0 @@ -nextflow_process { - - name "Test Process ENSEMBLVEP_VEP" - script "../main.nf" - process "ENSEMBLVEP_VEP" - config "./nextflow.config" - - tag "modules" - tag "modules_nfcore" - tag "ensemblvep" - tag "ensemblvep/vep" - - test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") { - config "./vcf.config" - - when { - process { - """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - [] - ]) - input[1] = params.vep_genome - input[2] = params.vep_species - input[3] = params.vep_cache_version - input[4] = vep_cache - input[5] = Channel.value([ - [id:"fasta"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[6] = [] - """ - } - } - - then { - assert process.success - assertAll( - { assert snapshot( - file(process.out.vcf[0][1]).name + ",variantsMD5:" + path(process.out.vcf[0][1]).vcf.variantsMD5, - file(process.out.tbi[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() } - ) - } - - } - - test("test_ensemblvep_vep_fasta_tab_gz") { - config "./tab.gz.config" - - when { - process { - """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - [] - ]) - input[1] = params.vep_genome - input[2] = params.vep_species - input[3] = params.vep_cache_version - input[4] = vep_cache - input[5] = Channel.value([ - [id:"fasta"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[6] = [] - """ - } - } - - then { - assert process.success - assertAll( - { assert snapshot( - file(process.out.tab[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() }, - { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } - ) - } - } -} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap deleted file mode 100644 index 00a27d57b..000000000 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap +++ /dev/null @@ -1,55 +0,0 @@ -{ - "test_ensemblvep_vep_fasta_tab_gz": { - "content": [ - "test.tab.gz", - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_VEP", - "ensemblvep", - "115.2" - ] - ], - "versions_tabix": [ - [ - "ENSEMBLVEP_VEP", - "tabix", - "1.21" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-16T13:49:54.784347273" - }, - "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { - "content": [ - "test.vcf.gz,variantsMD5:d41d8cd98f00b204e9800998ecf8427e", - "test.vcf.gz.tbi", - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_VEP", - "ensemblvep", - "115.2" - ] - ], - "versions_tabix": [ - [ - "ENSEMBLVEP_VEP", - "tabix", - "1.21" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-16T13:49:36.798576341" - } -} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config deleted file mode 100644 index 8e68fe24a..000000000 --- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -params { - vep_cache_version = "115" - vep_genome = "WBcel235" - vep_species = "caenorhabditis_elegans" -} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config deleted file mode 100644 index 40eb03e59..000000000 --- a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: ENSEMBLVEP_VEP { - ext.args = '--tab --compress_output bgzip' - } -} diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config deleted file mode 100644 index ad8955a37..000000000 --- a/modules/nf-core/ensemblvep/vep/tests/vcf.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: ENSEMBLVEP_VEP { - ext.args = '--vcf' - } -} diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 184d26fda..5cb97333a 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -109,9 +109,6 @@ "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", @@ -226,9 +223,6 @@ "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", @@ -242,7 +236,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:23:15.456518407" + "timestamp": "2026-01-25T21:20:12.412575747" }, "align mt - bwa": { "content": [ @@ -354,9 +348,6 @@ "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", @@ -471,9 +462,6 @@ "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", - "versions.yml:md5,a7d670ab01994f84ce85fae59ca624c5", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", @@ -487,6 +475,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:26:33.086288065" + "timestamp": "2026-01-25T21:22:23.024924094" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 2e6539e20..29eb1a4bc 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -67,7 +67,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta, ch_genome_fai ) + SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta, ch_genome_fai, [[:], []] ) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index d80dda6ff..0ae402e15 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -111,7 +111,7 @@ workflow ANNOTATE_GENOME_SNVS { TABIX_BCFTOOLS_VIEW (BCFTOOLS_VIEW.out.vcf) BCFTOOLS_VIEW.out.vcf - .join(TABIX_BCFTOOLS_VIEW.out.tbi, failOnMismatch:true, failOnDuplicate:true) + .join(TABIX_BCFTOOLS_VIEW.out.index, failOnMismatch:true, failOnDuplicate:true) .set { ch_cadd_in } ANNOTATE_CADD ( @@ -123,7 +123,6 @@ workflow ANNOTATE_GENOME_SNVS { ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) - ch_versions = ch_versions.mix(TABIX_BCFTOOLS_VIEW.out.versions) } BCFTOOLS_VIEW.out.vcf @@ -158,7 +157,7 @@ workflow ANNOTATE_GENOME_SNVS { TABIX_VEP (ch_vep_out) ch_vep_out - .join(TABIX_VEP.out.tbi, failOnMismatch:true) + .join(TABIX_VEP.out.index, failOnMismatch:true) .groupTuple() .map { meta, vcfs, tbis -> def sortedvcfs = vcfs.sort { vcf -> vcf.baseName } @@ -183,7 +182,6 @@ workflow ANNOTATE_GENOME_SNVS { CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed) CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]]) - BCFTOOLS_CONCAT.out.vcf .map { meta, vcf -> [meta - meta.subMap('prefix'), vcf] } .set { ch_concat_out } @@ -191,8 +189,8 @@ workflow ANNOTATE_GENOME_SNVS { TABIX_BCFTOOLS_CONCAT (ch_concat_out) ch_vep_ann = ch_concat_out - ch_vep_index = TABIX_BCFTOOLS_CONCAT.out.tbi - ch_vep_ann_index = ch_concat_out.join(TABIX_BCFTOOLS_CONCAT.out.tbi) + ch_vep_index = TABIX_BCFTOOLS_CONCAT.out.index + ch_vep_ann_index = ch_concat_out.join(TABIX_BCFTOOLS_CONCAT.out.index) //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) @@ -205,8 +203,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO.out.versions) ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) - ch_versions = ch_versions.mix(TABIX_VEP.out.versions) - ch_versions = ch_versions.mix(TABIX_BCFTOOLS_CONCAT.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) emit: diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 6707ab11b..38a877913 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -113,9 +113,9 @@ workflow ANNOTATE_MT_SNVS { ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) emit: - haplog = ch_haplog // channel: [ val(meta), path(txt) ] - report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] - tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ] - vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] + haplog = ch_haplog // channel: [ val(meta), path(txt) ] + report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] + tbi = TABIX_TABIX_VEP_MT.out.index // channel: [ val(meta), path(tbi) ] + vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 9ff4f0882..0d2119abd 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -30,7 +30,7 @@ workflow ANNOTATE_RHOCALLVIZ { TABIX_TABIX(BCFTOOLS_VIEW_RHOCALL.out.vcf) BCFTOOLS_VIEW_RHOCALL.out.vcf - .join(TABIX_TABIX.out.tbi) + .join(TABIX_TABIX.out.index) .set {ch_roh_in } BCFTOOLS_ROH(ch_roh_in, [[],[]], [], [], [], []) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 34982ea4c..7f3384afa 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -101,10 +101,9 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) ch_versions = ch_versions.mix(PICARD_SORTVCF.out.versions) - ch_versions = ch_versions.mix(TABIX_VEP.out.versions) emit: - tbi = TABIX_VEP.out.tbi // channel: [ val(meta), path(tbi) ] + tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 088246a63..40dd7099f 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -91,13 +91,13 @@ workflow CALL_MOBILE_ELEMENTS { } .set { ch_vcfs } - TABIX_ME_SPLIT.out.tbi - .map { meta, vcf -> - [ groupKey( meta - meta.subMap('interval'), meta.nr_of_intervals ), vcf ] + TABIX_ME_SPLIT.out.index + .map { meta, tbi -> + [ groupKey( meta - meta.subMap('interval'), meta.nr_of_intervals ), tbi ] } .groupTuple() - .map { meta, vcf -> - [ meta - meta.subMap('nr_of_intervals'), vcf ] + .map { meta, tbi -> + [ meta - meta.subMap('nr_of_intervals'), tbi ] } .set { ch_tbis } @@ -123,12 +123,10 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) - ch_versions = ch_versions.mix(TABIX_ME_SPLIT.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) - ch_versions = ch_versions.mix(TABIX_ME.out.versions) emit: - tbi = TABIX_ME.out.tbi // channel: [ val(meta), path(tbi) ] + tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 64a7d5589..045358ef0 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -41,7 +41,7 @@ workflow CALL_REPEAT_EXPANSIONS { // Split multi allelelic SPLIT_MULTIALLELICS_EXP ( - RENAMESAMPLE_EXP.out.vcf.join(TABIX_EXP_RENAME.out.tbi, failOnMismatch:true, failOnDuplicate:true), + RENAMESAMPLE_EXP.out.vcf.join(TABIX_EXP_RENAME.out.index, failOnMismatch:true, failOnDuplicate:true), ch_genome_fasta ) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 80d73cbb0..935b0206d 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -75,7 +75,7 @@ workflow CALL_SNV_DEEPVARIANT { .set{ch_varcallerbed} REMOVE_DUPLICATES_GL.out.vcf - .join(TABIX_GL.out.tbi) + .join(TABIX_GL.out.index) .combine(ch_varcallerbed) .set { ch_annotate_in } @@ -90,7 +90,7 @@ workflow CALL_SNV_DEEPVARIANT { emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] - tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + tabix = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 04394f7fc..87a2d40bd 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -42,7 +42,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } .set{ manta_vcf } - ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions) } if (val_analysis_type.equals("wgs")) { @@ -109,7 +108,7 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf - ch_merged_tbi = TABIX_TABIX.out.tbi + ch_merged_tbi = TABIX_TABIX.out.index ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 4729955be..0bb0f47eb 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -61,7 +61,7 @@ workflow POSTPROCESS_MT_CALLS { // Removing duplicates and merging if there is more than one sample SPLIT_MULTIALLELICS_MT.out.vcf - .join(TABIX_TABIX_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) + .join(TABIX_TABIX_MT.out.index, failOnMismatch:true, failOnDuplicate:true) .set { ch_in_remdup } REMOVE_DUPLICATES_MT(ch_in_remdup, ch_genome_fasta) TABIX_TABIX_MT2(REMOVE_DUPLICATES_MT.out.vcf) @@ -72,7 +72,7 @@ workflow POSTPROCESS_MT_CALLS { .toList() .set { file_list_vcf } - TABIX_TABIX_MT2.out.tbi + TABIX_TABIX_MT2.out.index .map{ _meta, vcf -> vcf} .toSortedList{a, b -> a.name <=> b.name} .toList() @@ -113,7 +113,7 @@ workflow POSTPROCESS_MT_CALLS { .set{ch_varcallerbed} ch_addfoundintag_in - .join(TABIX_TABIX_MERGE.out.tbi) + .join(TABIX_TABIX_MERGE.out.index) .combine(ch_varcallerbed) .set { ch_annotate_in } @@ -125,10 +125,9 @@ workflow POSTPROCESS_MT_CALLS { ch_versions = ch_versions.mix(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.versions) ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) emit: - tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index f29fb4258..e205e18ce 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -88,7 +88,7 @@ workflow PREPARE_REFERENCES { // Genome indices // if (!val_fai) { - ch_genome_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]]).fai.collect() + ch_genome_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[:],[]], false).fai.collect() } else { ch_genome_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() } @@ -134,13 +134,12 @@ workflow PREPARE_REFERENCES { // if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { if (!val_mtfasta) { - ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_genome_fai).fa.collect() - ch_versions = ch_versions.mix(SAMTOOLS_EXTRACT_MT.out.versions) + ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_genome_fai, false).fa.collect() } else { ch_mt_fasta = channel.fromPath(val_mtfasta).map { it -> [[id:it.simpleName], it] }.collect() } - ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() + ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[:],[]], false).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) @@ -189,7 +188,7 @@ workflow PREPARE_REFERENCES { if (val_known_dbsnp_tbi) { ch_dbsnp_tbi = channel.fromPath(val_known_dbsnp_tbi).map{ it -> [[id:it.simpleName], it] }.collect() } else { - ch_dbsnp_tbi = TABIX_DBSNP(ch_dbsnp).tbi.collect() + ch_dbsnp_tbi = TABIX_DBSNP(ch_dbsnp).index.collect() } } @@ -198,7 +197,7 @@ workflow PREPARE_REFERENCES { if (val_gnomad_af_idx) { ch_gnomad_idx = channel.fromPath(val_gnomad_af_idx).map{ it -> [[id:it.simpleName], it] }.collect() } else { - ch_gnomad_idx = TABIX_GNOMAD_AF(ch_gnomad_af).tbi.collect() + ch_gnomad_idx = TABIX_GNOMAD_AF(ch_gnomad_af).index.collect() } ch_gnomad_af_idx = ch_gnomad_af.join(ch_gnomad_idx).map {_meta, tab, idx -> [tab,idx]}.collect() } @@ -239,7 +238,7 @@ workflow PREPARE_REFERENCES { ch_vcfanno_tabix_in = channel.fromPath(val_vcfanno_extra).map { it -> [[id:it.baseName], it] } if (val_vcfanno_extra.endsWith(".gz")) { - TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in).tbi + TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in).index .join(ch_vcfanno_tabix_in) .map { _meta, tbi, vcf -> return [[vcf,tbi]]} .set {ch_vcfanno_extra} diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 162c9d459..cc51e69da 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -56,7 +56,7 @@ workflow QC_BAM { .set { ch_hsmetrics_in} if (val_target_bed) { - ch_hsmetrics = PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]]).metrics + ch_hsmetrics = PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[:],[]], [[:],[]]).metrics } if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 3c4cdf24d..85af4dfff 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,159 +2,61 @@ "QC_BAM - test, bwamem2": { "content": [ [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ - "earlycasualcaiman_mosdepth.per-base.d4" + ], [ - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] + ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-05T11:04:56.134850832" + "timestamp": "2026-01-26T08:22:35.617440867" }, "QC_BAM - test, sentieon": { "content": [ [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ - "earlycasualcaiman_mosdepth.per-base.d4" + ], [ - "earlycasualcaiman_wgsmetrics.txt" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T11:05:48.291219333" + "timestamp": "2026-01-26T08:23:33.958003807" } } \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index c02e9a2bd..1e451568f 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -24,7 +24,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { [], [] ) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bebce756d..6084018a5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,908 +1,15 @@ { "-profile test": { "content": [ - { - "ADD_VARCALLER_TO_BED": { - "tabix": 1.12 - }, - "BCFTOOLS_ANNOTATE": { - "bcftools": 1.22 - }, - "BCFTOOLS_CONCAT": { - "bcftools": 1.2 - }, - "BCFTOOLS_CONCAT_ME": { - "bcftools": 1.2 - }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.2 - }, - "BCFTOOLS_REHEADER_EXP": { - "bcftools": 1.21 - }, - "BCFTOOLS_REHEADER_ME": { - "bcftools": 1.21 - }, - "BCFTOOLS_ROH": { - "bcftools": 1.2 - }, - "BCFTOOLS_SORT": { - "bcftools": 1.2 - }, - "BCFTOOLS_SORT_ME": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_CNVNATOR": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_FILTER": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_MANTA": { - "bcftools": 1.2 - }, - "BCFTOOLS_VIEW_RHOCALL": { - "bcftools": 1.2 - }, - 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"smncopynumbercaller", - "smncopynumbercaller/out", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", - "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_2.fastp.fastq.gz", - "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "pipeline_info" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-24T00:51:35.621202872" + "timestamp": "2026-01-25T21:12:28.093929424" } } \ No newline at end of file From b587c756dbe245c4f4f8584dcb1feed72ffa64d5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:08:25 +0100 Subject: [PATCH 274/872] move to annotate mt subwf --- conf/modules/annotate_mt_snvs.config | 6 ++ .../vcf_filter_bcftools_ensemblvep.config | 7 --- modules.json | 5 +- subworkflows/local/annotate_mt_snvs.nf | 57 ++++++++++++------- .../vcf_filter_bcftools_ensemblvep/main.nf | 13 ----- .../vcf_filter_bcftools_ensemblvep.diff | 56 ------------------ workflows/raredisease.nf | 13 ++--- 7 files changed, 50 insertions(+), 107 deletions(-) delete mode 100644 subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config index cda985d99..c41f0d465 100644 --- a/conf/modules/annotate_mt_snvs.config +++ b/conf/modules/annotate_mt_snvs.config @@ -62,6 +62,12 @@ process { ext.prefix = { "${meta.prefix}" } } + withName: '.*:ANNOTATE_MT_SNVS:BCFTOOLS_PLUGINSETGT' { + ext.prefix = { "${meta.id}_mt_${meta.set}_modifiedgt" } + ext.args = "--output-type z --write-index=tbi" + ext.args2 = "-i 'FMT/AF>=0.95 && FMT/DP>=100'" + } + withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' { ext.args = '--tree phylotree-rsrs@17.1' ext.prefix = { "${meta.prefix}_haplogrep" } diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_ensemblvep.config index 69867e0c2..83b282b21 100644 --- a/conf/modules/vcf_filter_bcftools_ensemblvep.config +++ b/conf/modules/vcf_filter_bcftools_ensemblvep.config @@ -48,13 +48,6 @@ process { ext.prefix = { "${meta.id}_mt_${meta.set}" } ext.args = { "-Oz -i 'AF>0.05' --write-index=tbi" } } - - withName: '.*:GENERATE_CLINICAL_SET_MT:BCFTOOLS_PLUGINSETGT' { - ext.prefix = { "${meta.id}_mt_${meta.set}_modifiedgt" } - ext.args = "--output-type z --write-index=tbi" - ext.args2 = "-i 'FMT/AF>=0.95 && FMT/DP>=100'" - } - } // ME variants diff --git a/modules.json b/modules.json index a85d7067d..2e683df77 100644 --- a/modules.json +++ b/modules.json @@ -33,7 +33,7 @@ "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", @@ -580,8 +580,7 @@ "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": ["subworkflows"], - "patch": "subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff" + "installed_by": ["subworkflows"] } } } diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 6c327c1c0..a3961ae28 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -3,6 +3,7 @@ // include { REPLACE_SPACES_IN_VCFINFO } from '../../modules/local/replace_spaces_in_vcfinfo' +include { BCFTOOLS_PLUGINSETGT } from '../../modules/nf-core/bcftools/pluginsetgt' include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../modules/nf-core/tabix/tabix/main' include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../modules/nf-core/tabix/bgziptabix/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../modules/nf-core/ensemblvep/vep/main' @@ -14,21 +15,22 @@ include { HMTNOTE_ANNOTATE } from '../../modules/n workflow ANNOTATE_MT_SNVS { take: - ch_cadd_header // channel: [mandatory] [ path(txt) ] - ch_cadd_resources // channel: [mandatory] [ path(annotation) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_fai // channel: [mandatory] [ path(fai) ] - ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] - ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] - ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] - ch_vep_cache // channel: [mandatory] [ path(cache) ] - ch_vep_extra_files // channel: [mandatory] [ path(files) ] - skip_haplogrep3 // boolean - val_cadd_resources // string: path to cadd resources file - val_genome // string: GRCh37 or GRCh38 - val_vep_cache_version // string: vep version ex: 107 + ch_cadd_header // channel: [mandatory] [ path(txt) ] + ch_cadd_resources // channel: [mandatory] [ path(annotation) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_fai // channel: [mandatory] [ path(fai) ] + ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] + ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] + ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] + ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] + ch_vep_cache // channel: [mandatory] [ path(cache) ] + ch_vep_extra_files // channel: [mandatory] [ path(files) ] + skip_haplogrep3 // boolean + val_cadd_resources // string: path to cadd resources file + val_genome // string: GRCh37 or GRCh38 + val_homoplasmy_af_threshold // float: 0-1 + val_vep_cache_version // string: vep version ex: 107 main: ch_versions = channel.empty() @@ -100,12 +102,27 @@ workflow ANNOTATE_MT_SNVS { TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf) + ch_vcf = ENSEMBLVEP_MT.out.vcf + ch_tbi = TABIX_TABIX_VEP_MT.out.tbi + // Running haplogrep3 if (!skip_haplogrep3) { HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in) ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt } + if (val_homoplasmy_af_threshold<1) { + BCFTOOLS_PLUGINSETGT ( + ENSEMBLVEP_MT.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, + channel.value('q'), + channel.value("c:'1/1'"), + [], + [] + ) + ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf + ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi + } + ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions) ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) @@ -115,9 +132,9 @@ workflow ANNOTATE_MT_SNVS { ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) emit: - haplog = ch_haplog // channel: [ val(meta), path(txt) ] - report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] - tbi = TABIX_TABIX_VEP_MT.out.tbi // channel: [ val(meta), path(tbi) ] - vcf_ann = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] + haplog = ch_haplog // channel: [ val(meta), path(txt) ] + report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf_ann = ch_vcf // channel: [ val(meta), path(vcf) ] + versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index a51e39191..1c1616590 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -10,7 +10,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] filter_with_bcftools // bool: should bcftools view be run filter_with_filter_vep // bool: should filter_vep be run - homoplasmy_af_threshold // float: 0-1 main: ch_versions = channel.empty() @@ -30,18 +29,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi - if (homoplasmy_af_threshold<1) { - BCFTOOLS_PLUGINSETGT ( - BCFTOOLS_VIEW.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, - channel.value('q'), - channel.value("c:'1/1'"), - [], - [] - ) - ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf - ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi - } - } if(filter_with_filter_vep) { diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff deleted file mode 100644 index fc2f472b0..000000000 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/vcf_filter_bcftools_ensemblvep.diff +++ /dev/null @@ -1,56 +0,0 @@ -Changes in component 'nf-core/vcf_filter_bcftools_ensemblvep' -'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config' is unchanged -'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml' is unchanged -Changes in 'vcf_filter_bcftools_ensemblvep/main.nf': ---- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf -+++ subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf -@@ -1,5 +1,6 @@ - include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' - include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -+include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt/main' - include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' - // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config - workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { -@@ -9,10 +10,11 @@ - ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] - filter_with_bcftools // bool: should bcftools view be run - filter_with_filter_vep // bool: should filter_vep be run -+ homoplasmy_af_threshold // float: 0-1 - - main: -- ch_versions = Channel.empty() -- ch_tbi = Channel.empty() -+ ch_versions = channel.empty() -+ ch_tbi = channel.empty() - - // Since bcftools is likely much faster than filter_vep, - // we run it first to reduce the number of variants that filter_vep has to process. -@@ -25,9 +27,21 @@ - [] - ) - ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) -+ ch_vcf = BCFTOOLS_VIEW.out.vcf -+ ch_tbi = BCFTOOLS_VIEW.out.tbi - -- ch_vcf = BCFTOOLS_VIEW.out.vcf -- ch_tbi = BCFTOOLS_VIEW.out.tbi -+ if (homoplasmy_af_threshold<1) { -+ BCFTOOLS_PLUGINSETGT ( -+ BCFTOOLS_VIEW.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, -+ channel.value('q'), -+ channel.value("c:'1/1'"), -+ [], -+ [] -+ ) -+ ch_vcf = BCFTOOLS_PLUGINSETGT.out.vcf -+ ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi -+ } -+ - } - - if(filter_with_filter_vep) { - -'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config' is unchanged -'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test' is unchanged -'subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap' is unchanged -************************************************************ diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3edd7c9f9..67efcbe3b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -438,8 +438,7 @@ workflow RAREDISEASE { ch_clin_research_snv_vcf.clinical, ch_hgnc_ids, false, - true, - null + true ) GENERATE_CLINICAL_SET_SNV.out.vcf .set { ch_clinical_snv_vcf } @@ -494,6 +493,7 @@ workflow RAREDISEASE { skip_haplogrep3, val_cadd_resources, val_genome, + val_homoplasmy_af_threshold, val_vep_cache_version ).set { ch_mt_annotate } ch_versions = ch_versions.mix(ch_mt_annotate.versions) @@ -511,8 +511,7 @@ workflow RAREDISEASE { ch_clin_research_mt_vcf.clinical, ch_hgnc_ids, true, - false, - val_homoplasmy_af_threshold + false ) GENERATE_CLINICAL_SET_MT.out.vcf .set { ch_clinical_mtsnv_vcf } @@ -610,8 +609,7 @@ workflow RAREDISEASE { ch_clin_research_sv_vcf.clinical, ch_hgnc_ids, false, - true, - null + true ) GENERATE_CLINICAL_SET_SV.out.vcf .set { ch_clinical_sv_vcf } @@ -689,8 +687,7 @@ workflow RAREDISEASE { ch_clin_research_me_vcf.clinical, ch_hgnc_ids, false, - true, - null + true ) GENERATE_CLINICAL_SET_ME.out.vcf .set { ch_clinical_me_vcf } From 4fae2675607bdc0726ec0c6c439e967aee12daec Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:14:18 +0100 Subject: [PATCH 275/872] revert changes --- .../nf-core/vcf_filter_bcftools_ensemblvep/main.nf | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 1c1616590..204369666 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -1,6 +1,5 @@ include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt/main' include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { @@ -12,8 +11,8 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { filter_with_filter_vep // bool: should filter_vep be run main: - ch_versions = channel.empty() - ch_tbi = channel.empty() + ch_versions = Channel.empty() + ch_tbi = Channel.empty() // Since bcftools is likely much faster than filter_vep, // we run it first to reduce the number of variants that filter_vep has to process. @@ -26,8 +25,8 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { [] ) ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) - ch_vcf = BCFTOOLS_VIEW.out.vcf - ch_tbi = BCFTOOLS_VIEW.out.tbi + ch_vcf = BCFTOOLS_VIEW.out.vcf + ch_tbi = BCFTOOLS_VIEW.out.tbi } From d000088f3a1ea8e5a1b9f9ef6c98c3bc0fc802ea Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:15:44 +0100 Subject: [PATCH 276/872] revert changes 2 --- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 204369666..862f8de4e 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -27,7 +27,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi - } if(filter_with_filter_vep) { From 1ffd55c0415c1a17c4934a89d20c7f2212d437dc Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:24:24 +0100 Subject: [PATCH 277/872] fix lint error --- subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 862f8de4e..39b8aafc2 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -25,6 +25,7 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { [] ) ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions) + ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi } From 5c161fac02b44c830558ea839a07ab3640ac3e5c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:36:57 +0100 Subject: [PATCH 278/872] prettier --- modules.json | 457 +++++++++++++-------------------------------------- 1 file changed, 114 insertions(+), 343 deletions(-) diff --git a/modules.json b/modules.json index b407cfec4..295ba1a6a 100644 --- a/modules.json +++ b/modules.json @@ -8,771 +8,550 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": 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"installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -781,33 +560,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From bf11aa7b6c3618e4a61a81213f93fe93e75218c7 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 26 Jan 2026 14:57:13 +0000 Subject: [PATCH 279/872] [automated] Fix code linting --- modules.json | 457 +++++++++++++-------------------------------------- 1 file changed, 114 insertions(+), 343 deletions(-) diff --git a/modules.json b/modules.json index b407cfec4..295ba1a6a 100644 --- a/modules.json +++ b/modules.json @@ -8,771 +8,550 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": 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"installed_by": ["modules"] }, "sentieon/readwriter": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stranger": { "branch": "master", "git_sha": "72717e1f3feabaa57a6a71ba5a85d9c4ceeba514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/query": { "branch": "master", "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -781,33 +560,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 657686b58aba409e6c0e433920438344c4354ea2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 27 Jan 2026 10:51:04 +0100 Subject: [PATCH 280/872] update snaps --- subworkflows/local/align/main.nf | 2 +- .../local/align/tests/main.nf.test.snap | 39 +- .../tests/main.nf.test.snap | 12 +- .../align_sentieon/tests/main.nf.test.snap | 48 +- .../tests/main.nf.test.snap | 16 +- .../local/qc_bam/tests/main.nf.test.snap | 126 ++- .../local/qc_bam/tests/nextflow.config | 1 - tests/default.nf.test.snap | 878 +++++++++++++++++- tests/test_bam.nf.test.snap | 820 +++++++++++++++- tests/test_singleton.nf.test.snap | 638 ++++++++++++- 10 files changed, 2465 insertions(+), 115 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 224149535..661b9b7e8 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -54,7 +54,7 @@ workflow ALIGN { ch_versions = channel.empty() if (!skip_fastp) { - FASTP (ch_input_reads, [], false, false, false) + FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) ch_input_reads = FASTP.out.reads ch_fastp_json = FASTP.out.json } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index e04faf30d..8b83d6ca7 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -253,21 +253,12 @@ "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", @@ -283,18 +274,12 @@ "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" @@ -304,7 +289,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:10:54.26947033" + "timestamp": "2026-01-27T09:03:18.529621306" }, "align bwameme - wgs": { "content": [ @@ -445,15 +430,9 @@ "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", "versions.yml:md5,6cbf152be76b9a14bb7eccb2658cabb3", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", - "versions.yml:md5,76abbad692af483cd9c6bc9c5d29b330", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", "versions.yml:md5,914929705542ec69faf26ad6c672e2af", @@ -472,18 +451,12 @@ "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", - "versions.yml:md5,bc6e997423a4d7b3c3db4374ae26b64f", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", "versions.yml:md5,d19b223e2ea8c907b23c9b301c15f3fb", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", - "versions.yml:md5,deacbc4b4196d58efb6dab2e2d333ee9", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65", "versions.yml:md5,f8dd98ba8455bb8d00379fba39cc9e65" @@ -493,7 +466,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:19:59.751912776" + "timestamp": "2026-01-26T23:13:51.08952732" }, "align bwamem2 - wes": { "content": [ @@ -575,12 +548,6 @@ "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,81cee5ff00c008209a5c6fb06ac57de5", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", - "versions.yml:md5,87e7da5e82b70b42f06b30a245a5750e", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7", "versions.yml:md5,c31eb465488334212645bd43296d8bd7" @@ -590,6 +557,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-23T09:11:40.672538153" + "timestamp": "2026-01-27T09:04:50.753630765" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 879f7dbf8..378aee009 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -32,20 +32,18 @@ ] ], [ - "versions.yml:md5,22d2871963a6cdc14c58d98fc3c3c9c3", "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-04T12:30:00.835976838" + "timestamp": "2026-01-26T23:20:05.423583715" }, "align bwameme": { "content": [ @@ -80,19 +78,17 @@ ] ], [ - "versions.yml:md5,22d2871963a6cdc14c58d98fc3c3c9c3", "versions.yml:md5,390a09ae83280da84de93856149cc3a1", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,e9e514dbea5a822d1978acac57bee61e", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-04T12:30:47.082179053" + "timestamp": "2026-01-26T23:21:26.123323889" } } \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 8bc1129d0..61e2f2be2 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,eecb176fcd4ba3862cd8a87584d29d7f" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], "1": [ @@ -29,7 +29,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,2c3892c0b7dd38008f812936f19edcfd" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], "2": [ @@ -44,7 +44,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_mq_metrics.txt:md5,d924101f16a609cfe2381fb2904c1157" + "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" ] ], "3": [ @@ -59,7 +59,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_qd_metrics.txt:md5,5d823326eaf59b00e31b7a10b8e1a09e" + "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" ] ], "4": [ @@ -74,7 +74,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_metrics.txt:md5,6d373e38fcaa29620eb2c1c62bd9ece9" + "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" ] ], "5": [ @@ -89,7 +89,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_summary.txt:md5,123abd2c83e7df6f141a30c7d38bff27" + "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" ] ], "6": [ @@ -104,7 +104,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_aln_metrics.txt:md5,609454bf43dd880e347da719e1868432" + "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" ] ], "7": [ @@ -119,14 +119,9 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_is_metrics.txt:md5,04eb7da7a2b7acea2bf02f860535c2e8" + "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" ] ], - "8": [ - "versions.yml:md5,081d0fd598d1279f3025f39626df5a10", - "versions.yml:md5,9f88074c5a7336a02eeb30461af26fd1", - "versions.yml:md5,f084363cb6d662d82d09a289b6b68346" - ], "aln_metrics": [ [ { @@ -139,7 +134,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_aln_metrics.txt:md5,609454bf43dd880e347da719e1868432" + "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" ] ], "gc_metrics": [ @@ -154,7 +149,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_metrics.txt:md5,6d373e38fcaa29620eb2c1c62bd9ece9" + "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" ] ], "gc_summary": [ @@ -169,7 +164,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_gc_summary.txt:md5,123abd2c83e7df6f141a30c7d38bff27" + "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" ] ], "is_metrics": [ @@ -184,7 +179,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_is_metrics.txt:md5,04eb7da7a2b7acea2bf02f860535c2e8" + "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" ] ], "marked_bai": [ @@ -199,7 +194,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,2c3892c0b7dd38008f812936f19edcfd" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], "marked_bam": [ @@ -214,7 +209,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,eecb176fcd4ba3862cd8a87584d29d7f" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], "mq_metrics": [ @@ -229,7 +224,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_mq_metrics.txt:md5,d924101f16a609cfe2381fb2904c1157" + "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" ] ], "qd_metrics": [ @@ -244,20 +239,15 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_datametrics_qd_metrics.txt:md5,5d823326eaf59b00e31b7a10b8e1a09e" + "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" ] - ], - "versions": [ - "versions.yml:md5,081d0fd598d1279f3025f39626df5a10", - "versions.yml:md5,9f88074c5a7336a02eeb30461af26fd1", - "versions.yml:md5,f084363cb6d662d82d09a289b6b68346" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-06-25T17:05:48.914189124" + "timestamp": "2026-01-26T23:22:09.03170299" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index d7aab6732..b240fb809 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -387,22 +387,15 @@ "29": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", - "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", - "versions.yml:md5,3d14ad719ad5095ae199e915140148b6", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", - "versions.yml:md5,4e8ef14026e5c035dd4c36c30fe76e0e", - "versions.yml:md5,6a0d25217268ed42e4cfe4f77972ba9b", - "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", - "versions.yml:md5,dac6d3657264cb33a64b581c43e6a0de", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ], "3": [ @@ -910,22 +903,15 @@ "versions": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", - "versions.yml:md5,1dd7f004d62b304a49613a400bdb20c8", "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", - "versions.yml:md5,3d14ad719ad5095ae199e915140148b6", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,4c809981aaef975a666ac3812651bec6", - "versions.yml:md5,4e8ef14026e5c035dd4c36c30fe76e0e", - "versions.yml:md5,6a0d25217268ed42e4cfe4f77972ba9b", - "versions.yml:md5,6c2f65dfa53a173a7f7ba8ee03933dc0", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,77768b2bc91b4934bd8a3e3c392f11d2", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", - "versions.yml:md5,dac6d3657264cb33a64b581c43e6a0de", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] } @@ -934,6 +920,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-17T13:36:20.294622928" + "timestamp": "2026-01-26T23:24:35.811727654" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 85af4dfff..b1d3ef2cf 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,61 +2,159 @@ "QC_BAM - test, bwamem2": { "content": [ [ - + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ], [ - + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ ], [ - + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T08:22:35.617440867" + "timestamp": "2026-01-27T10:15:41.947673274" }, "QC_BAM - test, sentieon": { "content": [ [ - + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ], [ - + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ ], [ - + "earlycasualcaiman_wgsmetrics.txt" ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T08:23:33.958003807" + "timestamp": "2026-01-27T10:17:32.616739257" } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config index 785869e7a..4f1859433 100644 --- a/subworkflows/local/qc_bam/tests/nextflow.config +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -30,7 +30,6 @@ process { } withName: '.*QC_BAM:MOSDEPTH' { - ext.args = "--d4" ext.prefix = { "${meta.id}_mosdepth" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6084018a5..86448783a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,15 +1,887 @@ { "-profile test": { "content": [ - null, + { + "ADD_VARCALLER_TO_BED": { + "tabix": 1.12 + }, + "BCFTOOLS_ANNOTATE": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.22 + }, + "BCFTOOLS_REHEADER_EXP": { + "bcftools": 1.22 + }, + "BCFTOOLS_REHEADER_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_ROH": { + "bcftools": 1.22 + }, + "BCFTOOLS_SORT": { + "bcftools": 1.22 + }, + "BCFTOOLS_SORT_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_CNVNATOR": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_FILTER": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_MANTA": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_RHOCALL": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_TIDDIT": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_UNCOMPRESS": { + "bcftools": 1.22 + }, + "BEDTOOLS_PAD_TARGET_BED": { + "bedtools": "2.31.1" + }, + "BWAMEM2_INDEX_GENOME": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_INDEX_MT": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_INDEX_MT_SHIFT": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, + "BWAMEM2_MEM_MT": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, + "BWA_INDEX_GENOME": { + "bwa": "0.7.18-r1243-dirty" + }, + "CAT_CAT_BAIT": { + "pigz": 2.8 + }, + "CHROMOGRAPH_AUTOZYG": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_COV": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, + "CNVNATOR_CALL": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_CONVERT2VCF": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_HIST": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_PARTITION": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_RD": { + "CNVnator": "0.4.1" + }, + "CNVNATOR_STAT": { + "CNVnator": "0.4.1" + }, + "CREATE_PEDIGREE_FILE": { + "create_pedigree_file": "v1.0", + "python": "3.8.3" + }, + "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { + "add_most_severe_consequence": 1.1, + "bgzip": 1.21 + }, + "CUSTOM_ADDMOSTSEVEREPLI": { + "add_most_severe_pli": 1.1, + "bgzip": 1.21 + }, + "DEEPVARIANT": { + "deepvariant": "1.8.0" + }, + "EKLIPSE": { + "eklipse": 1.8 + }, + "EXPANSIONHUNTER": { + "expansionhunter": "5.0.0", + "bgzip": 1.18 + }, + "FASTP": { + "fastp": "1.0.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_FILTERMUTECTCALLS_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEBAMALIGNMENT_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_MUTECT2_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_PRINTREADS_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_REVERTSAM_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_SAMTOFASTQ_MT": { + "gatk4": "4.5.0.0" + }, + "GATK4_SELECTVARIANTS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION_MT": { + "gatk4": "4.5.0.0" + }, + "GATK_BILT": { + "gatk4": "4.5.0.0" + }, + "GATK_ILT": { + "gatk4": "4.5.0.0" + }, + "GATK_SD": { + "gatk4": "4.5.0.0" + }, + "GATK_SD_MT": { + "gatk4": "4.5.0.0" + }, + "GATK_SHIFTFASTA": { + "gatk4": "4.5.0.0" + }, + "GAWK": { + "gawk": "5.3.0" + }, + "GENMOD_ANNOTATE": { + "genmod": "3.10.2" + }, + "GENMOD_COMPOUND": { + "genmod": "3.10.2" + }, + "GENMOD_MODELS": { + "genmod": "3.10.2" + }, + "GENMOD_SCORE": { + "genmod": "3.10.2" + }, + "GET_CHROM_SIZES": { + "coreutils": 8.31 + }, + "GLNEXUS": { + "glnexus": "1.4.1-0-g68e25e5" + }, + 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"annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", + "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz", + "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", + "annotate_snv", + "annotate_snv/genome", + "annotate_snv/genome/hugelymodelbat_rhocallviz", + "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", + "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", + "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", + "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", + "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/mitochondria", + "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", + "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", + "annotate_sv", + "annotate_sv/justhusky_svdbquery_vep.json.gz", + "annotate_sv/justhusky_svdbquery_vep.summary.html", + "annotate_sv/justhusky_svdbquery_vep.tab.gz", + "annotate_sv/justhusky_svdbquery_vep.vcf.gz", + "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/genome", + "call_sv/genome/justhusky_sv.vcf.gz", + "call_sv/genome/justhusky_sv.vcf.gz.tbi", + "call_sv/mitochondria", + "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", + "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", + "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "fastqc", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "haplocheck", + "haplocheck/hugelymodelbat.raw.txt", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/.stub", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "peddy", + "peddy/justhusky.het_check.csv", + "peddy/justhusky.html", + "peddy/justhusky.ped_check.csv", + "peddy/justhusky.peddy.ped", + "peddy/justhusky.sex_check.csv", + "peddy/justhusky.vs.html", + "pedigree", + "pedigree/justhusky.ped", + "pipeline_info", + "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", + "qc_bam", + "qc_bam/hugelymodelbat", + "qc_bam/hugelymodelbat/css", + "qc_bam/hugelymodelbat/css/agogo.css", + "qc_bam/hugelymodelbat/css/ajax-loader.gif", + "qc_bam/hugelymodelbat/css/basic.css", + "qc_bam/hugelymodelbat/css/bgfooter.png", + "qc_bam/hugelymodelbat/css/bgtop.png", + "qc_bam/hugelymodelbat/css/comment-bright.png", + "qc_bam/hugelymodelbat/css/comment-close.png", + "qc_bam/hugelymodelbat/css/comment.png", + "qc_bam/hugelymodelbat/css/doctools.js", + "qc_bam/hugelymodelbat/css/down-pressed.png", + "qc_bam/hugelymodelbat/css/down.png", + "qc_bam/hugelymodelbat/css/file.png", + "qc_bam/hugelymodelbat/css/jquery.js", + "qc_bam/hugelymodelbat/css/minus.png", + "qc_bam/hugelymodelbat/css/plus.png", + "qc_bam/hugelymodelbat/css/pygments.css", + "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", + "qc_bam/hugelymodelbat/css/report.css", + "qc_bam/hugelymodelbat/css/searchtools.js", + "qc_bam/hugelymodelbat/css/underscore.js", + "qc_bam/hugelymodelbat/css/up-pressed.png", + "qc_bam/hugelymodelbat/css/up.png", + "qc_bam/hugelymodelbat/css/websupport.js", + "qc_bam/hugelymodelbat/genome_results.txt", + "qc_bam/hugelymodelbat/images_qualimapReport", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/hugelymodelbat/qualimapReport.html", + "qc_bam/hugelymodelbat/raw_data_qualimapReport", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/hugelymodelbat_chromographcov", + "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.per-base.d4", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.summary.txt", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/hugelymodelbat_tidditcov.bed", + "qc_bam/hugelymodelbat_tidditcov.bw", + "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "rank_and_filter", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", + "repeat_expansions", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "smncopynumbercaller", + "smncopynumbercaller/out", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", + "vcf2cytosure", + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T21:12:28.093929424" + "timestamp": "2026-01-27T10:50:06.243055556" } } \ No newline at end of file From 5442cfa721378451fb1a9b1455a9305b6dab867e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 27 Jan 2026 14:11:00 +0100 Subject: [PATCH 281/872] update vep --- modules.json | 2 +- .../ensemblvep/vep/ensemblvep-vep.diff | 41 +++++++++++++-- modules/nf-core/ensemblvep/vep/main.nf | 17 ++----- .../vcf_filter_bcftools_ensemblvep/main.nf | 42 +++++++-------- .../tests/main.nf.test | 26 +++++----- .../tests/main.nf.test.snap | 51 ++++++++++--------- 6 files changed, 104 insertions(+), 75 deletions(-) diff --git a/modules.json b/modules.json index 295ba1a6a..0eb97dec9 100644 --- a/modules.json +++ b/modules.json @@ -574,7 +574,7 @@ }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", - "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8", + "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index ef4a555c1..f141ba410 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -3,14 +3,49 @@ Changes in component 'nf-core/ensemblvep/vep' Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf +++ modules/nf-core/ensemblvep/vep/main.nf -@@ -20,7 +20,7 @@ +@@ -4,8 +4,8 @@ + + conda "bioconda::ensembl-vep=110.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : +- 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : ++ 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" + + input: + tuple val(meta), path(vcf), path(custom_extra_files) +@@ -20,8 +20,8 @@ tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , emit: report -+ path "*.summary.html" , optional:true, emit: report - path "versions.yml" , emit: versions +- path "versions.yml" , emit: versions ++ tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true ++ tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep when: + task.ext.when == null || task.ext.when +@@ -48,11 +48,6 @@ + --fork $task.cpus \\ + --stats_file ${prefix}.summary.html \\ + +- +- cat <<-END_VERSIONS > versions.yml +- "${task.process}": +- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') +- END_VERSIONS + """ + + stub: +@@ -63,9 +58,5 @@ + touch ${prefix}.json.gz + touch ${prefix}.summary.html + +- cat <<-END_VERSIONS > versions.yml +- "${task.process}": +- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') +- END_VERSIONS + """ + } ************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 4886b05e6..61da45d06 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "bioconda::ensembl-vep=110.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : + 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" input: tuple val(meta), path(vcf), path(custom_extra_files) @@ -20,8 +20,8 @@ process ENSEMBLVEP_VEP { tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , optional:true, emit: report - path "versions.yml" , emit: versions + tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true + tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep when: task.ext.when == null || task.ext.when @@ -48,11 +48,6 @@ process ENSEMBLVEP_VEP { --fork $task.cpus \\ --stats_file ${prefix}.summary.html \\ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ stub: @@ -63,9 +58,5 @@ process ENSEMBLVEP_VEP { touch ${prefix}.json.gz touch ${prefix}.summary.html - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 1e451568f..e98e54d40 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -1,52 +1,52 @@ -include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep/main' -include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view' +include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix' + // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { - take: - ch_vcf // channel: [ val(meta), path(vcf) ] + ch_vcf // channel: [ val(meta), path(vcf) ] ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] - filter_with_bcftools // bool: should bcftools view be run - filter_with_filter_vep // bool: should filter_vep be run + filter_with_bcftools // bool: should bcftools view be run + filter_with_filter_vep // bool: should filter_vep be run main: - ch_versions = Channel.empty() - ch_tbi = Channel.empty() + ch_versions = channel.empty() + ch_tbi = channel.empty() // Since bcftools is likely much faster than filter_vep, // we run it first to reduce the number of variants that filter_vep has to process. - if(filter_with_bcftools) { + if (filter_with_bcftools) { - BCFTOOLS_VIEW ( - ch_vcf.map { meta, vcf -> [ meta, vcf, [] ] }, + BCFTOOLS_VIEW( + ch_vcf.map { meta, vcf -> [meta, vcf, []] }, + [], [], [], - [] ) ch_vcf = BCFTOOLS_VIEW.out.vcf ch_tbi = BCFTOOLS_VIEW.out.tbi } - if(filter_with_filter_vep) { + if (filter_with_filter_vep) { - ENSEMBLVEP_FILTERVEP ( + ENSEMBLVEP_FILTERVEP( ch_vcf, - ch_filter_vep_feature_file.map { _meta, file -> file } + ch_filter_vep_feature_file.map { _meta, file -> file }, ) - TABIX_BGZIPTABIX ( + TABIX_BGZIPTABIX( ENSEMBLVEP_FILTERVEP.out.output ) ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) - ch_vcf = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, vcf, _tbi -> [ meta, vcf ] } - ch_tbi = TABIX_BGZIPTABIX.out.gz_tbi.map { meta, _vcf, tbi -> [ meta, tbi ] } + ch_vcf = TABIX_BGZIPTABIX.out.gz_index.map { meta, vcf, _tbi -> [meta, vcf] } + ch_tbi = TABIX_BGZIPTABIX.out.gz_index.map { meta, _vcf, tbi -> [meta, tbi] } } emit: - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test index 811929877..fb000d16a 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test @@ -34,10 +34,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.versions, - file(workflow.out.tbi.get(0).get(1)).name, - path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, - path(workflow.out.vcf.get(0).get(1)).vcf.summary, + workflow.out.versions.collect { it instanceof String ? path(it).yaml : it }, + file(workflow.out.tbi[0][1]).name, + path(workflow.out.vcf[0][1]).vcf.variantsMD5, + path(workflow.out.vcf[0][1]).vcf.summary, ).match() } ) } @@ -65,10 +65,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.versions, - file(workflow.out.tbi.get(0).get(1)).name, - path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, - path(workflow.out.vcf.get(0).get(1)).vcf.summary, + workflow.out.versions.collect { it instanceof String ? path(it).yaml : it }, + file(workflow.out.tbi[0][1]).name, + path(workflow.out.vcf[0][1]).vcf.variantsMD5, + path(workflow.out.vcf[0][1]).vcf.summary, ).match() } ) } @@ -96,10 +96,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.versions, - file(workflow.out.tbi.get(0).get(1)).name, - path(workflow.out.vcf.get(0).get(1)).vcf.variantsMD5, - path(workflow.out.vcf.get(0).get(1)).vcf.summary, + workflow.out.versions.collect { it instanceof String ? path(it).yaml : it }, + file(workflow.out.tbi[0][1]).name, + path(workflow.out.vcf[0][1]).vcf.variantsMD5, + path(workflow.out.vcf[0][1]).vcf.summary, ).match() } ) } @@ -133,4 +133,4 @@ nextflow_workflow { } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap index 731a41068..19d0c6f18 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap @@ -2,50 +2,57 @@ "vcf, hgnc_ids - filter on hgnc ids": { "content": [ [ - "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", - "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f" + { + "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": { + "bgzip": 1.21, + "tabix": 1.21 + } + } ], "test.vcf.gz.tbi", "18e010447bd23a05a202d44daf66bcd2", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-29T09:51:55.795875" + "timestamp": "2026-01-07T17:55:42.872290536" }, "vcf, hgnc_ids - filter on hgnc ids and expression": { "content": [ [ - "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", - "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", - "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + { + "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": { + "bgzip": 1.21, + "tabix": 1.21 + } + } ], "test.vcf.gz.tbi", "18e010447bd23a05a202d44daf66bcd2", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-29T09:52:06.507756" + "timestamp": "2026-01-20T12:45:00.851156984" }, "vcf, hgnc_ids - filter on expression": { "content": [ [ - "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + ], "test_filtered.vcf.gz.tbi", "9236236d782191442193a20355604927", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=37, phased=false, phasedAutodetect=false]" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-19T16:47:44.418033098" + "timestamp": "2026-01-20T12:44:40.698598144" }, "vcf, hgnc_ids - filter on hgnc ids and expression - stub": { "content": [ @@ -67,9 +74,7 @@ ] ], "2": [ - "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", - "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", - "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f" ], "tbi": [ [ @@ -88,16 +93,14 @@ ] ], "versions": [ - "versions.yml:md5,16af11013f788015f8d81f43d2c36c68", - "versions.yml:md5,947e9db984ae77df9c8445edc82ee36f", - "versions.yml:md5,f1157acfb79970703c753901c0555ad5" + "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-29T09:52:17.525437" + "timestamp": "2026-01-20T12:45:09.964268419" } } \ No newline at end of file From ef215cf7f138fb64936e4a30bb7e1555e146cdd5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 27 Jan 2026 20:36:46 +0100 Subject: [PATCH 282/872] review suggestions --- CHANGELOG.md | 2 +- conf/modules/annotate_mt_snvs.config | 4 ++-- nextflow_schema.json | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f98eb2f48..c7d62acfa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPath to create channels in a readable fashion in main.nf [#766](https://github.com/nf-core/raredisease/pull/766) - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) -- A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1(homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) +- A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1 (homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) ### `Changed` diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config index c41f0d465..afed4b153 100644 --- a/conf/modules/annotate_mt_snvs.config +++ b/conf/modules/annotate_mt_snvs.config @@ -63,9 +63,9 @@ process { } withName: '.*:ANNOTATE_MT_SNVS:BCFTOOLS_PLUGINSETGT' { - ext.prefix = { "${meta.id}_mt_${meta.set}_modifiedgt" } + ext.prefix = { "${meta.prefix}_mt_modifiedgt" } ext.args = "--output-type z --write-index=tbi" - ext.args2 = "-i 'FMT/AF>=0.95 && FMT/DP>=100'" + ext.args2 = { "-i 'FMT/AF>=${params.homoplasmy_af_threshold} && FMT/DP>=100'" } } withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' { diff --git a/nextflow_schema.json b/nextflow_schema.json index 8b6b41a4e..b2cf39513 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -545,7 +545,7 @@ "homoplasmy_af_threshold": { "type": "number", "default": 1, - "description": "Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homooplasmic and assigned a 1/1 genotype. Range 0-1.0.", + "description": "Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homoplasmic and assigned a 1/1 genotype. Range 0-1.0.", "fa_icon": "fas fa-less-than" }, "platform": { From ab4a8817944174e9f00d963fa1e536551a260841 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 27 Jan 2026 20:37:44 +0100 Subject: [PATCH 283/872] fix alignment --- subworkflows/local/annotate_mt_snvs.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index a3961ae28..0f4c65e5b 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -27,10 +27,10 @@ workflow ANNOTATE_MT_SNVS { ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] skip_haplogrep3 // boolean - val_cadd_resources // string: path to cadd resources file - val_genome // string: GRCh37 or GRCh38 + val_cadd_resources // string: path to cadd resources file + val_genome // string: GRCh37 or GRCh38 val_homoplasmy_af_threshold // float: 0-1 - val_vep_cache_version // string: vep version ex: 107 + val_vep_cache_version // string: vep version ex: 107 main: ch_versions = channel.empty() From 80c45b42ae32c67e8cfab379840e3bb2ac623573 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 31 Jan 2026 15:10:12 +0100 Subject: [PATCH 284/872] update tabix modules --- modules.json | 8 +- .../ensemblvep/filtervep/environment.yml | 5 +- modules/nf-core/ensemblvep/filtervep/main.nf | 32 +-- modules/nf-core/ensemblvep/filtervep/meta.yml | 43 +++- .../ensemblvep/filtervep/tests/main.nf.test | 49 +---- .../filtervep/tests/main.nf.test.snap | 36 ++-- .../filtervep/tests/nextflow.config | 2 +- .../ensemblvep/filtervep/tests/tab.gz.config | 6 - .../ensemblvep/filtervep/tests/tags.yml | 2 - .../ensemblvep/filtervep/tests/vcf.config | 6 - modules/nf-core/tabix/bgzip/environment.yml | 5 +- modules/nf-core/tabix/bgzip/main.nf | 21 +- modules/nf-core/tabix/bgzip/meta.yml | 41 +++- .../nf-core/tabix/bgzip/tests/main.nf.test | 2 +- .../tabix/bgzip/tests/main.nf.test.snap | 80 ++++--- modules/nf-core/tabix/bgzip/tests/tags.yml | 2 - .../nf-core/tabix/bgziptabix/environment.yml | 5 +- modules/nf-core/tabix/bgziptabix/main.nf | 20 +- modules/nf-core/tabix/bgziptabix/meta.yml | 78 ++++--- .../tabix/bgziptabix/tests/main.nf.test | 48 ++--- .../tabix/bgziptabix/tests/main.nf.test.snap | 196 ++++++++++-------- .../{tabix_csi.config => nextflow.config} | 2 +- .../tabix/bgziptabix/tests/tabix_tbi.config | 5 - .../nf-core/tabix/bgziptabix/tests/tags.yml | 2 - subworkflows/local/annotate_genome_snvs.nf | 6 +- subworkflows/local/annotate_mt_snvs.nf | 8 +- .../local/call_snv_deepvariant/main.nf | 1 - subworkflows/local/call_sv_cnvnator/main.nf | 3 +- subworkflows/local/call_sv_tiddit/main.nf | 3 +- subworkflows/local/prepare_references/main.nf | 9 +- subworkflows/local/rank_variants.nf | 3 +- .../vcf_filter_bcftools_ensemblvep/main.nf | 2 - .../tests/main.nf.test.snap | 32 +-- 33 files changed, 396 insertions(+), 367 deletions(-) delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/tags.yml delete mode 100644 modules/nf-core/tabix/bgzip/tests/tags.yml rename modules/nf-core/tabix/bgziptabix/tests/{tabix_csi.config => nextflow.config} (56%) delete mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config delete mode 100644 modules/nf-core/tabix/bgziptabix/tests/tags.yml diff --git a/modules.json b/modules.json index 0eb97dec9..c33f16502 100644 --- a/modules.json +++ b/modules.json @@ -138,7 +138,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4", + "git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { @@ -500,12 +500,12 @@ }, "tabix/bgzip": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", + "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { @@ -574,7 +574,7 @@ }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 3d36eb17c..d9ed9b6bd 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::ensembl-vep=113.0 + # renovate: datasource=conda depName=bioconda/ensembl-vep + - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index 69245df0e..dcf0148ef 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -1,49 +1,39 @@ process ENSEMBLVEP_FILTERVEP { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' + : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" input: tuple val(meta), path(input) - path (feature_file) + path feature_file output: tuple val(meta), path("*.${extension}"), emit: output - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ filter_vep \\ - $args \\ - --input_file $input \\ + ${args} \\ + --input_file ${input} \\ --output_file ${prefix}.${extension} \\ --only_matched - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" + extension = task.ext.suffix ?: "vcf" """ touch ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index a73e3b7a7..68928cfc8 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -24,13 +24,16 @@ input: type: file description: VCF/TAB file annotated with vep pattern: "*.{vcf,tab,tsv,txt}" - - - feature_file: - type: file - description: File containing features on separate lines. To be used with --filter - option. + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - feature_file: + type: file + description: File containing features on separate lines. To be used with --filter + option. + ontologies: [] output: - - output: - - meta: + output: + - - meta: type: map description: | Groovy Map containing sample information @@ -39,11 +42,29 @@ output: type: file description: VCF/TAB file pattern: "*.{vcf,tab,txt,tsv}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_ensemblvep: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test index 7147792f7..044934579 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test @@ -10,32 +10,18 @@ nextflow_process { tag "ensemblvep" tag "ensemblvep/vep" tag "ensemblvep/filtervep" - tag "ensemblvep/download" - // Test for filtering VCF file test("test_ensemblvep_filtervep_vcf") { config "./vcf.config" setup { - run("ENSEMBLVEP_DOWNLOAD") { - script "../../download/main.nf" - - process { - """ - input[0] = Channel.of([ - [id:"113_WBcel235"], - params.vep_genome, - params.vep_species, - params.vep_cache_version - ]) - """ - } - } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -44,7 +30,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[4] = vep_cache input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -65,38 +51,25 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match() }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, { assert path(process.out.output.get(0).get(1)).readLines().first().contains("##fileformat=VCFv4.2") } ) } } - // Test for filtering TAB file test("test_ensemblvep_filtervep_tab_gz") { config "./tab.gz.config" setup { - run("ENSEMBLVEP_DOWNLOAD") { - script "../../download/main.nf" - - process { - """ - input[0] = Channel.of([ - [id:"113_WBcel235"], - params.vep_genome, - params.vep_species, - params.vep_cache_version - ]) - """ - } - } run("ENSEMBLVEP_VEP") { script "../../vep/main.nf" process { """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), @@ -105,7 +78,7 @@ nextflow_process { input[1] = params.vep_genome input[2] = params.vep_species input[3] = params.vep_cache_version - input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[4] = vep_cache input[5] = Channel.value([ [id:"fasta"], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) @@ -126,10 +99,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, + { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } ) } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 065d747ba..1559d7e79 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -1,26 +1,38 @@ { "test_ensemblvep_filtervep_vcf": { "content": [ - [ - "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" - ] + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_FILTERVEP", + "ensemblvep", + "115.2" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-21T09:10:47.874831491" + "timestamp": "2026-01-07T17:41:53.157363596" }, "test_ensemblvep_filtervep_tab_gz": { "content": [ - [ - "versions.yml:md5,1e8906572b04dd21d8c6973efac773c6" - ] + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_FILTERVEP", + "ensemblvep", + "115.2" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-21T09:11:18.765461163" + "timestamp": "2026-01-07T17:42:10.309756999" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config index 40b3a3bd6..32ff2cb6f 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params { - vep_cache_version = "113" + vep_cache_version = "115" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index cdad2d94d..f1eb11d65 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -6,12 +6,6 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ENSEMBLVEP_DOWNLOAD { - ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' - } - withName: ENSEMBLVEP_VEP { ext.args = '--tab' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml b/modules/nf-core/ensemblvep/filtervep/tests/tags.yml deleted file mode 100644 index b43bf40d6..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -ensemblvep/filtervep: - - "modules/nf-core/ensemblvep/filtervep/**" diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index ee2aef574..a737274ef 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -6,12 +6,6 @@ process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ENSEMBLVEP_DOWNLOAD { - ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' - } - withName: ENSEMBLVEP_VEP { ext.args = '--vcf' ext.prefix = { "${meta.id}_vep" } diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 017c259da..771b13870 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::tabix=1.11 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 67991c74b..e80919bfd 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -4,16 +4,16 @@ process TABIX_BGZIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : - 'biocontainers/htslib:1.20--h5efdd21_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' : + 'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }" input: tuple val(meta), path(input) output: - tuple val(meta), path("${output}") , emit: output - tuple val(meta), path("${output}.gzi"), emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${output}"), emit: output + tuple val(meta), path("*.gzi") , emit: gzi, optional: true + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix when: task.ext.when == null || task.ext.when @@ -26,16 +26,13 @@ process TABIX_BGZIP { output = in_bgzip ? "${prefix}.${extension}" : "${prefix}.${extension}.gz" command = in_bgzip ? '-d' : '' // Name the index according to $prefix, unless a name has been requested - if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) { + split_args = args.split(' +|=') + if ((split_args.contains('-i') || split_args.contains('--index')) && !split_args.contains('-I') && !split_args.contains('--index-name')) { args = args + " -I ${output}.gzi" } """ bgzip $command -c $args -@${task.cpus} $input > ${output} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -47,9 +44,5 @@ process TABIX_BGZIP { echo "" | gzip > ${output} touch ${output}.gzi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index 131e92cfd..7b56e897c 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -23,9 +23,10 @@ input: - input: type: file description: file to compress or to decompress + ontologies: [] output: - - output: - - meta: + output: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,21 +35,41 @@ output: type: file description: Output compressed/decompressed file pattern: "*." - - gzi: - - meta: + ontologies: [] + gzi: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - ${output}.gzi: + - "*.gzi": type: file description: Optional gzip index file for compressed inputs pattern: "*.gzi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_tabix: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test index d784aa070..00e7c0984 100644 --- a/modules/nf-core/tabix/bgzip/tests/main.nf.test +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test Process TABIX_BGZIP" - script "modules/nf-core/tabix/bgzip/main.nf" + script "../main.nf" process "TABIX_BGZIP" tag "modules" diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap index 0748143f0..28388109f 100644 --- a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -24,7 +24,11 @@ ], "2": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ], "gzi": [ @@ -37,16 +41,20 @@ "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "versions": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + "versions_tabix": [ + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-19T11:28:34.159992362" + "timestamp": "2026-01-27T15:05:31.678626" }, "test_stub": { "content": [ @@ -73,7 +81,11 @@ ], "2": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ], "gzi": [ @@ -86,16 +98,20 @@ "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + "versions_tabix": [ + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-19T11:28:22.087769106" + "timestamp": "2026-01-27T15:05:27.928712" }, "sarscov2_vcf_bgzip_compress_gzi": { "content": [ @@ -117,7 +133,11 @@ ] ], "2": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ], "gzi": [ [ @@ -135,16 +155,20 @@ "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], - "versions": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + "versions_tabix": [ + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-19T11:28:57.15091665" + "timestamp": "2026-01-27T15:05:39.49628" }, "bgzip_test": { "content": [ @@ -186,7 +210,11 @@ ] ], "2": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ], "gzi": [ [ @@ -204,15 +232,19 @@ "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + "versions_tabix": [ + [ + "TABIX_BGZIP", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-19T11:28:45.219404786" + "timestamp": "2026-01-27T15:05:35.726067" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml deleted file mode 100644 index de0eec86f..000000000 --- a/modules/nf-core/tabix/bgzip/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tabix/bgzip: - - "modules/nf-core/tabix/bgzip/**" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index 017c259da..771b13870 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::tabix=1.11 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 22f37a773..30eae745f 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,16 +4,16 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : - 'biocontainers/htslib:1.20--h5efdd21_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' : + 'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }" input: tuple val(meta), path(input) output: - tuple val(meta), path("*.gz"), path("*.tbi"), optional: true, emit: gz_tbi - tuple val(meta), path("*.gz"), path("*.csi"), optional: true, emit: gz_csi - path "versions.yml" , emit: versions + tuple val(meta), path("*.gz"), path("*.{tbi,csi}"), emit: gz_index + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -23,13 +23,9 @@ process TABIX_BGZIPTABIX { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz + bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -40,9 +36,5 @@ process TABIX_BGZIPTABIX { echo "" | gzip > ${prefix}.${input.getExtension()}.gz touch ${prefix}.${input.getExtension()}.gz.${index} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 806fbc121..2a3078c55 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -1,5 +1,6 @@ name: tabix_bgziptabix -description: bgzip a sorted tab-delimited genome file and then create tabix index +description: bgzip a sorted tab-delimited genome file and then create tabix + index keywords: - bgzip - compress @@ -23,9 +24,10 @@ input: - input: type: file description: Sorted tab-delimited genome file + ontologies: [] output: - - gz_tbi: - - meta: + gz_index: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,29 +36,55 @@ output: type: file description: bgzipped tab-delimited genome file pattern: "*.gz" - - "*.tbi": + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - "*.{tbi,csi}": type: file - description: tabix index file - pattern: "*.tbi" - - gz_csi: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.gz": - type: file - description: bgzipped tab-delimited genome file - pattern: "*.gz" - - "*.csi": - type: file - description: csi index file - pattern: "*.csi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: Tabix index file (either tbi or csi) + pattern: "*.{tbi,csi}" + ontologies: [] + versions_tabix: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bgzip: + type: string + description: The tool name + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - bgzip: + type: string + description: The tool name + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + authors: - "@maxulysse" - "@DLBPointon" diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 4d4130dc0..1955b143e 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -1,7 +1,7 @@ nextflow_process { name "Test Process TABIX_BGZIPTABIX" - script "modules/nf-core/tabix/bgziptabix/main.nf" + script "../main.nf" process "TABIX_BGZIPTABIX" tag "modules" @@ -9,10 +9,13 @@ nextflow_process { tag "tabix" tag "tabix/bgziptabix" - test("sarscov2_bed_tbi") { - config "./tabix_tbi.config" + config "./nextflow.config" + test("sarscov2_bed_tbi") { when { + params { + module_args = '-p vcf' + } process { """ input[0] = [ @@ -26,19 +29,16 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.gz_tbi[0][1]).name - ).match("tbi_test") - } + { assert snapshot(process.out).match() } ) } } test("sarscov2_bed_csi") { - config "./tabix_csi.config" - when { + params { + module_args = '-p vcf --csi' + } process { """ input[0] = [ @@ -52,22 +52,19 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.gz_csi[0][1]).name - ).match("csi_test") - } + { assert snapshot(process.out).match() } ) } } test("sarscov2_bed_csi_stub") { - config "./tabix_csi.config" - options "-stub" when { + params { + module_args = '-p vcf --csi' + } process { """ input[0] = [ @@ -81,22 +78,19 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.gz_csi[0][1]).name - ).match("csi_stub") - } + { assert snapshot(process.out).match() } ) } } test("sarscov2_bed_tbi_stub") { - config "./tabix_tbi.config" - options "-stub" when { + params { + module_args = '-p vcf' + } process { """ input[0] = [ @@ -110,11 +104,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, - { assert snapshot( - file(process.out.gz_tbi[0][1]).name - ).match("tbi_stub") - } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap index fb87799b2..cf3ce8aa8 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -12,15 +12,20 @@ ] ], "1": [ - + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ], "2": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" - ], - "gz_csi": [ - + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "gz_tbi": [ + "gz_index": [ [ { "id": "tbi_test" @@ -29,24 +34,32 @@ "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" ] ], - "versions": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + "versions_bgzip": [ + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] + ], + "versions_tabix": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-19T11:29:16.053817543" + "timestamp": "2026-01-29T23:36:32.823417" }, "sarscov2_bed_csi": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "csi_test" @@ -55,10 +68,21 @@ "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], + "1": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] + ], "2": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "gz_csi": [ + "gz_index": [ [ { "id": "csi_test" @@ -67,29 +91,27 @@ "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], - "gz_tbi": [ - + "versions_bgzip": [ + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "versions": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + "versions_tabix": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-19T11:29:27.667745444" - }, - "csi_test": { - "content": [ - "csi_test.bed.gz" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-02-19T14:51:00.548801" + "timestamp": "2026-01-29T23:36:36.715208" }, "sarscov2_bed_tbi_stub": { "content": [ @@ -104,15 +126,20 @@ ] ], "1": [ - + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ], "2": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" - ], - "gz_csi": [ - + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "gz_tbi": [ + "gz_index": [ [ { "id": "test" @@ -121,54 +148,32 @@ "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + "versions_bgzip": [ + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] + ], + "versions_tabix": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-25T14:45:18.533169949" - }, - "csi_stub": { - "content": [ - "test.bed.gz" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-02-19T14:51:09.218454" - }, - "tbi_stub": { - "content": [ - "test.bed.gz" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-25T14:45:18.550930179" - }, - "tbi_test": { - "content": [ - "tbi_test.bed.gz" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-02-19T14:50:51.579654" + "timestamp": "2026-01-29T23:36:45.016007" }, "sarscov2_bed_csi_stub": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "test" @@ -177,10 +182,21 @@ "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "1": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] + ], "2": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "gz_csi": [ + "gz_index": [ [ { "id": "test" @@ -189,18 +205,26 @@ "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "gz_tbi": [ - + "versions_bgzip": [ + [ + "TABIX_BGZIPTABIX", + "bgzip", + "1.21" + ] ], - "versions": [ - "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + "versions_tabix": [ + [ + "TABIX_BGZIPTABIX", + "tabix", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-09-25T14:44:19.786135972" + "timestamp": "2026-01-29T23:36:40.5401" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/nextflow.config similarity index 56% rename from modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config rename to modules/nf-core/tabix/bgziptabix/tests/nextflow.config index fb41a3142..5b2316c88 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config +++ b/modules/nf-core/tabix/bgziptabix/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: TABIX_BGZIPTABIX { - ext.args2 = '-p vcf --csi' + ext.args2 = params.module_args } } diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config deleted file mode 100644 index c1915dc4b..000000000 --- a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: TABIX_BGZIPTABIX { - ext.args2 = '-p vcf' - } -} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml deleted file mode 100644 index 5052b4d70..000000000 --- a/modules/nf-core/tabix/bgziptabix/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tabix/bgziptabix: - - "modules/nf-core/tabix/bgziptabix/**" diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 0ae402e15..8a1f7b486 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -62,7 +62,7 @@ workflow ANNOTATE_GENOME_SNVS { ZIP_TABIX_ROHCALL (RHOCALL_ANNOTATE.out.vcf) ch_vcf - .join(ZIP_TABIX_ROHCALL.out.gz_tbi, remainder: true) + .join(ZIP_TABIX_ROHCALL.out.gz_index, remainder: true) .combine(ch_split_intervals) .map { it -> def meta = it[0] @@ -104,7 +104,7 @@ workflow ANNOTATE_GENOME_SNVS { ZIP_TABIX_VCFANNO (VCFANNO.out.vcf) - BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_tbi, [], [], []) // filter on frequencies + BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_index, [], [], []) // filter on frequencies // Annotating with CADD if (!val_cadd_resources.equals(null)) { @@ -195,13 +195,11 @@ workflow ANNOTATE_GENOME_SNVS { ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(ZIP_TABIX_ROHCALL.out.versions) ch_versions = ch_versions.mix(VCFANNO.out.versions) ch_versions = ch_versions.mix(UPD_SITES.out.versions) ch_versions = ch_versions.mix(UPD_REGIONS.out.versions) ch_versions = ch_versions.mix(CHROMOGRAPH_SITES.out.versions) ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) - ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO.out.versions) ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 38a877913..08c7e5002 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -47,7 +47,7 @@ workflow ANNOTATE_MT_SNVS { ZIP_TABIX_HMTNOTE_MT(REPLACE_SPACES_IN_VCFINFO.out.vcf) // Vcfanno - ZIP_TABIX_HMTNOTE_MT.out.gz_tbi + ZIP_TABIX_HMTNOTE_MT.out.gz_index .combine(ch_vcfanno_extra) .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } @@ -55,7 +55,7 @@ workflow ANNOTATE_MT_SNVS { VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) ZIP_TABIX_VCFANNO_MT(VCFANNO_MT.out.vcf) - ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_tbi.map{meta, vcf, _tbi -> return [meta, vcf]} + ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_index.map{meta, vcf, _tbi -> return [meta, vcf]} // Annotating with CADD if (!val_cadd_resources.equals(null)) { @@ -63,7 +63,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_resources, ch_fai, ch_cadd_header, - ZIP_TABIX_VCFANNO_MT.out.gz_tbi, + ZIP_TABIX_VCFANNO_MT.out.gz_index, val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf @@ -108,8 +108,6 @@ workflow ANNOTATE_MT_SNVS { ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(ZIP_TABIX_VCFANNO_MT.out.versions) - ch_versions = ch_versions.mix(ZIP_TABIX_HMTNOTE_MT.out.versions) ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) emit: diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 935b0206d..b4cb395ee 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -32,7 +32,6 @@ workflow CALL_SNV_DEEPVARIANT { ch_bam_bai .combine (TABIX_BGZIP.out.output.map {_meta, bed -> return bed}) .set { ch_deepvar_in } - ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions) } else if (val_analysis_type.equals("wgs")) { ch_bam_bai .map { meta, bam, bai -> diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 153928c94..13e656bb4 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -29,7 +29,7 @@ workflow CALL_SV_CNVNATOR { CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]], "call" ) CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab) INDEX_CNVNATOR (CNVNATOR_CONVERT2VCF.out.vcf) - BCFTOOLS_VIEW_CNVNATOR (INDEX_CNVNATOR.out.gz_tbi, [], [], []).vcf + BCFTOOLS_VIEW_CNVNATOR (INDEX_CNVNATOR.out.gz_index, [], [], []).vcf .collect{_meta, vcf -> vcf} .toList() .set { vcf_file_list } @@ -47,7 +47,6 @@ workflow CALL_SV_CNVNATOR { ch_versions = ch_versions.mix(CNVNATOR_CALL.out.versions) ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions) ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions) - ch_versions = ch_versions.mix(INDEX_CNVNATOR.out.versions) emit: vcf = SVDB_MERGE_CNVNATOR.out.vcf // channel: [ val(meta), path(*.tar.gz) ] diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index d368a8049..eb83777e8 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -18,7 +18,7 @@ workflow CALL_SV_TIDDIT { TIDDIT_SV ( ch_bam_bai, ch_genome_fasta, ch_bwa_index ) INDEX_TIDDIT (TIDDIT_SV.out.vcf) - BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_tbi, [], [], []).vcf + BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_index, [], [], []).vcf .collect{ _meta, vcf -> vcf} .toList() .set { vcf_file_list } @@ -31,7 +31,6 @@ workflow CALL_SV_TIDDIT { ch_versions = TIDDIT_SV.out.versions ch_versions = ch_versions.mix(SVDB_MERGE_TIDDIT.out.versions) - ch_versions = ch_versions.mix(INDEX_TIDDIT.out.versions) emit: vcf = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index e205e18ce..65eec3db6 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -211,7 +211,7 @@ workflow PREPARE_REFERENCES { ch_target_bed, ch_genome_fai.map { _meta, fai -> return fai } ) - ch_target_bed_gz_tbi = TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_tbi + ch_target_bed_gz_tbi = TABIX_BGZIPINDEX_PADDED_BED(BEDTOOLS_PAD_TARGET_BED.out.bed).gz_index ch_target_intervals = GATK_BILT(ch_target_bed, ch_genome_dict).interval_list.map{ _meta, inter -> inter}.collect() @@ -227,9 +227,7 @@ workflow PREPARE_REFERENCES { ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) - ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_PADDED_BED.out.versions, - GATK_BILT.out.versions, - GATK_ILT.out.versions) + ch_versions = ch_versions.mix(GATK_BILT.out.versions, GATK_ILT.out.versions) } // // Prepare vcfanno extra files @@ -245,10 +243,9 @@ workflow PREPARE_REFERENCES { } else { TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in) channel.empty() - .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_tbi, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) + .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_index, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) .map { _meta, vcf, index -> return [[vcf,index]] } .set {ch_vcfanno_extra} - ch_versions = ch_versions.mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.versions) } } // diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 2d297a1b7..7dc4589b7 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -36,8 +36,7 @@ workflow RANK_VARIANTS { if (process_with_sort) { ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf).vcf // SV file needs to be sorted before indexing } else { - ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_tbi.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs - ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) + ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_index.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs } emit: diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index e98e54d40..33b4d9a8d 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -39,7 +39,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { TABIX_BGZIPTABIX( ENSEMBLVEP_FILTERVEP.out.output ) - ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions) ch_vcf = TABIX_BGZIPTABIX.out.gz_index.map { meta, vcf, _tbi -> [meta, vcf] } ch_tbi = TABIX_BGZIPTABIX.out.gz_index.map { meta, _vcf, tbi -> [meta, tbi] } @@ -48,5 +47,4 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { emit: vcf = ch_vcf // channel: [ val(meta), path(vcf) ] tbi = ch_tbi // channel: [ val(meta), path(tbi) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap index 19d0c6f18..03ac1e7b0 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap @@ -2,12 +2,7 @@ "vcf, hgnc_ids - filter on hgnc ids": { "content": [ [ - { - "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": { - "bgzip": 1.21, - "tabix": 1.21 - } - } + ], "test.vcf.gz.tbi", "18e010447bd23a05a202d44daf66bcd2", @@ -15,19 +10,14 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-07T17:55:42.872290536" + "timestamp": "2026-01-27T19:43:16.754963" }, "vcf, hgnc_ids - filter on hgnc ids and expression": { "content": [ [ - { - "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": { - "bgzip": 1.21, - "tabix": 1.21 - } - } + ], "test.vcf.gz.tbi", "18e010447bd23a05a202d44daf66bcd2", @@ -35,9 +25,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-20T12:45:00.851156984" + "timestamp": "2026-01-27T19:43:25.968654" }, "vcf, hgnc_ids - filter on expression": { "content": [ @@ -73,9 +63,6 @@ "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ - "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f" - ], "tbi": [ [ { @@ -91,16 +78,13 @@ }, "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "versions": [ - "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-20T12:45:09.964268419" + "timestamp": "2026-01-27T19:43:35.16804" } } \ No newline at end of file From 821184682510d034d003969fdbb37ec980050784 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 2 Feb 2026 08:55:43 +0100 Subject: [PATCH 285/872] nf-tests completed --- conf/modules/call_sv_MT.config | 1 + modules/local/mitosalt/main.nf | 5 +- nextflow.config | 22 +-- tests/default.nf.test.snap | 32 ++-- tests/test_bam.nf.test.snap | 94 ++++++++-- tests/test_singleton.nf.test.snap | 282 ++++++++++++++++++++++++++++-- 6 files changed, 377 insertions(+), 59 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 4fa1a01e5..deedd506d 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -34,4 +34,5 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + } diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index fbbd7cd1b..81cf574b2 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -3,10 +3,6 @@ process MITOSALT { label "process_low" conda "${moduleDir}/environment.yml" -// container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -// 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': -// 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? '/home/proj/production/dropbox/RN/mitosalt.sif': 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" @@ -49,6 +45,7 @@ process MITOSALT { """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} touch ${prefix}.breakpoint + touch ${prefix}.cluster cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/nextflow.config b/nextflow.config index 04a8aa046..56a42e479 100644 --- a/nextflow.config +++ b/nextflow.config @@ -121,21 +121,21 @@ params { sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE' variant_type = 'snp,indel' - // Mitosalt options - score_threshold = 80 - evalue_threshold = 0.00001 - split_length = 15 - paired_distance = 1000 - deletion_threshold_min = 30 - deletion_threshold_max = 30000 + // Mitosalt/saltshaker options + breakspan = 15 breakthreshold = 2 cluster_threshold = 2 - breakspan = 15 - sizelimit = 10000 - hplimit = 0.01 + deletion_threshold_max = 30000 + deletion_threshold_min = 30 + evalue_threshold = 0.00001 + exclude = 5 flank = 15 + hplimit = 0.01 + paired_distance = 1000 + score_threshold = 80 + sizelimit = 10000 split_distance_threshold = 5 - exclude = 5 + split_length = 15 // MultiQC options multiqc_config = null diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bebce756d..dd9d09f3b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -124,9 +124,6 @@ "DEEPVARIANT": { "deepvariant": "1.8.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -221,6 +218,9 @@ "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, + "HISAT2_INDEX_GENOME": { + "hisat2": "2.2.1" + }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" }, @@ -230,6 +230,9 @@ "INDEX_TIDDIT": { "tabix": 1.2 }, + "LAST_INDEX_MT": { + "last": 1611 + }, "MANTA": { "manta": "1.6.0" }, @@ -239,6 +242,9 @@ "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, "MOSDEPTH": { "mosdepth": "0.3.10" }, @@ -339,6 +345,9 @@ "SAM_TO_BAM": { "samtools": "1.22.1" }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -553,17 +562,14 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman.png", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_deletions.csv", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_genes.csv", - "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck.png", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_deletions.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_genes.csv", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -903,6 +909,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-18T17:13:55.314547424" + "timestamp": "2026-02-02T07:56:08.820059386" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 7ce7c0353..7543a67ca 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 795, + 823, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -66,6 +66,10 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -121,9 +125,6 @@ "DEEPVARIANT": { "deepvariant": "1.8.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -143,6 +144,12 @@ "expansionhunter": "5.0.0", "bgzip": 1.18 }, + "FASTP": { + "fastp": "0.23.4" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.5.0.0" }, @@ -212,6 +219,9 @@ "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, + "HISAT2_INDEX_GENOME": { + "hisat2": "2.2.1" + }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" }, @@ -221,12 +231,21 @@ "INDEX_TIDDIT": { "tabix": 1.2 }, + "LAST_INDEX_MT": { + "last": 1611 + }, "MANTA": { "manta": "1.6.0" }, + "MARKDUPLICATES": { + "picard": "3.3.0" + }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, "MOSDEPTH": { "mosdepth": "0.3.10" }, @@ -306,18 +325,30 @@ "SAMTOOLS_FAIDX_MT": { "samtools": 1.21 }, + "SAMTOOLS_INDEX_ALIGN": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX_MARKDUP": { + "samtools": 1.21 + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -333,6 +364,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -458,10 +492,19 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -520,18 +563,25 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman.png", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_deletions.csv", - "call_sv/mitochondria/eKLIPse_earlycasualcaiman_genes.csv", - "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck.png", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_deletions.csv", - "call_sv/mitochondria/eKLIPse_slowlycivilbuck_genes.csv", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "fastqc", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -834,6 +884,22 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -844,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-18T17:30:21.579519047" + "timestamp": "2026-02-02T07:58:42.049734691" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a537d5f6c..a186d27e7 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 361, + 823, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -15,6 +15,9 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.2 }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.2 + }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.21 }, @@ -83,6 +86,12 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, "CNVNATOR_CALL": { "CNVnator": "0.4.1" }, @@ -116,9 +125,6 @@ "DEEPVARIANT": { "deepvariant": "1.8.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -213,6 +219,9 @@ "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, + "HISAT2_INDEX_GENOME": { + "hisat2": "2.2.1" + }, "HMTNOTE_ANNOTATE": { "hmtnote": "0.7.2" }, @@ -222,6 +231,9 @@ "INDEX_TIDDIT": { "tabix": 1.2 }, + "LAST_INDEX_MT": { + "last": 1611 + }, "MANTA": { "manta": "1.6.0" }, @@ -231,6 +243,9 @@ "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, "MOSDEPTH": { "mosdepth": "0.3.10" }, @@ -331,6 +346,9 @@ "SAM_TO_BAM": { "samtools": "1.22.1" }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -346,6 +364,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.21 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.9.4", "tabix": 1.21 @@ -436,6 +457,12 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, + "UPD_REGIONS": { + "upd": 0.1 + }, + "UPD_SITES": { + "upd": 0.1 + }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -463,11 +490,21 @@ }, [ "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.csi", @@ -477,6 +514,13 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", + "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", + "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", + "annotate_snv/genome/hugelymodelbat_chromograph_regions", + "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", @@ -485,6 +529,11 @@ "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.csi", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", + "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -514,22 +563,37 @@ "call_sv/genome/justhusky_sv.vcf.gz.csi", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/eKLIPse_hugelymodelbat.png", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_deletions.csv", - "call_sv/mitochondria/eKLIPse_hugelymodelbat_genes.csv", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", + "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/hugelymodelbat_LNUMBER1", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -542,6 +606,89 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman", + "qc_bam/earlycasualcaiman/css", + "qc_bam/earlycasualcaiman/css/agogo.css", + "qc_bam/earlycasualcaiman/css/ajax-loader.gif", + "qc_bam/earlycasualcaiman/css/basic.css", + "qc_bam/earlycasualcaiman/css/bgfooter.png", + "qc_bam/earlycasualcaiman/css/bgtop.png", + "qc_bam/earlycasualcaiman/css/comment-bright.png", + "qc_bam/earlycasualcaiman/css/comment-close.png", + "qc_bam/earlycasualcaiman/css/comment.png", + "qc_bam/earlycasualcaiman/css/doctools.js", + "qc_bam/earlycasualcaiman/css/down-pressed.png", + "qc_bam/earlycasualcaiman/css/down.png", + "qc_bam/earlycasualcaiman/css/file.png", + "qc_bam/earlycasualcaiman/css/jquery.js", + "qc_bam/earlycasualcaiman/css/minus.png", + "qc_bam/earlycasualcaiman/css/plus.png", + "qc_bam/earlycasualcaiman/css/pygments.css", + "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", + "qc_bam/earlycasualcaiman/css/report.css", + "qc_bam/earlycasualcaiman/css/searchtools.js", + "qc_bam/earlycasualcaiman/css/underscore.js", + "qc_bam/earlycasualcaiman/css/up-pressed.png", + "qc_bam/earlycasualcaiman/css/up.png", + "qc_bam/earlycasualcaiman/css/websupport.js", + "qc_bam/earlycasualcaiman/genome_results.txt", + "qc_bam/earlycasualcaiman/images_qualimapReport", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/earlycasualcaiman/qualimapReport.html", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/earlycasualcaiman_chromographcov", + "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.summary.txt", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/earlycasualcaiman_tidditcov.bed", + "qc_bam/earlycasualcaiman_tidditcov.bw", + "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", "qc_bam/hugelymodelbat/css", "qc_bam/hugelymodelbat/css/agogo.css", @@ -625,6 +772,89 @@ "qc_bam/hugelymodelbat_tidditcov.wig", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck", + "qc_bam/slowlycivilbuck/css", + "qc_bam/slowlycivilbuck/css/agogo.css", + "qc_bam/slowlycivilbuck/css/ajax-loader.gif", + "qc_bam/slowlycivilbuck/css/basic.css", + "qc_bam/slowlycivilbuck/css/bgfooter.png", + "qc_bam/slowlycivilbuck/css/bgtop.png", + "qc_bam/slowlycivilbuck/css/comment-bright.png", + "qc_bam/slowlycivilbuck/css/comment-close.png", + "qc_bam/slowlycivilbuck/css/comment.png", + "qc_bam/slowlycivilbuck/css/doctools.js", + "qc_bam/slowlycivilbuck/css/down-pressed.png", + "qc_bam/slowlycivilbuck/css/down.png", + "qc_bam/slowlycivilbuck/css/file.png", + "qc_bam/slowlycivilbuck/css/jquery.js", + "qc_bam/slowlycivilbuck/css/minus.png", + "qc_bam/slowlycivilbuck/css/plus.png", + "qc_bam/slowlycivilbuck/css/pygments.css", + "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", + "qc_bam/slowlycivilbuck/css/report.css", + "qc_bam/slowlycivilbuck/css/searchtools.js", + "qc_bam/slowlycivilbuck/css/underscore.js", + "qc_bam/slowlycivilbuck/css/up-pressed.png", + "qc_bam/slowlycivilbuck/css/up.png", + "qc_bam/slowlycivilbuck/css/websupport.js", + "qc_bam/slowlycivilbuck/genome_results.txt", + "qc_bam/slowlycivilbuck/images_qualimapReport", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/slowlycivilbuck/qualimapReport.html", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/slowlycivilbuck_chromographcov", + "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.summary.txt", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/slowlycivilbuck_tidditcov.bed", + "qc_bam/slowlycivilbuck_tidditcov.bw", + "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -639,29 +869,47 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "vcf2cytosure/earlycasualcaiman.cgh", + "vcf2cytosure/hugelymodelbat.cgh", + "vcf2cytosure/slowlycivilbuck.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2025-12-18T17:37:33.421833397" + "timestamp": "2026-02-02T08:01:16.155264316" } } \ No newline at end of file From 5868857f2101982f0433ceb0d00401e9ff0828f8 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 2 Feb 2026 11:31:50 +0100 Subject: [PATCH 286/872] fix subdepth channel --- main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/main.nf b/main.nf index 347d84487..a5507c1a4 100644 --- a/main.nf +++ b/main.nf @@ -97,6 +97,7 @@ workflow NFCORE_RAREDISEASE { val_sequence_dictionary val_skip_tools val_skip_subworkflows + val_subdepth val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed @@ -191,6 +192,7 @@ workflow NFCORE_RAREDISEASE { ch_score_config_mt = channelFromPath(val_score_config_mt, true) ch_score_config_snv = channelFromPath(val_score_config_snv, true) ch_score_config_sv = channelFromPath(val_score_config_sv, true) + ch_subdepth = channelFromPath(val_subdepth, true) ch_vcf2cytosure_blacklist = channelFromPath(val_vcf2cytosure_blacklist, true) ch_vcfanno_lua = channelFromPath(val_vcfanno_lua, true) ch_vcfanno_toml = channelFromPath(val_vcfanno_toml, true) @@ -551,6 +553,7 @@ workflow { params.skip_subworkflows, params.svdb_query_bedpedbs, params.svdb_query_dbs, + params.mitosalt_depth, params.target_bed, params.variant_caller, params.variant_catalog, From 451517fa60f02b4d3135fa9e1bad06b8a03dc151 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Feb 2026 08:55:16 +0100 Subject: [PATCH 287/872] fixed subdepth channel and updated snapshots --- main.nf | 2 +- tests/default.nf.test.snap | 2 +- tests/test_bam.nf.test.snap | 2 +- tests/test_singleton.nf.test.snap | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index a5507c1a4..1a41e100b 100644 --- a/main.nf +++ b/main.nf @@ -551,9 +551,9 @@ workflow { params.sequence_dictionary, params.skip_tools, params.skip_subworkflows, + params.mitosalt_depth, params.svdb_query_bedpedbs, params.svdb_query_dbs, - params.mitosalt_depth, params.target_bed, params.variant_caller, params.variant_catalog, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dd9d09f3b..4089d31cc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -909,6 +909,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-02T07:56:08.820059386" + "timestamp": "2026-02-04T08:48:40.592550098" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 7543a67ca..ff0377ced 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -910,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-02T07:58:42.049734691" + "timestamp": "2026-02-04T08:51:39.820380268" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a186d27e7..1a099f754 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -910,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-02T08:01:16.155264316" + "timestamp": "2026-02-04T08:54:08.345773451" } } \ No newline at end of file From d28ed0df0f8f4a1c7589a75bfeffdcbf775f9baf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 4 Feb 2026 08:18:07 +0000 Subject: [PATCH 288/872] [automated] Fix code linting --- modules/local/mitosalt/environment.yml | 28 ++--- modules/local/mitosalt/main.nf | 2 +- .../resources/usr/bin/MitoSAlt1.1.1.pl | 110 +++++++++--------- modules/local/prep_mitosalt/main.nf | 2 +- nextflow.config | 1 - subworkflows/local/call_sv_MT/main.nf | 40 +++---- subworkflows/local/prepare_references/main.nf | 2 +- 7 files changed, 91 insertions(+), 94 deletions(-) diff --git a/modules/local/mitosalt/environment.yml b/modules/local/mitosalt/environment.yml index fb034f855..3bb5bb046 100644 --- a/modules/local/mitosalt/environment.yml +++ b/modules/local/mitosalt/environment.yml @@ -1,16 +1,16 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bioconda::bbmap=39.37 -- bioconda::bedtools=2.31.1 -- bioconda::bioconductor-biostrings=2.74.0 -- bioconda::bioconductor-pwalign=1.2.0 -- bioconda::hisat2=2.2.1 -- bioconda::last=1648 -- bioconda::sambamba=1.0.1 -- bioconda::samtools=1.22.1 -- bioconda::ucsc-bedgraphtobigwig=482 -- bioconda::ucsc-fasize=482 -- bioconda::ucsc-fasomerecords=482 -- conda-forge::r-rcolorbrewer=1.1_3 + - bioconda::bbmap=39.37 + - bioconda::bedtools=2.31.1 + - bioconda::bioconductor-biostrings=2.74.0 + - bioconda::bioconductor-pwalign=1.2.0 + - bioconda::hisat2=2.2.1 + - bioconda::last=1648 + - bioconda::sambamba=1.0.1 + - bioconda::samtools=1.22.1 + - bioconda::ucsc-bedgraphtobigwig=482 + - bioconda::ucsc-fasize=482 + - bioconda::ucsc-fasomerecords=482 + - conda-forge::r-rcolorbrewer=1.1_3 diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 81cf574b2..546da48af 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -38,7 +38,7 @@ process MITOSALT { mitosalt: $VERSION END_VERSIONS """ - + stub: def VERSION = "1.1.1" def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl index e8300bf78..5c6739daf 100755 --- a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl +++ b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl @@ -4,7 +4,7 @@ use List::Util qw(first min max sum); use Data::Dumper; -#INPUT +#INPUT my $config_file = $ARGV[0]; my $p1 = $ARGV[1]; my $p2 = $ARGV[2]; @@ -44,7 +44,7 @@ $User_Preferences->{$var} = $value; my $line = $_; print $line."\n"; -} +} #PROGRAMS my $hisat2 = $User_Preferences->{hisat2}; @@ -124,7 +124,7 @@ #EXTRACT READS print scalar(localtime).": Extract reads\n"; - system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); + system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); system("$samtools index tmp_$tag.bam"); system("$samtools idxstats tmp_$tag.bam > indel/$tag.count.txt"); system("$samtools view -u -@ $threads -f 12 tmp_$tag.bam > tmp1_$tag.bam"); #flag to extract unmapped reads with mate also unmapped @@ -187,7 +187,7 @@ my $bedfile = "indel/$tag.bed"; my $breakpointfile = "indel/$tag.breakpoint"; my $clusterfile = "indel/$tag.cluster"; - + my $check_paired = &check_paired($infile); print scalar(localtime).": Build split read hash\n"; $hash = &build_hash($infile,$check_paired); @@ -264,7 +264,7 @@ sub build_hash{ } elsif($check_paired == 1){ my @name = split(/\//,$elements[6]); $id = $name[0]; - $mate = $name[1]; + $mate = $name[1]; } my $strand = $elements[9]; @@ -273,12 +273,12 @@ sub build_hash{ next if exists $check_hash->{$id}->{$start.$length}; $check_hash->{$id}->{$start.$length}++; $mate = 2 if $mate > 1; - #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; + #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; #FILTER BY SCORE AND MAP EVALUE next if $score < $score_threshold; next if $evalue > $evalue_threshold; - + push(@{$hash->{$id}->{$mate}->{starts}},$start); push(@{$hash->{$id}->{$mate}->{ends}},$end); push(@{$hash->{$id}->{$mate}->{rstarts}},$read_start); @@ -324,7 +324,7 @@ sub remove_duplicates{ my @signatures = ($signature1,$signature2); @signatures = sort @signatures; - my $signature = join("",@signatures); + my $signature = join("",@signatures); if(exists $check_duplicates->{$signature} && $count1>0 && $count2>0){ @@ -345,17 +345,17 @@ sub print_bed{ open(ABED,">$filename"); for my $id (keys %{$hash}){ #print $id."\n"; - + for my $read(keys %{$hash->{$id}}){ my $name = $id."_".$read; #CHECK IF READ IS SPLIT ALIGNED my $count = @{$hash->{$id}->{$read}->{starts}}; next if $count > 1; - my $start = @{$hash->{$id}->{$read}->{starts}}[0]; + my $start = @{$hash->{$id}->{$read}->{starts}}[0]; my $end = @{$hash->{$id}->{$read}->{ends}}[0]; - print ABED "$refchr\t$start\t$end\t$name\n"; - } + print ABED "$refchr\t$start\t$end\t$name\n"; + } } system("sort -k2,2n $filename -o $filename"); close(ABED); @@ -385,7 +385,7 @@ sub process_hash{ next unless $min_len >= $split_length; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -397,11 +397,11 @@ sub process_hash{ elsif($read_starts[0]>$read_starts[1] && $read_local_starts[0]<$read_local_starts[1]){$read_check = 'yes';} elsif($read_starts[0]<=$read_starts[1] && $read_local_starts[0]<$read_local_starts[1] && $read_starts[1]<$read_ends[0] ){$read_check = 'yes';} elsif($read_starts[0]>=$read_starts[1] && $read_local_starts[0]>$read_local_starts[1] && $read_ends[1]>$read_starts[0] ){$read_check = 'yes';} - + #CHECK IF THE SPLIT READ FRAGMENTS SPAN THE DLOOP - my $min_start = min @{$hash->{$id}->{$read}->{starts}}; + my $min_start = min @{$hash->{$id}->{$read}->{starts}}; my $max_end = max @{$hash->{$id}->{$read}->{ends}}; - next if $min_start <= $dloop1 && $max_end >= $dloop2; + next if $min_start <= $dloop1 && $max_end >= $dloop2; my ($size,$start,$end) = &get_frag_distance(\@read_starts,\@read_ends,$read_check,$msize); next if $size < $deletion_threshold_min; @@ -410,7 +410,7 @@ sub process_hash{ #print "$name\t$start\t$end\t$size\n"; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #CHECK IF PAIRED READ EXISTS AND ITS ALIGNMENT POSITION SUPPORTS THE SPLIT READ my $pair = 1 if $read == 2; @@ -435,7 +435,7 @@ sub process_hash{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + $start = $len[2]; $end = $len[3]; $size = $len[4]; @@ -463,7 +463,7 @@ sub process_hash1{ my $bpe = shift; my $delhash; - + open(BP,">$breakpointfile"); open(BED,">$bedfile"); open(BPS,">$bps"); @@ -478,7 +478,7 @@ sub process_hash1{ next unless $count == 3; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -548,7 +548,7 @@ sub process_hash1{ #CHECK IF THE SPLIT READ FRAGMENTS ARE ABOVE LENGTH THRESHOLD my $min_len = min @read_lengthsN; next unless $min_len >= $split_length; - + #LOOK FOR SPLIT READS WHICH MAP INVERSELY SPANNING THE D'LOOP my $read_check = 'no'; @@ -566,7 +566,7 @@ sub process_hash1{ $paired_support = 'yes' if $distance_paired_support <= $paired_distance; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #LOOK FOR SPLIT READS WITH LARGE UNMAPPED AREA my ($split_distance) = &get_split_distance(\@read_local_startsN,\@read_lengthsN); @@ -582,7 +582,7 @@ sub process_hash1{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + #$start = $len[2]; #$end = $len[3]; #$size = $len[4]; @@ -611,10 +611,10 @@ sub paired_support{ my $distance1 = 0; my $distance2=0; - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; - - my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; + + my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; my $pair_end = @{$hash->{$id}->{$pair}->{ends}}[0]; $distance1 = $read_starts[0] - $pair_end if $read_starts[0] > $pair_end; @@ -640,10 +640,10 @@ sub get_frag_distance{ my $frag1_end = @{$ends}[0]; my $frag2_end = @{$ends}[1]; - + if($read_check eq 'no'){ if($frag1_start > $frag2_end){ - my $size = $frag1_start - $frag2_end; + my $size = $frag1_start - $frag2_end; @res = ($size,$frag2_end,$frag1_start); } elsif($frag2_start > $frag1_end){ @@ -670,7 +670,7 @@ sub get_frag_distance{ if($read_check eq 'yes'){ if($frag1_start > $frag2_end){ - my $size = ($msize -$frag1_end) + $frag2_start; + my $size = ($msize -$frag1_end) + $frag2_start; @res = ($size,$frag2_start,$frag1_end); } elsif($frag2_start > $frag1_end){ @@ -708,7 +708,7 @@ sub get_split_distance{ my $local1_length = @{$lengths}[0]; my $local2_length = @{$lengths}[1]; - + if($local1_start>$local2_start){ my $distance = $local1_start - $local2_start - $local2_length; @res = ($distance); @@ -716,7 +716,7 @@ sub get_split_distance{ if($local2_start>$local1_start){ my $distance = $local2_start - $local1_start - $local1_length; @res = ($distance); - } + } return @res; } @@ -729,7 +729,7 @@ sub generate_bed{ my $lengths = shift; my $scores = shift; my $strand = shift; - + my $size = shift; my $bstart = shift; my $bend = shift; @@ -759,7 +759,7 @@ sub generate_bed{ $size = $frag1_start - $frag2_end; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag1_start > $frag2_end && $strand eq '+'){ @@ -770,53 +770,53 @@ sub generate_bed{ $size = 1 + $msize- $frag1_end + $frag2_start; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_end; $bend = $frag2_start; $size = $frag2_start - $frag1_end; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '-'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_start; $bend = $frag2_end; $size = 1 + $msize - $frag2_end + $frag1_start; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag2_start < $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag2_start; - $bend = $frag1_end; + $bend = $frag1_end; $size = $msize - $frag1_end + $frag2_start; my $block_start=$frag1_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } elsif($frag1_start < $frag2_end && $strand eq '-'){ $start = $frag2_start; - $end = $frag1_end; + $end = $frag1_end; $bstart = $frag1_start; - $bend = $frag2_end; + $bend = $frag2_end; $size = $msize - $frag2_end + $frag1_start; my $block_start=$frag2_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } return @len; } @@ -852,14 +852,14 @@ sub generate_bed1{ $start = $frag2_start; $end = $frag1_end; my $block_start=$frag1_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length); } elsif($frag2_start > $frag1_end){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; my $block_start=$frag2_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length); } return @len; @@ -901,7 +901,7 @@ sub get_cluster{ $bpe_hash->{$readid} = $clusterid; } close(BPE); - + for my $readid(keys %{$delhash}){ next unless exists $bps_hash->{$readid}; next unless exists $bpe_hash->{$readid}; @@ -920,17 +920,17 @@ sub build_results{ my $refchr = shift; my $cluster_read_count_threshold = shift; my $tag = shift; - my $clustercount; + my $clustercount; my $nosplitbed_file = "tmp_".$tag."_nosplit.bed";; for my $clusterid (keys %{$clusterhash}){ - my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; - next if $cluster_read_count < $cluster_read_count_threshold; + my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; + next if $cluster_read_count < $cluster_read_count_threshold; print "Check $clusterid\n"; my $clustercheck; $clustercount->{$clusterid}->{wt} = 0; - $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; + $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; my $splitbed_fileS = "tmp_".$tag.".split.start.bed"; my $splitbed_fileE = "tmp_".$tag.".split.end.bed"; @@ -1041,5 +1041,3 @@ sub print_result{ } close(CF); } - - diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf index 8ef1f5b95..41b0caa4f 100644 --- a/modules/local/prep_mitosalt/main.nf +++ b/modules/local/prep_mitosalt/main.nf @@ -24,7 +24,7 @@ process PREP_MITOSALT { val sizelimit val split_distance_threshold val split_length - + output: path "mitosalt_config.txt", emit: msconfig diff --git a/nextflow.config b/nextflow.config index f5d90a8a8..e7bb7bb3c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -514,4 +514,3 @@ validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } - diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 9c83ac8d1..14131b335 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -45,30 +45,30 @@ workflow CALL_SV_MT { PREP_MITOSALT( ch_genome_chrsizes, - ch_genome_fai, - ch_genome_hisat2index, - ch_mt_fai, + ch_genome_fai, + ch_genome_hisat2index, + ch_mt_fai, ch_mt_fasta, - ch_mt_lastdb, - val_breakspan, - val_breakthreshold, - val_cluster_threshold, - val_deletion_threshold_max, - val_deletion_threshold_min, - val_evalue_threshold, - val_exclude, - val_flank, - val_hplimit, + ch_mt_lastdb, + val_breakspan, + val_breakthreshold, + val_cluster_threshold, + val_deletion_threshold_max, + val_deletion_threshold_min, + val_evalue_threshold, + val_exclude, + val_flank, + val_hplimit, val_mito_name, - val_paired_distance, - val_score_threshold, - val_sizelimit, + val_paired_distance, + val_score_threshold, + val_sizelimit, val_split_distance_threshold, - val_split_length - ) + val_split_length + ) - MITOSALT( - SEQTK_SAMPLE.out.reads, + MITOSALT( + SEQTK_SAMPLE.out.reads, PREP_MITOSALT.out.msconfig, ch_genome_chrsizes, ch_genome_fai, diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 5f889286b..fed86336c 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -149,7 +149,7 @@ workflow PREPARE_REFERENCES { ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[],[]]).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() - ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).index.collect() + ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).index.collect() ch_mt_last_index = LAST_INDEX_MT(ch_mt_fasta).index.collect() GATK_SHIFTFASTA(ch_mt_fasta, ch_mt_fai, ch_mt_dict) From 94b5f52b509fe03c7449d5ff790a00115d377541 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Feb 2026 10:48:04 +0100 Subject: [PATCH 289/872] updated nf schema --- main.nf | 2 +- nextflow.config | 1 + nextflow_schema.json | 170 +++++++++++++++++++++++++++--- tests/default.nf.test.snap | 2 +- tests/test_bam.nf.test.snap | 2 +- tests/test_singleton.nf.test.snap | 2 +- 6 files changed, 160 insertions(+), 19 deletions(-) diff --git a/main.nf b/main.nf index 001ddf4e5..2a18e6be6 100644 --- a/main.nf +++ b/main.nf @@ -193,7 +193,6 @@ workflow NFCORE_RAREDISEASE { ch_score_config_mt = channelFromPath(val_score_config_mt, true) ch_score_config_snv = channelFromPath(val_score_config_snv, true) ch_score_config_sv = channelFromPath(val_score_config_sv, true) - ch_subdepth = channelFromPath(val_subdepth, true) ch_vcf2cytosure_blacklist = channelFromPath(val_vcf2cytosure_blacklist, true) ch_vcfanno_lua = channelFromPath(val_vcfanno_lua, true) ch_vcfanno_toml = channelFromPath(val_vcfanno_toml, true) @@ -238,6 +237,7 @@ workflow NFCORE_RAREDISEASE { ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_ngsbits_method = channel.value(val_ngsbits_samplegender_method) ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model) + ch_subdepth = channel.value(val_subdepth) ch_vcfanno_resources = val_vcfanno_resources ? channel.fromPath(val_vcfanno_resources).splitText().map{it -> it.trim()}.collect() : channel.value([]) ch_gcnvcaller_model = val_gcnvcaller_model ? channel.fromPath(val_gcnvcaller_model) diff --git a/nextflow.config b/nextflow.config index f5d90a8a8..89120689e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -132,6 +132,7 @@ params { exclude = 5 flank = 15 hplimit = 0.01 + mitosalt_depth = 10000000 paired_distance = 1000 score_threshold = 80 sizelimit = 10000 diff --git a/nextflow_schema.json b/nextflow_schema.json index 97ff47652..016564048 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,9 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["outdir"], + "required": [ + "outdir" + ], "properties": { "input": { "type": "string", @@ -122,7 +124,10 @@ "fa_icon": "fas fa-align-center", "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.", "default": "GRCh38", - "enum": ["GRCh37", "GRCh38"] + "enum": [ + "GRCh37", + "GRCh38" + ] }, "gens_gnomad_pos": { "type": "string", @@ -516,7 +521,11 @@ "description": "Path to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep." } }, - "required": ["fasta", "intervals_wgs", "intervals_y"] + "required": [ + "fasta", + "intervals_wgs", + "intervals_y" + ] }, "analysis_options": { "title": "Analysis options", @@ -529,7 +538,11 @@ "default": "wgs", "description": "Specifies which analysis type for the pipeline- either 'wgs', 'wes' or 'mito'. This changes resources consumed and tools used.", "fa_icon": "fas fa-align-center", - "enum": ["wgs", "wes", "mito"] + "enum": [ + "wgs", + "wes", + "mito" + ] }, "concatenate_snv_calls": { "type": "boolean", @@ -544,7 +557,7 @@ }, "homoplasmy_af_threshold": { "type": "number", - "default": 1, + "default": 1.0, "description": "Allele frequency threshold for mitochondrial variants. Variants with an AF above this threshold will be treated as homoplasmic and assigned a 1/1 genotype. Range 0-1.0.", "fa_icon": "fas fa-less-than" }, @@ -559,7 +572,11 @@ "default": "xy", "description": "Method selection for ngs-bits samplegender", "fa_icon": "fas fa-align-center", - "enum": ["xy", "hetx", "sry"] + "enum": [ + "xy", + "hetx", + "sry" + ] }, "restrict_to_contigs": { "type": "string", @@ -614,14 +631,23 @@ "default": "bwamem2", "description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa', 'bwameme' and 'sentieon'.", "fa_icon": "fas fa-align-center", - "enum": ["bwa", "bwamem2", "bwameme", "sentieon"] + "enum": [ + "bwa", + "bwamem2", + "bwameme", + "sentieon" + ] }, "mt_aligner": { "type": "string", "default": "bwamem2", "description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa' and 'sentieon'.", "fa_icon": "fas fa-align-center", - "enum": ["bwa", "bwamem2", "sentieon"] + "enum": [ + "bwa", + "bwamem2", + "sentieon" + ] }, "samtools_sort_threads": { "type": "integer", @@ -648,7 +674,10 @@ "type": "string", "default": "reads", "description": "Subsample mitochondria based on fraction of reads or number of reads", - "enum": ["fraction", "reads"], + "enum": [ + "fraction", + "reads" + ], "fa_icon": "fas fa-align-center" }, "mt_subsample_reads": { @@ -703,21 +732,33 @@ "fa_icon": "fas fa-bacon", "description": "Option for selecting the PCR indel model used by Sentieon Dnascope.", "help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.", - "enum": ["NONE", "HOSTILE", "AGGRESSIVE", "CONSERVATIVE"] + "enum": [ + "NONE", + "HOSTILE", + "AGGRESSIVE", + "CONSERVATIVE" + ] }, "variant_caller": { "type": "string", "default": "deepvariant", "description": "Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.", "fa_icon": "fas fa-random", - "enum": ["deepvariant", "sentieon"] + "enum": [ + "deepvariant", + "sentieon" + ] }, "variant_type": { "type": "string", "default": "snp,indel", "description": "Specifies the variant types for sentieon variant caller.", "fa_icon": "fas fa-align-center", - "enum": ["snp", "indel", "snp,indel"] + "enum": [ + "snp", + "indel", + "snp,indel" + ] } } }, @@ -747,6 +788,92 @@ } } }, + "mitosalt_options": { + "title": "Mitosalt and saltshaker options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to run mitosalt and saltshaker", + "properties": { + "hisat2": { + "type": "string" + }, + "breakspan": { + "type": "integer", + "default": 15, + "description": "minimum number of bases a non-split read must span either side of a breakpoint to be considered in the heteroplasmy count" + }, + "breakthreshold": { + "type": "integer", + "default": 2, + "description": "the maximum deviation a given set of split read breakpoints can have to be considered within the same cluster" + }, + "cluster_threshold": { + "type": "integer", + "default": 2, + "description": "minimum number of reads supporting a cluster" + }, + "deletion_threshold_max": { + "type": "integer", + "default": 30000, + "description": "the maximum size of the gap between fragments of a split read for the split read to be considered as potentially spanning a deletion" + }, + "deletion_threshold_min": { + "type": "integer", + "default": 30, + "description": "the minimum size of the gap between fragemtns of a split read for the split read to be considered as potentially spanning a deletion" + }, + "evalue_threshold": { + "type": "number", + "default": 1e-05, + "description": "alignment e-value cutoff" + }, + "exclude": { + "type": "integer", + "default": 5, + "description": "filter split reads if both fragments fall within the regions at the start and end to avoid pseudo-gapped alignments due to a circular genome" + }, + "flank": { + "type": "integer", + "default": 15, + "description": "basepairs flanking a deletion" + }, + "hplimit": { + "type": "number", + "default": 0.01, + "description": "detected heteroplasmy threshold" + }, + "mitosalt_depth": { + "type": "integer", + "default": 10000000, + "description": "depth to subsample fastq files to before running mitosalt" + }, + "paired_distance": { + "type": "integer", + "default": 1000, + "description": "the maximum distance of a paired read from its split counterpart for paired support to be considered positive" + }, + "score_threshold": { + "type": "integer", + "default": 80, + "description": "alignemnt score cutoff" + }, + "sizelimit": { + "type": "integer", + "default": 10000, + "description": "maximum size of deletions tolerated, beyond which they are reclassified as potential duplications in the reverse orientation" + }, + "split_distance_threshold": { + "type": "integer", + "default": 5, + "description": "the maximum length of unmapped distance between two fragments of a split read" + }, + "split_length": { + "type": "integer", + "default": 15, + "description": "minimum number of bases in a split read fragment for the read to be considered as potentially spanning a deletion" + } + } + }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -814,7 +941,14 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email_on_fail": { @@ -907,7 +1041,10 @@ "hidden": true }, "help": { - "type": ["boolean", "string"], + "type": [ + "boolean", + "string" + ], "description": "Display the help message." }, "help_full": { @@ -940,11 +1077,14 @@ { "$ref": "#/$defs/annotation_options" }, + { + "$ref": "#/$defs/mitosalt_options" + }, { "$ref": "#/$defs/institutional_config_options" }, { "$ref": "#/$defs/generic_options" } - ] + ], } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4089d31cc..fe6430ef1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -909,6 +909,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T08:48:40.592550098" + "timestamp": "2026-02-04T10:39:36.534853957" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index ff0377ced..db51408bf 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -910,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T08:51:39.820380268" + "timestamp": "2026-02-04T10:43:55.12867456" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 1a099f754..c336d5be1 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -910,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T08:54:08.345773451" + "timestamp": "2026-02-04T10:46:59.255846426" } } \ No newline at end of file From b1fb941cfb232d5707e53c20b52f34c9b3c13370 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 10:55:01 +0100 Subject: [PATCH 290/872] fix CI error --- .../tests/main.nf.test.snap | 4 +- tests/default.nf.test.snap | 41 +++++++++++++++---- tests/test_bam.nf.test.snap | 41 +++++++++++++++---- tests/test_singleton.nf.test.snap | 41 +++++++++++++++---- workflows/raredisease.nf | 5 --- 5 files changed, 97 insertions(+), 35 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index b240fb809..6ac191684 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -390,7 +390,6 @@ "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", - "versions.yml:md5,4c809981aaef975a666ac3812651bec6", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", @@ -906,7 +905,6 @@ "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", - "versions.yml:md5,4c809981aaef975a666ac3812651bec6", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", @@ -920,6 +918,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T23:24:35.811727654" + "timestamp": "2026-01-31T15:59:04.629155265" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 86448783a..b47286abc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -127,6 +127,21 @@ "EKLIPSE": { "eklipse": 1.8 }, + "ENSEMBLVEP_FILTERVEP": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_ME": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_MT": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SNV": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SV": { + "ensemblvep": 110.0 + }, "EXPANSIONHUNTER": { "expansionhunter": "5.0.0", "bgzip": 1.18 @@ -210,10 +225,12 @@ "hmtnote": "0.7.2" }, "INDEX_CNVNATOR": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "INDEX_TIDDIT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "MANTA": { "manta": "1.6.0" @@ -376,10 +393,12 @@ "tabix": 1.21 }, "TABIX_BGZIPINDEX_PADDED_BED": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_BGZIPTABIX": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_DBSNP": { "tabix": 1.21 @@ -451,16 +470,20 @@ "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_HMTNOTE_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_ROHCALL": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 } }, [ @@ -882,6 +905,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-27T09:27:15.497975481" + "timestamp": "2026-01-31T20:55:04.269156792" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 55881d4e1..e290a2ac7 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -124,6 +124,21 @@ "EKLIPSE": { "eklipse": 1.8 }, + "ENSEMBLVEP_FILTERVEP": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_ME": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_MT": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SNV": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SV": { + "ensemblvep": 110.0 + }, "EXPANSIONHUNTER": { "expansionhunter": "5.0.0", "bgzip": 1.18 @@ -201,10 +216,12 @@ "hmtnote": "0.7.2" }, "INDEX_CNVNATOR": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "INDEX_TIDDIT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "MANTA": { "manta": "1.6.0" @@ -352,10 +369,12 @@ "tabix": 1.21 }, "TABIX_BGZIPINDEX_PADDED_BED": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_BGZIPTABIX": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_DBSNP": { "tabix": 1.21 @@ -427,16 +446,20 @@ "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_HMTNOTE_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_ROHCALL": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 } }, [ @@ -823,6 +846,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-27T10:13:08.294315267" + "timestamp": "2026-01-31T22:23:45.894751961" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 087712330..5c5e7e05e 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -119,6 +119,21 @@ "EKLIPSE": { "eklipse": 1.8 }, + "ENSEMBLVEP_FILTERVEP": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_ME": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_MT": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SNV": { + "ensemblvep": 110.0 + }, + "ENSEMBLVEP_SV": { + "ensemblvep": 110.0 + }, "EXPANSIONHUNTER": { "expansionhunter": "5.0.0", "bgzip": 1.18 @@ -202,10 +217,12 @@ "hmtnote": "0.7.2" }, "INDEX_CNVNATOR": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "INDEX_TIDDIT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "MANTA": { "manta": "1.6.0" @@ -365,10 +382,12 @@ "tabix": 1.21 }, "TABIX_BGZIPINDEX_PADDED_BED": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_BGZIPTABIX": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "TABIX_DBSNP": { "tabix": 1.21 @@ -434,16 +453,20 @@ "nf-core/raredisease": "v2.7.0dev" }, "ZIP_TABIX_HMTNOTE_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_ROHCALL": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 }, "ZIP_TABIX_VCFANNO_MT": { - "tabix": 1.2 + "bgzip": 1.21, + "tabix": 1.21 } }, [ @@ -641,6 +664,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-27T10:50:06.243055556" + "timestamp": "2026-02-01T18:23:51.512604286" } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 530873679..6173976c7 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -439,7 +439,6 @@ workflow RAREDISEASE { ) GENERATE_CLINICAL_SET_SNV.out.vcf .set { ch_clinical_snv_vcf } - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SNV.out.versions) } ch_ann_csq_snv_in = ch_clinical_snv_vcf.mix(ch_clin_research_snv_vcf.research) @@ -511,8 +510,6 @@ workflow RAREDISEASE { ) GENERATE_CLINICAL_SET_MT.out.vcf .set { ch_clinical_mtsnv_vcf } - - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_MT.out.versions) } ch_ann_csq_mtsnv_in = ch_clinical_mtsnv_vcf.mix(ch_clin_research_mt_vcf.research) @@ -609,7 +606,6 @@ workflow RAREDISEASE { ) GENERATE_CLINICAL_SET_SV.out.vcf .set { ch_clinical_sv_vcf } - ch_versions = ch_versions.mix(GENERATE_CLINICAL_SET_SV.out.versions) } ch_ann_csq_sv_in = ch_clinical_sv_vcf.mix(ch_clin_research_sv_vcf.research) @@ -687,7 +683,6 @@ workflow RAREDISEASE { ) GENERATE_CLINICAL_SET_ME.out.vcf .set { ch_clinical_me_vcf } - ch_versions = ch_versions.mix( GENERATE_CLINICAL_SET_ME.out.versions ) } ch_ann_csq_me_in = ch_clinical_me_vcf.mix(ch_clin_research_me_vcf.research) From b3cec88067551a56b242633d5ad288bae287e8df Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 11:05:29 +0100 Subject: [PATCH 291/872] tbi to index --- subworkflows/local/annotate_mt_snvs.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 2f5847b8e..b6c6d4630 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -103,7 +103,7 @@ workflow ANNOTATE_MT_SNVS { TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf) ch_vcf = ENSEMBLVEP_MT.out.vcf - ch_tbi = TABIX_TABIX_VEP_MT.out.tbi + ch_tbi = TABIX_TABIX_VEP_MT.out.index // Running haplogrep3 if (!skip_haplogrep3) { From ca083ffb31e1ab5d5f24a9db6db63e2c5b597b88 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 11:13:56 +0100 Subject: [PATCH 292/872] remove ensemblvep versions --- subworkflows/local/annotate_mt_snvs.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index b6c6d4630..c5f45329a 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -123,7 +123,6 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } - ch_versions = ch_versions.mix(ENSEMBLVEP_MT.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions) ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) From 20d4247e8bb8742e9fca68304da7905161657b25 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 11:20:16 +0100 Subject: [PATCH 293/872] remove tabix versions --- subworkflows/local/annotate_mt_snvs.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index c5f45329a..d855ebd2d 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -123,7 +123,6 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } - ch_versions = ch_versions.mix(TABIX_TABIX_VEP_MT.out.versions) ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) From c26f54719a798e2143c5eeddbadf739185a3c0c1 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Feb 2026 11:59:39 +0100 Subject: [PATCH 294/872] remove mitodepth from test conf --- conf/test.config | 6 ++++-- nextflow_schema.json | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index 9ddb93393..acae9c950 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,8 +26,12 @@ process { env { MPLCONFIGDIR="." + SINGULARITY_CACHE_DIR="/home/proj/stage/singularity_cache" } +singularity.pullTimeout='2h' +singularity.cacheDir='/home/proj/stage/singularity_cache' + params { config_profile_name = 'Test profile - default' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -64,6 +68,4 @@ params { vep_filters = params.pipelines_testdata_base_path + '/reference/hgnc.txt' vep_cache_version = 107 vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' - mitosalt_config = 'data/config_human.txt' - mitosalt_depth = '100000' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 016564048..d3df992c0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1086,5 +1086,5 @@ { "$ref": "#/$defs/generic_options" } - ], + ] } From 9cf7a17b64d36240b7e54a6db9e79141033c5434 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Feb 2026 12:00:45 +0100 Subject: [PATCH 295/872] remove singularity cache from test conf --- conf/test.config | 2 -- 1 file changed, 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index acae9c950..dc6dd262e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,11 +26,9 @@ process { env { MPLCONFIGDIR="." - SINGULARITY_CACHE_DIR="/home/proj/stage/singularity_cache" } singularity.pullTimeout='2h' -singularity.cacheDir='/home/proj/stage/singularity_cache' params { config_profile_name = 'Test profile - default' From 4a53e580e209a306a68179166e2681b49b64180c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 4 Feb 2026 11:02:43 +0000 Subject: [PATCH 296/872] [automated] Fix code linting --- nextflow_schema.json | 81 ++++++++------------------------------------ 1 file changed, 15 insertions(+), 66 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d3df992c0..c4113ff6c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,9 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "outdir" - ], + "required": ["outdir"], "properties": { "input": { "type": "string", @@ -124,10 +122,7 @@ "fa_icon": "fas fa-align-center", "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.", "default": "GRCh38", - "enum": [ - "GRCh37", - "GRCh38" - ] + "enum": ["GRCh37", "GRCh38"] }, "gens_gnomad_pos": { "type": "string", @@ -521,11 +516,7 @@ "description": "Path to a bed-like file exported by scout, which contains HGNC_IDs to be used in filter_vep." } }, - "required": [ - "fasta", - "intervals_wgs", - "intervals_y" - ] + "required": ["fasta", "intervals_wgs", "intervals_y"] }, "analysis_options": { "title": "Analysis options", @@ -538,11 +529,7 @@ "default": "wgs", "description": "Specifies which analysis type for the pipeline- either 'wgs', 'wes' or 'mito'. This changes resources consumed and tools used.", "fa_icon": "fas fa-align-center", - "enum": [ - "wgs", - "wes", - "mito" - ] + "enum": ["wgs", "wes", "mito"] }, "concatenate_snv_calls": { "type": "boolean", @@ -572,11 +559,7 @@ "default": "xy", "description": "Method selection for ngs-bits samplegender", "fa_icon": "fas fa-align-center", - "enum": [ - "xy", - "hetx", - "sry" - ] + "enum": ["xy", "hetx", "sry"] }, "restrict_to_contigs": { "type": "string", @@ -631,23 +614,14 @@ "default": "bwamem2", "description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa', 'bwameme' and 'sentieon'.", "fa_icon": "fas fa-align-center", - "enum": [ - "bwa", - "bwamem2", - "bwameme", - "sentieon" - ] + "enum": ["bwa", "bwamem2", "bwameme", "sentieon"] }, "mt_aligner": { "type": "string", "default": "bwamem2", "description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa' and 'sentieon'.", "fa_icon": "fas fa-align-center", - "enum": [ - "bwa", - "bwamem2", - "sentieon" - ] + "enum": ["bwa", "bwamem2", "sentieon"] }, "samtools_sort_threads": { "type": "integer", @@ -674,10 +648,7 @@ "type": "string", "default": "reads", "description": "Subsample mitochondria based on fraction of reads or number of reads", - "enum": [ - "fraction", - "reads" - ], + "enum": ["fraction", "reads"], "fa_icon": "fas fa-align-center" }, "mt_subsample_reads": { @@ -732,33 +703,21 @@ "fa_icon": "fas fa-bacon", "description": "Option for selecting the PCR indel model used by Sentieon Dnascope.", "help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.", - "enum": [ - "NONE", - "HOSTILE", - "AGGRESSIVE", - "CONSERVATIVE" - ] + "enum": ["NONE", "HOSTILE", "AGGRESSIVE", "CONSERVATIVE"] }, "variant_caller": { "type": "string", "default": "deepvariant", "description": "Specifies the variant caller to use - available options are 'deepvariant' and 'sentieon'.", "fa_icon": "fas fa-random", - "enum": [ - "deepvariant", - "sentieon" - ] + "enum": ["deepvariant", "sentieon"] }, "variant_type": { "type": "string", "default": "snp,indel", "description": "Specifies the variant types for sentieon variant caller.", "fa_icon": "fas fa-align-center", - "enum": [ - "snp", - "indel", - "snp,indel" - ] + "enum": ["snp", "indel", "snp,indel"] } } }, @@ -824,7 +783,7 @@ }, "evalue_threshold": { "type": "number", - "default": 1e-05, + "default": 1e-5, "description": "alignment e-value cutoff" }, "exclude": { @@ -873,7 +832,7 @@ "description": "minimum number of bases in a split read fragment for the read to be considered as potentially spanning a deletion" } } - }, + }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -941,14 +900,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email_on_fail": { @@ -1041,10 +993,7 @@ "hidden": true }, "help": { - "type": [ - "boolean", - "string" - ], + "type": ["boolean", "string"], "description": "Display the help message." }, "help_full": { From e53bd011156be791adf71aeb5b84a770be09ef43 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 16:20:10 +0100 Subject: [PATCH 297/872] update changelog --- CHANGELOG.md | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c7d62acfa..752e2badd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -51,13 +51,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ----------------------------------- | ----------- | ----------- | | bcftools | 1.20 | 1.21 | | htslib | 1.20 | 1.21 | -| mosdepth | 0.3.8 | 0.3.10 | +| mosdepth | 0.3.8 | 0.3.11 | | ngs-bits | 2023_02 | 2024_11 | | gatk4/determinegermlinecontigploidy | 4.5.0.0 | 4.6.2.0 | | gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | | gens-preproc | 1.0.11 | 1.1.2 | -| samtools (sort & view) | 1.21 | 1.22.1 | +| pigz | 2.3.4 | 2.8 | +| samtools | 1.21 | 1.22.1 | | sambamba | | 1.0.1 | +| ensemblverp/filtervep | 113 | 115.2 | +| fastp | 0.23.4 | 1.0.1 | +| genmod | 3.9 | 3.10.2 | +| multiqc | 1.32 | 1.33 | +| picard | 3.3.0 | 3.4.0 | +| sentieon | 202503 | 202503.02 | +| stranger | 0.9.4 | 0.10.0 | ## 2.6.0 - Cacofonix [2025-06-25] From 79c224519281284576529ee24db6f3f40e59a17c Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Feb 2026 22:03:39 +0100 Subject: [PATCH 298/872] update modules --- modules.json | 68 ++-- modules/nf-core/chromograph/main.nf | 102 ++--- modules/nf-core/chromograph/meta.yml | 35 +- .../nf-core/chromograph/tests/main.nf.test | 143 ++++++- .../chromograph/tests/main.nf.test.snap | 382 ++++++++++++++++++ .../nf-core/chromograph/tests/nextflow.config | 5 + .../nf-core/cnvnator/cnvnator/environment.yml | 2 + modules/nf-core/cnvnator/cnvnator/main.nf | 33 +- modules/nf-core/cnvnator/cnvnator/meta.yml | 44 +- .../cnvnator/cnvnator/tests/main.nf.test | 127 ++++++ .../cnvnator/cnvnator/tests/main.nf.test.snap | 102 +++++ .../cnvnator/cnvnator/tests/nextflow.config | 21 + .../cnvnator/convert2vcf/environment.yml | 2 + modules/nf-core/cnvnator/convert2vcf/main.nf | 18 +- modules/nf-core/cnvnator/convert2vcf/meta.yml | 35 +- .../cnvnator/convert2vcf/tests/main.nf.test | 136 +++++++ .../convert2vcf/tests/main.nf.test.snap | 64 +++ .../convert2vcf/tests/nextflow.config | 20 + .../deepvariant/rundeepvariant/main.nf | 32 +- .../deepvariant/rundeepvariant/meta.yml | 75 +++- .../rundeepvariant/tests/main.nf.test | 106 ++++- .../rundeepvariant/tests/main.nf.test.snap | 374 ++++++++++++++--- .../tests/nextflow-intervals.config | 8 - .../nextflow-non-autosomal-calling.config | 8 - .../rundeepvariant/tests/nextflow.config | 8 +- .../deepvariant/rundeepvariant/tests/tags.yml | 2 - .../nf-core/expansionhunter/environment.yml | 1 - modules/nf-core/expansionhunter/main.nf | 17 +- modules/nf-core/expansionhunter/meta.yml | 45 ++- .../expansionhunter/tests/main.nf.test.snap | 72 +++- .../gatk4/bedtointervallist/environment.yml | 7 +- .../nf-core/gatk4/bedtointervallist/main.nf | 35 +- .../nf-core/gatk4/bedtointervallist/meta.yml | 38 +- .../bedtointervallist/tests/main.nf.test | 31 +- .../bedtointervallist/tests/main.nf.test.snap | 61 ++- .../gatk4/bedtointervallist/tests/tags.yml | 2 - .../gatk4/collectreadcounts/environment.yml | 7 +- .../nf-core/gatk4/collectreadcounts/main.nf | 59 ++- .../nf-core/gatk4/collectreadcounts/meta.yml | 58 ++- .../collectreadcounts/tests/main.nf.test.snap | 40 +- .../createsequencedictionary/environment.yml | 7 +- .../gatk4/createsequencedictionary/main.nf | 37 +- .../gatk4/createsequencedictionary/meta.yml | 36 +- .../tests/main.nf.test.snap | 40 +- .../createsequencedictionary/tests/tags.yml | 2 - .../gatk4/denoisereadcounts/environment.yml | 7 +- .../nf-core/gatk4/denoisereadcounts/main.nf | 30 +- .../nf-core/gatk4/denoisereadcounts/meta.yml | 42 +- .../denoisereadcounts/tests/main.nf.test | 2 +- .../denoisereadcounts/tests/main.nf.test.snap | 18 +- .../gatk4/denoisereadcounts/tests/tags.yml | 6 - .../determinegermlinecontigploidy/main.nf | 10 +- .../determinegermlinecontigploidy/meta.yml | 26 +- .../tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 38 +- .../gatk4/filtermutectcalls/environment.yml | 7 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 51 +-- .../nf-core/gatk4/filtermutectcalls/meta.yml | 68 +++- .../filtermutectcalls/tests/main.nf.test | 30 +- .../filtermutectcalls/tests/main.nf.test.snap | 95 +++-- .../gatk4/filtermutectcalls/tests/tags.yml | 2 - .../nf-core/gatk4/germlinecnvcaller/main.nf | 10 +- .../nf-core/gatk4/germlinecnvcaller/meta.yml | 26 +- .../germlinecnvcaller/tests/main.nf.test | 4 +- .../germlinecnvcaller/tests/main.nf.test.snap | 36 +- .../gatk4/intervallisttools/environment.yml | 7 +- .../nf-core/gatk4/intervallisttools/main.nf | 31 +- .../nf-core/gatk4/intervallisttools/meta.yml | 36 +- .../intervallisttools/tests/main.nf.test.snap | 40 +- .../gatk4/intervallisttools/tests/tags.yml | 2 - .../gatk4/mergebamalignment/environment.yml | 7 +- .../nf-core/gatk4/mergebamalignment/main.nf | 33 +- .../nf-core/gatk4/mergebamalignment/meta.yml | 36 +- .../mergebamalignment/tests/main.nf.test | 2 +- .../mergebamalignment/tests/main.nf.test.snap | 38 +- .../nf-core/gatk4/mergevcfs/environment.yml | 7 +- modules/nf-core/gatk4/mergevcfs/main.nf | 39 +- modules/nf-core/gatk4/mergevcfs/meta.yml | 46 ++- .../gatk4/mergevcfs/tests/main.nf.test | 3 + .../gatk4/mergevcfs/tests/main.nf.test.snap | 45 ++- .../nf-core/gatk4/mergevcfs/tests/tags.yml | 2 - modules/nf-core/gatk4/mutect2/environment.yml | 7 +- modules/nf-core/gatk4/mutect2/main.nf | 75 ++-- modules/nf-core/gatk4/mutect2/meta.yml | 131 ++++-- .../nf-core/gatk4/mutect2/tests/f1r2.config | 3 - .../nf-core/gatk4/mutect2/tests/main.nf.test | 308 +++++++++++--- .../gatk4/mutect2/tests/main.nf.test.snap | 350 ++++++++++++---- .../nf-core/gatk4/mutect2/tests/mito.config | 3 - .../gatk4/mutect2/tests/nextflow.config | 5 + .../nf-core/gatk4/mutect2/tests/pair.config | 3 - modules/nf-core/gatk4/mutect2/tests/tags.yml | 2 - .../postprocessgermlinecnvcalls/README.md | 9 - .../environment.yml | 10 + .../gatk4/postprocessgermlinecnvcalls/main.nf | 51 ++- .../postprocessgermlinecnvcalls/meta.yml | 48 ++- .../tests/main.nf.test | 154 +++++++ .../tests/main.nf.test.snap | 44 ++ .../tests/nextflow.config | 15 + .../nf-core/gatk4/printreads/environment.yml | 7 +- modules/nf-core/gatk4/printreads/main.nf | 41 +- modules/nf-core/gatk4/printreads/meta.yml | 46 ++- .../gatk4/printreads/tests/main.nf.test | 4 +- .../gatk4/printreads/tests/main.nf.test.snap | 38 +- .../nf-core/gatk4/revertsam/environment.yml | 7 +- modules/nf-core/gatk4/revertsam/main.nf | 33 +- modules/nf-core/gatk4/revertsam/meta.yml | 33 +- .../gatk4/revertsam/tests/main.nf.test | 2 +- .../gatk4/revertsam/tests/main.nf.test.snap | 38 +- .../nf-core/gatk4/samtofastq/environment.yml | 7 +- modules/nf-core/gatk4/samtofastq/main.nf | 41 +- modules/nf-core/gatk4/samtofastq/meta.yml | 38 +- .../gatk4/samtofastq/tests/main.nf.test | 6 +- .../gatk4/samtofastq/tests/main.nf.test.snap | 54 ++- .../gatk4/selectvariants/environment.yml | 7 +- modules/nf-core/gatk4/selectvariants/main.nf | 33 +- modules/nf-core/gatk4/selectvariants/meta.yml | 38 +- .../gatk4/selectvariants/tests/main.nf.test | 6 +- .../selectvariants/tests/main.nf.test.snap | 38 ++ .../gatk4/selectvariants/tests/tags.yml | 2 - .../nf-core/gatk4/shiftfasta/environment.yml | 7 +- modules/nf-core/gatk4/shiftfasta/main.nf | 45 +-- modules/nf-core/gatk4/shiftfasta/meta.yml | 67 +-- .../gatk4/shiftfasta/tests/main.nf.test.snap | 20 +- .../gatk4/splitintervals/environment.yml | 7 +- modules/nf-core/gatk4/splitintervals/main.nf | 35 +- modules/nf-core/gatk4/splitintervals/meta.yml | 41 +- .../splitintervals/tests/main.nf.test.snap | 60 ++- .../splitintervals/tests/nextflow.config | 2 +- .../gatk4/variantfiltration/environment.yml | 7 +- .../nf-core/gatk4/variantfiltration/main.nf | 53 +-- .../nf-core/gatk4/variantfiltration/meta.yml | 59 ++- .../variantfiltration/tests/main.nf.test | 62 ++- .../variantfiltration/tests/main.nf.test.snap | 64 ++- .../gatk4/variantfiltration/tests/tags.yml | 2 - .../addorreplacereadgroups/environment.yml | 5 +- .../picard/addorreplacereadgroups/main.nf | 14 +- .../picard/addorreplacereadgroups/meta.yml | 46 ++- .../addorreplacereadgroups/tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 56 ++- .../addorreplacereadgroups/tests/tags.yml | 2 - .../collectmultiplemetrics/environment.yml | 3 +- .../picard/collectmultiplemetrics/main.nf | 14 +- .../picard/collectmultiplemetrics/meta.yml | 28 +- .../collectmultiplemetrics/tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 54 ++- .../picard/collectwgsmetrics/environment.yml | 3 +- .../nf-core/picard/collectwgsmetrics/main.nf | 15 +- .../nf-core/picard/collectwgsmetrics/meta.yml | 27 +- .../collectwgsmetrics/tests/main.nf.test | 4 +- .../collectwgsmetrics/tests/main.nf.test.snap | 36 +- .../picard/liftovervcf/environment.yml | 5 +- modules/nf-core/picard/liftovervcf/main.nf | 14 +- modules/nf-core/picard/liftovervcf/meta.yml | 42 +- .../picard/liftovervcf/tests/main.nf.test | 4 +- .../liftovervcf/tests/main.nf.test.snap | 36 +- .../picard/markduplicates/environment.yml | 5 +- modules/nf-core/picard/markduplicates/main.nf | 15 +- .../nf-core/picard/markduplicates/meta.yml | 51 ++- .../picard/markduplicates/tests/main.nf.test | 6 +- .../markduplicates/tests/main.nf.test.snap | 162 ++++++-- .../picard/markduplicates/tests/tags.yml | 2 - .../picard/renamesampleinvcf/environment.yml | 3 +- .../nf-core/picard/renamesampleinvcf/main.nf | 19 +- .../nf-core/picard/renamesampleinvcf/meta.yml | 28 +- .../renamesampleinvcf/tests/main.nf.test | 2 +- .../renamesampleinvcf/tests/main.nf.test.snap | 18 +- .../nf-core/picard/sortvcf/environment.yml | 5 +- modules/nf-core/picard/sortvcf/main.nf | 18 +- modules/nf-core/picard/sortvcf/meta.yml | 35 +- .../nf-core/picard/sortvcf/tests/main.nf.test | 2 +- .../picard/sortvcf/tests/main.nf.test.snap | 18 +- modules/nf-core/stranger/environment.yml | 2 +- modules/nf-core/stranger/main.nf | 6 +- modules/nf-core/stranger/meta.yml | 12 +- .../nf-core/stranger/tests/main.nf.test.snap | 16 +- modules/nf-core/svdb/merge/environment.yml | 5 +- modules/nf-core/svdb/merge/main.nf | 18 +- modules/nf-core/svdb/merge/meta.yml | 48 ++- modules/nf-core/svdb/merge/tests/main.nf.test | 16 +- .../svdb/merge/tests/main.nf.test.snap | 336 +++++++++++---- modules/nf-core/svdb/query/environment.yml | 5 +- modules/nf-core/svdb/query/main.nf | 14 +- modules/nf-core/svdb/query/meta.yml | 78 ++-- modules/nf-core/svdb/query/tests/main.nf.test | 5 +- .../svdb/query/tests/main.nf.test.snap | 18 +- modules/nf-core/svdb/query/tests/tags.yml | 2 - subworkflows/local/align/main.nf | 2 +- subworkflows/local/align_MT/main.nf | 4 - .../local/align_bwa_bwamem2_bwameme/main.nf | 1 - subworkflows/local/annotate_genome_snvs.nf | 3 - .../local/annotate_mobile_elements.nf | 5 - .../local/annotate_rhocallviz/main.nf | 1 - .../local/annotate_structural_variants.nf | 4 - subworkflows/local/call_mobile_elements.nf | 1 - .../local/call_repeat_expansions/main.nf | 6 - subworkflows/local/call_snv.nf | 2 - subworkflows/local/call_snv_MT/main.nf | 3 - .../local/call_snv_deepvariant/main.nf | 1 - .../local/call_structural_variants.nf | 1 - subworkflows/local/call_sv_cnvnator/main.nf | 10 - .../local/call_sv_germlinecnvcaller/main.nf | 8 - subworkflows/local/call_sv_tiddit/main.nf | 1 - .../local/convert_mt_bam_to_fastq/main.nf | 6 - subworkflows/local/gens.nf | 3 - .../local/postprocess_MT_calls/main.nf | 3 - subworkflows/local/prepare_references/main.nf | 4 - subworkflows/local/qc_bam/main.nf | 3 - subworkflows/local/scatter_genome/main.nf | 1 - 208 files changed, 5215 insertions(+), 1945 deletions(-) create mode 100644 modules/nf-core/chromograph/tests/main.nf.test.snap create mode 100644 modules/nf-core/chromograph/tests/nextflow.config create mode 100644 modules/nf-core/cnvnator/cnvnator/tests/main.nf.test create mode 100644 modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap create mode 100644 modules/nf-core/cnvnator/cnvnator/tests/nextflow.config create mode 100644 modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test create mode 100644 modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap create mode 100644 modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config delete mode 100644 modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config delete mode 100644 modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config delete mode 100644 modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/denoisereadcounts/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/filtermutectcalls/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/intervallisttools/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/mergevcfs/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/mutect2/tests/f1r2.config delete mode 100644 modules/nf-core/gatk4/mutect2/tests/mito.config create mode 100644 modules/nf-core/gatk4/mutect2/tests/nextflow.config delete mode 100644 modules/nf-core/gatk4/mutect2/tests/pair.config delete mode 100644 modules/nf-core/gatk4/mutect2/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config create mode 100644 modules/nf-core/gatk4/selectvariants/tests/main.nf.test.snap delete mode 100644 modules/nf-core/gatk4/selectvariants/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/variantfiltration/tests/tags.yml delete mode 100644 modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml delete mode 100644 modules/nf-core/picard/markduplicates/tests/tags.yml delete mode 100644 modules/nf-core/svdb/query/tests/tags.yml diff --git a/modules.json b/modules.json index b308e6230..b1af329d7 100644 --- a/modules.json +++ b/modules.json @@ -107,18 +107,18 @@ }, "chromograph": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", "installed_by": ["modules"] }, "cnvnator/cnvnator": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "e657cdd0198cc26f2e501325eb7f70fbd740b6ee", "installed_by": ["modules"], "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" }, "cnvnator/convert2vcf": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "9d43cc3f4b065a99d62dcd58f10d5f4e9feb4bd8", "installed_by": ["modules"] }, "custom/addmostsevereconsequence": { @@ -133,7 +133,7 @@ }, "deepvariant/rundeepvariant": { "branch": "master", - "git_sha": "470ac76fb4fbba2a9284c8b65191119c8bfe5a69", + "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", "installed_by": ["modules"] }, "eklipse": { @@ -154,7 +154,7 @@ }, "expansionhunter": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", "installed_by": ["modules"] }, "fastp": { @@ -169,97 +169,97 @@ }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", "installed_by": ["modules"] }, "gatk4/denoisereadcounts": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", "installed_by": ["modules"] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", + "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", "installed_by": ["modules"] }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", + "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", "installed_by": ["modules"] }, "gatk4/mergebamalignment": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", "installed_by": ["modules"] }, "gatk4/postprocessgermlinecnvcalls": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", "installed_by": ["modules"] }, "gatk4/printreads": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/revertsam": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/samtofastq": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/selectvariants": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/shiftfasta": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/splitintervals": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", "installed_by": ["modules"] }, "gawk": { @@ -335,7 +335,7 @@ }, "picard/addorreplacereadgroups": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", "installed_by": ["modules"] }, "picard/collecthsmetrics": { @@ -345,32 +345,32 @@ }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", "installed_by": ["modules"] }, "picard/renamesampleinvcf": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", "installed_by": ["modules"] }, "qualimap/bamqc": { @@ -490,17 +490,17 @@ }, "stranger": { "branch": "master", - "git_sha": "72717e1f3feabaa57a6a71ba5a85d9c4ceeba514", + "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", "installed_by": ["modules"] }, "svdb/query": { "branch": "master", - "git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c", + "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", "installed_by": ["modules"] }, "tabix/bgzip": { diff --git a/modules/nf-core/chromograph/main.nf b/modules/nf-core/chromograph/main.nf index e1374e483..f575a4cf6 100644 --- a/modules/nf-core/chromograph/main.nf +++ b/modules/nf-core/chromograph/main.nf @@ -1,11 +1,12 @@ process CHROMOGRAPH { - tag "$meta.id" + // $meta.id can be [] because autozyg is not required, so use all ids + tag "${[meta, meta2, meta3, meta4, meta5, meta6, meta7].collect { meta_map -> meta_map.id }.findAll().unique().join('_') ?: 'chromograph'}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2': - 'biocontainers/chromograph:1.3.1--pyhdfd78af_2' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2' + : 'biocontainers/chromograph:1.3.1--pyhdfd78af_2'}" input: tuple val(meta), path(autozyg) @@ -17,79 +18,54 @@ process CHROMOGRAPH { tuple val(meta7), path(sites) output: - tuple val(meta), path("${prefix}"), emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.png"), emit: plots, optional: true + tuple val("${task.process}"), val('chromograph'), eval("chromograph --version | sed 's/.* //'") , topic: versions , emit: versions_chromograph when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def autozyg_param = autozyg ? "--autozyg ${autozyg}" : '' - def coverage_param = coverage ? "--coverage ${coverage}" : '' - def exome_param = exome ? "--exom ${exome}" : '' - def fracsnp_param = fracsnp ? "--fracsnp ${fracsnp}" : '' - def ideogram_param = ideogram ? "--ideogram ${ideogram}" : '' - def regions_param = regions ? "--regions ${regions}" : '' - def sites_param = sites ? "--sites ${sites}" : '' + def args = task.ext.args ?: '' + def autozyg_param = autozyg ? "--autozyg ${autozyg}" : '' + def coverage_param = coverage ? "--coverage ${coverage}" : '' + def exome_param = exome ? "--exom ${exome}" : '' + def fracsnp_param = fracsnp ? "--fracsnp ${fracsnp}" : '' + def ideogram_param = ideogram ? "--ideogram ${ideogram}" : '' + def regions_param = regions ? "--regions ${regions}" : '' + def sites_param = sites ? "--sites ${sites}" : '' - if (autozyg) { - prefix = task.ext.prefix ?: "${meta.id}" - } else if (coverage) { - prefix = task.ext.prefix ?: "${meta2.id}" - } else if (exome) { - prefix = task.ext.prefix ?: "${meta3.id}" - } else if (fracsnp) { - prefix = task.ext.prefix ?: "${meta4.id}" - } else if (ideogram) { - prefix = task.ext.prefix ?: "${meta5.id}" - } else if (regions) { - prefix = task.ext.prefix ?: "${meta6.id}" - } else { - prefix = task.ext.prefix ?: "${meta7.id}" - } """ chromograph \\ - $args \\ - $autozyg_param \\ - $coverage_param \\ - $exome_param \\ - $fracsnp_param \\ - $ideogram_param \\ - $regions_param \\ - $sites_param \\ - --outd ${prefix} + ${args} \\ + ${autozyg_param} \\ + ${coverage_param} \\ + ${exome_param} \\ + ${fracsnp_param} \\ + ${ideogram_param} \\ + ${regions_param} \\ + ${sites_param} \\ + --outd . - cat <<-END_VERSIONS > versions.yml - "${task.process}": - chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' ) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' + euploidy = args.contains('-e') || args.contains('--euploid') - if (autozyg) { - prefix = task.ext.prefix ?: "${meta.id}" - } else if (coverage) { - prefix = task.ext.prefix ?: "${meta2.id}" - } else if (exome) { - prefix = task.ext.prefix ?: "${meta3.id}" - } else if (fracsnp) { - prefix = task.ext.prefix ?: "${meta4.id}" - } else if (ideogram) { - prefix = task.ext.prefix ?: "${meta5.id}" - } else if (regions) { - prefix = task.ext.prefix ?: "${meta6.id}" - } else { - prefix = task.ext.prefix ?: "${meta7.id}" - } """ - mkdir ${prefix} + ${touchCmd(euploidy, autozyg)} + ${touchCmd(euploidy, coverage)} + ${touchCmd(euploidy, exome)} + ${touchCmd(euploidy, fracsnp)} + ${touchCmd(euploidy, ideogram)} + ${touchCmd(euploidy, regions)} + ${touchCmd(euploidy, sites)} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' ) - END_VERSIONS """ } + +// Helper function to generate touch commands +def touchCmd(euploidy, input_file) { + def chrs = euploidy ? (1..22) + ['X', 'Y', 'M'] : [1] + input_file ? chrs.collect { chr -> "touch ${input_file}_chr${chr}.png" }.join(' ') : '' +} diff --git a/modules/nf-core/chromograph/meta.yml b/modules/nf-core/chromograph/meta.yml index c61482807..b9899f0e0 100644 --- a/modules/nf-core/chromograph/meta.yml +++ b/modules/nf-core/chromograph/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "chromograph" description: Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. @@ -88,18 +88,33 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - ${prefix}: + - "*.png": type: file - description: Directory containing the plots in png format - pattern: "*.png" + description: Plot(s) in PNG format ontologies: [] + versions_chromograph: + - - ${task.process}: + type: string + description: The process the versions were collected from + - chromograph: + type: string + description: The tool name + - chromograph --version | sed 's/.* //': + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - chromograph: + type: string + description: The tool name + - chromograph --version | sed 's/.* //': + type: eval + description: The expression to obtain the version of the tool + authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/chromograph/tests/main.nf.test b/modules/nf-core/chromograph/tests/main.nf.test index 8643afe3a..050c470cb 100644 --- a/modules/nf-core/chromograph/tests/main.nf.test +++ b/modules/nf-core/chromograph/tests/main.nf.test @@ -6,33 +6,152 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "chromograph" + config "./nextflow.config" - test("test_chromograph_sites") { + test("test_chromograph_sites_wig") { + when { + params { + module_args = '' + } + process { + """ + input[0] = [[],[]] + input[1] = Channel.of( + 'fixedStep chrom=chr3 start=400601 step=100', + '11', + '22', + '33') + .collectFile(name: 'wig_input.wig', newLine: true) + .map { file -> [ [ id: file.name ], file ] } + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] + input[6] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_chromograph_sites_wig_euploid") { + when { + params { + module_args = '--euploid' + } + process { + """ + input[0] = [[],[]] + input[1] = Channel.of( + 'fixedStep chrom=chr3 start=400601 step=100', + '11', + '22', + '33') + .collectFile(name: 'wig_input.wig', newLine: true) + .map { file -> [ [ id: file.name ], file ] } + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] + input[6] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_chromograph_sites_wig_stub") { + + options "-stub" when { + params { + module_args = '' + } process { """ - input[0] = [[:],[]] - input[1] = [[:],[]] - input[2] = [[:],[]] - input[3] = [[:],[]] - input[4] = [[:],[]] - input[5] = [[:],[]] + input[0] = [[],[]] + input[1] = Channel.of( + 'fixedStep chrom=chr3 start=400601 step=100', + '11', + '22', + '33') + .collectFile(name: 'wig_input.wig', newLine: true) + .map { file -> [ [ id: file.name ], file ] } + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true) - ] + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true) + ] """ } } then { assertAll( - {assert process.success}, - {assert process.out.plots.get(0).get(1) ==~ ".*/test"} + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("test_chromograph_sites_wig_euploid_stub") { + + options "-stub" + + when { + params { + module_args = '--euploid' + } + process { + """ + input[0] = [[],[]] + input[1] = Channel.of( + 'fixedStep chrom=chr3 start=400601 step=100', + '11', + '22', + '33') + .collectFile(name: 'wig_input.wig', newLine: true) + .map { file -> [ [ id: file.name ], file ] } + input[2] = [[],[]] + input[3] = [[],[]] + input[4] = [[],[]] + input[5] = [[],[]] + input[6] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/chromograph/tests/main.nf.test.snap b/modules/nf-core/chromograph/tests/main.nf.test.snap new file mode 100644 index 000000000..1bf107b8a --- /dev/null +++ b/modules/nf-core/chromograph/tests/main.nf.test.snap @@ -0,0 +1,382 @@ +{ + "test_chromograph_sites_wig": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "updsites_21.png:md5,819946a2718817268668ee73f5062351", + "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75" + ] + ] + ], + "1": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ], + "plots": [ + [ + [ + + ], + [ + "updsites_21.png:md5,819946a2718817268668ee73f5062351", + "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75" + ] + ] + ], + "versions_chromograph": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-01-28T11:38:25.707495" + }, + "test_chromograph_sites_wig_euploid": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "updsites_1.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_10.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_11.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_12.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_13.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_14.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_15.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_16.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_17.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_18.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_19.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_2.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_20.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_21.png:md5,819946a2718817268668ee73f5062351", + "updsites_22.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_3.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_4.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_5.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_6.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_7.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_8.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_9.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_M.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_X.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_Y.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr1.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr10.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr11.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr12.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr13.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr14.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr15.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr16.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr17.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr18.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr19.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr2.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr20.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr21.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr22.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75", + "wig_input_chr4.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr5.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr6.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr7.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr8.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr9.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrM.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrX.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrY.png:md5,33d95212be5bf91fbea53500bcbba19c" + ] + ] + ], + "1": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ], + "plots": [ + [ + [ + + ], + [ + "updsites_1.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_10.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_11.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_12.png:md5,33d95212be5bf91fbea53500bcbba19c", + 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"updsites_9.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_M.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_X.png:md5,33d95212be5bf91fbea53500bcbba19c", + "updsites_Y.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr1.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr10.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr11.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr12.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr13.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr14.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr15.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr16.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr17.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr18.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr19.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr2.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr20.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr21.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr22.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75", + "wig_input_chr4.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr5.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr6.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr7.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr8.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chr9.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrM.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrX.png:md5,33d95212be5bf91fbea53500bcbba19c", + "wig_input_chrY.png:md5,33d95212be5bf91fbea53500bcbba19c" + ] + ] + ], + "versions_chromograph": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-01-28T11:38:34.365039" + }, + "test_chromograph_sites_wig_stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ], + "plots": [ + [ + [ + + ], + [ + "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_chromograph": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-01-28T11:38:41.365186" + }, + "test_chromograph_sites_wig_euploid_stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ], + "plots": [ + [ + [ + + ], + [ + "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "updsites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "wig_input.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_chromograph": [ + [ + "CHROMOGRAPH", + "chromograph", + "1.3.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-01-28T11:38:48.971868" + } +} \ No newline at end of file diff --git a/modules/nf-core/chromograph/tests/nextflow.config b/modules/nf-core/chromograph/tests/nextflow.config new file mode 100644 index 000000000..a0db35bc9 --- /dev/null +++ b/modules/nf-core/chromograph/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: CHROMOGRAPH { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/cnvnator/cnvnator/environment.yml b/modules/nf-core/cnvnator/cnvnator/environment.yml index 9cd8ebf35..6f421c9cc 100644 --- a/modules/nf-core/cnvnator/cnvnator/environment.yml +++ b/modules/nf-core/cnvnator/cnvnator/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf index 66427cd12..e891d4cf6 100644 --- a/modules/nf-core/cnvnator/cnvnator/main.nf +++ b/modules/nf-core/cnvnator/cnvnator/main.nf @@ -4,20 +4,19 @@ process CNVNATOR_CNVNATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvnator:0.4.1--py310h2dce045_7': - 'biocontainers/cnvnator:0.4.1--py310h2dce045_7' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a5/a54de0a286dcc6f73972be37104995ba96e37ef404f9d2bff294a7e8be5b7a92/data': + 'community.wave.seqera.io/library/cnvnator:0.4.1--5a467cfadbbc668d' }" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(root) tuple val(meta3), path(fasta) tuple val(meta4), path(fai) - val step output: - tuple val(output_meta), path("${output_meta.id}_${step}.root"), emit: root - tuple val(output_meta), path("*.tab") , emit: tab, optional: true - path "versions.yml" , emit: versions + tuple val(output_meta), path("${prefix}.root"), emit: root + tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true + tuple val("${task.process}"), val('cnvnator'), eval("cnvnator 2>&1 | sed -n '3s/CNVnator v//p'"), topic: versions, emit: versions_cnvnator when: task.ext.when == null || task.ext.when @@ -32,38 +31,24 @@ process CNVNATOR_CNVNATOR { } else { reference = '' } - calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' - mv_cmd = "mv ${prefix}.root ${prefix}_${step}.root" - steps = ["his", "stat", "partition", "call"] - cp_cmd = steps.contains(step) ? "cp ${root} ${prefix}.root" :"" + def calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' """ - $cp_cmd cnvnator \\ -root ${prefix}.root \\ $args \\ $reference \\ $input_cmd \\ $calls_cmd - - $mv_cmd - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) - END_VERSIONS """ stub: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" output_meta = bam ? meta : meta2 - def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : '' + def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : '' """ - touch ${prefix}_${step}.root - $calls_cmd + touch ${prefix}.root + $calls_cmd_opt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) - END_VERSIONS """ } diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 7ad6b4068..39643a6de 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -23,10 +23,12 @@ input: type: file description: Sorted BAM/CRAM/SAM file pattern: "*.bam" + ontologies: [] - bai: type: file description: Sorted BAM/CRAM/SAM file pattern: "*.bam" + ontologies: [] - - meta2: type: map description: | @@ -36,6 +38,7 @@ input: type: file description: ROOT file pattern: "*.root" + ontologies: [] - - meta3: type: map description: | @@ -45,6 +48,7 @@ input: type: file description: Path to a directory containing fasta files or a fasta file pattern: "*.fa" + ontologies: [] - - meta4: type: map description: | @@ -54,9 +58,10 @@ input: type: file description: Path to a fasta file index pattern: "*.fai" + ontologies: [] output: - - root: - - output_meta: + root: + - - output_meta: type: map description: | Groovy Map containing sample information @@ -65,8 +70,9 @@ output: type: file description: A ROOT file pattern: "*.root" - - tab: - - output_meta: + ontologies: [] + tab: + - - output_meta: type: map description: | Groovy Map containing sample information @@ -75,11 +81,31 @@ output: type: file description: A tab file containing cnvnator calls pattern: "*.tab" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_cnvnator: + - - ${task.process}: + type: string + description: The name of the process + - cnvnator: + type: string + description: The name of the tool + - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - cnvnator: + type: string + description: The name of the tool + - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test new file mode 100644 index 000000000..bc24b893f --- /dev/null +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test @@ -0,0 +1,127 @@ +nextflow_process { + + name "Test Process CNVNATOR_CNVNATOR" + config "./nextflow.config" + script "../main.nf" + process "CNVNATOR_CNVNATOR" + + tag "modules" + tag "modules_nfcore" + tag "cnvnator" + tag "cnvnator/cnvnator" + + setup { + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_RD") { + script "../main.nf" + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.bam.bai', checkIfExists:true) + ] + input[1] = [[:],[]] + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_HIST") { + script "../main.nf" + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_RD.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_STAT") { + script "../main.nf" + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_HIST.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_PARTITION") { + script "../main.nf" + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_STAT.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + } + + test("test_cnvnator") { + when { + params { + cnvnator_rd_args = '-chrom chr22' + cnvnator_hist_args = '-his 1000' + cnvnator_stat_args = '-stat 1000' + cnvnator_partition_args = '-partition 1000' + cnvnator_args = '-call 1000' + } + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_PARTITION.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.tab, + process.out.findAll { key, val -> key.startsWith("versions") }, + process.out.root.collect{ file(it[1]).name } + ).match()} + ) + } + } + + + test("test_cnvnator -- stub") { + options '-stub' + when { + params { + cnvnator_rd_args = '' + cnvnator_hist_args = '-his 1000' + cnvnator_stat_args = '-stat 1000' + cnvnator_partition_args = '-partition 1000' + cnvnator_args = '-call 1000' + } + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_PARTITION.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + } +} diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap new file mode 100644 index 000000000..879b22990 --- /dev/null +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "test_cnvnator": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.tab:md5,56246f1dab5e62cd7902963562f889fd" + ] + ], + { + "versions_cnvnator": [ + [ + "CNVNATOR_CNVNATOR", + "cnvnator", + "0.4.1" + ] + ] + }, + [ + "test.root" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-02T15:01:39.090472" + }, + "test_cnvnator -- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + "CNVNATOR_CNVNATOR", + "cnvnator", + "0.4.1" + ] + ], + "root": [ + [ + { + "id": "test", + "single_end": false + }, + "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tab": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_cnvnator": [ + [ + "CNVNATOR_CNVNATOR", + "cnvnator", + "0.4.1" + ] + ] + }, + { + "versions_cnvnator": [ + [ + "CNVNATOR_CNVNATOR", + "cnvnator", + "0.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-02T15:01:50.842069" + } +} \ No newline at end of file diff --git a/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config new file mode 100644 index 000000000..f971334b1 --- /dev/null +++ b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config @@ -0,0 +1,21 @@ +process { + withName: "CNVNATOR_RD" { + ext.args = params.cnvnator_rd_args + } + + withName: "CNVNATOR_HIST" { + ext.args = params.cnvnator_hist_args + } + + withName: "CNVNATOR_STAT" { + ext.args = params.cnvnator_stat_args + } + + withName: "CNVNATOR_PARTITION" { + ext.args = params.cnvnator_partition_args + } + + withName: "CNVNATOR_CNVNATOR" { + ext.args = params.cnvnator_args + } +} diff --git a/modules/nf-core/cnvnator/convert2vcf/environment.yml b/modules/nf-core/cnvnator/convert2vcf/environment.yml index 9cd8ebf35..6f421c9cc 100644 --- a/modules/nf-core/cnvnator/convert2vcf/environment.yml +++ b/modules/nf-core/cnvnator/convert2vcf/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvnator/convert2vcf/main.nf b/modules/nf-core/cnvnator/convert2vcf/main.nf index 87dd031a3..0d52b80fb 100644 --- a/modules/nf-core/cnvnator/convert2vcf/main.nf +++ b/modules/nf-core/cnvnator/convert2vcf/main.nf @@ -4,15 +4,15 @@ process CNVNATOR_CONVERT2VCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/cnvnator:0.4.1--py310h2dce045_7': - 'biocontainers/cnvnator:0.4.1--py310h2dce045_7' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a5/a54de0a286dcc6f73972be37104995ba96e37ef404f9d2bff294a7e8be5b7a92/data': + 'community.wave.seqera.io/library/cnvnator:0.4.1--5a467cfadbbc668d' }" input: tuple val(meta), path(calls) output: tuple val(meta), path("*.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('cnvnator'), eval("cnvnator 2>&1 | sed -n '3s/CNVnator v//p'"), topic: versions, emit: versions_cnvnator when: task.ext.when == null || task.ext.when @@ -25,22 +25,14 @@ process CNVNATOR_CONVERT2VCF { ${calls} \\ $args \\ > ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator : \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) - END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf + echo ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator : \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) - END_VERSIONS + touch ${prefix}.vcf """ } diff --git a/modules/nf-core/cnvnator/convert2vcf/meta.yml b/modules/nf-core/cnvnator/convert2vcf/meta.yml index 3d686c2f1..57960b81f 100644 --- a/modules/nf-core/cnvnator/convert2vcf/meta.yml +++ b/modules/nf-core/cnvnator/convert2vcf/meta.yml @@ -23,9 +23,11 @@ input: type: file description: A tab file containing CNVnator calls pattern: "*.tab" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,11 +36,30 @@ output: type: file description: CNVnator calls in vcf format pattern: "*.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_cnvnator: + - - ${task.process}: + type: string + description: The name of the process + - cnvnator: + type: string + description: The name of the tool + - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - cnvnator: + type: string + description: The name of the tool + - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test new file mode 100644 index 000000000..723a32226 --- /dev/null +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_process { + + name "Test Process CNVNATOR_CONVERT2VCF" + config "./nextflow.config" + script "../main.nf" + process "CNVNATOR_CONVERT2VCF" + + tag "modules" + tag "modules_nfcore" + tag "cnvnator" + tag "cnvnator/cnvnator" + tag "cnvnator/convert2vcf" + + setup { + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_RD") { + script "../../cnvnator/main.nf" + + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam.bai', checkIfExists:true) + ] + input[1] = [[:],[]] + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_HIST") { + script "../../cnvnator/main.nf" + + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_RD.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_STAT") { + script "../../cnvnator/main.nf" + + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_HIST.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_PARTITION") { + script "../../cnvnator/main.nf" + + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_STAT.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + + run("CNVNATOR_CNVNATOR", alias: "CNVNATOR_CALL") { + script "../../cnvnator/main.nf" + + process { + """ + input[0] = [[:],[],[]] + input[1] = CNVNATOR_PARTITION.out.root + input[2] = [[:],[]] + input[3] = [[:],[]] + """ + } + } + } + + test("test_cnvnator_convert2vcf") { + + when { + params { + cnvnator_rd_args = '-chrom chr22' + cnvnator_hist_args = '-his 1000' + cnvnator_stat_args = '-stat 1000' + cnvnator_partition_args = '-partition 1000' + cnvnator_call_args = '-call 1000' + } + process { + """ + input[0] = CNVNATOR_CALL.out.tab + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf[0][1]).vcf.variantsMD5 + ).match() } + ) + } + } + + + test("test_cnvnator_convert2vcf -- stub") { + options '-stub' + when { + params { + cnvnator_rd_args = '-chrom chr22' + cnvnator_hist_args = '-his 1000' + cnvnator_stat_args = '-stat 1000' + cnvnator_partition_args = '-partition 1000' + cnvnator_call_args = '-call 1000' + } + process { + """ + input[0] = CNVNATOR_CALL.out.tab + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap new file mode 100644 index 000000000..c8e740009 --- /dev/null +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap @@ -0,0 +1,64 @@ +{ + "test_cnvnator_convert2vcf": { + "content": [ + { + "versions_cnvnator": [ + [ + "CNVNATOR_CONVERT2VCF", + "cnvnator", + "0.4.1" + ] + ] + }, + "b47837c71432a5ffc854c7936b5966d0" + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-02T15:02:17.740405" + }, + "test_cnvnator_convert2vcf -- stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "CNVNATOR_CONVERT2VCF", + "cnvnator", + "0.4.1" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_cnvnator": [ + [ + "CNVNATOR_CONVERT2VCF", + "cnvnator", + "0.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-02T15:02:31.268041" + } +} \ No newline at end of file diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config new file mode 100644 index 000000000..f056ed315 --- /dev/null +++ b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + withName: "CNVNATOR_RD" { + ext.args = params.cnvnator_rd_args + } + withName: "CNVNATOR_HIST" { + ext.args = params.cnvnator_hist_args + } + + withName: "CNVNATOR_STAT" { + ext.args = params.cnvnator_stat_args + } + + withName: "CNVNATOR_PARTITION" { + ext.args = params.cnvnator_partition_args + } + + withName: "CNVNATOR_CALL" { + ext.args = params.cnvnator_call_args + } +} diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf index 41338f28c..77889e2e8 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/main.nf +++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf @@ -6,7 +6,7 @@ process DEEPVARIANT_RUNDEEPVARIANT { // https://github.com/bioconda/bioconda-recipes/pull/45214#issuecomment-1890937836 // BUG https://github.com/nf-core/modules/issues/1754 // BUG https://github.com/bioconda/bioconda-recipes/issues/30310 - container "docker.io/google/deepvariant:1.8.0" + container "docker.io/google/deepvariant:1.9.0" input: tuple val(meta), path(input), path(index), path(intervals) @@ -16,11 +16,12 @@ process DEEPVARIANT_RUNDEEPVARIANT { tuple val(meta5), path(par_bed) output: - tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf - tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi - tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf - tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi + tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf + tuple val(meta), path("${prefix}.g.vcf.gz.tbi") , emit: gvcf_tbi + tuple val(meta), path("${prefix}.visual_report.html"), emit: report, optional: true + tuple val("${task.process}"), val('deepvariant'), eval("/opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //'"), topic: versions, emit: versions_deepvariant when: task.ext.when == null || task.ext.when @@ -46,11 +47,6 @@ process DEEPVARIANT_RUNDEEPVARIANT { ${par_regions} \\ --intermediate_results_dir=tmp \\ --num_shards=${task.cpus} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) - END_VERSIONS """ stub: @@ -60,14 +56,8 @@ process DEEPVARIANT_RUNDEEPVARIANT { } prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz - touch ${prefix}.vcf.gz.tbi - touch ${prefix}.g.vcf.gz - touch ${prefix}.g.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) - END_VERSIONS - """ + echo "stub" | gzip > ${prefix}.vcf.gz + echo "stub" | gzip > ${prefix}.vcf.gz.tbi + echo "stub" | gzip > ${prefix}.g.vcf.gz + echo "stub" | gzip > ${prefix}.g.vcf.gz.tbi """ } diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml index 29b45ff91..3e4e97efb 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/meta.yml +++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml @@ -1,14 +1,14 @@ name: deepvariant_rundeepvariant -description: DeepVariant is an analysis pipeline that uses a deep neural network to - call genetic variants from next-generation DNA sequencing data +description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network - to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural + network to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant @@ -25,13 +25,16 @@ input: type: file description: BAM/CRAM file pattern: "*.bam/cram" + ontologies: [] - index: type: file description: Index of BAM/CRAM file pattern: "*.bai/crai" + ontologies: [] - intervals: type: file description: file containing intervals + ontologies: [] - - meta2: type: map description: | @@ -41,6 +44,7 @@ input: type: file description: The reference fasta file pattern: "*.fasta" + ontologies: [] - - meta3: type: map description: | @@ -50,6 +54,7 @@ input: type: file description: Index of reference fasta file pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -59,6 +64,7 @@ input: type: file description: GZI index of reference fasta file pattern: "*.gzi" + ontologies: [] - - meta5: type: map description: | @@ -68,9 +74,10 @@ input: type: file description: BED file containing PAR regions pattern: "*.bed" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -79,8 +86,10 @@ output: type: file description: Compressed VCF file pattern: "*.vcf.gz" - - vcf_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + vcf_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -89,8 +98,9 @@ output: type: file description: Tabix index file of compressed VCF pattern: "*.vcf.gz.tbi" - - gvcf: - - meta: + ontologies: [] + gvcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -99,8 +109,10 @@ output: type: file description: Compressed GVCF file pattern: "*.g.vcf.gz" - - gvcf_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + gvcf_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -109,11 +121,42 @@ output: type: file description: Tabix index file of compressed GVCF pattern: "*.g.vcf.gz.tbi" - - versions: - - versions.yml: + ontologies: [] + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.visual_report.html: type: file - description: File containing software versions - pattern: "versions.yml" + description: Visual report in HTML format + pattern: "*.html" + optional: true + ontologies: [] + versions_deepvariant: + - - ${task.process}: + type: string + description: The process the versions were collected from + - deepvariant: + type: string + description: The tool name + - /opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - deepvariant: + type: string + description: The tool name + - /opt/deepvariant/bin/run_deepvariant --version | sed 's/^.*version //': + type: eval + description: The expression to obtain the version of the tool + authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test index 0790fb813..b22ca383f 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test @@ -8,11 +8,14 @@ nextflow_process { tag "deepvariant" tag "modules" tag "modules_nfcore" + config "./nextflow.config" test("homo_sapiens - [bam, bai] - fasta - fai") { - when { - config "./nextflow.config" + when { + params { + module_args = '--regions=\"chr22:0-40001\" --model_type=WGS' + } process { """ input[0] = [ @@ -48,9 +51,11 @@ nextflow_process { } test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai") { - config "./nextflow-intervals.config" when { + params { + module_args = '--model_type=WGS' + } process { """ input[0] = [ @@ -86,9 +91,11 @@ nextflow_process { } test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed") { - config "./nextflow-non-autosomal-calling.config" - tag "test" + when { + params { + module_args = '--model_type=WGS --haploid_contigs chr22' + } process { """ input[0] = [ @@ -125,9 +132,96 @@ nextflow_process { } test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai") { + + when { + params { + module_args = '--regions=\"chr22:0-40001\" --model_type=WGS' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [bam, bai] - fasta - fai - stub") { + + options "-stub" + when { - config "./nextflow.config" + params { + module_args = '' + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai - stub") { + + options "-stub" + + when { + params { + module_args = '' + } process { """ input[0] = [ diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap index 8e836336d..4ed36cb84 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "1": [ @@ -17,7 +17,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], "2": [ @@ -26,7 +26,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "3": [ @@ -35,11 +35,18 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] ], "4": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ], "gvcf": [ [ @@ -47,7 +54,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "gvcf_tbi": [ @@ -56,8 +63,11 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] + ], + "report": [ + ], "vcf": [ [ @@ -65,7 +75,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "vcf_tbi": [ @@ -74,19 +84,23 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], - "versions": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-14T08:16:22.036932742" + "timestamp": "2026-01-30T10:26:37.893603098" }, "homo_sapiens - [bam, bai] - fasta - fai": { "content": [ @@ -97,7 +111,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "1": [ @@ -106,7 +120,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], "2": [ @@ -115,7 +129,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "3": [ @@ -124,11 +138,18 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] ], "4": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ], "gvcf": [ [ @@ -136,7 +157,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "gvcf_tbi": [ @@ -145,8 +166,11 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] + ], + "report": [ + ], "vcf": [ [ @@ -154,7 +178,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "vcf_tbi": [ @@ -163,19 +187,23 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], - "versions": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-14T08:13:35.621497498" + "timestamp": "2026-01-30T10:23:01.002396661" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": { "content": [ @@ -186,7 +214,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "1": [ @@ -195,7 +223,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], "2": [ @@ -204,7 +232,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "3": [ @@ -213,11 +241,18 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] ], "4": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ], "gvcf": [ [ @@ -225,7 +260,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc" + "test_out.g.vcf.gz:md5,89b2e47883a65bb9cae8f173e782bb17" ] ], "gvcf_tbi": [ @@ -234,8 +269,11 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9" + "test_out.g.vcf.gz.tbi:md5,1680c67fe988bc1d8220fbb4127c2c18" ] + ], + "report": [ + ], "vcf": [ [ @@ -243,7 +281,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee" + "test_out.vcf.gz:md5,707212230030c8c3efbe5c2e0428da03" ] ], "vcf_tbi": [ @@ -252,19 +290,23 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59" + "test_out.vcf.gz.tbi:md5,248648ca03f5fda904ebbef8821e0e37" ] ], - "versions": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-14T08:14:32.23781232" + "timestamp": "2026-01-30T10:24:41.218929693" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": { "content": [ @@ -275,7 +317,213 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,b79936a7bf53fa4ee7e5866664e37d56" + "test_out.vcf.gz:md5,b3d1a03998c435d8c37be7c9c868f3c0" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz.tbi:md5,d57a16c0fda381a7bf659789d889a9d4" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz:md5,61833a909ae1bc176b47a5afc9fdc517" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz.tbi:md5,673ce95e6701a5e7d58ea2ab93440b27" + ] + ], + "4": [ + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz:md5,61833a909ae1bc176b47a5afc9fdc517" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz.tbi:md5,673ce95e6701a5e7d58ea2ab93440b27" + ] + ], + "report": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz:md5,b3d1a03998c435d8c37be7c9c868f3c0" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz.tbi:md5,d57a16c0fda381a7bf659789d889a9d4" + ] + ], + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-30T10:25:39.678376571" + }, + "homo_sapiens - [bam, bai] - fasta - fai - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] + ], + "4": [ + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] + ], + "report": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] + ], + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-30T10:27:08.029325062" + }, + "homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_out.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "1": [ @@ -284,7 +532,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,22f9f4c6c8c1faa8b129eddf32b445b8" + "test_out.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "2": [ @@ -293,7 +541,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,c82ce85ed16dcabe411995c52aaffd85" + "test_out.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "3": [ @@ -302,11 +550,18 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,6420a456b0507c70c8423293395c29bc" + "test_out.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "4": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + + ], + "5": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ], "gvcf": [ [ @@ -314,7 +569,7 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz:md5,c82ce85ed16dcabe411995c52aaffd85" + "test_out.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "gvcf_tbi": [ @@ -323,8 +578,11 @@ "id": "test", "single_end": false }, - "test_out.g.vcf.gz.tbi:md5,6420a456b0507c70c8423293395c29bc" + "test_out.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] + ], + "report": [ + ], "vcf": [ [ @@ -332,7 +590,7 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz:md5,b79936a7bf53fa4ee7e5866664e37d56" + "test_out.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "vcf_tbi": [ @@ -341,18 +599,22 @@ "id": "test", "single_end": false }, - "test_out.vcf.gz.tbi:md5,22f9f4c6c8c1faa8b129eddf32b445b8" + "test_out.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], - "versions": [ - "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01" + "versions_deepvariant": [ + [ + "DEEPVARIANT_RUNDEEPVARIANT", + "deepvariant", + "1.9.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-01-14T08:15:29.680851997" + "timestamp": "2026-01-30T10:27:35.653099478" } } \ No newline at end of file diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config deleted file mode 100644 index 78d8d5982..000000000 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - withName: DEEPVARIANT_RUNDEEPVARIANT { - ext.args = '--model_type=WGS ' - ext.prefix = { "${meta.id}_out" } - } - -} diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config deleted file mode 100644 index 6d265292a..000000000 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - withName: DEEPVARIANT_RUNDEEPVARIANT { - ext.args = '--model_type=WGS --haploid_contigs chr22' - ext.prefix = { "${meta.id}_out" } - } - -} diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config index 77e355cae..9693059b8 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config @@ -1,8 +1,6 @@ process { - withName: DEEPVARIANT_RUNDEEPVARIANT { - ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS ' - ext.prefix = { "${meta.id}_out" } - } - + ext.args = params.module_args + ext.prefix = { "${meta.id}_out" } + } } diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml deleted file mode 100644 index 958b8e414..000000000 --- a/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -deepvariant/rundeepvariant: - - modules/nf-core/deepvariant/rundeepvariant/** diff --git a/modules/nf-core/expansionhunter/environment.yml b/modules/nf-core/expansionhunter/environment.yml index 951de76c0..97f251f51 100644 --- a/modules/nf-core/expansionhunter/environment.yml +++ b/modules/nf-core/expansionhunter/environment.yml @@ -6,4 +6,3 @@ channels: dependencies: - bioconda::expansionhunter=5.0.0 - - bioconda::htslib=1.18 diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index dbcb175fc..82b6ec9c1 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -4,8 +4,8 @@ process EXPANSIONHUNTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/expansionhunter:5.0.0--hf366f20_0' : - 'biocontainers/expansionhunter:5.0.0--hf366f20_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/14/14e1d96665f934a98e569fc5a6fa237f98d3753eee2b6f60d0aea8ff9d44f406/data' : + 'community.wave.seqera.io/library/expansionhunter:5.0.0--389ada7e191a4fba' }" input: tuple val(meta), path(bam), path(bai) @@ -17,7 +17,8 @@ process EXPANSIONHUNTER { tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.json.gz") , emit: json tuple val(meta), path("*_realigned.bam") , emit: bam - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//'"), topic: versions, emit: versions_expansionhunter + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -38,11 +39,6 @@ process EXPANSIONHUNTER { bgzip --threads ${task.cpus} ${args2} ${prefix}.vcf bgzip --threads ${task.cpus} ${args2} ${prefix}.json - cat <<-END_VERSIONS > versions.yml - "${task.process}": - expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | head -1 | sed 's/^.*ExpansionHunter v//') - bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//') - END_VERSIONS """ stub: @@ -52,10 +48,5 @@ process EXPANSIONHUNTER { echo "" | gzip > ${prefix}.json.gz touch ${prefix}_realigned.bam - cat <<-END_VERSIONS > versions.yml - "${task.process}": - expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | head -1 | sed 's/^.*ExpansionHunter v//') - bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//') - END_VERSIONS """ } diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml index 44ca3361c..f9e5475cc 100644 --- a/modules/nf-core/expansionhunter/meta.yml +++ b/modules/nf-core/expansionhunter/meta.yml @@ -98,13 +98,46 @@ output: description: BAM/CRAM file pattern: "*.{bam,cram}" ontologies: [] + versions_expansionhunter: + - - ${task.process}: + type: string + description: The process the versions were collected from + - expansionhunter: + type: string + description: The tool name + - ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//': + type: eval + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bgzip: + type: string + description: The tool name + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - expansionhunter: + type: string + description: The tool name + - ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - bgzip: + type: string + description: The tool name + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@jemten" maintainers: diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test.snap b/modules/nf-core/expansionhunter/tests/main.nf.test.snap index a4e09f4c3..4cf42a7c5 100644 --- a/modules/nf-core/expansionhunter/tests/main.nf.test.snap +++ b/modules/nf-core/expansionhunter/tests/main.nf.test.snap @@ -23,18 +23,29 @@ { "id": "test" }, - "test_realigned.bam:md5,b37a72c0b97b45e63636a9758f3144d7" + "test_realigned.bam:md5,3f9de11932f2548f8259c063ac37ab94" ] ], "3": [ - "versions.yml:md5,056b525f67ba23c361f0c65f47256dca" + [ + "EXPANSIONHUNTER", + "expansionhunter", + "5.0.0]" + ] + ], + "4": [ + [ + "EXPANSIONHUNTER", + "bgzip", + "1.22.1" + ] ], "bam": [ [ { "id": "test" }, - "test_realigned.bam:md5,b37a72c0b97b45e63636a9758f3144d7" + "test_realigned.bam:md5,3f9de11932f2548f8259c063ac37ab94" ] ], "json": [ @@ -53,16 +64,27 @@ "test.vcf.gz:md5,cfd4a1d35c0e469b99eb6aaa6d22de76" ] ], - "versions": [ - "versions.yml:md5,056b525f67ba23c361f0c65f47256dca" + "versions_bgzip": [ + [ + "EXPANSIONHUNTER", + "bgzip", + "1.22.1" + ] + ], + "versions_expansionhunter": [ + [ + "EXPANSIONHUNTER", + "expansionhunter", + "5.0.0]" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-03T12:20:15.18545069" + "timestamp": "2026-01-29T15:38:57.19607229" }, "stub": { "content": [ @@ -92,7 +114,18 @@ ] ], "3": [ - "versions.yml:md5,056b525f67ba23c361f0c65f47256dca" + [ + "EXPANSIONHUNTER", + "expansionhunter", + "5.0.0]" + ] + ], + "4": [ + [ + "EXPANSIONHUNTER", + "bgzip", + "1.22.1" + ] ], "bam": [ [ @@ -118,15 +151,26 @@ "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,056b525f67ba23c361f0c65f47256dca" + "versions_bgzip": [ + [ + "EXPANSIONHUNTER", + "bgzip", + "1.22.1" + ] + ], + "versions_expansionhunter": [ + [ + "EXPANSIONHUNTER", + "expansionhunter", + "5.0.0]" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-03T12:20:28.430115" + "timestamp": "2026-01-29T15:39:11.490611694" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 68863d677..60b10ed1c 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -1,11 +1,11 @@ process GATK4_BEDTOINTERVALLIST { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(bed) @@ -13,7 +13,7 @@ process GATK4_BEDTOINTERVALLIST { output: tuple val(meta), path('*.interval_list'), emit: interval_list - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -24,33 +24,24 @@ process GATK4_BEDTOINTERVALLIST { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ BedToIntervalList \\ - --INPUT $bed \\ + --INPUT ${bed} \\ --OUTPUT ${prefix}.interval_list \\ - --SEQUENCE_DICTIONARY $dict \\ + --SEQUENCE_DICTIONARY ${dict} \\ --TMP_DIR . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.interval_list - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 25348e162..a3e2f2347 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -26,6 +26,7 @@ input: type: file description: Input bed file pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -35,25 +36,40 @@ input: type: file description: Sequence dictionary pattern: "*.dict" + ontologies: [] output: - - interval_list: - - meta: + interval_list: + - - meta: type: file description: gatk interval list file pattern: "*.interval_list" + ontologies: [] - "*.interval_list": type: file description: gatk interval list file pattern: "*.interval_list" - - _list: - type: file - description: gatk interval list file - pattern: "*.interval_list" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test index 2289f73fa..8d318e906 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - [file(params.modules_testdata_base_path + + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] ] input[1] = [ [ id:'dict' ], // meta map @@ -27,12 +27,35 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } -} \ No newline at end of file + test("test_gatk4_bedtointervallist - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + input[1] = [ [ id:'dict' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap index 48c322fd0..554425060 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -1,4 +1,45 @@ { + "test_gatk4_bedtointervallist - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GATK4_BEDTOINTERVALLIST", + "gatk4", + "4.6.2.0" + ] + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_gatk4": [ + [ + "GATK4_BEDTOINTERVALLIST", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-22T09:52:55.698969373" + }, "test_gatk4_bedtointervallist": { "content": [ { @@ -11,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + [ + "GATK4_BEDTOINTERVALLIST", + "gatk4", + "4.6.2.0" + ] ], "interval_list": [ [ @@ -21,15 +66,19 @@ "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" ] ], - "versions": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions_gatk4": [ + [ + "GATK4_BEDTOINTERVALLIST", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-19T14:20:12.168775" + "timestamp": "2026-01-22T09:52:46.629308651" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml deleted file mode 100644 index b4d54f129..000000000 --- a/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/bedtointervallist: - - "modules/nf-core/gatk4/bedtointervallist/**" diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 2c545d224..750923375 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -1,11 +1,11 @@ process GATK4_COLLECTREADCOUNTS { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(input), path(input_index), path(intervals) @@ -14,9 +14,9 @@ process GATK4_COLLECTREADCOUNTS { tuple val(meta4), path(dict) output: - tuple val(meta), path("*.hdf5"), optional: true, emit: hdf5 - tuple val(meta), path("*.tsv") , optional: true, emit: tsv - path "versions.yml" , emit: versions + tuple val(meta), path("*.hdf5"), emit: hdf5, optional: true + tuple val(meta), path("*.tsv"), emit: tsv, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -25,45 +25,42 @@ process GATK4_COLLECTREADCOUNTS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--reference $fasta" : "" - def extension = args.contains("--format HDF5") ? "hdf5" : - args.contains("--format TSV") ? "tsv" : - "hdf5" + def reference = fasta ? "--reference ${fasta}" : "" + def extension = args.contains("--format HDF5") + ? "hdf5" + : args.contains("--format TSV") + ? "tsv" + : "hdf5" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK COLLECTREADCOUNTS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK COLLECTREADCOUNTS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ CollectReadCounts \\ - --input $input \\ - --intervals $intervals \\ - --output ${prefix}.$extension \\ - $reference \\ + --input ${input} \\ + --intervals ${intervals} \\ + --output ${prefix}.${extension} \\ + ${reference} \\ --tmp-dir . \\ - $args + ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--format HDF5") ? "hdf5" : - args.contains("--format TSV") ? "tsv" : - "hdf5" + def extension = args.contains("--format HDF5") + ? "hdf5" + : args.contains("--format TSV") + ? "tsv" + : "hdf5" """ touch ${prefix}.${extension} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index cf8c7731d..a65f7f065 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,6 +1,7 @@ name: "gatk4_collectreadcounts" -description: Collects read counts at specified intervals. The count for each interval - is calculated by counting the number of read starts that lie in the interval. +description: Collects read counts at specified intervals. The count for each + interval is calculated by counting the number of read starts that lie in the + interval. keywords: - collectreadcounts - bam @@ -8,11 +9,11 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform - at the Broad Institute, the toolkit offers a wide variety of tools with a primary - focus on variant discovery and genotyping. Its powerful processing engine and - high-performance computing features make it capable of taking on projects of - any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences + Platform at the Broad Institute, the toolkit offers a wide variety of + tools with a primary focus on variant discovery and genotyping. Its + powerful processing engine and high-performance computing features make it + capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk @@ -29,14 +30,17 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - input_index: type: file description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" + ontologies: [] - intervals: type: file description: A file containing the specified intervals pattern: "*.{bed,intervals}" + ontologies: [] - - meta2: type: map description: | @@ -46,6 +50,7 @@ input: type: file description: Optional - Reference FASTA pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -55,6 +60,7 @@ input: type: file description: Optional - Index of the reference FASTA file pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -64,9 +70,10 @@ input: type: file description: Optional - Sequence dictionary of the reference FASTA file pattern: "*.dict" + ontologies: [] output: - - hdf5: - - meta: + hdf5: + - - meta: type: map description: | Groovy Map containing sample information @@ -75,8 +82,9 @@ output: type: file description: The read counts in hdf5 format pattern: "*.hdf5" - - tsv: - - meta: + ontologies: [] + tsv: + - - meta: type: map description: | Groovy Map containing sample information @@ -85,11 +93,29 @@ output: type: file description: The read counts in TSV format pattern: "*.tsv" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index 28a3a6e15..ca6304c51 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -15,7 +15,11 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] ], "hdf5": [ @@ -29,16 +33,20 @@ "test.tsv:md5,d9a32039b7a84f5bb74e8382e5427670" ] ], - "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions_gatk4": [ + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T12:58:19.610687" + "timestamp": "2026-02-03T11:04:47.877494" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ @@ -69,7 +77,11 @@ ] ], "2": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] ], "hdf5": [ @@ -83,15 +95,19 @@ "test.tsv:md5,8e45a6164916c303387f39f02ce45841" ] ], - "versions": [ - "versions.yml:md5,ebf23f4ab63948ba97df07035f8d2659" + "versions_gatk4": [ + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T12:58:07.500024" + "timestamp": "2026-02-03T11:04:25.535499" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b3..750e9c411 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,18 +1,18 @@ process GATK4_CREATESEQUENCEDICTIONARY { - tag "$fasta" - label 'process_medium' + tag "${fasta}" + label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(fasta) output: - tuple val(meta), path('*.dict') , emit: dict - path "versions.yml" , emit: versions + tuple val(meta), path('*.dict'), emit: dict + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -22,31 +22,22 @@ process GATK4_CREATESEQUENCEDICTIONARY { def avail_mem = 6144 if (!task.memory) { - log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ CreateSequenceDictionary \\ - --REFERENCE $fasta \\ - --URI $fasta \\ + --REFERENCE ${fasta} \\ + --URI ${fasta} \\ --TMP_DIR . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: """ touch ${fasta.baseName}.dict - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 7b5156bb3..9a5c9f235 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -14,7 +14,8 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] + licence: + - "Apache-2.0" identifier: "" input: - - meta: @@ -26,21 +27,40 @@ input: type: file description: Input fasta file pattern: "*.{fasta,fa}" + ontologies: [] output: - - dict: - - meta: + dict: + - - meta: type: file description: gatk dictionary file pattern: "*.{dict}" + ontologies: [] - "*.dict": type: file description: gatk dictionary file pattern: "*.{dict}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f954..497c8cf09 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + [ + "GATK4_CREATESEQUENCEDICTIONARY", + "gatk4", + "4.6.2.0" + ] ], "dict": [ [ @@ -21,16 +25,20 @@ "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions_gatk4": [ + [ + "GATK4_CREATESEQUENCEDICTIONARY", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-16T10:16:16.34453" + "timestamp": "2026-02-03T11:24:16.167358" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + [ + "GATK4_CREATESEQUENCEDICTIONARY", + "gatk4", + "4.6.2.0" + ] ], "dict": [ [ @@ -54,15 +66,19 @@ "genome.dict:md5,7362679f176e0f52add03c08f457f646" ] ], - "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions_gatk4": [ + [ + "GATK4_CREATESEQUENCEDICTIONARY", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-16T13:58:25.822068" + "timestamp": "2026-02-03T11:24:00.222321" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml deleted file mode 100644 index 035c5e4c7..000000000 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/createsequencedictionary: - - "modules/nf-core/gatk4/createsequencedictionary/**" diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 878e85c6f..73790c636 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -1,11 +1,11 @@ process GATK4_DENOISEREADCOUNTS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(counts) @@ -13,8 +13,8 @@ process GATK4_DENOISEREADCOUNTS { output: tuple val(meta), path("*_standardizedCR.tsv"), emit: standardized - tuple val(meta), path("*_denoisedCR.tsv") , emit: denoised - path "versions.yml" , emit: versions + tuple val(meta), path("*_denoisedCR.tsv"), emit: denoised + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -25,9 +25,10 @@ process GATK4_DENOISEREADCOUNTS { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK DenoiseReadCounts] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK DenoiseReadCounts] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ @@ -38,23 +39,12 @@ process GATK4_DENOISEREADCOUNTS { --count-panel-of-normals ${pon} \\ --standardized-copy-ratios ${prefix}_standardizedCR.tsv \\ --denoised-copy-ratios ${prefix}_denoisedCR.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_standardizedCR.tsv touch ${prefix}_denoisedCR.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/denoisereadcounts/meta.yml b/modules/nf-core/gatk4/denoisereadcounts/meta.yml index 367321ba2..0c7835a7e 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/meta.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/meta.yml @@ -26,6 +26,8 @@ input: type: file description: Read counts in hdf5 or tsv format. pattern: "*.{hdf5,tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV - - meta2: type: map description: | @@ -35,9 +37,10 @@ input: type: file description: Panel of normals file hdf5 or tsv format. pattern: "*.{hdf5}" + ontologies: [] output: - - standardized: - - meta: + standardized: + - - meta: type: map description: | Groovy Map containing sample information @@ -46,8 +49,10 @@ output: type: file description: Standardized copy ratios file. pattern: "*.{tsv}" - - denoised: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + denoised: + - - meta: type: map description: | Groovy Map containing sample information @@ -56,11 +61,30 @@ output: type: file description: Denoised copy ratios file pattern: "*.{tsv}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test index e5fef2a2a..34268f630 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test @@ -67,7 +67,7 @@ nextflow_process { { assert snapshot( process.out.standardized, process.out.denoised, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index f35eb283d..26892e208 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -19,14 +19,20 @@ "test_denoisedCR.tsv:md5,f9e56b8e12b4dadc91a6d977fa79c6a8" ] ], - [ - "versions.yml:md5,140780e1af7318cc9259b8970bc70c81" - ] + { + "versions_gatk4": [ + [ + "GATK4_DENOISEREADCOUNTS", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-16T12:34:12.568925" + "timestamp": "2026-02-03T11:36:00.92882" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/tags.yml b/modules/nf-core/gatk4/denoisereadcounts/tests/tags.yml deleted file mode 100644 index 5f105a82a..000000000 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/tags.yml +++ /dev/null @@ -1,6 +0,0 @@ -gatk4/denoisereadcounts: - - "modules/nf-core/gatk4/denoisereadcounts/**" - - "modules/nf-core/gatk4/createreadcountpanelofnormals/**" - - "modules/nf-core/gatk4/collectreadcounts/**" - - "modules/nf-core/gatk4/preprocessintervals/**" - - "modules/nf-core/gatk4/denoisereadcounts/**" diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 4db496933..f23d3ee9d 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -15,7 +15,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { output: tuple val(meta), path("${prefix}-calls"), emit: calls tuple val(meta), path("${prefix}-model"), emit: model, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -54,10 +54,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { --tmp-dir . \\ ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -66,9 +62,5 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { touch ${prefix}-calls touch ${prefix}-model - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 45e717651..0e0c1610d 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -81,13 +81,27 @@ output: A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). pattern: "*-model/" + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index a6d0fb7b7..e7187b03c 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -63,7 +63,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, ).match() } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap index ac6caa6ab..213238f85 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -1,9 +1,15 @@ { "homo sapiens - bam": { "content": [ - [ - "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" - ], + { + "versions_gatk4": [ + [ + "GATK4_DETERMINEGERMLINECONTIGPLOIDY", + "gatk4", + "4.6.2.0" + ] + ] + }, [ "SAMPLE_0", "SAMPLE_1" @@ -20,10 +26,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-15T12:53:00.186632174" + "timestamp": "2026-02-03T13:46:07.36352943" }, "homo sapiens - bam - stub": { "content": [ @@ -45,7 +51,11 @@ ] ], "2": [ - "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" + [ + "GATK4_DETERMINEGERMLINECONTIGPLOIDY", + "gatk4", + "4.6.2.0" + ] ], "calls": [ [ @@ -63,15 +73,19 @@ "test-model:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,42bacd108c52aae6228da94d0779ec6f" + "versions_gatk4": [ + [ + "GATK4_DETERMINEGERMLINECONTIGPLOIDY", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-15T12:53:17.594899648" + "timestamp": "2026-02-03T13:47:11.516191863" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index 0532ec025..b3fb9116d 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -1,11 +1,11 @@ process GATK4_FILTERMUTECTCALLS { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate) @@ -14,10 +14,10 @@ process GATK4_FILTERMUTECTCALLS { tuple val(meta4), path(dict) output: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val(meta), path("*.filteringStats.tsv"), emit: stats - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -26,34 +26,31 @@ process GATK4_FILTERMUTECTCALLS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def orientationbias_command = orientationbias ? orientationbias.collect{"--orientation-bias-artifact-priors $it"}.join(' ') : '' - def segmentation_command = segmentation ? segmentation.collect{"--tumor-segmentation $it"}.join(' ') : '' - def estimate_command = estimate ? " --contamination-estimate ${estimate} " : '' - def table_command = table ? table.collect{"--contamination-table $it"}.join(' ') : '' + def orientationbias_command = orientationbias ? orientationbias.collect { "--orientation-bias-artifact-priors ${it}" }.join(' ') : '' + def segmentation_command = segmentation ? segmentation.collect { "--tumor-segmentation ${it}" }.join(' ') : '' + def estimate_command = estimate ? " --contamination-estimate ${estimate} " : '' + def table_command = table ? table.collect { "--contamination-table ${it}" }.join(' ') : '' def avail_mem = 3072 if (!task.memory) { - log.info '[GATK FilterMutectCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK FilterMutectCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ FilterMutectCalls \\ - --variant $vcf \\ + --variant ${vcf} \\ --output ${prefix}.vcf.gz \\ - --reference $fasta \\ - $orientationbias_command \\ - $segmentation_command \\ - $estimate_command \\ - $table_command \\ + --reference ${fasta} \\ + ${orientationbias_command} \\ + ${segmentation_command} \\ + ${estimate_command} \\ + ${table_command} \\ --tmp-dir . \\ - $args + ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -63,9 +60,5 @@ process GATK4_FILTERMUTECTCALLS { touch ${prefix}.vcf.gz.tbi touch ${prefix}.vcf.gz.filteringStats.tsv - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/filtermutectcalls/meta.yml b/modules/nf-core/gatk4/filtermutectcalls/meta.yml index 9287277eb..eb3e9baf4 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/meta.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/meta.yml @@ -27,28 +27,36 @@ input: type: file description: compressed vcf file of mutect2calls pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - vcf_tbi: type: file description: Tabix index of vcf file pattern: "*vcf.gz.tbi" + ontologies: [] - stats: type: file description: Stats file that pairs with output vcf file pattern: "*vcf.gz.stats" + ontologies: [] - orientationbias: type: file description: files containing artifact priors for input vcf. Optional input. pattern: "*.artifact-prior.tar.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - segmentation: type: file description: tables containing segmentation information for input vcf. Optional input. pattern: "*.segmentation.table" + ontologies: [] - table: type: file description: table(s) containing contamination data for input vcf. Optional input, takes priority over estimate. pattern: "*.contamination.table" + ontologies: [] - estimate: type: float description: estimation of contamination value as a double. Optional input, @@ -62,6 +70,7 @@ input: type: file description: The reference fasta file pattern: "*.fasta" + ontologies: [] - - meta3: type: map description: | @@ -71,6 +80,7 @@ input: type: file description: Index of reference fasta file pattern: "*.fasta.fai" + ontologies: [] - - meta4: type: map description: | @@ -80,39 +90,67 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: file description: file containing filtered mutect2 calls. pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.vcf.gz": type: file description: file containing filtered mutect2 calls. pattern: "*.vcf.gz" - - tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: type: file - description: tbi file that pairs with vcf. - pattern: "*.vcf.gz.tbi" + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.vcf.gz.tbi": type: file description: tbi file that pairs with vcf. pattern: "*.vcf.gz.tbi" - - stats: - - meta: + ontologies: [] + stats: + - - meta: type: file - description: file containing statistics of the filtermutectcalls run. - pattern: "*.filteringStats.tsv" + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.filteringStats.tsv": type: file description: file containing statistics of the filtermutectcalls run. pattern: "*.filteringStats.tsv" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test index 83c3703fc..f775f3ed2 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test @@ -42,10 +42,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("versions_base") }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, - { assert path(process.out.tbi.get(0).get(1)).linesGzip.toString().contains("TBI")}, - { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0]).match() } + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), + file(process.out.stats[0][1]).readLines()[0] + ).match() } ) } @@ -83,10 +85,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("versions_with-files") }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, - { assert path(process.out.tbi.get(0).get(1)).linesGzip.toString().contains("TBI")}, - { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() } + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), + file(process.out.stats[0][1]).readLines()[0..5] + ).match() } ) } @@ -124,10 +128,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("versions_use-val") }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, - { assert path(process.out.tbi.get(0).get(1)).linesGzip.toString().contains("TBI")}, - { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0]).match() } + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), + file(process.out.stats[0][1]).readLines()[0] + ).match() } ) } diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 1c39e3b5d..6856af7e7 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -1,25 +1,36 @@ { "human - vcf - use-val": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_FILTERMUTECTCALLS", + "gatk4", + "4.6.2.0" + ] + ] + }, + "4f8cfebe28e5fd097a7bfc2e556983d3", + true, "#Ln prior of deletion of length 10=-20.72326583694641" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T12:46:03.887912" + "timestamp": "2026-02-03T13:24:33.782781" }, "versions_with-files": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.7" }, - "timestamp": "2024-05-15T12:45:43.679571" + "timestamp": "2025-09-15T14:22:04.77036932" }, "human - vcf - stub": { "content": [ @@ -49,7 +60,11 @@ ] ], "3": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + [ + "GATK4_FILTERMUTECTCALLS", + "gatk4", + "4.6.2.0" + ] ], "stats": [ [ @@ -75,43 +90,58 @@ "test.filtered.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions_gatk4": [ + [ + "GATK4_FILTERMUTECTCALLS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T12:46:32.666273" + "timestamp": "2026-02-03T13:24:52.944908" }, "versions_use-val": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.7" }, - "timestamp": "2024-05-15T12:46:03.876073" + "timestamp": "2025-09-15T14:22:18.790658915" }, "versions_base": { "content": [ [ - "versions.yml:md5,1e86368bd682668a6777ccf2cfd90689" + "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.7" }, - "timestamp": "2024-05-15T12:47:39.930795" + "timestamp": "2025-09-15T14:21:49.569533374" }, "human - vcf - with-files": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_FILTERMUTECTCALLS", + "gatk4", + "4.6.2.0" + ] + ] + }, + "54e439a79e4b6956a7f2c5b0730c9918", + true, [ "#Ln prior of deletion of length 10=-20.72326583694641", "#Ln prior of deletion of length 9=-20.72326583694641", @@ -122,19 +152,30 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T12:45:43.699286" + "timestamp": "2026-02-03T13:24:11.396747" }, "human - vcf - base": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_FILTERMUTECTCALLS", + "gatk4", + "4.6.2.0" + ] + ] + }, + "5352aa0f3ea986008a2652eba7c0fdba", + true, "#Ln prior of deletion of length 10=-20.72326583694641" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T12:47:39.949405" + "timestamp": "2026-02-03T13:23:48.108444" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/tags.yml b/modules/nf-core/gatk4/filtermutectcalls/tests/tags.yml deleted file mode 100644 index 447310318..000000000 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/filtermutectcalls: - - "modules/nf-core/gatk4/filtermutectcalls/**" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index 6da848d2e..c3e6b114e 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -14,7 +14,7 @@ process GATK4_GERMLINECNVCALLER { tuple val(meta), path("*-cnv-model/*-calls"), emit: cohortcalls, optional: true tuple val(meta), path("*-cnv-model/*-model"), emit: cohortmodel, optional: true tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -51,10 +51,6 @@ process GATK4_GERMLINECNVCALLER { ${intervals_command} \\ ${model_command} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -64,9 +60,5 @@ process GATK4_GERMLINECNVCALLER { mkdir -p ${prefix}-cnv-model/${prefix}-model mkdir -p ${prefix}-cnv-model/${prefix}-calls - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml index 4d8bb1d54..f820c629a 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml @@ -78,13 +78,27 @@ output: description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode pattern: "*-cnv-calls/*-calls" + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index d14ef9a0f..a3bb985ea 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -84,7 +84,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, ).match() } @@ -114,7 +114,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, ).match() } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index b7f71b5f1..311076984 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -1,9 +1,15 @@ { "homo sapiens - bam": { "content": [ - [ - "versions.yml:md5,abc17734413b02fbe4d397ac105213c2" - ], + { + "versions_gatk4": [ + [ + "GATK4_GERMLINECNVCALLER", + "gatk4", + "4.6.2.0" + ] + ] + }, [ "SAMPLE_0", "SAMPLE_1", @@ -29,16 +35,22 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-15T12:09:54.937398398" + "timestamp": "2026-02-03T15:09:50.216500599" }, "homo sapiens - bam - stub": { "content": [ - [ - "versions.yml:md5,abc17734413b02fbe4d397ac105213c2" - ], + { + "versions_gatk4": [ + [ + "GATK4_GERMLINECNVCALLER", + "gatk4", + "4.6.2.0" + ] + ] + }, [ ], @@ -47,9 +59,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-15T12:10:16.833243771" + "timestamp": "2026-02-03T15:12:05.192665905" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 400fa0380..2d69d3819 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -1,18 +1,18 @@ process GATK4_INTERVALLISTTOOLS { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(intervals) output: tuple val(meta), path("*_split/*/*.interval_list"), emit: interval_list - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -23,9 +23,10 @@ process GATK4_INTERVALLISTTOOLS { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK IntervalListTools] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK IntervalListTools] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ @@ -33,10 +34,10 @@ process GATK4_INTERVALLISTTOOLS { gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ IntervalListTools \\ - --INPUT $intervals \\ + --INPUT ${intervals} \\ --OUTPUT ${prefix}_split \\ --TMP_DIR . \\ - $args + ${args} python3 < versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -66,9 +63,5 @@ process GATK4_INTERVALLISTTOOLS { touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/intervallisttools/meta.yml b/modules/nf-core/gatk4/intervallisttools/meta.yml index 8ee15a297..7ed79afe0 100644 --- a/modules/nf-core/gatk4/intervallisttools/meta.yml +++ b/modules/nf-core/gatk4/intervallisttools/meta.yml @@ -26,9 +26,10 @@ input: - intervals: type: file description: Interval file + ontologies: [] output: - - interval_list: - - meta: + interval_list: + - - meta: type: map description: | Groovy Map containing sample information @@ -37,15 +38,28 @@ output: type: file description: Interval list files pattern: "*.interval_list" - - _list: - type: file - description: Interval list files - pattern: "*.interval_list" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@praveenraj2018" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 7718ed003..143136148 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -16,7 +16,11 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + [ + "GATK4_INTERVALLISTTOOLS", + "gatk4", + "4.6.2.0" + ] ], "interval_list": [ [ @@ -31,16 +35,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions_gatk4": [ + [ + "GATK4_INTERVALLISTTOOLS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-22T21:26:22.252885" + "timestamp": "2026-02-03T15:44:06.410817008" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -59,7 +67,11 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + [ + "GATK4_INTERVALLISTTOOLS", + "gatk4", + "4.6.2.0" + ] ], "interval_list": [ [ @@ -74,15 +86,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions_gatk4": [ + [ + "GATK4_INTERVALLISTTOOLS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-22T22:15:11.772344" + "timestamp": "2026-02-03T15:45:07.987268525" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/tests/tags.yml b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml deleted file mode 100644 index bf85ff5fa..000000000 --- a/modules/nf-core/gatk4/intervallisttools/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/intervallisttools: - - "modules/nf-core/gatk4/intervallisttools/**" diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 0085026c8..016b275f3 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -1,11 +1,11 @@ process GATK4_MERGEBAMALIGNMENT { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(aligned), path(unmapped) @@ -14,7 +14,7 @@ process GATK4_MERGEBAMALIGNMENT { output: tuple val(meta), path('*.bam'), emit: bam - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -25,24 +25,21 @@ process GATK4_MERGEBAMALIGNMENT { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK MergeBamAlignment] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK MergeBamAlignment] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ MergeBamAlignment \\ - --UNMAPPED_BAM $unmapped \\ - --ALIGNED_BAM $aligned \\ + --UNMAPPED_BAM ${unmapped} \\ + --ALIGNED_BAM ${aligned} \\ --OUTPUT ${prefix}.bam \\ - --REFERENCE_SEQUENCE $fasta \\ + --REFERENCE_SEQUENCE ${fasta} \\ --TMP_DIR . \\ - $args + ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -50,9 +47,5 @@ process GATK4_MERGEBAMALIGNMENT { """ touch ${prefix}.bam - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/mergebamalignment/meta.yml b/modules/nf-core/gatk4/mergebamalignment/meta.yml index 7bde93459..0d9bda912 100644 --- a/modules/nf-core/gatk4/mergebamalignment/meta.yml +++ b/modules/nf-core/gatk4/mergebamalignment/meta.yml @@ -27,10 +27,12 @@ input: type: file description: The aligned bam file pattern: "*.{bam}" + ontologies: [] - unmapped: type: file description: The unmapped bam file pattern: "*.{bam}" + ontologies: [] - - meta2: type: map description: | @@ -39,6 +41,7 @@ input: - fasta: type: file description: The reference fasta file + ontologies: [] - - meta3: type: map description: | @@ -47,21 +50,40 @@ input: - dict: type: file description: GATK sequence dictionary + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: file description: The merged bam file pattern: "*.bam" + ontologies: [] - "*.bam": type: file description: The merged bam file pattern: "*.bam" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test index 96e93bb19..d5878f4de 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test @@ -35,7 +35,7 @@ nextflow_process { { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 719a7bb33..2ebca8687 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + [ + "GATK4_MERGEBAMALIGNMENT", + "gatk4", + "4.6.2.0" + ] ], "bam": [ [ @@ -21,28 +25,38 @@ "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" + "versions_gatk4": [ + [ + "GATK4_MERGEBAMALIGNMENT", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T12:02:15.41024" + "timestamp": "2026-02-03T19:42:44.250559934" }, "test-gatk4-mergebamalignment": { "content": [ "30c325e1e032eb1782a280d34c0fb1c7", - [ - "versions.yml:md5,a72cfce8c9d171260cbb82b492be4372" - ] + { + "versions_gatk4": [ + [ + "GATK4_MERGEBAMALIGNMENT", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T12:02:08.379035" + "timestamp": "2026-02-03T19:42:06.516476761" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d43915..95f1eccc9 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_MERGEVCFS { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(vcf) @@ -13,8 +13,8 @@ process GATK4_MERGEVCFS { output: tuple val(meta), path('*.vcf.gz'), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -22,28 +22,25 @@ process GATK4_MERGEVCFS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input_list = vcf.collect{ "--INPUT $it"}.join(' ') - def reference_command = dict ? "--SEQUENCE_DICTIONARY $dict" : "" + def input_list = vcf.collect { "--INPUT ${it}" }.join(' ') + def reference_command = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK MergeVcfs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK MergeVcfs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ MergeVcfs \\ - $input_list \\ + ${input_list} \\ --OUTPUT ${prefix}.vcf.gz \\ - $reference_command \\ + ${reference_command} \\ --TMP_DIR . \\ - $args + ${args} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -52,9 +49,5 @@ process GATK4_MERGEVCFS { touch ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index b4f61d780..146eaf893 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -34,30 +34,54 @@ input: type: file description: Optional Sequence Dictionary as input pattern: "*.dict" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: file description: merged vcf file pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.vcf.gz": type: file description: merged vcf file pattern: "*.vcf.gz" - - tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: type: file - description: index files for the merged vcf files - pattern: "*.tbi" + description: merged vcf file + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.tbi": type: file description: index files for the merged vcf files pattern: "*.tbi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a2..f9765aab5 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs") @@ -48,6 +49,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict") @@ -75,6 +77,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict_stub") diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 62cceed57..14170940e 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,35 +1,62 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_MERGEVCFS", + "gatk4", + "4.6.2.0" + ] + ] + }, "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-02-14T14:57:40.784590995" + "timestamp": "2026-02-03T20:51:23.679671657" }, "test_gatk4_mergevcfs": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_MERGEVCFS", + "gatk4", + "4.6.2.0" + ] + ] + }, "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-02-14T14:56:42.178255913" + "timestamp": "2026-02-03T20:49:37.159554677" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + { + "versions_gatk4": [ + [ + "GATK4_MERGEVCFS", + "gatk4", + "4.6.2.0" + ] + ] + }, "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-02-14T14:57:11.404322124" + "timestamp": "2026-02-03T20:50:41.376990748" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/tests/tags.yml b/modules/nf-core/gatk4/mergevcfs/tests/tags.yml deleted file mode 100644 index d2a74ba2c..000000000 --- a/modules/nf-core/gatk4/mergevcfs/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/mergevcfs: - - "modules/nf-core/gatk4/mergevcfs/**" diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 79d8d2826..269c605f5 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -1,28 +1,30 @@ process GATK4_MUTECT2 { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(input), path(input_index), path(intervals) tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) + tuple val(meta3), path(fai), path(gzi) tuple val(meta4), path(dict) - path(germline_resource) - path(germline_resource_tbi) - path(panel_of_normals) - path(panel_of_normals_tbi) + path alleles + path alleles_tbi + path germline_resource + path germline_resource_tbi + path panel_of_normals + path panel_of_normals_tbi output: - tuple val(meta), path("*.vcf.gz") , emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi - tuple val(meta), path("*.stats") , emit: stats - tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2 - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.stats"), emit: stats + tuple val(meta), path("*.f1r2.tar.gz"), emit: f1r2, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -30,46 +32,39 @@ process GATK4_MUTECT2 { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def inputs = input.collect{ "--input $it"}.join(" ") - def interval_command = intervals ? "--intervals $intervals" : "" - def pon_command = panel_of_normals ? "--panel-of-normals $panel_of_normals" : "" - def gr_command = germline_resource ? "--germline-resource $germline_resource" : "" + def inputs = input.collect { vcf_ -> "--input ${vcf_}" }.join(" ") + def interval_command = intervals ? "--intervals ${intervals}" : "" + def pon_command = panel_of_normals ? "--panel-of-normals ${panel_of_normals}" : "" + def gr_command = germline_resource ? "--germline-resource ${germline_resource}" : "" + def a_command = alleles ? "--alleles ${alleles}": "" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ Mutect2 \\ - $inputs \\ + ${inputs} \\ --output ${prefix}.vcf.gz \\ - --reference $fasta \\ - $pon_command \\ - $gr_command \\ - $interval_command \\ + --reference ${fasta} \\ + ${pon_command} \\ + ${gr_command} \\ + ${a_command} \\ + ${interval_command} \\ --tmp-dir . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi touch ${prefix}.vcf.gz.stats - touch ${prefix}.f1r2.tar.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + echo "" | gzip > ${prefix}.f1r2.tar.gz """ } diff --git a/modules/nf-core/gatk4/mutect2/meta.yml b/modules/nf-core/gatk4/mutect2/meta.yml index 27fd63a24..46e21377f 100644 --- a/modules/nf-core/gatk4/mutect2/meta.yml +++ b/modules/nf-core/gatk4/mutect2/meta.yml @@ -37,6 +37,7 @@ input: type: file description: Specify region the tools is run on. pattern: ".{bed,interval_list}" + ontologies: [] - - meta2: type: map description: | @@ -45,7 +46,8 @@ input: - fasta: type: file description: The reference fasta file - pattern: "*.fasta" + pattern: "*.{fasta,fasta.gz}" + ontologies: [] - - meta3: type: map description: | @@ -54,7 +56,13 @@ input: - fai: type: file description: Index of reference fasta file - pattern: "*.fasta.fai" + pattern: "*.{fasta.fai,fasta.fai.gz}" + ontologies: [] + - gzi: + type: file + description: Index of bgzipped reference fasta file + pattern: "*.fasta.gz.gzi" + ontologies: [] - - meta4: type: map description: | @@ -64,66 +72,101 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - - - germline_resource: - type: file - description: Population vcf of germline sequencing, containing allele fractions. - pattern: "*.vcf.gz" - - - germline_resource_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" - - - panel_of_normals: - type: file - description: vcf file to be used as a panel of normals. - pattern: "*.vcf.gz" - - - panel_of_normals_tbi: - type: file - description: Index for the panel of normals. - pattern: "*.vcf.gz.tbi" + ontologies: [] + - alleles: + type: file + description: vcf file to be used to force-call alleles. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - alleles_tbi: + type: file + description: Index file for alleles to be force-called. + pattern: "*.vcf.gz.tbi" + ontologies: [] + - germline_resource: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - germline_resource_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + ontologies: [] + - panel_of_normals: + type: file + description: vcf file to be used as a panel of normals. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - panel_of_normals_tbi: + type: file + description: Index for the panel of normals. + pattern: "*.vcf.gz.tbi" + ontologies: [] output: - - vcf: - - meta: - type: file - description: compressed vcf file - pattern: "*.vcf.gz" + vcf: + - - meta: + type: map + description: A Groovy map containing sample information - "*.vcf.gz": type: file description: compressed vcf file pattern: "*.vcf.gz" - - tbi: - - meta: - type: file - description: Index of vcf file - pattern: "*vcf.gz.tbi" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: + type: map + description: A Groovy map containing sample information - "*.tbi": type: file description: Index of vcf file pattern: "*vcf.gz.tbi" - - stats: - - meta: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" + ontologies: [] + stats: + - - meta: + type: map + description: A Groovy map containing sample information - "*.stats": type: file description: Stats file that pairs with output vcf file pattern: "*vcf.gz.stats" - - f1r2: - - meta: - type: file - description: file containing information to be passed to LearnReadOrientationModel - (only outputted when tumor_normal_pair mode is run) - pattern: "*.f1r2.tar.gz" + ontologies: [] + f1r2: + - - meta: + type: map + description: A Groovy map containing sample information - "*.f1r2.tar.gz": type: file description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) pattern: "*.f1r2.tar.gz" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@GCJMackenzie" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/mutect2/tests/f1r2.config b/modules/nf-core/gatk4/mutect2/tests/f1r2.config deleted file mode 100644 index 2d3c8a170..000000000 --- a/modules/nf-core/gatk4/mutect2/tests/f1r2.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = { "--normal-sample $meta.normal_id --f1r2-tar-gz ${meta.id}.f1r2.tar.gz" } -} diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test b/modules/nf-core/gatk4/mutect2/tests/main.nf.test index aea8d2269..8917fd212 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test @@ -8,10 +8,13 @@ nextflow_process { tag "modules_nfcore" tag "gatk4" tag "gatk4/mutect2" + config "./nextflow.config" - test("tumor_normal_pair") { - config "./pair.config" + test("human - bam - tumor_normal_pair") { when { + params { + module_args = "--normal-sample normal" + } process { """ input[0] = [ @@ -36,16 +39,19 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) ] - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) - input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) - input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + input[4] = [] + input[5] = [] + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } @@ -55,20 +61,23 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("tumor_normal_pair_f1r2") { - config "./f1r2.config" + test("human - bam - tumor_normal_pair_f1r2") { + when { + params { + module_args = "--normal-sample normal --f1r2-tar-gz test.f1r2.tar.gz" + } process { """ input[0] = [ @@ -93,16 +102,19 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) ] - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) - input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) - input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + input[4] = [] + input[5] = [] + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } @@ -111,18 +123,22 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2.collect { file(it[1]).getName() }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("tumor_single"){ + + test("human - bam - tumor_only"){ when { + params { + module_args = '' + } process { """ input[0] = [ @@ -137,16 +153,19 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) ] - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) - input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) - input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + input[4] = [] + input[5] = [] + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } @@ -155,18 +174,22 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("cram_input"){ + + test("human - cram"){ when { + params { + module_args = '' + } process{ """ input[0] = [ @@ -181,16 +204,19 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) ] - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) - input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) - input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + input[4] = [] + input[5] = [] + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } @@ -199,19 +225,22 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("generate_pon") { + test("human - bam - generate_pon") { when { + params { + module_args = '' + } process { """ input[0] = [ @@ -226,7 +255,8 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], @@ -236,6 +266,8 @@ nextflow_process { input[5] = [] input[6] = [] input[7] = [] + input[8] = [] + input[9] = [] """ } } @@ -244,19 +276,22 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("mitochondria"){ + test("mitochondria - bam"){ when { + params { + module_args = "--mitochondria-mode" + } process { """ input[0] = [ @@ -271,7 +306,59 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)], + [] + ] + input[3] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[4] = [] + input[5] = [] + input[6] = [] + input[7] = [] + input[8] = [] + input[9] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } + ) + } + } + + test("mitochondria - bam - gz_ref"){ + when { + params { + module_args = "--mitochondria-mode" + } + process { + """ + input[0] = [ + [ id:'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam', checkIfExists: true)], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai', checkIfExists: true)], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true)], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true)] ] input[3] = [ [ id:'genome' ], @@ -281,6 +368,8 @@ nextflow_process { input[5] = [] input[6] = [] input[7] = [] + input[8] = [] + input[9] = [] """ } } @@ -289,20 +378,25 @@ nextflow_process { { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, process.out.stats, process.out.f1r2, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } } - test("tumor_normal_pair_f1r2_stubs"){ - options "-stub-run" + test("human - bam - tumor_normal_pair_f1r2 - stub"){ + + options "-stub" + when { + params { + module_args = '' + } process { """ input[0] = [ @@ -327,34 +421,142 @@ nextflow_process { ] input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] ] input[3] = [ [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) ] - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) - input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) - input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + input[4] = [] + input[5] = [] + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) """ } } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("human - bam - tumor_normal_pair - force_call") { + when { + params { + module_args = "" + } + process { + """ + input[0] = [ + [ + id:'test', + normal_id:'normal', + tumor_id:'tumour' + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true) + ], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] + ] + input[3] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + ] + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', checkIfExists: true) + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + """ + } + } + then { assertAll( { assert process.success }, { assert snapshot( - process.out.vcf.collect { file(it[1]).getName() }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats.collect { file(it[1]).getName() }, - process.out.f1r2.collect { file(it[1]).getName() }, - process.out.versions.collect { file(it[1]).getName() } + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } + } + test("human - bam - tumor_only - force_call"){ + when { + params { + module_args = '' + } + process { + """ + input[0] = [ + [ id:'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true)], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)], + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)], + [] + ] + input[3] = [ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + ] + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/axiom_exome_plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi', checkIfExists: true) + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) + input[8] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true) + input[9] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { + assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } + ) + } } } diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index f047af19d..76db52e05 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -1,33 +1,40 @@ { - "tumor_normal_pair_f1r2_stubs": { + "human - bam - generate_pon": { "content": [ - [ - "test.vcf.gz" - ], + "876aa6be01c0c8fc71ad8e99ed842240", [ "test.vcf.gz.tbi" ], [ - "test.vcf.gz.stats" + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,b569ce66bbffe9588b3d221e821023ee" + ] ], [ - "test.f1r2.tar.gz" + ], - [ - "h" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-21T10:14:45.599103891" + "timestamp": "2026-02-03T21:26:03.059145991" }, - "generate_pon": { + "human - bam - tumor_only - force_call": { "content": [ - [ - "test.vcf.gz" - ], + "9c2928d0e751262c048ac162b9223e4e", [ "test.vcf.gz.tbi" ], @@ -36,56 +43,66 @@ { "id": "test" }, - "test.vcf.gz.stats:md5,b569ce66bbffe9588b3d221e821023ee" + "test.vcf.gz.stats:md5,2398263886ecb546c8055af4fbad6040" ] ], [ ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-20T15:57:18.264453766" + "timestamp": "2026-02-03T21:37:31.740160738" }, - "mitochondria": { + "human - bam - tumor_normal_pair": { "content": [ - [ - "test.vcf.gz" - ], + "7418ed45a029394253817a5eb7149334", [ "test.vcf.gz.tbi" ], [ [ { - "id": "test" + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" }, - "test.vcf.gz.stats:md5,4f77301a125913170b8e9e7828b4ca3f" + "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6" ] ], [ ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-20T16:05:47.668766905" + "timestamp": "2026-02-03T21:10:46.039204223" }, - "cram_input": { + "human - cram": { "content": [ - [ - "test.vcf.gz" - ], + "1b65f1a163b517944bf2e4b74230e035", [ "test.vcf.gz.tbi" ], @@ -100,21 +117,58 @@ [ ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-20T15:52:27.894730554" + "timestamp": "2026-02-03T21:22:38.825106184" }, - "tumor_single": { + "mitochondria - bam": { "content": [ + "ea70f79e33805a2c0b47b32a48a8d26f", [ - "test.vcf.gz" + "test.vcf.gz.tbi" + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,fc6ea14ca2da346babe78161beea28c9" + ] ], + [ + + ], + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-03T21:26:44.448416009" + }, + "human - bam - tumor_only": { + "content": [ + "1b65f1a163b517944bf2e4b74230e035", [ "test.vcf.gz.tbi" ], @@ -129,21 +183,58 @@ [ ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-20T15:43:28.935723443" + "timestamp": "2026-02-03T21:19:10.024181048" }, - "tumor_normal_pair": { + "mitochondria - bam - gz_ref": { "content": [ + "ea70f79e33805a2c0b47b32a48a8d26f", + [ + "test.vcf.gz.tbi" + ], [ - "test.vcf.gz" + [ + { + "id": "test" + }, + "test.vcf.gz.stats:md5,fc6ea14ca2da346babe78161beea28c9" + ] ], + [ + + ], + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-03T21:27:29.464429837" + }, + "human - bam - tumor_normal_pair - force_call": { + "content": [ + "63c4ff01a8316f4243b6b12b06ded74e", [ "test.vcf.gz.tbi" ], @@ -154,27 +245,136 @@ "normal_id": "normal", "tumor_id": "tumour" }, - "test.vcf.gz.stats:md5,17d2091015d04cbd4a26b7a67dc659e6" + "test.vcf.gz.stats:md5,81390058f99b80db30c89020aa9fc546" ] ], [ ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-20T15:31:31.913366311" + "timestamp": "2026-02-03T21:33:21.41092687" }, - "tumor_normal_pair_f1r2": { + "human - bam - tumor_normal_pair_f1r2 - stub": { "content": [ - [ - "test.vcf.gz" - ], + { + "0": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.f1r2.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ], + "f1r2": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.f1r2.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "stats": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "normal_id": "normal", + "tumor_id": "tumour" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-03T21:28:08.170677731" + }, + "human - bam - tumor_normal_pair_f1r2": { + "content": [ + "7418ed45a029394253817a5eb7149334", [ "test.vcf.gz.tbi" ], @@ -191,14 +391,20 @@ [ "test.f1r2.tar.gz" ], - [ - "versions.yml:md5,d94731c50c20569fe9896235a843f382" - ] + { + "versions_gatk4": [ + [ + "GATK4_MUTECT2", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-03-21T09:45:52.321385704" + "timestamp": "2026-02-03T21:15:39.798158102" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mutect2/tests/mito.config b/modules/nf-core/gatk4/mutect2/tests/mito.config deleted file mode 100644 index de61d3e24..000000000 --- a/modules/nf-core/gatk4/mutect2/tests/mito.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = { "--mitochondria-mode" } -} diff --git a/modules/nf-core/gatk4/mutect2/tests/nextflow.config b/modules/nf-core/gatk4/mutect2/tests/nextflow.config new file mode 100644 index 000000000..08e942851 --- /dev/null +++ b/modules/nf-core/gatk4/mutect2/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_MUTECT2 { + ext.args = params.module_args + } +} diff --git a/modules/nf-core/gatk4/mutect2/tests/pair.config b/modules/nf-core/gatk4/mutect2/tests/pair.config deleted file mode 100644 index 2a812b825..000000000 --- a/modules/nf-core/gatk4/mutect2/tests/pair.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = { "--normal-sample $meta.normal_id" } -} diff --git a/modules/nf-core/gatk4/mutect2/tests/tags.yml b/modules/nf-core/gatk4/mutect2/tests/tags.yml deleted file mode 100644 index 461879274..000000000 --- a/modules/nf-core/gatk4/mutect2/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/mutect2: - - "modules/nf-core/gatk4/mutect2/**" diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md deleted file mode 100644 index c6a454565..000000000 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Conda is not supported at the moment - -The [bioconda](https://bioconda.github.io/recipes/gatk4/README.html) recipe is not fully working as expected, cf [github issue](https://github.com/broadinstitute/gatk/issues/7811) - -Hence, we are using the docker container provided by the authors of the tool: - -- [broadinstitute/gatk](https://hub.docker.com/r/broadinstitute/gatk) - -This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/gatk) for convenience. diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml new file mode 100644 index 000000000..67e0eb860 --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index 73d4a7158..f87511d5f 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -1,47 +1,48 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' - //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 - container "nf-core/gatk:4.5.0.0" //Biocontainers is missing a package + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(calls), path(model), path(ploidy) output: - tuple val(meta), path("*_genotyped_intervals.vcf.gz") , emit: intervals, optional: true - tuple val(meta), path("*_genotyped_segments.vcf.gz") , emit: segments, optional: true - tuple val(meta), path("*_denoised.vcf.gz") , emit: denoised, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*_genotyped_intervals.vcf.gz"), emit: intervals, optional: true + tuple val(meta), path("*_genotyped_segments.vcf.gz"), emit: segments, optional: true + tuple val(meta), path("*_denoised.vcf.gz"), emit: denoised, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : "" - def model_command = model ? model.collect{"--model-shard-path $it"}.join(' ') : "" - def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" + def calls_command = calls ? calls.collect { "--calls-shard-path ${it}" }.join(' ') : "" + def model_command = model ? model.collect { "--model-shard-path ${it}" }.join(' ') : "" + def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK GermlineCNVCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK PostProcessGermlineCnvCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ export THEANO_FLAGS="base_compiledir=\$PWD" + export PYTENSOR_FLAGS="base_compiledir=\$PWD" gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ PostprocessGermlineCNVCalls \\ - $calls_command \\ - $model_command \\ - $ploidy_command \\ + ${calls_command} \\ + ${model_command} \\ + ${ploidy_command} \\ + ${args} \\ --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\ --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\ --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz @@ -53,15 +54,11 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { """ stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." - } def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_genotyped_intervals.vcf.gz - touch ${prefix}_genotyped_segments.vcf.gz - touch ${prefix}_denoised.vcf.gz + echo "" | gzip > ${prefix}_genotyped_intervals.vcf.gz + echo "" | gzip > ${prefix}_genotyped_segments.vcf.gz + echo "" | gzip > ${prefix}_denoised.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml index d090169ab..c093baf1d 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml @@ -39,8 +39,8 @@ input: When a model is supplied to tool will run in CASE mode. pattern: "*-calls/" output: - - intervals: - - meta: + intervals: + - - meta: type: map description: | Groovy Map containing sample information @@ -49,12 +49,10 @@ output: type: file description: Intervals VCF file pattern: "*.vcf.gz" - - s: - type: file - description: Intervals VCF file - pattern: "*.vcf.gz" - - segments: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + segments: + - - meta: type: map description: | Groovy Map containing sample information @@ -63,8 +61,10 @@ output: type: file description: Segments VCF file pattern: "*.vcf.gz" - - denoised: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + denoised: + - - meta: type: map description: | Groovy Map containing sample information @@ -73,11 +73,29 @@ output: type: file description: Denoised copy ratio file pattern: "*.vcf.gz" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ryanjameskennedy" maintainers: diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test new file mode 100644 index 000000000..00415fd0a --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -0,0 +1,154 @@ +nextflow_process { + + name "Test Process GATK4_POSTPROCESSGERMLINECNVCALLS" + script "../main.nf" + config "./nextflow.config" + process "GATK4_POSTPROCESSGERMLINECNVCALLS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/germlinecnvcaller" + tag "gatk4/postprocessgermlinecnvcalls" + + setup { + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + intervals = [[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] + dict = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] + + input = [intervals, dict] + """ + } + } + run("GATK4_COLLECTREADCOUNTS"){ + script "../../collectreadcounts/main.nf" + process { + """ + input_bam = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + ]) + + fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() + + input = [input_bam, fasta, fai, dict] + """ + } + } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY", alias: "GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT") { + script "../../determinegermlinecontigploidy/main.nf" + process { + """ + bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + input = [ + GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(bed) + .map({ meta, counts, bed -> [ meta, counts, bed, [] ]}), + [[],[]], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists: true) + ] + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_COHORT") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) + """ + } + } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_CASE") { + script "../../germlinecnvcaller/main.nf" + process { + """ + input[0] = GATK4_COLLECTREADCOUNTS.out.tsv + .first() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) + """ + } + } + } + + test("homo sapiens - counts") { + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } + ) + } + + } + + test("homo sapiens - counts - stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") }, + file(process.out.intervals[0][1]).name, + file(process.out.segments[0][1]).name, + file(process.out.denoised[0][1]).name, + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap new file mode 100644 index 000000000..15ae1944a --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -0,0 +1,44 @@ +{ + "homo sapiens - counts - stub": { + "content": [ + { + "versions_gatk4": [ + [ + "GATK4_POSTPROCESSGERMLINECNVCALLS", + "gatk4", + "4.6.2.0" + ] + ] + }, + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-03T22:29:17.166798377" + }, + "homo sapiens - counts": { + "content": [ + { + "versions_gatk4": [ + [ + "GATK4_POSTPROCESSGERMLINECNVCALLS", + "gatk4", + "4.6.2.0" + ] + ] + }, + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz" + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-03T22:26:44.628515186" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config new file mode 100644 index 000000000..81566d90e --- /dev/null +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/nextflow.config @@ -0,0 +1,15 @@ +process { + withName: 'GATK4_COLLECTREADCOUNTS*' { + ext.args = "--format TSV --interval-merging-rule OVERLAPPING_ONLY" + } + withName: 'GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + ext.prefix = "ploidy" + } + withName: 'GATK4_GERMLINECNVCALLER_COHORT' { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY --run-mode COHORT" + } + withName: 'GATK4_GERMLINECNVCALLER_CASE' { + ext.args = "--run-mode CASE" + } +} diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index f97180adc..62b771650 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -1,11 +1,11 @@ process GATK4_PRINTREADS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(input), path(index) @@ -14,10 +14,10 @@ process GATK4_PRINTREADS { tuple val(meta4), path(dict) output: - tuple val(meta), path("${prefix}.bam") , emit: bam, optional: true - tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true - tuple val(meta), path("${prefix}.sam") , emit: sam, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -28,9 +28,10 @@ process GATK4_PRINTREADS { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK PrintReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK PrintReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } if ("${input}" == "${prefix}.${input.extension}") { error("Output filename is the same as input filename. Please specify a different prefix.") @@ -38,16 +39,11 @@ process GATK4_PRINTREADS { """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ PrintReads \\ - $args \\ - --reference $fasta \\ - --input $input \\ - --read-index $index \\ + ${args} \\ + --reference ${fasta} \\ + --input ${input} \\ + --read-index ${index} \\ --output ${prefix}.${input.getExtension()} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -56,10 +52,5 @@ process GATK4_PRINTREADS { touch ${prefix}.${input.getExtension()} touch ${prefix}.${input.getExtension()} touch ${prefix}.${input.getExtension()} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/printreads/meta.yml b/modules/nf-core/gatk4/printreads/meta.yml index de8da7c56..34de84ceb 100644 --- a/modules/nf-core/gatk4/printreads/meta.yml +++ b/modules/nf-core/gatk4/printreads/meta.yml @@ -27,10 +27,12 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + ontologies: [] - index: type: file description: BAM/CRAM/SAM file pattern: "*.{bai,crai,sai}" + ontologies: [] - - meta2: type: map description: | @@ -40,6 +42,7 @@ input: type: file description: reference fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -49,6 +52,7 @@ input: type: file description: reference fasta index file pattern: "*.{fai}" + ontologies: [] - - meta4: type: map description: | @@ -58,9 +62,10 @@ input: type: file description: reference fasta dictionary file pattern: "*.{dict}" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -69,8 +74,9 @@ output: type: file description: Sorted BAM file pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -79,8 +85,9 @@ output: type: file description: Sorted CRAM file pattern: "*.{cram}" - - sam: - - meta: + ontologies: [] + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -89,11 +96,28 @@ output: type: file description: Sorted SAM file pattern: "*.{sam}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test index c07886197..f86f08a1d 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test @@ -44,7 +44,7 @@ nextflow_process { bam(process.out.bam[0][1]).getReadsMD5(), process.out.cram, process.out.sam, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -85,7 +85,7 @@ nextflow_process { process.out.bam, bam(process.out.cram[0][1]).getHeaderMD5(), process.out.sam, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index 7f1266f26..e47cdcae4 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -8,33 +8,45 @@ [ ], - [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" - ] + { + "versions_gatk4": [ + [ + "GATK4_PRINTREADS", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:48:53.871683" + "timestamp": "2026-02-04T10:04:26.642559" }, "test-gatk4-printreads-cram": { "content": [ [ ], - "591299d00e262474250c5ccc241bba59", + "b1319b92694dfa02102224820fcc1ada", [ ], - [ - "versions.yml:md5,9b368270d802ed95c530a7f0105f6453" - ] + { + "versions_gatk4": [ + [ + "GATK4_PRINTREADS", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T13:42:29.968056" + "timestamp": "2026-02-04T10:04:46.522705" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/revertsam/main.nf b/modules/nf-core/gatk4/revertsam/main.nf index 635784ab2..8aa5747e0 100644 --- a/modules/nf-core/gatk4/revertsam/main.nf +++ b/modules/nf-core/gatk4/revertsam/main.nf @@ -1,18 +1,18 @@ process GATK4_REVERTSAM { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(bam) output: tuple val(meta), path('*.bam'), emit: bam - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -23,32 +23,23 @@ process GATK4_REVERTSAM { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK RevertSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK RevertSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ RevertSam \\ - --INPUT $bam \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.reverted.bam \\ --TMP_DIR . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.reverted.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/revertsam/meta.yml b/modules/nf-core/gatk4/revertsam/meta.yml index fb73b13f7..3cbc0cd1c 100644 --- a/modules/nf-core/gatk4/revertsam/meta.yml +++ b/modules/nf-core/gatk4/revertsam/meta.yml @@ -25,21 +25,40 @@ input: type: file description: The input bam/sam file pattern: "*.{bam,sam}" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: file description: The reverted bam/sam file pattern: "*.reverted.bam" + ontologies: [] - "*.bam": type: file description: The reverted bam/sam file pattern: "*.reverted.bam" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test index b52680485..e06c041f4 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 1cbb5ce6e..3858e13bf 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -2,15 +2,21 @@ "test-gatk4-revertsam": { "content": [ "e3cfa46b13cc4fc425cccae944f43b10", - [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" - ] + { + "versions_gatk4": [ + [ + "GATK4_REVERTSAM", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:45:39.712635" + "timestamp": "2026-02-04T10:08:17.497786" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -24,7 +30,11 @@ ] ], "1": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + [ + "GATK4_REVERTSAM", + "gatk4", + "4.6.2.0" + ] ], "bam": [ [ @@ -34,15 +44,19 @@ "test.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,ee8dfa21abb49349e4865984cc122b9e" + "versions_gatk4": [ + [ + "GATK4_REVERTSAM", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:45:46.856318" + "timestamp": "2026-02-04T10:08:32.702485" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/samtofastq/main.nf b/modules/nf-core/gatk4/samtofastq/main.nf index 35b9b76db..0e3867f87 100644 --- a/modules/nf-core/gatk4/samtofastq/main.nf +++ b/modules/nf-core/gatk4/samtofastq/main.nf @@ -1,18 +1,18 @@ process GATK4_SAMTOFASTQ { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(bam) output: tuple val(meta), path('*.fastq.gz'), emit: fastq - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -24,34 +24,25 @@ process GATK4_SAMTOFASTQ { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ SamToFastq \\ - --INPUT $bam \\ - $output \\ + --INPUT ${bam} \\ + ${output} \\ --TMP_DIR . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.fastq.gz - touch ${prefix}_1.fastq.gz - touch ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + echo "" | gzip > ${prefix}.fastq.gz + echo "" | gzip > ${prefix}_1.fastq.gz + echo "" | gzip > ${prefix}_2.fastq.gz """ } diff --git a/modules/nf-core/gatk4/samtofastq/meta.yml b/modules/nf-core/gatk4/samtofastq/meta.yml index 91a8e503f..b392f8bc1 100644 --- a/modules/nf-core/gatk4/samtofastq/meta.yml +++ b/modules/nf-core/gatk4/samtofastq/meta.yml @@ -25,21 +25,39 @@ input: type: file description: Input SAM/BAM file pattern: "*.{bam,sam}" + ontologies: [] output: - - fastq: - - meta: - type: file - description: converted fastq file - pattern: "*.fastq" + fastq: + - - meta: + type: map + description: A Groovy map containing sample information - "*.fastq.gz": type: file description: converted fastq file pattern: "*.fastq" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test index 30a41addd..b9af8b189 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { { assert process.success }, { assert snapshot( path(process.out.fastq[0][1]).linesGzip[3..7], - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -53,7 +53,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { path(it).linesGzip[3..7] }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -78,7 +78,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { file(it).name }, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index 0e1ec4b79..abeb9291f 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -8,15 +8,21 @@ "+", "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE versions.yml "${task.process}": @@ -47,7 +48,7 @@ process GATK4_SELECTVARIANTS { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gatk4/selectvariants/meta.yml b/modules/nf-core/gatk4/selectvariants/meta.yml index 5fd9c6f39..3297ea69b 100644 --- a/modules/nf-core/gatk4/selectvariants/meta.yml +++ b/modules/nf-core/gatk4/selectvariants/meta.yml @@ -34,9 +34,10 @@ input: type: file description: One or more genomic intervals over which to operate pattern: ".intervals" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -45,8 +46,10 @@ output: type: file description: Compressed VCF file pattern: "*.selectvariants.vcf.gz" - - tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,11 +58,28 @@ output: type: file description: Tabix index file pattern: "*.vcf.gz.tbi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@mjcipriano" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test index d8a97d2c5..3fea99ec1 100644 --- a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test @@ -30,7 +30,8 @@ nextflow_process { then { assertAll( {assert process.success}, - {assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2")} + {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, + {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} ) } @@ -55,7 +56,8 @@ nextflow_process { then { assertAll( {assert process.success}, - {assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2")} + {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, + {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} ) } diff --git a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test.snap b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test.snap new file mode 100644 index 000000000..6007162b1 --- /dev/null +++ b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test.snap @@ -0,0 +1,38 @@ +{ + "selectvariants - gz input": { + "content": [ + { + "versions_gatk4": [ + [ + "GATK4_SELECTVARIANTS", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T10:16:52.22932" + }, + "selectvariants - vcf input": { + "content": [ + { + "versions_gatk4": [ + [ + "GATK4_SELECTVARIANTS", + "gatk4", + "4.6.2.0" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T10:16:31.972787" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/selectvariants/tests/tags.yml b/modules/nf-core/gatk4/selectvariants/tests/tags.yml deleted file mode 100644 index d9fb50f77..000000000 --- a/modules/nf-core/gatk4/selectvariants/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/selectvariants: - - "modules/nf-core/gatk4/selectvariants/**" diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 350ff8d33..5ccc867ea 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -1,11 +1,11 @@ process GATK4_SHIFTFASTA { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(fasta) @@ -13,13 +13,13 @@ process GATK4_SHIFTFASTA { tuple val(meta3), path(dict) output: - tuple val(meta), path("*_shift.fasta") , emit: shift_fa - tuple val(meta), path("*_shift.fasta.fai") , emit: shift_fai - tuple val(meta), path("*_shift.back_chain") , emit: shift_back_chain - tuple val(meta), path("*_shift.dict") , emit: dict , optional: true - tuple val(meta), path("*.intervals") , emit: intervals , optional: true - tuple val(meta), path("*.shifted.intervals") , emit: shift_intervals , optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*_shift.fasta"), emit: shift_fa + tuple val(meta), path("*_shift.fasta.fai"), emit: shift_fai + tuple val(meta), path("*_shift.back_chain"), emit: shift_back_chain + tuple val(meta), path("*_shift.dict"), emit: dict, optional: true + tuple val(meta), path("*.intervals"), emit: intervals, optional: true + tuple val(meta), path("*.shifted.intervals"), emit: shift_intervals, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -31,24 +31,20 @@ process GATK4_SHIFTFASTA { def avail_mem = 3072 if (!task.memory) { - log.info '[GATK ShiftFasta] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK ShiftFasta] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ ShiftFasta \\ - --reference $fasta \\ + --reference ${fasta} \\ --output ${prefix}_shift.fasta \\ --shift-back-output ${prefix}_shift.back_chain \\ - $args \\ - $seq_dict \\ + ${args} \\ + ${seq_dict} \\ --tmp-dir . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -59,10 +55,5 @@ process GATK4_SHIFTFASTA { touch test.shifted.intervals touch test_shift.fasta touch test_shift.fasta.fai - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/shiftfasta/meta.yml b/modules/nf-core/gatk4/shiftfasta/meta.yml index 28b2ac555..fdcfe83e2 100644 --- a/modules/nf-core/gatk4/shiftfasta/meta.yml +++ b/modules/nf-core/gatk4/shiftfasta/meta.yml @@ -28,6 +28,7 @@ input: type: file description: fasta file pattern: "*.{fa,fasta}" + ontologies: [] - - meta2: type: map description: | @@ -37,6 +38,7 @@ input: type: file description: index for fasta file pattern: "*.{fai}" + ontologies: [] - - meta3: type: map description: | @@ -46,9 +48,10 @@ input: type: file description: sequence dictionary file pattern: "*.{dict}" + ontologies: [] output: - - shift_fa: - - meta: + shift_fa: + - - meta: type: map description: | Groovy Map containing fasta information @@ -57,8 +60,9 @@ output: type: file description: Shifted fasta file pattern: "*.{fa,fasta}" - - shift_fai: - - meta: + ontologies: [] + shift_fai: + - - meta: type: map description: | Groovy Map containing fasta information @@ -67,8 +71,9 @@ output: type: file description: Index file for the shifted fasta file pattern: "*.{fai}" - - shift_back_chain: - - meta: + ontologies: [] + shift_back_chain: + - - meta: type: map description: | Groovy Map containing fasta information @@ -77,8 +82,9 @@ output: type: file description: The shiftback chain file to use when lifting over pattern: "*.{back_chain}" - - dict: - - meta: + ontologies: [] + dict: + - - meta: type: map description: | Groovy Map containing fasta information @@ -87,8 +93,9 @@ output: type: file description: sequence dictionary file pattern: "*.{dict}" - - intervals: - - meta: + ontologies: [] + intervals: + - - meta: type: map description: | Groovy Map containing fasta information @@ -97,12 +104,9 @@ output: type: file description: Intervals file for the fasta file pattern: "*.{intervals}" - - s: - type: file - description: Intervals file for the fasta file - pattern: "*.{intervals}" - - shift_intervals: - - meta: + ontologies: [] + shift_intervals: + - - meta: type: map description: | Groovy Map containing fasta information @@ -111,15 +115,28 @@ output: type: file description: Intervals file for the shifted fasta file pattern: "*.{shifted.intervals}" - - s: - type: file - description: Intervals file for the shifted fasta file - pattern: "*.{shifted.intervals}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap index bb7e5aa01..a465dc485 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap @@ -60,7 +60,11 @@ ] ], "6": [ - "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54" + [ + "GATK4_SHIFTFASTA", + "gatk4", + "4.6.2.0" + ] ], "dict": [ [ @@ -119,15 +123,19 @@ "test.shifted.intervals:md5,6d8d74cd94813e56ec9f09933884f45d" ] ], - "versions": [ - "versions.yml:md5,afdffb5981aa10bdf40af3a50323fd54" + "versions_gatk4": [ + [ + "GATK4_SHIFTFASTA", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:11:50.342225" + "timestamp": "2026-02-04T10:25:05.997054" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf index d59b6afb1..5945c8655 100644 --- a/modules/nf-core/gatk4/splitintervals/main.nf +++ b/modules/nf-core/gatk4/splitintervals/main.nf @@ -1,11 +1,11 @@ process GATK4_SPLITINTERVALS { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(intervals) @@ -15,7 +15,7 @@ process GATK4_SPLITINTERVALS { output: tuple val(meta), path("**.interval_list"), emit: split_intervals - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -23,27 +23,23 @@ process GATK4_SPLITINTERVALS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--reference $fasta" : "" + def reference = fasta ? "--reference ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[GATK SplitIntervals] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK SplitIntervals] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ SplitIntervals \\ --output ${prefix} \\ - --intervals $intervals \\ - $reference \\ + --intervals ${intervals} \\ + ${reference} \\ --tmp-dir . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ stub: @@ -52,10 +48,5 @@ process GATK4_SPLITINTERVALS { mkdir ${prefix} touch ${prefix}/0000-scattered.interval_list touch ${prefix}/0001-scattered.interval_list - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/splitintervals/meta.yml b/modules/nf-core/gatk4/splitintervals/meta.yml index 6a1b869b0..695334563 100644 --- a/modules/nf-core/gatk4/splitintervals/meta.yml +++ b/modules/nf-core/gatk4/splitintervals/meta.yml @@ -23,6 +23,7 @@ input: - intervals: type: file description: Interval file + ontologies: [] - - meta2: type: map description: | @@ -32,6 +33,7 @@ input: type: file description: Reference FASTA pattern: "*.{fa,fasta}" + ontologies: [] - - meta3: type: map description: | @@ -41,6 +43,7 @@ input: type: file description: Reference FASTA index pattern: "*.fai" + ontologies: [] - - meta4: type: map description: | @@ -50,22 +53,42 @@ input: type: file description: Reference sequence dictionary pattern: "*.dict" + ontologies: [] output: - - split_intervals: - - meta: + split_intervals: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] + pattern: "*.interval_list" - "**.interval_list": - type: file - description: interval files + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] pattern: "*.interval_list" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap index d055a8737..092b26007 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap @@ -14,7 +14,11 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ], "split_intervals": [ [ @@ -27,16 +31,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions_gatk4": [ + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:06:41.633105" + "timestamp": "2026-02-04T10:27:38.084533" }, "test-gatk4-splitintervals-bed": { "content": [ @@ -53,7 +61,11 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ], "split_intervals": [ [ @@ -66,16 +78,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions_gatk4": [ + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-26T11:06:28.504041" + "timestamp": "2026-02-04T10:27:18.658962" }, "test-gatk4-splitintervals-intervals-stub": { "content": [ @@ -92,7 +108,11 @@ ] ], "1": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ], "split_intervals": [ [ @@ -105,15 +125,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,384addd364fb36fdac7593eba22fcdb7" + "versions_gatk4": [ + [ + "GATK4_SPLITINTERVALS", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T10:56:46.243594" + "timestamp": "2026-02-04T10:27:55.618457" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitintervals/tests/nextflow.config b/modules/nf-core/gatk4/splitintervals/tests/nextflow.config index 18f7dda02..f012109c4 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/nextflow.config +++ b/modules/nf-core/gatk4/splitintervals/tests/nextflow.config @@ -2,4 +2,4 @@ process { withName: GATK4_SPLITINTERVALS { ext.args = "--scatter-count 2" } -} \ No newline at end of file +} diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 55993f440..67e0eb860 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,5 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.2.0 + # renovate: datasource=conda depName=bioconda/gcnvkernel + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 388c60abf..b3c0e340f 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -1,22 +1,23 @@ process GATK4_VARIANTFILTRATION { - tag "$meta.id" - label 'process_medium' + tag "${meta.id}" + label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' + : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" input: tuple val(meta), path(vcf), path(tbi) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) + tuple val(meta5), path(gzi) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi") , emit: tbi - path "versions.yml" , emit: versions + tuple val(meta), path("*.tbi"), emit: tbi + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -25,35 +26,39 @@ process GATK4_VARIANTFILTRATION { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + // Infer .dict file name that gatk expects, even if ends in .fasta.gz + def dict_name = fasta.getBaseName() + if (dict_name ==~ /^.*\.(fasta|fna|fa)$/) { + dict_name = dict_name.replaceAll(/\.(fasta|fna|fa)$/, "") + } + dict_name = "${dict_name}.dict" + def avail_mem = 3072 if (!task.memory) { - log.info '[GATK VariantFiltration] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[GATK VariantFiltration] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ + # Make sure the .dict file is named correctly + if [[ ${dict_name} != ${dict} ]]; then + ln -s ${dict} ${dict_name} + fi + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ VariantFiltration \\ - --variant $vcf \\ + --variant ${vcf} \\ --output ${prefix}.vcf.gz \\ - --reference $fasta \\ + --reference ${fasta} \\ --tmp-dir . \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS + ${args} """ + stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/variantfiltration/meta.yml b/modules/nf-core/gatk4/variantfiltration/meta.yml index 8e23e205b..4177a706d 100644 --- a/modules/nf-core/gatk4/variantfiltration/meta.yml +++ b/modules/nf-core/gatk4/variantfiltration/meta.yml @@ -39,6 +39,7 @@ input: type: file description: Fasta file of reference genome pattern: "*.fasta" + ontologies: [] - - meta3: type: map description: | @@ -48,6 +49,7 @@ input: type: file description: Index of fasta file pattern: "*.fasta.fai" + ontologies: [] - - meta4: type: map description: | @@ -57,30 +59,65 @@ input: type: file description: Sequence dictionary of fastea file pattern: "*.dict" + ontologies: [] + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: Genome index file only needed when the genome file was compressed + with the BGZF algorithm. + pattern: "*.gzi" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: file description: Compressed VCF file pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.vcf.gz": type: file description: Compressed VCF file pattern: "*.vcf.gz" - - tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tbi: + - - meta: type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + description: Compressed VCF file + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format - "*.tbi": type: file description: Index of VCF file pattern: "*.vcf.gz.tbi" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test index 36b7438d3..65ba4124c 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "gatk4" tag "gatk4/variantfiltration" - test("test_gatk4_variantfiltration_vcf_input") { + test("gatk4_variantfiltration - human - vcf - fasta") { when { process { @@ -31,6 +31,10 @@ nextflow_process { [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ + [ id:'genome' ], // meta map + [] + ] """ } } @@ -38,15 +42,56 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions, - file(process.out.vcf.get(0).get(1)).name, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, file(process.out.tbi.get(0).get(1)).name).match() }, ) } } - test("test_gatk4_variantfiltration_gz_input") { + test("gatk4_variantfiltration - human - vcf - fasta.gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[4] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.tbi.get(0).get(1)).name).match() }, + ) + } + + } + + test("gatk4_variantfiltration - human - vcf.gz - fasta") { when { process { @@ -68,6 +113,10 @@ nextflow_process { [ id:'genome' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ + [ id:'genome' ], // meta map + [] + ] """ } } @@ -75,8 +124,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions, - file(process.out.vcf.get(0).get(1)).name, + { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, file(process.out.tbi.get(0).get(1)).name).match() }, ) } @@ -84,4 +133,3 @@ nextflow_process { } } - diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap index 36c03f7c1..3a621b227 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -1,30 +1,62 @@ { - "test_gatk4_variantfiltration_gz_input": { + "gatk4_variantfiltration - human - vcf - fasta.gz": { "content": [ - [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" - ], - "test.vcf.gz", + { + "versions_gatk4": [ + [ + "GATK4_VARIANTFILTRATION", + "gatk4", + "4.6.2.0" + ] + ] + }, + "cf0477cc14953b16caacbf5be507b88", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-22T22:43:27.609784" + "timestamp": "2026-02-04T10:38:33.543304" }, - "test_gatk4_variantfiltration_vcf_input": { + "gatk4_variantfiltration - human - vcf.gz - fasta": { "content": [ - [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" - ], - "test.vcf.gz", + { + "versions_gatk4": [ + [ + "GATK4_VARIANTFILTRATION", + "gatk4", + "4.6.2.0" + ] + ] + }, + "cf0477cc14953b16caacbf5be507b88", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-22T22:42:55.316294" + "timestamp": "2026-02-04T10:38:51.020309" + }, + "gatk4_variantfiltration - human - vcf - fasta": { + "content": [ + { + "versions_gatk4": [ + [ + "GATK4_VARIANTFILTRATION", + "gatk4", + "4.6.2.0" + ] + ] + }, + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T10:38:15.367356" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantfiltration/tests/tags.yml b/modules/nf-core/gatk4/variantfiltration/tests/tags.yml deleted file mode 100644 index 4818037d7..000000000 --- a/modules/nf-core/gatk4/variantfiltration/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/variantfiltration: - - "modules/nf-core/gatk4/variantfiltration/**" diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index 1d715d564..b4ac4fe08 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 5a71e085a..5ef3b7d8e 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(reads) @@ -16,7 +16,7 @@ process PICARD_ADDORREPLACEREADGROUPS { tuple val(meta), path("*.bam") , emit: bam, optional: true tuple val(meta), path("*.bai") , emit: bai, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -44,10 +44,6 @@ process PICARD_ADDORREPLACEREADGROUPS { --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: @@ -57,9 +53,5 @@ process PICARD_ADDORREPLACEREADGROUPS { """ touch ${prefix}.${suffix} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index 77ce85035..6c3ed7599 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -25,6 +25,7 @@ input: type: file description: Sequence reads file, can be SAM/BAM/CRAM format pattern: "*.{bam,cram,sam}" + ontologies: [] - - meta2: type: map description: | @@ -34,6 +35,7 @@ input: type: file description: Reference genome file pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + ontologies: [] - - meta3: type: map description: | @@ -43,9 +45,10 @@ input: type: file description: Reference genome index file pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -54,8 +57,9 @@ output: type: file description: Output BAM file pattern: "*.{bam}" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -64,8 +68,9 @@ output: type: file description: An optional BAM index file pattern: "*.{bai}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -74,11 +79,30 @@ output: type: file description: Output CRAM file pattern: "*.{cram}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": + type: string + description: The command used to generate the version of the tool + authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 9c029354f..45729f3b5 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -29,7 +29,7 @@ nextflow_process { { assert snapshot( file(process.out.bam[0][1]).name, file(process.out.bai[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, ) @@ -59,7 +59,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.cram[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() }, ) diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index 3ae6b9171..d2a99ee27 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -2,15 +2,21 @@ "homo_sapiens - cram": { "content": [ "test.replaced.cram", - [ - "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" - ] + { + "versions_picard": [ + [ + "PICARD_ADDORREPLACEREADGROUPS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:13:23.115450366" + "timestamp": "2026-02-02T09:36:16.966842212" }, "sarscov2 - bam - stub": { "content": [ @@ -30,7 +36,11 @@ ], "3": [ - "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" + [ + "PICARD_ADDORREPLACEREADGROUPS", + "picard", + "3.4.0" + ] ], "bai": [ @@ -46,29 +56,39 @@ "cram": [ ], - "versions": [ - "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" + "versions_picard": [ + [ + "PICARD_ADDORREPLACEREADGROUPS", + "picard", + "3.4.0" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:13:47.23694937" + "timestamp": "2026-02-02T09:36:29.861163004" }, "sarscov2 - bam": { "content": [ "null.replaced.bam", "null.replaced.bai", - [ - "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" - ] + { + "versions_picard": [ + [ + "PICARD_ADDORREPLACEREADGROUPS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:12:53.083677142" + "timestamp": "2026-02-02T09:36:00.935196996" } } \ No newline at end of file diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml b/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml deleted file mode 100644 index 733010d62..000000000 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -picard/addorreplacereadgroups: - - "modules/nf-core/picard/addorreplacereadgroups/**" diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index 8f34e975c..b4ac4fe08 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index cf1af40af..3c6152e5f 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta) , path(bam), path(bai) @@ -15,7 +15,7 @@ process PICARD_COLLECTMULTIPLEMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics tuple val(meta), path("*.pdf") , emit: pdf, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -39,10 +39,6 @@ process PICARD_COLLECTMULTIPLEMETRICS { --OUTPUT ${prefix}.CollectMultipleMetrics \\ $reference - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) - END_VERSIONS """ stub: @@ -59,9 +55,5 @@ process PICARD_COLLECTMULTIPLEMETRICS { touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 3f0bf6103..1ea47244c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -74,13 +74,29 @@ output: description: PDF plots of metrics pattern: "*.{pdf}" ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test index 5b67774f7..08456941b 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -36,7 +36,7 @@ nextflow_process { { assert snapshot( process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -66,7 +66,7 @@ nextflow_process { { assert snapshot( process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -102,7 +102,7 @@ nextflow_process { { assert snapshot( process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index a76a32375..1acf37765 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -15,15 +15,21 @@ "test.CollectMultipleMetrics.quality_distribution.pdf", "test.CollectMultipleMetrics.read_length_histogram.pdf" ], - [ - "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T11:05:12.591021247" + "timestamp": "2026-02-02T10:22:21.230301646" }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -41,15 +47,21 @@ "test.CollectMultipleMetrics.quality_distribution.pdf", "test.CollectMultipleMetrics.read_length_histogram.pdf" ], - [ - "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T11:06:08.499320579" + "timestamp": "2026-02-02T10:23:52.23446844" }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -67,14 +79,20 @@ "test.CollectMultipleMetrics.quality_distribution.pdf", "test.CollectMultipleMetrics.read_length_histogram.pdf" ], - [ - "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T11:05:42.117033611" + "timestamp": "2026-02-02T10:23:27.387621193" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 5f2dfc031..186d4a4bc 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -4,5 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 - conda-forge::r-base=4.4.1 diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 39cf7d2b7..aa77100c7 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(bam), path(bai) @@ -15,7 +15,7 @@ process PICARD_COLLECTWGSMETRICS { output: tuple val(meta), path("*_metrics"), emit: metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -40,11 +40,6 @@ process PICARD_COLLECTWGSMETRICS { --REFERENCE_SEQUENCE ${fasta} \\ $interval - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) - END_VERSIONS """ stub: @@ -52,9 +47,5 @@ process PICARD_COLLECTWGSMETRICS { """ touch ${prefix}.CollectWgsMetrics.coverage_metrics - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index a27e0a88c..c59811d58 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -69,13 +69,28 @@ output: description: Alignment metrics files generated by picard pattern: "*_{metrics}" ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test index a3984566d..d6a60e6bf 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test @@ -38,7 +38,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -73,7 +73,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index 1958fcdeb..375c2ef9d 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -2,27 +2,39 @@ "test-picard-collectwgsmetrics-with-interval": { "content": [ true, - [ - "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:15:18.13771243" + "timestamp": "2026-02-02T14:52:55.091876466" }, "test-picard-collectwgsmetrics": { "content": [ true, - [ - "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" - ] + { + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:14:57.786056996" + "timestamp": "2026-02-02T14:52:11.334274481" } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index 1d715d564..b4ac4fe08 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 69feb624a..186afc50f 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(input_vcf) @@ -16,7 +16,7 @@ process PICARD_LIFTOVERVCF { output: tuple val(meta), path("*.lifted.vcf.gz") , emit: vcf_lifted tuple val(meta), path("*.unlifted.vcf.gz"), emit: vcf_unlifted - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -41,10 +41,6 @@ process PICARD_LIFTOVERVCF { --REJECT ${prefix}.unlifted.vcf.gz \\ --REFERENCE_SEQUENCE $fasta - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: @@ -53,9 +49,5 @@ process PICARD_LIFTOVERVCF { echo | gzip > ${prefix}.lifted.vcf.gz echo | gzip > ${prefix}.unlifted.vcf.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index 10fbfc837..bc4baf2da 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -21,6 +21,7 @@ input: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] - - meta2: type: map description: | @@ -30,6 +31,7 @@ input: type: file description: dictionary for fasta file pattern: "*.{dict}" + ontologies: [] - - meta3: type: map description: | @@ -39,6 +41,7 @@ input: type: file description: fasta file pattern: "*.fasta" + ontologies: [] - - meta4: type: map description: | @@ -47,9 +50,10 @@ input: - chain: type: file description: The liftover chain file + ontologies: [] output: - - vcf_lifted: - - meta: + vcf_lifted: + - - meta: type: map description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] @@ -57,8 +61,9 @@ output: type: file description: VCF file containing successfully lifted variants pattern: "*.{lifted.vcf.gz}" - - vcf_unlifted: - - meta: + ontologies: [] + vcf_unlifted: + - - meta: type: map description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] @@ -66,11 +71,30 @@ output: type: file description: VCF file containing unsuccessfully lifted variants pattern: "*.{unlifted.vcf.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test index 7b42102de..d0e35b45d 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf_lifted[0][1]).vcf.summary, path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -74,7 +74,7 @@ nextflow_process { { assert snapshot( file(process.out.vcf_lifted[0][1]).name, file(process.out.vcf_unlifted[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index e88aa9706..9bb324bbe 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -3,28 +3,40 @@ "content": [ "test.lifted.vcf.gz", "test.unlifted.vcf.gz", - [ - "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" - ] + { + "versions_picard": [ + [ + "PICARD_LIFTOVERVCF", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T12:08:23.913395641" + "timestamp": "2026-02-02T11:41:30.546426132" }, "test-picard-liftovervcf": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "39a9de5185d94289283bd27cfcdeba97", - [ - "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" - ] + { + "versions_picard": [ + [ + "PICARD_LIFTOVERVCF", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T12:08:12.803193917" + "timestamp": "2026-02-02T11:40:19.064084452" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 1d715d564..b4ac4fe08 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 8a2ed64e6..10621e019 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(reads) @@ -17,7 +17,7 @@ process PICARD_MARKDUPLICATES { tuple val(meta), path("*.bai") , emit: bai, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.metrics.txt"), emit: metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -46,10 +46,6 @@ process PICARD_MARKDUPLICATES { $reference \\ --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: @@ -58,11 +54,8 @@ process PICARD_MARKDUPLICATES { if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.${suffix} + touch ${prefix}.${suffix}.bai touch ${prefix}.MarkDuplicates.metrics.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index bcaf91605..0ec99c7f1 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -26,6 +26,7 @@ input: type: file description: Sequence reads file, can be SAM/BAM/CRAM format pattern: "*.{bam,cram,sam}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +36,7 @@ input: type: file description: Reference genome fasta file, required for CRAM input pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -44,9 +46,10 @@ input: type: file description: Reference genome fasta index pattern: "*.{fai}" + ontologies: [] output: - - bam: - - meta: + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -55,8 +58,9 @@ output: type: file description: BAM file with duplicate reads marked/removed pattern: "*.{bam}" - - bai: - - meta: + ontologies: [] + bai: + - - meta: type: map description: | Groovy Map containing sample information @@ -66,8 +70,9 @@ output: description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag pattern: "*.{bai}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -76,8 +81,9 @@ output: type: file description: Output CRAM file pattern: "*.{cram}" - - metrics: - - meta: + ontologies: [] + metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -86,11 +92,30 @@ output: type: file description: Duplicate metrics file generated by picard pattern: "*.{metrics.txt}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index 9ed909659..e18723be0 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert snapshot( file(process.out.bam[0][1]).name, path(process.out.metrics.get(0).get(1)).readLines()[0..2], - process.out.versions) + process.out.findAll { key, val -> key.startsWith("versions") }) .match() } ) } @@ -57,7 +57,7 @@ nextflow_process { { assert snapshot( file(process.out.bam[0][1]).name, path(process.out.metrics.get(0).get(1)).readLines()[0..2], - process.out.versions) + process.out.findAll { key, val -> key.startsWith("versions") }) .match() } ) } @@ -90,7 +90,7 @@ nextflow_process { { assert snapshot( file(process.out.cram[0][1]).name, path(process.out.metrics.get(0).get(1)).readLines()[0..2], - process.out.versions) + process.out.findAll { key, val -> key.startsWith("versions") }) .match() } ) } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 13770a8e2..848013849 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -12,7 +12,13 @@ ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ @@ -27,10 +33,20 @@ ] ], "4": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ], "bai": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "bam": [ [ @@ -53,16 +69,20 @@ "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:58:50.046420643" + "timestamp": "2026-02-02T11:46:02.077382134" }, "sarscov2 [unsorted bam] - stub": { "content": [ @@ -77,7 +97,13 @@ ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ @@ -92,10 +118,20 @@ ] ], "4": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ], "bai": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "bam": [ [ @@ -118,16 +154,20 @@ "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:58:36.738907079" + "timestamp": "2026-02-02T11:45:49.985589186" }, "sarscov2 [unsorted bam]": { "content": [ @@ -137,15 +177,21 @@ "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], - [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" - ] + { + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:57:16.683233382" + "timestamp": "2026-02-02T11:42:49.704752548" }, "sarscov2 [sorted bam]": { "content": [ @@ -155,15 +201,21 @@ "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], - [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" - ] + { + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:57:47.416956759" + "timestamp": "2026-02-02T11:44:17.407572621" }, "homo_sapiens [cram]": { "content": [ @@ -173,15 +225,21 @@ "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], - [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" - ] + { + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:58:15.143314223" + "timestamp": "2026-02-02T11:45:33.412603893" }, "homo_sapiens [cram] - stub": { "content": [ @@ -190,7 +248,13 @@ ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ [ @@ -211,10 +275,20 @@ ] ], "4": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ], "bai": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "bam": [ @@ -237,15 +311,19 @@ "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + "versions_picard": [ + [ + "PICARD_MARKDUPLICATES", + "picard", + "3.4.0" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:59:03.402916523" + "timestamp": "2026-02-02T11:46:18.599127485" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml deleted file mode 100644 index 4f213d620..000000000 --- a/modules/nf-core/picard/markduplicates/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -picard/markduplicates: - - modules/nf-core/picard/markduplicates/** diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index 8f34e975c..b4ac4fe08 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 9e5e2e2dc..6b02886bf 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,22 +5,22 @@ process PICARD_RENAMESAMPLEINVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def extended_args = args.contains("--NEW_SAMPLE_NAME") ? $args : "${args} --NEW_SAMPLE_NAME ${meta.id}" + def extended_args = args.contains("--NEW_SAMPLE_NAME") ? args : "${args} --NEW_SAMPLE_NAME ${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { @@ -37,20 +37,11 @@ process PICARD_RENAMESAMPLEINVCF { --OUTPUT ${prefix}_renam.vcf.gz \\ $extended_args - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_renam.vcf.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS + echo "" | gzip > ${prefix}_renam.vcf.gz """ } diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 8af62051e..762780bd0 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -37,13 +37,29 @@ output: description: VCF file pattern: "*.{vcf,vcf.gz}" ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test index f755447ff..42e127a01 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { { assert process.success }, { assert snapshot( path(process.out.vcf[0][1]).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index 6a21666ad..86626ce81 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -2,14 +2,20 @@ "test-picard-renamesampleinvcf": { "content": [ "e21a2349f41663d1fc38f47fbe65a6d5", - [ - "versions.yml:md5,89be4b901aa05e78d449d11b00eff5e9" - ] + { + "versions_picard": [ + [ + "PICARD_RENAMESAMPLEINVCF", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-18T09:53:47.55538945" + "timestamp": "2026-02-02T15:51:56.010473" } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index 1d715d564..b4ac4fe08 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.3.0 + # renovate: datasource=conda depName=bioconda/picard + - bioconda::picard=3.4.0 diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index a094e6bfa..782deba2b 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : - 'biocontainers/picard:3.3.0--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : + 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process PICARD_SORTVCF { output: tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -40,23 +40,13 @@ process PICARD_SORTVCF { $seq_dict \\ $reference \\ --OUTPUT ${prefix}_sorted.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_sorted.vcf.gz + echo "" | gzip > ${prefix}_sorted.vcf.gz touch ${prefix}.bam.bai touch ${prefix}.MarkDuplicates.metrics.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS """ } diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index 6dc28e03f..f6e327ff9 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -22,6 +22,7 @@ input: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] - - meta2: type: map description: | @@ -31,6 +32,7 @@ input: type: file description: Reference genome fasta file pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -40,9 +42,10 @@ input: type: file description: Reference genome dictionary file pattern: "*.{dict}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -51,11 +54,29 @@ output: type: file description: Sorted VCF file pattern: "*.{vcf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_picard: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - picard: + type: string + description: The tool name + - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + type: string + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test index 9df73ad43..e8ef67501 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -34,7 +34,7 @@ nextflow_process { { assert process.success }, { assert snapshot( path(process.out.vcf[0][1]).linesGzip[3..7], - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index e4a02c4f3..9db773653 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -8,14 +8,20 @@ "##INFO=", "##INFO=" ], - [ - "versions.yml:md5,e6e6356d3b5b1b8e8cfd5d4958c694e6" - ] + { + "versions_picard": [ + [ + "PICARD_SORTVCF", + "picard", + "3.4.0" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-10-18T10:45:30.685264704" + "timestamp": "2026-02-02T11:47:50.61817621" } } \ No newline at end of file diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml index 788dd06ef..0cd211c25 100644 --- a/modules/nf-core/stranger/environment.yml +++ b/modules/nf-core/stranger/environment.yml @@ -4,7 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::tabix=1.11 + - bioconda::htslib=1.23 - conda-forge::pip=25.3 - conda-forge::python=3.14.2 - pip: diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf index a793f4375..14170010d 100644 --- a/modules/nf-core/stranger/main.nf +++ b/modules/nf-core/stranger/main.nf @@ -4,8 +4,8 @@ process STRANGER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bc/bc075f106c93d3bb9c786c73f897c8cb005962e4c31c08226bd55eef742e9025/data': - 'community.wave.seqera.io/library/tabix_pip_stranger:9685bd298256c94b' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/90/90f7f35b37e9e31c8680c18ef59c76e74500f44664887b3c1131daf07ff3043f/data': + 'community.wave.seqera.io/library/htslib_pip_stranger:de13e0cf88d77b50' }" input: tuple val(meta), path(vcf) @@ -15,7 +15,7 @@ process STRANGER { tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val("${task.process}"), val('stranger'), eval("stranger --version | sed 's/stranger, version //g'"), topic: versions, emit: versions_stranger - tuple val("${task.process}"), val('tabix'), eval("tabix --version | sed -n 's/^.*htslib) //p'"), topic: versions, emit: versions_tabix + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml index 15e513e60..623b6e13d 100644 --- a/modules/nf-core/stranger/meta.yml +++ b/modules/nf-core/stranger/meta.yml @@ -63,7 +63,7 @@ output: - stranger: type: string description: The name of the tool - - '"stranger --version | sed ''s/stranger': + - stranger --version | sed 's/stranger, version //g': type: eval description: The expression to obtain the version of the tool @@ -73,8 +73,8 @@ output: description: The name of the process - tabix: type: string - description: The name of the tool - - tabix --version | sed -n 's/^.*htslib) //p': + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': type: eval description: The expression to obtain the version of the tool @@ -86,7 +86,7 @@ topics: - stranger: type: string description: The name of the tool - - '"stranger --version | sed ''s/stranger': + - stranger --version | sed 's/stranger, version //g': type: eval description: The expression to obtain the version of the tool @@ -95,8 +95,8 @@ topics: description: The name of the process - tabix: type: string - description: The name of the tool - - tabix --version | sed -n 's/^.*htslib) //p': + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/stranger/tests/main.nf.test.snap b/modules/nf-core/stranger/tests/main.nf.test.snap index 50a0a98e6..922cb7f03 100644 --- a/modules/nf-core/stranger/tests/main.nf.test.snap +++ b/modules/nf-core/stranger/tests/main.nf.test.snap @@ -29,7 +29,7 @@ [ "STRANGER", "tabix", - "1.22.1" + "1.23" ] ], "tbi": [ @@ -59,16 +59,16 @@ [ "STRANGER", "tabix", - "1.22.1" + "1.23" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T09:36:05.482418969" + "timestamp": "2026-01-30T15:59:31.211437829" }, "homo_sapiens - vcf, repeat_catalogue": { "content": [ @@ -100,7 +100,7 @@ [ "STRANGER", "tabix", - "1.22.1" + "1.23" ] ], "tbi": [ @@ -130,15 +130,15 @@ [ "STRANGER", "tabix", - "1.22.1" + "1.23" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.2" + "nextflow": "25.10.2" }, - "timestamp": "2025-12-16T09:36:01.200222427" + "timestamp": "2026-01-30T15:59:14.37967244" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index dc587136e..dce89b7ea 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -3,7 +3,6 @@ channels: - conda-forge - bioconda - dependencies: - - bcftools=1.21 - - svdb=2.8.2 + - bioconda::bcftools=1.23 + - bioconda::svdb=2.8.3 diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 104f5ad79..8779a2ce4 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -1,10 +1,11 @@ process SVDB_MERGE { tag "$meta.id" label 'process_single' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd:b3615e06ef17566f2988a215ce9e10808c1d08bf-0': - 'biocontainers/mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd:b3615e06ef17566f2988a215ce9e10808c1d08bf-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ff995c756aa8a3c0af13b1d054eacd536a11d35de5fa288dacf558bc21696968/data': + 'community.wave.seqera.io/library/bcftools_svdb:ae3b14d2d608fd81' }" input: tuple val(meta), path(vcfs) @@ -15,7 +16,8 @@ process SVDB_MERGE { tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf tuple val(meta), path("*.tbi") , emit: tbi, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('svdb'), eval("svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'"), emit: versions_svdb, topic: versions + tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), emit: versions_bcftools, topic: versions when: task.ext.when == null || task.ext.when @@ -71,11 +73,6 @@ process SVDB_MERGE { --threads ${task.cpus} \\ --output ${prefix}.${extension} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ stub: @@ -96,10 +93,5 @@ process SVDB_MERGE { ${create_cmd} ${prefix}.${extension} ${create_index} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index 574fbad16..48d73e47e 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -1,5 +1,6 @@ name: svdb_merge -description: The merge module merges structural variants within one or more vcf files. +description: The merge module merges structural variants within one or more vcf + files. keywords: - structural variants - vcf @@ -68,13 +69,46 @@ output: description: Default VCF file index pattern: "*.csi" ontologies: [] + versions_svdb: + - - ${task.process}: + type: string + description: The name of the process + - svdb: + type: string + description: The name of the tool + - svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + versions_bcftools: + - - ${task.process}: + type: string + description: The name of the process + - bcftools: + type: string + description: The tool name + - bcftools --version | sed '1!d; s/^.*bcftools //': + type: eval + description: The command used to generate the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - svdb: + type: string + description: The name of the tool + - svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - bcftools: + type: string + description: The tool name + - bcftools --version | sed '1!d; s/^.*bcftools //': + type: eval + description: The command used to generate the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test index 6a79d7a09..23ea38209 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test +++ b/modules/nf-core/svdb/merge/tests/main.nf.test @@ -31,7 +31,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -59,7 +59,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -87,7 +87,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -115,7 +115,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -146,7 +146,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -177,7 +177,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -208,7 +208,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -239,7 +239,7 @@ nextflow_process { { assert snapshot( path(process.out.vcf.get(0).get(1)).vcf.summary, path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test.snap b/modules/nf-core/svdb/merge/tests/main.nf.test.snap index e86662e53..6e8e14d5e 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/merge/tests/main.nf.test.snap @@ -3,15 +3,28 @@ "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", "60fb4cab2aa891bebef8ffdbd0e41bc3", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:00:25.9277471" + "timestamp": "2026-02-03T09:51:10.673745" }, "2 samples, ['tiddit', 'cnvnator'], true - stub": { "content": [ @@ -31,7 +44,18 @@ ], "3": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ], + "4": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] ], "csi": [ @@ -47,114 +71,216 @@ "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:05:49.325618245" + "timestamp": "2026-02-03T09:52:04.81478" }, "2 samples, ['tiddit', 'cnvnator'], []": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", "254e56e4fc8356d68424828438da66e3", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:02:27.964808463" + "timestamp": "2026-02-03T09:51:39.788196" }, "2 samples, [], []": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", "7ad648266e57d405b5b01aaea4613d1c", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:02:11.013532413" + "timestamp": "2026-02-03T09:51:30.166443" }, "2 samples, ['tiddit', 'cnvnator'], true": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", "254e56e4fc8356d68424828438da66e3", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:02:35.956320871" + "timestamp": "2026-02-03T09:51:44.571583" }, "1 sample, ['tiddit'], []": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", "9dd588cd870672b78192f48ad440b5d", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:00:42.064583463" + "timestamp": "2026-02-03T09:51:20.286591" }, "1 sample, [], true": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", "60fb4cab2aa891bebef8ffdbd0e41bc3", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:00:33.88572601" + "timestamp": "2026-02-03T09:51:15.445349" }, "1 sample, ['tiddit'], true": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", "9dd588cd870672b78192f48ad440b5d", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:00:50.18149857" + "timestamp": "2026-02-03T09:51:25.013931" }, "2 samples, [], true": { "content": [ "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", "de0a3b56cdee89e4c9cd4fbb4ad3391d", - [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" - ] + { + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:02:19.556799178" + "timestamp": "2026-02-03T09:51:35.029226" }, "2 samples, ['tiddit', 'cnvnator'], [] - stub": { "content": [ @@ -174,7 +300,18 @@ ], "3": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ], + "4": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] ], "csi": [ @@ -190,16 +327,27 @@ "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:05:40.427970257" + "timestamp": "2026-02-03T09:51:59.208139" }, "2 samples, [], [] - stub": { "content": [ @@ -219,7 +367,18 @@ ], "3": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ], + "4": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] ], "csi": [ @@ -235,16 +394,27 @@ "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:05:24.34471465" + "timestamp": "2026-02-03T09:51:49.255901" }, "2 samples, [], true - stub": { "content": [ @@ -264,7 +434,18 @@ ], "3": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] + ], + "4": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] ], "csi": [ @@ -280,15 +461,26 @@ "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,bf8271626d334b2a827f94a2daacadd0" + "versions_bcftools": [ + [ + "SVDB_MERGE", + "bcftools", + "1.23" + ] + ], + "versions_svdb": [ + [ + "SVDB_MERGE", + "svdb", + "2.8.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-24T09:05:32.529261733" + "timestamp": "2026-02-03T09:51:54.851615" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml index 2af552205..dce89b7ea 100644 --- a/modules/nf-core/svdb/query/environment.yml +++ b/modules/nf-core/svdb/query/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::svdb=2.8.2 + - bioconda::bcftools=1.23 + - bioconda::svdb=2.8.3 diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 4ceb477a0..873e0f1c1 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -4,8 +4,8 @@ process SVDB_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/svdb:2.8.2--py39h5371cbf_0': - 'biocontainers/svdb:2.8.2--py39h5371cbf_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ff995c756aa8a3c0af13b1d054eacd536a11d35de5fa288dacf558bc21696968/data': + 'community.wave.seqera.io/library/bcftools_svdb:ae3b14d2d608fd81' }" input: tuple val(meta), path(vcf) @@ -18,7 +18,7 @@ process SVDB_QUERY { output: tuple val(meta), path("*_query.vcf") , emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('svdb'), eval("svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\\1/p'"), emit: versions_svdb, topic: versions when: task.ext.when == null || task.ext.when @@ -58,10 +58,6 @@ process SVDB_QUERY { --query_vcf $vcf \\ --prefix ${prefix} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - END_VERSIONS """ stub: @@ -69,9 +65,5 @@ process SVDB_QUERY { """ touch ${prefix}_query.vcf - cat <<-END_VERSIONS > versions.yml - "${task.process}": - svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) - END_VERSIONS """ } diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml index f8cd33c8d..0b91c8be1 100644 --- a/modules/nf-core/svdb/query/meta.yml +++ b/modules/nf-core/svdb/query/meta.yml @@ -11,7 +11,6 @@ tools: documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] identifier: "" - input: - - meta: type: map @@ -22,30 +21,34 @@ input: type: file description: query vcf file pattern: "*.{vcf,vcf.gz}" - - - in_occs: - type: list - description: A list of allele count tags - - - in_frqs: - type: list - description: A list of allele frequency tags - - - out_occs: - type: list - description: A list of allele count tags - - - out_frqs: - type: list - description: A list of allele frequency tags - - - vcf_dbs: - type: file - description: path to a database vcf, or a comma separated list of vcfs - pattern: "*.{vcf,vcf.gz}" - - - bedpe_dbs: - type: file - description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, - or a comma separated list of files - pattern: "*.{bedpe}" + ontologies: [] + - in_occs: + type: list + description: A list of allele count tags + - in_frqs: + type: list + description: A list of allele frequency tags + - out_occs: + type: list + description: A list of allele count tags + - out_frqs: + type: list + description: A list of allele frequency tags + - vcf_dbs: + type: file + description: path to a database vcf, or a comma separated list of vcfs + pattern: "*.{vcf,vcf.gz}" + ontologies: [] + - bedpe_dbs: + type: file + description: path to a SV database of the following format + chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of + files + pattern: "*.{bedpe}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -54,10 +57,27 @@ output: type: file description: Annotated output VCF file pattern: "*_query.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_svdb: + - - ${task.process}: + type: string + description: The name of the process + - svdb: + type: string + description: The name of the tool + - svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - svdb: + type: string + description: The name of the tool + - svdb | sed -nE 's/.*SVDB-([0-9.]+).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" diff --git a/modules/nf-core/svdb/query/tests/main.nf.test b/modules/nf-core/svdb/query/tests/main.nf.test index 72e829158..aed1be8eb 100644 --- a/modules/nf-core/svdb/query/tests/main.nf.test +++ b/modules/nf-core/svdb/query/tests/main.nf.test @@ -29,7 +29,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(file(process.out.vcf[0][1]).name, file(process.out.versions[0]).name).match()} + { assert snapshot(path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() + } ) } } diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap index 65f2fcfaa..966ea2707 100644 --- a/modules/nf-core/svdb/query/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/query/tests/main.nf.test.snap @@ -1,13 +1,21 @@ { "svdb query": { "content": [ - "test_query.vcf", - "versions.yml" + "eee99ddfe9ab0a94a2be80e3c1757fdf", + { + "versions_svdb": [ + [ + "SVDB_QUERY", + "svdb", + "2.8.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2023-11-22T14:56:08.90223505" + "timestamp": "2026-02-03T10:26:18.573659" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/query/tests/tags.yml b/modules/nf-core/svdb/query/tests/tags.yml deleted file mode 100644 index f40963780..000000000 --- a/modules/nf-core/svdb/query/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -svdb/query: - - modules/nf-core/svdb/query/** diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 661b9b7e8..88895ccdb 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -152,7 +152,7 @@ workflow ALIGN { ch_mtshift_bam_bai_gatksubwf = ALIGN_MT_SHIFT.out.marked_bam .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling ch_versions = ch_versions - .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions, CONVERT_MT_BAM_TO_FASTQ.out.versions) + .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions) } if (val_save_mapped_as_cram) { diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 4030d370c..5a1dbbf4f 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -48,10 +48,6 @@ workflow ALIGN_MT { SAMTOOLS_SORT_MT (PICARD_MARKDUPLICATES_MT.out.bam, [[:],[]], 'bai') - ch_versions = ch_versions.mix(GATK4_MERGEBAMALIGNMENT_MT.out.versions) - ch_versions = ch_versions.mix(PICARD_ADDORREPLACEREADGROUPS_MT.out.versions) - ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES_MT.out.versions) - emit: marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 29eb1a4bc..0c95d6ef1 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -84,7 +84,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) - ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) emit: diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 8a1f7b486..1f2bd6953 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -198,9 +198,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_versions = ch_versions.mix(VCFANNO.out.versions) ch_versions = ch_versions.mix(UPD_SITES.out.versions) ch_versions = ch_versions.mix(UPD_REGIONS.out.versions) - ch_versions = ch_versions.mix(CHROMOGRAPH_SITES.out.versions) - ch_versions = ch_versions.mix(CHROMOGRAPH_REGIONS.out.versions) - ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) emit: diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements.nf index 80e0594f5..4de40d209 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements.nf @@ -21,7 +21,6 @@ workflow ANNOTATE_MOBILE_ELEMENTS { ch_vep_extra_files // channel: [mandatory] [ path(files) ] main: - ch_versions = channel.empty() ch_svdb_dbs = channel.empty() ch_me_svdb_resources @@ -71,10 +70,6 @@ workflow ANNOTATE_MOBILE_ELEMENTS { BCFTOOLS_VIEW_FILTER( ch_bcftools_filter_input, [], [], [] ) - ch_versions = ch_versions.mix( SVDB_QUERY_DB.out.versions ) - ch_versions = ch_versions.mix( PICARD_SORTVCF.out.versions ) - emit: vcf_ann = BCFTOOLS_VIEW_FILTER.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 0d2119abd..ac5db5cc8 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -54,7 +54,6 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_versions = ch_versions.mix(CHROMOGRAPH_AUTOZYG.out.versions) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 7f3384afa..63cd40b07 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -49,7 +49,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ) ch_vcf = SVDB_QUERY_DB.out.vcf - ch_versions = ch_versions.mix(SVDB_QUERY_DB.out.versions) } if (val_svdb_query_bedpedbs) { @@ -74,7 +73,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ) ch_vcf = SVDB_QUERY_BEDPE.out.vcf - ch_versions = ch_versions.mix(SVDB_QUERY_BEDPE.out.versions) } PICARD_SORTVCF(ch_vcf, ch_genome_fasta, ch_genome_dictionary) @@ -100,8 +98,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) - ch_versions = ch_versions.mix(PICARD_SORTVCF.out.versions) - emit: tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 40dd7099f..b4506c741 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -123,7 +123,6 @@ workflow CALL_MOBILE_ELEMENTS { ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) - ch_versions = ch_versions.mix(SVDB_MERGE_ME.out.versions) emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 045358ef0..14ec4fb61 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -19,7 +19,6 @@ workflow CALL_REPEAT_EXPANSIONS { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] main: - ch_versions = channel.empty() EXPANSIONHUNTER ( ch_bam, @@ -58,11 +57,6 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) - ch_versions = ch_versions.mix(EXPANSIONHUNTER.out.versions) - ch_versions = ch_versions.mix(RENAMESAMPLE_EXP.out.versions ) - ch_versions = ch_versions.mix(SVDB_MERGE_REPEATS.out.versions) - emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 77ee74df0..e301ef109 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -143,8 +143,6 @@ workflow CALL_SNV { ch_mt_txt = CALL_SNV_MT.out.txt ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions) ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions) - ch_versions = ch_versions.mix(POSTPROCESS_MT_CALLS.out.versions) - ch_versions = ch_versions.mix(GATK4_SELECTVARIANTS.out.versions) } if (val_concatenate_snv_calls) { diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 4456f3585..b1df3c7fd 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -34,9 +34,6 @@ workflow CALL_SNV_MT { GATK4_FILTERMUTECTCALLS_MT (ch_to_filt, ch_fasta, ch_fai, ch_dict) - ch_versions = ch_versions.mix(GATK4_MUTECT2_MT.out.versions) - ch_versions = ch_versions.mix(GATK4_FILTERMUTECTCALLS_MT.out.versions) - emit: filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] html = HAPLOCHECK_MT.out.html // channel: [ val(meta), path(html) ] diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index b4cb395ee..4a9fb1b22 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -82,7 +82,6 @@ workflow CALL_SNV_DEEPVARIANT { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(DEEPVARIANT.out.versions) ch_versions = ch_versions.mix(GLNEXUS.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 87a2d40bd..f7bb9104d 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -109,7 +109,6 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - ch_versions = ch_versions.mix(SVDB_MERGE.out.versions) } emit: diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 13e656bb4..36756a898 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -20,7 +20,6 @@ workflow CALL_SV_CNVNATOR { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - ch_versions = channel.empty() CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]], "rd" ) CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai, "his" ) @@ -40,15 +39,6 @@ workflow CALL_SV_CNVNATOR { SVDB_MERGE_CNVNATOR ( merge_input_vcfs, [], true ) - ch_versions = ch_versions.mix(CNVNATOR_RD.out.versions) - ch_versions = ch_versions.mix(CNVNATOR_HIST.out.versions) - ch_versions = ch_versions.mix(CNVNATOR_STAT.out.versions) - ch_versions = ch_versions.mix(CNVNATOR_PARTITION.out.versions) - ch_versions = ch_versions.mix(CNVNATOR_CALL.out.versions) - ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions) - ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions) - emit: vcf = SVDB_MERGE_CNVNATOR.out.vcf // channel: [ val(meta), path(*.tar.gz) ] - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index 1687c7079..e388fd4b4 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -22,7 +22,6 @@ workflow CALL_SV_GERMLINECNVCALLER { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - ch_versions = channel.empty() input = ch_bam_bai.combine( ch_readcount_intervals ) @@ -76,16 +75,9 @@ workflow CALL_SV_GERMLINECNVCALLER { SVDB_MERGE_GCNVCALLER ( merge_input_vcfs, [], true ) - ch_versions = ch_versions.mix(GATK4_COLLECTREADCOUNTS.out.versions) - ch_versions = ch_versions.mix(GATK4_DETERMINEGERMLINECONTIGPLOIDY.out.versions) - ch_versions = ch_versions.mix(GATK4_GERMLINECNVCALLER.out.versions) - ch_versions = ch_versions.mix(GATK4_POSTPROCESSGERMLINECNVCALLS.out.versions) - ch_versions = ch_versions.mix(SVDB_MERGE_GCNVCALLER.out.versions) - emit: genotyped_intervals_vcf = GATK4_POSTPROCESSGERMLINECNVCALLS.out.intervals // channel: [ val(meta), path(*.vcf.gz) ] genotyped_segments_vcf = GATK4_POSTPROCESSGERMLINECNVCALLS.out.segments // channel: [ val(meta), path(*.vcf.gz) ] genotyped_filtered_segments_vcf = SVDB_MERGE_GCNVCALLER.out.vcf // channel: [ val(meta), path(*.vcf.gz) ] denoised_vcf = GATK4_POSTPROCESSGERMLINECNVCALLS.out.denoised // channel: [ val(meta), path(*.vcf.gz) ] - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index eb83777e8..fc3b79817 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -30,7 +30,6 @@ workflow CALL_SV_TIDDIT { SVDB_MERGE_TIDDIT ( merge_input_vcfs, [], true ) ch_versions = TIDDIT_SV.out.versions - ch_versions = ch_versions.mix(SVDB_MERGE_TIDDIT.out.versions) emit: vcf = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/convert_mt_bam_to_fastq/main.nf b/subworkflows/local/convert_mt_bam_to_fastq/main.nf index 160e3837a..135721f06 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/main.nf +++ b/subworkflows/local/convert_mt_bam_to_fastq/main.nf @@ -15,7 +15,6 @@ workflow CONVERT_MT_BAM_TO_FASTQ { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] main: - ch_versions = channel.empty() // Outputs bam containing only MT GATK4_PRINTREADS_MT ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_genome_dict ) @@ -28,13 +27,8 @@ workflow CONVERT_MT_BAM_TO_FASTQ { // Outputs fastq files GATK4_SAMTOFASTQ_MT ( GATK4_REVERTSAM_MT.out.bam ) - ch_versions = ch_versions.mix(GATK4_PRINTREADS_MT.out.versions) - ch_versions = ch_versions.mix(GATK4_REVERTSAM_MT.out.versions) - ch_versions = ch_versions.mix(GATK4_SAMTOFASTQ_MT.out.versions) - emit: bam_bai = ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] fastq = GATK4_SAMTOFASTQ_MT.out.fastq // channel: [ val(meta), [ path(fastq) ] ] ubam = GATK4_REVERTSAM_MT.out.bam // channel: [ val(meta), path(bam) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index 68b8ba99b..e882f64c2 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -65,9 +65,6 @@ workflow GENS { GENS_GENERATE_COV_INDEX (GENS_GENERATE.out.cov) - ch_versions = ch_versions.mix(COLLECTREADCOUNTS.out.versions) - ch_versions = ch_versions.mix(DENOISEREADCOUNTS_FEMALE.out.versions) - ch_versions = ch_versions.mix(DENOISEREADCOUNTS_MALE.out.versions) ch_versions = ch_versions.mix(GENS_GENERATE.out.versions) ch_versions = ch_versions.mix(GENS_GENERATE_BAF_INDEX.out.versions) ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 0bb0f47eb..d87ec5b13 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -121,9 +121,6 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(PICARD_LIFTOVERVCF.out.versions) - ch_versions = ch_versions.mix(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.versions) - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION_MT.out.versions) ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) emit: diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 65eec3db6..0054b1e54 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -97,7 +97,6 @@ workflow PREPARE_REFERENCES { if (!val_genome_dict) { ch_genome_dict = GATK_SD(ch_genome_fasta).dict.collect() - ch_versions = ch_versions.mix(GATK_SD.out.versions) } else { ch_genome_dict = channel.fromPath(val_genome_dict).map {it -> [[id:it.simpleName], it]}.collect() } @@ -160,8 +159,6 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix(GATK_SD_MT.out.versions, - GATK_SHIFTFASTA.out.versions) } // // MT alignment indices @@ -227,7 +224,6 @@ workflow PREPARE_REFERENCES { ch_bait_intervals = CAT_CAT_BAIT ( ch_bait_intervals_cat_in ).file_out.map {_meta, inter -> inter}.collect().ifEmpty([[]]) - ch_versions = ch_versions.mix(GATK_BILT.out.versions, GATK_ILT.out.versions) } // // Prepare vcfanno extra files diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index cc51e69da..8b755908b 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -82,7 +82,6 @@ workflow QC_BAM { PICARD_COLLECTWGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y ) ch_cov = PICARD_COLLECTWGSMETRICS_WG.out.metrics ch_cov_y = PICARD_COLLECTWGSMETRICS_Y.out.metrics - ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS_WG.out.versions, PICARD_COLLECTWGSMETRICS_Y.out.versions) } else if (val_aligner.equals("sentieon")) { SENTIEON_WGSMETRICS_WG ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_wgs.map{ interval -> [[:], interval]} ) SENTIEON_WGSMETRICS_Y ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_intervals_y.map{ interval -> [[:], interval]} ) @@ -100,8 +99,6 @@ workflow QC_BAM { ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) - ch_versions = ch_versions.mix(CHROMOGRAPH_COV.out.versions) - ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions) ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index fc17c338b..c2c47cdb3 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -20,7 +20,6 @@ workflow SCATTER_GENOME { GATK4_SPLITINTERVALS(BUILD_BED.out.bed, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) ch_versions = ch_versions.mix(BUILD_BED.out.versions) - ch_versions = ch_versions.mix(GATK4_SPLITINTERVALS.out.versions) emit: bed = BUILD_BED.out.bed.collect() // channel: [ val(meta), path(bed) ] From a856ac167393b8115a8fa240926ad9d4e92f3c23 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 6 Feb 2026 12:22:34 +0100 Subject: [PATCH 299/872] new mitosalt container --- modules/local/mitosalt/main.nf | 2 +- tests/test_bam.nf.test.snap | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index 546da48af..ecde28237 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -4,7 +4,7 @@ process MITOSALT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - '/home/proj/production/dropbox/RN/mitosalt.sif': + 'https://depot.galaxyproject.org/singularity/mitosalt%3A1.1.1--hdfd78af_3': 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index db51408bf..88c7c1bcd 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -910,6 +910,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T10:43:55.12867456" + "timestamp": "2026-02-06T10:46:03.189728524" } } \ No newline at end of file From 7139e6c39fe49d4049309a2e6a1f27e45d58b3ee Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Feb 2026 15:44:19 +0100 Subject: [PATCH 300/872] update module --- modules.json | 5 +- .../cnvnator/cnvnator/cnvnator-cnvnator.diff | 50 ------------------- modules/nf-core/cnvnator/cnvnator/main.nf | 25 +++++----- modules/nf-core/cnvnator/cnvnator/meta.yml | 14 +++--- .../cnvnator/cnvnator/tests/main.nf.test | 8 ++- .../cnvnator/cnvnator/tests/main.nf.test.snap | 20 ++------ .../cnvnator/cnvnator/tests/nextflow.config | 10 ++-- 7 files changed, 39 insertions(+), 93 deletions(-) delete mode 100644 modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff diff --git a/modules.json b/modules.json index b1af329d7..5bcb733be 100644 --- a/modules.json +++ b/modules.json @@ -112,9 +112,8 @@ }, "cnvnator/cnvnator": { "branch": "master", - "git_sha": "e657cdd0198cc26f2e501325eb7f70fbd740b6ee", - "installed_by": ["modules"], - "patch": "modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff" + "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", + "installed_by": ["modules"] }, "cnvnator/convert2vcf": { "branch": "master", diff --git a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff b/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff deleted file mode 100644 index f06d7f6c1..000000000 --- a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff +++ /dev/null @@ -1,50 +0,0 @@ -Changes in module 'nf-core/cnvnator/cnvnator' ---- modules/nf-core/cnvnator/cnvnator/main.nf -+++ modules/nf-core/cnvnator/cnvnator/main.nf -@@ -12,11 +12,12 @@ - tuple val(meta2), path(root) - tuple val(meta3), path(fasta) - tuple val(meta4), path(fai) -+ val step - - output: -- tuple val(output_meta), path("${prefix}.root"), emit: root -- tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true -- path "versions.yml" , emit: versions -+ tuple val(output_meta), path("${output_meta.id}_${step}.root"), emit: root -+ tuple val(output_meta), path("*.tab") , emit: tab, optional: true -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -32,7 +33,11 @@ - reference = '' - } - calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' -+ mv_cmd = "mv ${prefix}.root ${prefix}_${step}.root" -+ steps = ["his", "stat", "partition", "call"] -+ cp_cmd = steps.contains(step) ? "cp ${root} ${prefix}.root" :"" - """ -+ $cp_cmd - cnvnator \\ - -root ${prefix}.root \\ - $args \\ -@@ -40,6 +45,7 @@ - $input_cmd \\ - $calls_cmd - -+ $mv_cmd - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) -@@ -52,7 +58,7 @@ - output_meta = bam ? meta : meta2 - def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : '' - """ -- touch ${prefix}.root -+ touch ${prefix}_${step}.root - $calls_cmd - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf index e891d4cf6..b7362cba0 100644 --- a/modules/nf-core/cnvnator/cnvnator/main.nf +++ b/modules/nf-core/cnvnator/cnvnator/main.nf @@ -9,12 +9,13 @@ process CNVNATOR_CNVNATOR { input: tuple val(meta), path(bam), path(bai) - tuple val(meta2), path(root) + tuple val(meta2), path(root, stageAs:'input/') tuple val(meta3), path(fasta) tuple val(meta4), path(fai) + val step // Without this parameter Nextflow can't distinguish between different steps, and resume becomes unreliable across the workflow chain output: - tuple val(output_meta), path("${prefix}.root"), emit: root + tuple val(output_meta), path("${prefix}.root"), emit: root, optional: true tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true tuple val("${task.process}"), val('cnvnator'), eval("cnvnator 2>&1 | sed -n '3s/CNVnator v//p'"), topic: versions, emit: versions_cnvnator @@ -25,30 +26,30 @@ process CNVNATOR_CNVNATOR { def args = task.ext.args ?: '' def input_cmd = bam ? "-tree ${bam}" : '' output_meta = bam ? meta : meta2 - prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" + prefix = task.ext.prefix ?: "${output_meta.id}" if (fasta) { reference = fasta.isDirectory() ? "-d ${fasta}" : "-fasta ${fasta}" } else { reference = '' } def calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' + cp_cmd = root ? "cp input/* ${prefix}.root" :"" """ + ${cp_cmd} cnvnator \\ -root ${prefix}.root \\ - $args \\ - $reference \\ - $input_cmd \\ - $calls_cmd + ${args} \\ + ${reference} \\ + ${input_cmd} \\ + ${calls_cmd} """ stub: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" output_meta = bam ? meta : meta2 - def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : '' + prefix = task.ext.prefix ?: "${output_meta.id}" + def touch_cmd = args.contains("-call") ? "touch ${prefix}.tab" : "touch ${prefix}.root" """ - touch ${prefix}.root - $calls_cmd_opt - + ${touch_cmd} """ } diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 39643a6de..c347493e0 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -1,6 +1,6 @@ name: "cnvnator_cnvnator" -description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage - by mapped reads. +description: CNVnator is a command line tool for CNV/CNA analysis from + depth-of-coverage by mapped reads. keywords: - cnvnator - cnv @@ -11,7 +11,8 @@ tools: homepage: "https://github.com/abyzovlab/CNVnator" documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:cnvnator input: - - meta: @@ -59,6 +60,9 @@ input: description: Path to a fasta file index pattern: "*.fai" ontologies: [] + - step: + type: string + description: One of "his", "rd", "call", "stat", and "partition" output: root: - - output_meta: @@ -82,7 +86,7 @@ output: description: A tab file containing cnvnator calls pattern: "*.tab" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_cnvnator: - - ${task.process}: type: string @@ -93,7 +97,6 @@ output: - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': type: eval description: The expression to obtain the version of the tool - topics: versions: - - ${task.process}: @@ -105,7 +108,6 @@ topics: - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': type: eval description: The expression to obtain the version of the tool - authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test index bc24b893f..fc086ef97 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test @@ -23,6 +23,7 @@ nextflow_process { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "rd" """ } } @@ -35,6 +36,7 @@ nextflow_process { input[1] = CNVNATOR_RD.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "his" """ } } @@ -47,6 +49,7 @@ nextflow_process { input[1] = CNVNATOR_HIST.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "stat" """ } } @@ -59,6 +62,7 @@ nextflow_process { input[1] = CNVNATOR_STAT.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "partition" """ } } @@ -79,6 +83,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } @@ -99,7 +104,7 @@ nextflow_process { options '-stub' when { params { - cnvnator_rd_args = '' + cnvnator_rd_args = '-chrom chr22' cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' @@ -111,6 +116,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap index 879b22990..07ebd04fb 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap @@ -27,19 +27,13 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:01:39.090472" + "timestamp": "2026-02-06T10:36:02.494664" }, "test_cnvnator -- stub": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ [ @@ -58,13 +52,7 @@ ] ], "root": [ - [ - { - "id": "test", - "single_end": false - }, - "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "tab": [ [ @@ -97,6 +85,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:01:50.842069" + "timestamp": "2026-02-06T13:37:25.433539" } } \ No newline at end of file diff --git a/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config index f971334b1..9a9f9a920 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config +++ b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config @@ -1,21 +1,21 @@ process { withName: "CNVNATOR_RD" { - ext.args = params.cnvnator_rd_args + ext.args = {params.cnvnator_rd_args} } withName: "CNVNATOR_HIST" { - ext.args = params.cnvnator_hist_args + ext.args = {params.cnvnator_hist_args} } withName: "CNVNATOR_STAT" { - ext.args = params.cnvnator_stat_args + ext.args = {params.cnvnator_stat_args} } withName: "CNVNATOR_PARTITION" { - ext.args = params.cnvnator_partition_args + ext.args = {params.cnvnator_partition_args} } withName: "CNVNATOR_CNVNATOR" { - ext.args = params.cnvnator_args + ext.args = {params.cnvnator_args} } } From 7702d8b17fc9c52172bf6c83f2ce90c519ed56a7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Feb 2026 15:45:37 +0100 Subject: [PATCH 301/872] update subwfs --- modules.json | 461 +++++++++++++----- subworkflows/local/call_snv_MT/main.nf | 2 +- .../local/call_structural_variants.nf | 1 - .../local/postprocess_MT_calls/main.nf | 2 +- workflows/raredisease.nf | 2 - 5 files changed, 348 insertions(+), 120 deletions(-) diff --git a/modules.json b/modules.json index b1af329d7..da72cf90c 100644 --- a/modules.json +++ b/modules.json @@ -8,555 +8,778 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -565,25 +788,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index b1df3c7fd..353e96e0e 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -19,7 +19,7 @@ workflow CALL_SNV_MT { ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) - GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai, ch_dict, [], [], [],[]) + GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf) ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index f7bb9104d..4fe09ca8b 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -55,7 +55,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .vcf .collect{ _meta, vcf -> vcf } .set { cnvnator_vcf } - ch_versions = ch_versions.mix(CALL_SV_CNVNATOR.out.versions) } if (!skip_germlinecnvcaller) { diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index d87ec5b13..90e501db7 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -50,7 +50,7 @@ workflow POSTPROCESS_MT_CALLS { GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.vcf .join(GATK4_MERGEVCFS_LIFT_UNLIFT_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) .set { ch_filt_vcf } - GATK4_VARIANTFILTRATION_MT (ch_filt_vcf, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) + GATK4_VARIANTFILTRATION_MT (ch_filt_vcf, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary, [[:],[]]) // Spliting multiallelic calls GATK4_VARIANTFILTRATION_MT.out.vcf diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 443f714fc..2a3833dc6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -345,7 +345,6 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) - ch_versions = ch_versions.mix(CALL_REPEAT_EXPANSIONS.out.versions) if (!skip_repeat_annotation) { STRANGER ( @@ -666,7 +665,6 @@ workflow RAREDISEASE { val_vep_cache_version, ch_vep_extra_files ).set { ch_me_annotate } - ch_versions = ch_versions.mix(ANNOTATE_MOBILE_ELEMENTS.out.versions) ch_me_annotate.vcf_ann .multiMap { meta, vcf -> From 3025c5b7024996027d3086294b30a9d14c80d5ea Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Feb 2026 16:11:06 +0100 Subject: [PATCH 302/872] update cnvnator --- modules.json | 464 +++++------------- .../cnvnator/cnvnator/cnvnator-cnvnator.diff | 50 -- modules/nf-core/cnvnator/cnvnator/main.nf | 25 +- modules/nf-core/cnvnator/cnvnator/meta.yml | 14 +- .../cnvnator/cnvnator/tests/main.nf.test | 8 +- .../cnvnator/cnvnator/tests/main.nf.test.snap | 20 +- .../cnvnator/cnvnator/tests/nextflow.config | 10 +- 7 files changed, 153 insertions(+), 438 deletions(-) delete mode 100644 modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff diff --git a/modules.json b/modules.json index da72cf90c..5bcb733be 100644 --- a/modules.json +++ b/modules.json @@ -8,778 +8,554 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - 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"installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff b/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff deleted file mode 100644 index f06d7f6c1..000000000 --- a/modules/nf-core/cnvnator/cnvnator/cnvnator-cnvnator.diff +++ /dev/null @@ -1,50 +0,0 @@ -Changes in module 'nf-core/cnvnator/cnvnator' ---- modules/nf-core/cnvnator/cnvnator/main.nf -+++ modules/nf-core/cnvnator/cnvnator/main.nf -@@ -12,11 +12,12 @@ - tuple val(meta2), path(root) - tuple val(meta3), path(fasta) - tuple val(meta4), path(fai) -+ val step - - output: -- tuple val(output_meta), path("${prefix}.root"), emit: root -- tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true -- path "versions.yml" , emit: versions -+ tuple val(output_meta), path("${output_meta.id}_${step}.root"), emit: root -+ tuple val(output_meta), path("*.tab") , emit: tab, optional: true -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -32,7 +33,11 @@ - reference = '' - } - calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' -+ mv_cmd = "mv ${prefix}.root ${prefix}_${step}.root" -+ steps = ["his", "stat", "partition", "call"] -+ cp_cmd = steps.contains(step) ? "cp ${root} ${prefix}.root" :"" - """ -+ $cp_cmd - cnvnator \\ - -root ${prefix}.root \\ - $args \\ -@@ -40,6 +45,7 @@ - $input_cmd \\ - $calls_cmd - -+ $mv_cmd - cat <<-END_VERSIONS > versions.yml - "${task.process}": - CNVnator: \$(echo \$(cnvnator 2>&1 | sed -n '3p' | sed 's/CNVnator v//')) -@@ -52,7 +58,7 @@ - output_meta = bam ? meta : meta2 - def calls_cmd = args.contains("-call") ? "touch ${prefix}.tab" : '' - """ -- touch ${prefix}.root -+ touch ${prefix}_${step}.root - $calls_cmd - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/cnvnator/cnvnator/main.nf b/modules/nf-core/cnvnator/cnvnator/main.nf index e891d4cf6..b7362cba0 100644 --- a/modules/nf-core/cnvnator/cnvnator/main.nf +++ b/modules/nf-core/cnvnator/cnvnator/main.nf @@ -9,12 +9,13 @@ process CNVNATOR_CNVNATOR { input: tuple val(meta), path(bam), path(bai) - tuple val(meta2), path(root) + tuple val(meta2), path(root, stageAs:'input/') tuple val(meta3), path(fasta) tuple val(meta4), path(fai) + val step // Without this parameter Nextflow can't distinguish between different steps, and resume becomes unreliable across the workflow chain output: - tuple val(output_meta), path("${prefix}.root"), emit: root + tuple val(output_meta), path("${prefix}.root"), emit: root, optional: true tuple val(output_meta), path("${prefix}.tab") , emit: tab, optional: true tuple val("${task.process}"), val('cnvnator'), eval("cnvnator 2>&1 | sed -n '3s/CNVnator v//p'"), topic: versions, emit: versions_cnvnator @@ -25,30 +26,30 @@ process CNVNATOR_CNVNATOR { def args = task.ext.args ?: '' def input_cmd = bam ? "-tree ${bam}" : '' output_meta = bam ? meta : meta2 - prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" + prefix = task.ext.prefix ?: "${output_meta.id}" if (fasta) { reference = fasta.isDirectory() ? "-d ${fasta}" : "-fasta ${fasta}" } else { reference = '' } def calls_cmd = args.contains("-call") ? "> ${prefix}.tab" : '' + cp_cmd = root ? "cp input/* ${prefix}.root" :"" """ + ${cp_cmd} cnvnator \\ -root ${prefix}.root \\ - $args \\ - $reference \\ - $input_cmd \\ - $calls_cmd + ${args} \\ + ${reference} \\ + ${input_cmd} \\ + ${calls_cmd} """ stub: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: bam ? "${meta.id}" : "${meta2.id}" output_meta = bam ? meta : meta2 - def calls_cmd_opt = args.contains("-call") ? "touch ${prefix}.tab" : '' + prefix = task.ext.prefix ?: "${output_meta.id}" + def touch_cmd = args.contains("-call") ? "touch ${prefix}.tab" : "touch ${prefix}.root" """ - touch ${prefix}.root - $calls_cmd_opt - + ${touch_cmd} """ } diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 39643a6de..c347493e0 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -1,6 +1,6 @@ name: "cnvnator_cnvnator" -description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage - by mapped reads. +description: CNVnator is a command line tool for CNV/CNA analysis from + depth-of-coverage by mapped reads. keywords: - cnvnator - cnv @@ -11,7 +11,8 @@ tools: homepage: "https://github.com/abyzovlab/CNVnator" documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:cnvnator input: - - meta: @@ -59,6 +60,9 @@ input: description: Path to a fasta file index pattern: "*.fai" ontologies: [] + - step: + type: string + description: One of "his", "rd", "call", "stat", and "partition" output: root: - - output_meta: @@ -82,7 +86,7 @@ output: description: A tab file containing cnvnator calls pattern: "*.tab" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_cnvnator: - - ${task.process}: type: string @@ -93,7 +97,6 @@ output: - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': type: eval description: The expression to obtain the version of the tool - topics: versions: - - ${task.process}: @@ -105,7 +108,6 @@ topics: - cnvnator 2>&1 | sed -n '3s/CNVnator v//p': type: eval description: The expression to obtain the version of the tool - authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test index bc24b893f..fc086ef97 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test @@ -23,6 +23,7 @@ nextflow_process { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "rd" """ } } @@ -35,6 +36,7 @@ nextflow_process { input[1] = CNVNATOR_RD.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "his" """ } } @@ -47,6 +49,7 @@ nextflow_process { input[1] = CNVNATOR_HIST.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "stat" """ } } @@ -59,6 +62,7 @@ nextflow_process { input[1] = CNVNATOR_STAT.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "partition" """ } } @@ -79,6 +83,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } @@ -99,7 +104,7 @@ nextflow_process { options '-stub' when { params { - cnvnator_rd_args = '' + cnvnator_rd_args = '-chrom chr22' cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' @@ -111,6 +116,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap index 879b22990..07ebd04fb 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap +++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test.snap @@ -27,19 +27,13 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:01:39.090472" + "timestamp": "2026-02-06T10:36:02.494664" }, "test_cnvnator -- stub": { "content": [ { "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ [ @@ -58,13 +52,7 @@ ] ], "root": [ - [ - { - "id": "test", - "single_end": false - }, - "test.root:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "tab": [ [ @@ -97,6 +85,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:01:50.842069" + "timestamp": "2026-02-06T13:37:25.433539" } } \ No newline at end of file diff --git a/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config index f971334b1..9a9f9a920 100644 --- a/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config +++ b/modules/nf-core/cnvnator/cnvnator/tests/nextflow.config @@ -1,21 +1,21 @@ process { withName: "CNVNATOR_RD" { - ext.args = params.cnvnator_rd_args + ext.args = {params.cnvnator_rd_args} } withName: "CNVNATOR_HIST" { - ext.args = params.cnvnator_hist_args + ext.args = {params.cnvnator_hist_args} } withName: "CNVNATOR_STAT" { - ext.args = params.cnvnator_stat_args + ext.args = {params.cnvnator_stat_args} } withName: "CNVNATOR_PARTITION" { - ext.args = params.cnvnator_partition_args + ext.args = {params.cnvnator_partition_args} } withName: "CNVNATOR_CNVNATOR" { - ext.args = params.cnvnator_args + ext.args = {params.cnvnator_args} } } From a62a600be64ff56b9fe9bd56b6b97ee01e7d9580 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Feb 2026 16:25:59 +0100 Subject: [PATCH 303/872] update changelog --- CHANGELOG.md | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 752e2badd..5dfb73cce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,25 +47,25 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| ----------------------------------- | ----------- | ----------- | -| bcftools | 1.20 | 1.21 | -| htslib | 1.20 | 1.21 | -| mosdepth | 0.3.8 | 0.3.11 | -| ngs-bits | 2023_02 | 2024_11 | -| gatk4/determinegermlinecontigploidy | 4.5.0.0 | 4.6.2.0 | -| gatk4/germlinecnvcaller | 4.5.0.0 | 4.6.2.0 | -| gens-preproc | 1.0.11 | 1.1.2 | -| pigz | 2.3.4 | 2.8 | -| samtools | 1.21 | 1.22.1 | -| sambamba | | 1.0.1 | -| ensemblverp/filtervep | 113 | 115.2 | -| fastp | 0.23.4 | 1.0.1 | -| genmod | 3.9 | 3.10.2 | -| multiqc | 1.32 | 1.33 | -| picard | 3.3.0 | 3.4.0 | -| sentieon | 202503 | 202503.02 | -| stranger | 0.9.4 | 0.10.0 | +| Tool | Old version | New version | +| --------------------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| htslib | 1.20 | 1.21 | +| mosdepth | 0.3.8 | 0.3.11 | +| ngs-bits | 2023_02 | 2024_11 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | +| gens-preproc | 1.0.11 | 1.1.2 | +| pigz | 2.3.4 | 2.8 | +| samtools | 1.21 | 1.22.1 | +| sambamba | | 1.0.1 | +| ensemblverp/filtervep | 113 | 115.2 | +| fastp | 0.23.4 | 1.0.1 | +| genmod | 3.9 | 3.10.2 | +| multiqc | 1.32 | 1.33 | +| picard | 3.3.0 | 3.4.0 | +| sentieon | 202503 | 202503.02 | +| stranger | 0.9.4 | 0.10.0 | +| deepvarian | 1.8.0 | 1.9.0 | ## 2.6.0 - Cacofonix [2025-06-25] From 7ec0ce46c1b7b5bc98daf44306fd8cb43d5affff Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 6 Feb 2026 16:39:29 +0100 Subject: [PATCH 304/872] new containers --- modules/local/mitosalt/main.nf | 4 ++-- tests/default.nf.test.snap | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index ecde28237..d0ed62b98 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -4,8 +4,8 @@ process MITOSALT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mitosalt%3A1.1.1--hdfd78af_3': - 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc2631dac526622d28ea1109b0f714d536606d0e5b3b85fe24407c8206e7e6b6/data': + 'community.wave.seqera.io/library/mitosalt:1.1.1--5fd87ac48a683358' }" input: diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index fe6430ef1..07e080180 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -909,6 +909,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T10:39:36.534853957" + "timestamp": "2026-02-06T14:15:40.865749779" } } \ No newline at end of file From 38e86369548c7f915f4a94567bde549beeff38d3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 7 Feb 2026 23:02:32 +0100 Subject: [PATCH 305/872] update snap --- modules.json | 2 +- modules/nf-core/expansionhunter/main.nf | 2 +- modules/nf-core/expansionhunter/meta.yml | 4 +- .../expansionhunter/tests/main.nf.test.snap | 16 +- .../local/align/tests/main.nf.test.snap | 73 +---- .../local/align_MT/tests/main.nf.test.snap | 72 ++--- .../tests/main.nf.test.snap | 10 +- .../tests/main.nf.test.snap | 12 +- .../scatter_genome/tests/main.nf.test.snap | 12 +- tests/default.nf.test.snap | 301 +++++++++++++++--- tests/test_bam.nf.test.snap | 299 ++++++++++++++--- tests/test_singleton.nf.test.snap | 145 ++++++--- 12 files changed, 638 insertions(+), 310 deletions(-) diff --git a/modules.json b/modules.json index 5bcb733be..505f5fc66 100644 --- a/modules.json +++ b/modules.json @@ -153,7 +153,7 @@ }, "expansionhunter": { "branch": "master", - "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "fastp": { diff --git a/modules/nf-core/expansionhunter/main.nf b/modules/nf-core/expansionhunter/main.nf index 82b6ec9c1..f389a04a4 100644 --- a/modules/nf-core/expansionhunter/main.nf +++ b/modules/nf-core/expansionhunter/main.nf @@ -17,7 +17,7 @@ process EXPANSIONHUNTER { tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.json.gz") , emit: json tuple val(meta), path("*_realigned.bam") , emit: bam - tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//'"), topic: versions, emit: versions_expansionhunter + tuple val("${task.process}"), val('expansionhunter'), eval("ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p'"), topic: versions, emit: versions_expansionhunter tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml index f9e5475cc..c6b070739 100644 --- a/modules/nf-core/expansionhunter/meta.yml +++ b/modules/nf-core/expansionhunter/meta.yml @@ -105,7 +105,7 @@ output: - expansionhunter: type: string description: The tool name - - ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//': + - ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p': type: eval description: The expression to obtain the version of the tool versions_bgzip: @@ -126,7 +126,7 @@ topics: - expansionhunter: type: string description: The tool name - - ExpansionHunter --version 2>&1 | head -1 | sed 's/^.*ExpansionHunter v//': + - ExpansionHunter --version | head -1 | sed -n 's/^.*ExpansionHunter v//; s/]//p': type: eval description: The expression to obtain the version of the tool - - ${task.process}: diff --git a/modules/nf-core/expansionhunter/tests/main.nf.test.snap b/modules/nf-core/expansionhunter/tests/main.nf.test.snap index 4cf42a7c5..04b55ca14 100644 --- a/modules/nf-core/expansionhunter/tests/main.nf.test.snap +++ b/modules/nf-core/expansionhunter/tests/main.nf.test.snap @@ -30,7 +30,7 @@ [ "EXPANSIONHUNTER", "expansionhunter", - "5.0.0]" + "5.0.0" ] ], "4": [ @@ -75,16 +75,16 @@ [ "EXPANSIONHUNTER", "expansionhunter", - "5.0.0]" + "5.0.0" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-29T15:38:57.19607229" + "timestamp": "2026-02-04T13:49:22.036774" }, "stub": { "content": [ @@ -117,7 +117,7 @@ [ "EXPANSIONHUNTER", "expansionhunter", - "5.0.0]" + "5.0.0" ] ], "4": [ @@ -162,15 +162,15 @@ [ "EXPANSIONHUNTER", "expansionhunter", - "5.0.0]" + "5.0.0" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-29T15:39:11.490611694" + "timestamp": "2026-02-04T13:53:07.012233" } } \ No newline at end of file diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 8b83d6ca7..07d7157f9 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -238,58 +238,28 @@ ] ], [ - "versions.yml:md5,04cb590a101237e8d8726039ee466819", - "versions.yml:md5,04cb590a101237e8d8726039ee466819", - "versions.yml:md5,04cb590a101237e8d8726039ee466819", - "versions.yml:md5,210790d64830e81c512ff898e8d888db", - "versions.yml:md5,210790d64830e81c512ff898e8d888db", - "versions.yml:md5,210790d64830e81c512ff898e8d888db", 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"nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T23:13:51.08952732" + "timestamp": "2026-02-06T17:31:32.266454329" }, "align bwamem2 - wes": { "content": [ @@ -542,9 +482,6 @@ "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", - "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", - "versions.yml:md5,7b799d18a80d6d144122cc97f83748c3", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", @@ -557,6 +494,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-27T09:04:50.753630765" + "timestamp": "2026-02-06T16:48:59.035282254" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 5cb97333a..7537c0bd6 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -67,7 +67,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" ], [ { @@ -83,7 +83,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" ], [ { @@ -99,22 +99,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] ], "2": [ - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" ], "marked_bai": [ [ @@ -181,7 +172,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,3f1d065d74ead7620a1fa3fe66404811" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" ], [ { @@ -197,7 +188,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,4ad1f7b8172388d7ab801de09a58aa8e" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" ], [ { @@ -213,22 +204,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,53f26c6136de14bddb7392a737db457a" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] ], "versions": [ - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" + "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" ] } ], @@ -236,7 +218,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T21:20:12.412575747" + "timestamp": "2026-02-06T17:37:55.606130634" }, "align mt - bwa": { "content": [ @@ -306,7 +288,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" ], [ { @@ -322,7 +304,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" ], [ { @@ -338,22 +320,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] ], "2": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" ], "marked_bai": [ [ @@ -420,7 +393,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,06cebfd2ccd12a52d53196b71b633ba2" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" ], [ { @@ -436,7 +409,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d1484f44f615bfa8eb0097307870c7de" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" ], [ { @@ -452,22 +425,13 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,866d2992afa71e50f5978244ef6a5b2b" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] ], "versions": [ "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,7ab78da5d9523074122d0c961d3bdb89", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ca3c0437f05cbf946185cd80b16744ef", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970", - "versions.yml:md5,ee160a842ca6cba016914a1d7a69e970" + "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" ] } ], @@ -475,6 +439,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-25T21:22:23.024924094" + "timestamp": "2026-02-06T17:44:37.818378883" } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 378aee009..3b33ea9a7 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "13f1d6d13abf640bc42f5692510b9a7a" + "da588ff12491da491e3059326ffef0de" ] ], [ @@ -34,7 +34,6 @@ [ "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] @@ -43,7 +42,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T23:20:05.423583715" + "timestamp": "2026-02-06T17:47:53.965738943" }, "align bwameme": { "content": [ @@ -59,7 +58,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "2b9969e02527b37fdfb5852fc2583bc5" + "91efdc668b5f6e075743e414c7afd0f8" ] ], [ @@ -80,7 +79,6 @@ [ "versions.yml:md5,390a09ae83280da84de93856149cc3a1", "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,9d7492d23e5995a4955de5f751df05af", "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] @@ -89,6 +87,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-26T23:21:26.123323889" + "timestamp": "2026-02-06T17:50:27.94216545" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 6ac191684..92f305466 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -386,15 +386,10 @@ ], "29": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", - "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", - "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ], "3": [ @@ -901,15 +896,10 @@ ], "versions": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,18ec352f630429e7d036f31a45b4cc9d", - "versions.yml:md5,26eb7437d00ad47436fb6f377c232a27", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,467b7fc47b7222904619e8b2b789709d", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,c18e81b268596fc9050cc8af016b09e8", - "versions.yml:md5,d73bccf32c40dcb80a722652878c6c43", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] } @@ -918,6 +908,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-31T15:59:04.629155265" + "timestamp": "2026-02-06T18:02:00.602808407" } } \ No newline at end of file diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 93e51e4d5..08c213bb6 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -73,8 +73,7 @@ ] ], "2": [ - "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", - "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" + "versions.yml:md5,005c9777d9befd3821945bc05709dfc8" ], "bed": [ [ @@ -147,15 +146,14 @@ ] ], "versions": [ - "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", - "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" + "versions.yml:md5,005c9777d9befd3821945bc05709dfc8" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-03-31T11:51:27.737317" + "timestamp": "2026-02-06T18:19:24.751974831" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b47286abc..288acbcca 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -92,22 +92,22 @@ "chromograph": "1.3.1" }, "CNVNATOR_CALL": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_HIST": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_RD": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_STAT": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", @@ -122,7 +122,7 @@ "bgzip": 1.21 }, "DEEPVARIANT": { - "deepvariant": "1.8.0" + "deepvariant": "1.9.0" }, "EKLIPSE": { "eklipse": 1.8 @@ -143,8 +143,8 @@ "ensemblvep": 110.0 }, "EXPANSIONHUNTER": { - "expansionhunter": "5.0.0", - "bgzip": 1.18 + "bgzip": "1.22.1", + "expansionhunter": "5.0.0" }, "FASTP": { "fastp": "1.0.1" @@ -153,46 +153,49 @@ "fastqc": "0.12.1" }, "GATK4_FILTERMUTECTCALLS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEBAMALIGNMENT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MUTECT2_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_PRINTREADS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_REVERTSAM_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SAMTOFASTQ_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SELECTVARIANTS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" + }, + "GATK4_SPLITINTERVALS": { + "gatk4": "4.6.2.0" }, "GATK4_VARIANTFILTRATION_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_BILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_ILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GAWK": { "gawk": "5.3.0" @@ -236,7 +239,7 @@ "manta": "1.6.0" }, "MARKDUPLICATES": { - "picard": "3.3.0" + "picard": "3.4.0" }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" @@ -254,28 +257,28 @@ "peddy": "0.4.8" }, "PICARD_ADDORREPLACEREADGROUPS_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTHSMETRICS": { "picard": "3.4.0" }, "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_WG": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_Y": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_LIFTOVERVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_MARKDUPLICATES_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_SORTVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "QUALIMAP_BAMQC": { "qualimap": 2.3 @@ -287,7 +290,7 @@ "bcftools": 1.22 }, "RENAMESAMPLE_EXP": { - "picard": "3.3.0" + "picard": "3.4.0" }, "RENAME_BAI": { "coreutils": 8.31 @@ -361,30 +364,30 @@ }, "STRANGER": { "stranger": "0.10.0", - "tabix": "1.22.1" + "tabix": 1.23 }, "SVDB_MERGE": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_CNVNATOR": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_ME": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_REPEATS": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_TIDDIT": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_QUERY_DB": { - "svdb": "2.8.2" + "svdb": "2.8.3" }, "TABIX_ANNOTATE": { "tabix": 1.21 @@ -511,24 +514,144 @@ "annotate_snv", "annotate_snv/genome", "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", - "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/hugelymodelbat_chromograph_regions", - "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrY.png", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", - "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -655,7 +778,6 @@ "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/earlycasualcaiman_chromographcov", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", @@ -682,6 +804,31 @@ "qc_bam/earlycasualcaiman_tidditcov.bed", "qc_bam/earlycasualcaiman_tidditcov.bw", "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", @@ -738,7 +885,6 @@ "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/hugelymodelbat_chromographcov", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -765,6 +911,31 @@ "qc_bam/hugelymodelbat_tidditcov.bed", "qc_bam/hugelymodelbat_tidditcov.bw", "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck", @@ -821,7 +992,6 @@ "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/slowlycivilbuck_chromographcov", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", @@ -848,6 +1018,31 @@ "qc_bam/slowlycivilbuck_tidditcov.bed", "qc_bam/slowlycivilbuck_tidditcov.bw", "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", @@ -905,6 +1100,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-31T20:55:04.269156792" + "timestamp": "2026-02-07T11:46:41.611269933" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index e290a2ac7..2f175af14 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -89,22 +89,22 @@ "chromograph": "1.3.1" }, "CNVNATOR_CALL": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_HIST": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_RD": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_STAT": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", @@ -119,7 +119,7 @@ "bgzip": 1.21 }, "DEEPVARIANT": { - "deepvariant": "1.8.0" + "deepvariant": "1.9.0" }, "EKLIPSE": { "eklipse": 1.8 @@ -140,50 +140,53 @@ "ensemblvep": 110.0 }, "EXPANSIONHUNTER": { - "expansionhunter": "5.0.0", - "bgzip": 1.18 + "bgzip": "1.22.1", + "expansionhunter": "5.0.0" }, "GATK4_FILTERMUTECTCALLS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEBAMALIGNMENT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MUTECT2_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_PRINTREADS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_REVERTSAM_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SAMTOFASTQ_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SELECTVARIANTS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" + }, + "GATK4_SPLITINTERVALS": { + "gatk4": "4.6.2.0" }, "GATK4_VARIANTFILTRATION_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_BILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_ILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GAWK": { "gawk": "5.3.0" @@ -242,28 +245,28 @@ "peddy": "0.4.8" }, "PICARD_ADDORREPLACEREADGROUPS_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTHSMETRICS": { "picard": "3.4.0" }, "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_WG": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_Y": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_LIFTOVERVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_MARKDUPLICATES_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_SORTVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "QUALIMAP_BAMQC": { "qualimap": 2.3 @@ -275,7 +278,7 @@ "bcftools": 1.22 }, "RENAMESAMPLE_EXP": { - "picard": "3.3.0" + "picard": "3.4.0" }, "RENAME_BAI": { "coreutils": 8.31 @@ -337,30 +340,30 @@ }, "STRANGER": { "stranger": "0.10.0", - "tabix": "1.22.1" + "tabix": 1.23 }, "SVDB_MERGE": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_CNVNATOR": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_ME": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_REPEATS": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_TIDDIT": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_QUERY_DB": { - "svdb": "2.8.2" + "svdb": "2.8.3" }, "TABIX_ANNOTATE": { "tabix": 1.21 @@ -478,24 +481,144 @@ "annotate_snv", "annotate_snv/genome", "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", - "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/hugelymodelbat_chromograph_regions", - "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrY.png", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", - "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -612,7 +735,6 @@ "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/earlycasualcaiman_chromographcov", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", @@ -639,6 +761,31 @@ "qc_bam/earlycasualcaiman_tidditcov.bed", "qc_bam/earlycasualcaiman_tidditcov.bw", "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", @@ -695,7 +842,6 @@ "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/hugelymodelbat_chromographcov", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -722,6 +868,31 @@ "qc_bam/hugelymodelbat_tidditcov.bed", "qc_bam/hugelymodelbat_tidditcov.bw", "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck", @@ -778,7 +949,6 @@ "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/slowlycivilbuck_chromographcov", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", @@ -805,6 +975,31 @@ "qc_bam/slowlycivilbuck_tidditcov.bed", "qc_bam/slowlycivilbuck_tidditcov.bw", "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", @@ -846,6 +1041,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-01-31T22:23:45.894751961" + "timestamp": "2026-02-07T12:27:20.306676608" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 5c5e7e05e..ab5180d12 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -84,22 +84,22 @@ "chromograph": "1.3.1" }, "CNVNATOR_CALL": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_CONVERT2VCF": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_HIST": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_PARTITION": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_RD": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CNVNATOR_STAT": { - "CNVnator": "0.4.1" + "cnvnator": "0.4.1" }, "CREATE_PEDIGREE_FILE": { "create_pedigree_file": "v1.0", @@ -114,7 +114,7 @@ "bgzip": 1.21 }, "DEEPVARIANT": { - "deepvariant": "1.8.0" + "deepvariant": "1.9.0" }, "EKLIPSE": { "eklipse": 1.8 @@ -135,8 +135,8 @@ "ensemblvep": 110.0 }, "EXPANSIONHUNTER": { - "expansionhunter": "5.0.0", - "bgzip": 1.18 + "bgzip": "1.22.1", + "expansionhunter": "5.0.0" }, "FASTP": { "fastp": "1.0.1" @@ -145,46 +145,49 @@ "fastqc": "0.12.1" }, "GATK4_FILTERMUTECTCALLS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEBAMALIGNMENT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_MUTECT2_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_PRINTREADS_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_REVERTSAM_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SAMTOFASTQ_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK4_SELECTVARIANTS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" + }, + "GATK4_SPLITINTERVALS": { + "gatk4": "4.6.2.0" }, "GATK4_VARIANTFILTRATION_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_BILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_ILT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SD_MT": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.2.0" }, "GAWK": { "gawk": "5.3.0" @@ -228,7 +231,7 @@ "manta": "1.6.0" }, "MARKDUPLICATES": { - "picard": "3.3.0" + "picard": "3.4.0" }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" @@ -246,28 +249,28 @@ "peddy": "0.4.8" }, "PICARD_ADDORREPLACEREADGROUPS_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTHSMETRICS": { "picard": "3.4.0" }, "PICARD_COLLECTMULTIPLEMETRICS": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_WG": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_COLLECTWGSMETRICS_Y": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_LIFTOVERVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_MARKDUPLICATES_MT": { - "picard": "3.3.0" + "picard": "3.4.0" }, "PICARD_SORTVCF": { - "picard": "3.3.0" + "picard": "3.4.0" }, "QUALIMAP_BAMQC": { "qualimap": 2.3 @@ -279,7 +282,7 @@ "bcftools": 1.22 }, "RENAMESAMPLE_EXP": { - "picard": "3.3.0" + "picard": "3.4.0" }, "RENAME_BAI": { "coreutils": 8.31 @@ -350,30 +353,30 @@ }, "STRANGER": { "stranger": "0.10.0", - "tabix": "1.22.1" + "tabix": 1.23 }, "SVDB_MERGE": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_CNVNATOR": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_ME": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_REPEATS": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_MERGE_TIDDIT": { - "svdb": "2.8.2", - "bcftools": 1.21 + "bcftools": 1.23, + "svdb": "2.8.3" }, "SVDB_QUERY_DB": { - "svdb": "2.8.2" + "svdb": "2.8.3" }, "TABIX_ANNOTATE": { "tabix": 1.21 @@ -484,10 +487,34 @@ "annotate_snv", "annotate_snv/genome", "annotate_snv/genome/hugelymodelbat_rhocallviz", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chrY.png", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_rhocallviz_autozyg_chromograph", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", "annotate_snv/mitochondria", @@ -598,7 +625,6 @@ "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/hugelymodelbat_chromographcov", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -625,6 +651,31 @@ "qc_bam/hugelymodelbat_tidditcov.bed", "qc_bam/hugelymodelbat_tidditcov.bw", "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", @@ -664,6 +715,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-01T18:23:51.512604286" + "timestamp": "2026-02-07T12:48:58.554399668" } } \ No newline at end of file From eb167b406e23602f1e580e0154a4ea5939b1d50f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 08:54:52 +0100 Subject: [PATCH 306/872] Update CHANGELOG.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5dfb73cce..e085629f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -65,7 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | picard | 3.3.0 | 3.4.0 | | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | -| deepvarian | 1.8.0 | 1.9.0 | +| deepvariant | 1.8.0 | 1.9.0 | ## 2.6.0 - Cacofonix [2025-06-25] From 8180ca8df7ed2cdd8b066b187993f18077ad039e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 9 Feb 2026 11:03:34 +0100 Subject: [PATCH 307/872] change version capture to match updates --- subworkflows/local/prepare_references/main.nf | 7 ++---- tests/default.nf.test.snap | 8 +------ tests/test_bam.nf.test.snap | 24 +++++++------------ tests/test_singleton.nf.test.snap | 22 +++++++---------- 4 files changed, 20 insertions(+), 41 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 5f28db0c3..1eb29f9ff 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -167,11 +167,8 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT.out.versions, - GATK_SD_MT.out.versions, - HISAT2_INDEX_GENOME.out.versions, - LAST_INDEX_MT.out.versions, - GATK_SHIFTFASTA.out.versions) + ch_versions = ch_versions.mix (HISAT2_INDEX_GENOME.out.versions, + LAST_INDEX_MT.out.versions) } // // MT alignment indices diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 25febcc1c..5ed87444f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -185,12 +185,6 @@ "GATK_SD": { "gatk4": "4.5.0.0" }, - "GATK_SD_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" - }, "GAWK": { "gawk": "5.3.0" }, @@ -911,6 +905,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-06T14:15:40.865749779" + "timestamp": "2026-02-09T09:41:15.778427811" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 074383120..49fe1805f 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -145,7 +145,7 @@ "bgzip": 1.18 }, "FASTP": { - "fastp": "0.23.4" + "fastp": "1.0.1" }, "FASTQC": { "fastqc": "0.12.1" @@ -186,12 +186,6 @@ "GATK_SD": { "gatk4": "4.5.0.0" }, - "GATK_SD_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" - }, "GAWK": { "gawk": "5.3.0" }, @@ -340,7 +334,7 @@ "samtools": "1.22.1" }, "SAMTOOLS_STATS": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" @@ -890,18 +884,18 @@ "trimming/earlycasualcaiman_LNUMBER1.fastp.html", "trimming/earlycasualcaiman_LNUMBER1.fastp.json", "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", "trimming/hugelymodelbat_LNUMBER3.fastp.html", "trimming/hugelymodelbat_LNUMBER3.fastp.json", "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", "trimming/slowlycivilbuck_LNUMBER2.fastp.html", "trimming/slowlycivilbuck_LNUMBER2.fastp.json", "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -912,6 +906,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-06T10:46:03.189728524" + "timestamp": "2026-02-09T10:07:25.308697516" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index b57b53361..a9e9a84aa 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -16,7 +16,7 @@ "bcftools": 1.22 }, "BCFTOOLS_MERGE_MT": { - "bcftools": 1.2 + "bcftools": 1.22 }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 @@ -186,12 +186,6 @@ "GATK_SD": { "gatk4": "4.5.0.0" }, - "GATK_SD_MT": { - "gatk4": "4.5.0.0" - }, - "GATK_SHIFTFASTA": { - "gatk4": "4.5.0.0" - }, "GAWK": { "gawk": "5.3.0" }, @@ -890,18 +884,18 @@ "trimming/earlycasualcaiman_LNUMBER1.fastp.html", "trimming/earlycasualcaiman_LNUMBER1.fastp.json", "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", "trimming/hugelymodelbat_LNUMBER3.fastp.html", "trimming/hugelymodelbat_LNUMBER3.fastp.json", "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", "trimming/slowlycivilbuck_LNUMBER2.fastp.html", "trimming/slowlycivilbuck_LNUMBER2.fastp.json", "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -912,6 +906,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-04T10:46:59.255846426" + "timestamp": "2026-02-09T10:39:58.934868309" } } \ No newline at end of file From a965a16f64356c09cf646c10eefd7ce598967535 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 11:51:39 +0100 Subject: [PATCH 308/872] update local modules --- conf/modules/scatter_genome.config | 5 ++ .../add_varcallername_to_bed/environment.yml | 7 +++ .../local/add_varcallername_to_bed/main.nf | 19 ++------ .../calculate_seed_fraction/environment.yml | 8 ++++ modules/local/calculate_seed_fraction/main.nf | 21 ++------- modules/local/create_bed_from_fai/main.nf | 39 --------------- .../local/create_hgncids_file/environment.yml | 8 ++++ modules/local/create_hgncids_file/main.nf | 47 ++++--------------- .../resources/usr/bin/create_hgncids_file.py | 42 +++++++++++++++++ .../create_pedigree_file/environment.yml | 7 +++ modules/local/create_pedigree_file/main.nf | 20 ++------ modules/local/gens/main.nf | 13 +---- modules/local/get_chrom_sizes/environment.yml | 7 +++ modules/local/get_chrom_sizes/main.nf | 20 ++------ .../local/mt_deletion_script/environment.yml | 7 +++ modules/local/mt_deletion_script/main.nf | 20 ++------ .../local/rename_align_files/environment.yml | 7 +++ modules/local/rename_align_files/main.nf | 19 ++------ .../replace_spaces_in_vcfinfo/environment.yml | 8 ++++ .../local/replace_spaces_in_vcfinfo/main.nf | 43 +++-------------- .../usr/bin/replace_spaces_in_vcfinfo.py | 34 ++++++++++++++ modules/local/retroseq/call/environment.yml | 7 +++ modules/local/retroseq/call/main.nf | 20 ++------ .../local/retroseq/discover/environment.yml | 7 +++ modules/local/retroseq/discover/main.nf | 19 ++------ subworkflows/local/prepare_references/main.nf | 10 ++-- subworkflows/local/scatter_genome/main.nf | 12 ++--- .../scatter_genome/tests/main.nf.test.snap | 18 ++----- 28 files changed, 222 insertions(+), 272 deletions(-) create mode 100644 modules/local/add_varcallername_to_bed/environment.yml create mode 100644 modules/local/calculate_seed_fraction/environment.yml delete mode 100644 modules/local/create_bed_from_fai/main.nf create mode 100644 modules/local/create_hgncids_file/environment.yml create mode 100644 modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py create mode 100644 modules/local/create_pedigree_file/environment.yml create mode 100644 modules/local/get_chrom_sizes/environment.yml create mode 100644 modules/local/mt_deletion_script/environment.yml create mode 100644 modules/local/rename_align_files/environment.yml create mode 100644 modules/local/replace_spaces_in_vcfinfo/environment.yml create mode 100644 modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py create mode 100644 modules/local/retroseq/call/environment.yml create mode 100644 modules/local/retroseq/discover/environment.yml diff --git a/conf/modules/scatter_genome.config b/conf/modules/scatter_genome.config index b5efa9bff..60730ea45 100644 --- a/conf/modules/scatter_genome.config +++ b/conf/modules/scatter_genome.config @@ -17,6 +17,11 @@ process { + withName: '.*SCATTER_GENOME:GAWK' { + ext.args2 = { '\'BEGIN {SEP="\t"}; {print \$1 SEP "0" SEP \$2}\'' } + ext.suffix = "bed" + } + withName: '.*SCATTER_GENOME:GATK4_SPLITINTERVALS' { ext.args = { "--scatter-count ${params.scatter_count}" } ext.prefix = { "${meta.id}_genome_intervals" } diff --git a/modules/local/add_varcallername_to_bed/environment.yml b/modules/local/add_varcallername_to_bed/environment.yml new file mode 100644 index 000000000..c0ba63205 --- /dev/null +++ b/modules/local/add_varcallername_to_bed/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 diff --git a/modules/local/add_varcallername_to_bed/main.nf b/modules/local/add_varcallername_to_bed/main.nf index 566402559..d584c1f14 100644 --- a/modules/local/add_varcallername_to_bed/main.nf +++ b/modules/local/add_varcallername_to_bed/main.nf @@ -2,17 +2,18 @@ process ADD_VARCALLER_TO_BED { tag "$meta.id" label 'process_single' - conda "bioconda::tabix=1.11" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' : + 'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }" input: tuple val(meta), path(chromsizes) output: tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -26,11 +27,6 @@ process ADD_VARCALLER_TO_BED { awk '{print \$1"\t0\t"\$2"\t$variant_caller\"}' $chromsizes > ${variant_caller}.bed bgzip --threads ${task.cpus} -c $args ${variant_caller}.bed > ${prefix}.bed.gz tabix $args2 ${prefix}.bed.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -38,10 +34,5 @@ process ADD_VARCALLER_TO_BED { """ touch ${prefix}.bed.gz touch ${prefix}.bed.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/local/calculate_seed_fraction/environment.yml b/modules/local/calculate_seed_fraction/environment.yml new file mode 100644 index 000000000..c38e0465e --- /dev/null +++ b/modules/local/calculate_seed_fraction/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.23 + - conda-forge::python=3.14.3 diff --git a/modules/local/calculate_seed_fraction/main.nf b/modules/local/calculate_seed_fraction/main.nf index 6d3dd2596..65fbac484 100644 --- a/modules/local/calculate_seed_fraction/main.nf +++ b/modules/local/calculate_seed_fraction/main.nf @@ -2,10 +2,10 @@ process CALCULATE_SEED_FRACTION { tag "$meta.id" label 'process_low' - conda "conda-forge::python=3.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2f/2fdb3ffa4bac62e98ec062e991217df2ab96e67bbd45a502bd25ff2effecb96e/data': + 'community.wave.seqera.io/library/htslib_python:d1e4474cbf76f4e9' }" input: tuple val(meta), path(cov) @@ -14,7 +14,8 @@ process CALCULATE_SEED_FRACTION { output: tuple val(meta), path("seedfrac.csv"), emit: csv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('calculate_seed_fraction'), val("1.0"), topic: versions, emit: versions_tabix + tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions, emit: versions_python when: task.ext.when == null || task.ext.when @@ -24,22 +25,10 @@ process CALCULATE_SEED_FRACTION { export MT_COVERAGE=`awk '{cov += \$3}END{ if (NR > 0) print cov / NR }' $cov` python -c "import os;print('%0.6f' % ($seed+ $rd/float(os.environ['MT_COVERAGE'])))" >seedfrac.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - calculate_seed_fraction: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS """ stub: """ touch seedfrac.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - calculate_seed_fraction: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS """ } diff --git a/modules/local/create_bed_from_fai/main.nf b/modules/local/create_bed_from_fai/main.nf deleted file mode 100644 index 6b96b6aee..000000000 --- a/modules/local/create_bed_from_fai/main.nf +++ /dev/null @@ -1,39 +0,0 @@ -process BUILD_BED { - tag "$meta.id" - label 'process_single' - - conda "anaconda::gawk=5.1.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'biocontainers/gawk:5.1.0' }" - - input: - tuple val(meta), path(fasta_fai) - - output: - tuple val(meta), path("*.bed") , emit: bed - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - """ - awk 'BEGIN {SEP="\t"}; {print \$1 SEP "0" SEP \$2}' ${fasta_fai} > ${fasta_fai.baseName}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS - """ - - stub: - """ - touch chr.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS - """ -} diff --git a/modules/local/create_hgncids_file/environment.yml b/modules/local/create_hgncids_file/environment.yml new file mode 100644 index 000000000..c38e0465e --- /dev/null +++ b/modules/local/create_hgncids_file/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.23 + - conda-forge::python=3.14.3 diff --git a/modules/local/create_hgncids_file/main.nf b/modules/local/create_hgncids_file/main.nf index f842d6a2c..ecf73e495 100644 --- a/modules/local/create_hgncids_file/main.nf +++ b/modules/local/create_hgncids_file/main.nf @@ -2,60 +2,31 @@ process CREATE_HGNCIDS_FILE { tag "$meta.id" label 'process_single' - conda "conda-forge::python=3.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2f/2fdb3ffa4bac62e98ec062e991217df2ab96e67bbd45a502bd25ff2effecb96e/data': + 'community.wave.seqera.io/library/htslib_python:d1e4474cbf76f4e9' }" input: tuple val(meta), path(input) output: tuple val(meta), path("*_reformatted.txt"), emit: txt - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('create_hgncids_file'), val("1.0"), topic: versions, emit: versions_create_hgncids_file + tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions, emit: versions_python when: task.ext.when == null || task.ext.when script: """ - python3 < versions.yml - "${task.process}": - create_hgncids_file: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS + create_hgncids_file.py --input ${input} --meta-id ${meta.id} + """ stub: """ - python3 < versions.yml - "${task.process}": - create_hgncids_file: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS + create_hgncids_file.py --input ${input} --meta-id ${meta.id} + """ } diff --git a/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py b/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py new file mode 100644 index 000000000..6f0261922 --- /dev/null +++ b/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 + +# Written by Ramprasad Neethiraj and released under the MIT license. +# See git repository (https://github.com/nf-core/raredisease) for full license text. + +from pathlib import Path +import argparse + +def main(): + parser = argparse.ArgumentParser( + description="Reformat input file based on meta.id" + ) + parser.add_argument( + "--input", + required=True, + help="Path to input file" + ) + parser.add_argument( + "--meta-id", + required=True, + help="Value of meta.id (e.g. scout)" + ) + + args = parser.parse_args() + + input_path = Path(args.input) + output_fn = input_path.stem + "_reformatted.txt" + + with input_path.open() as input_file, open(output_fn, "w") as output: + if args.meta_id == "scout": + for line in input_file: + if not line.startswith("#") and line.strip(): + spl = line.rstrip("\n").split("\t") + if len(spl) > 3: + output.write(spl[3] + "\n") + else: + for line in input_file: + if not line.startswith("#"): + output.write(line) + +if __name__ == "__main__": + main() diff --git a/modules/local/create_pedigree_file/environment.yml b/modules/local/create_pedigree_file/environment.yml new file mode 100644 index 000000000..7560fdd31 --- /dev/null +++ b/modules/local/create_pedigree_file/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: +- conda-forge +- bioconda +dependencies: +- conda-forge::coreutils=9.5 \ No newline at end of file diff --git a/modules/local/create_pedigree_file/main.nf b/modules/local/create_pedigree_file/main.nf index 79f2aef0e..45f3b7101 100644 --- a/modules/local/create_pedigree_file/main.nf +++ b/modules/local/create_pedigree_file/main.nf @@ -2,17 +2,17 @@ process CREATE_PEDIGREE_FILE { tag "pedigree" label 'process_single' - conda "conda-forge::python=3.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: val(samples) output: path("*.ped"), emit: ped - path "versions.yml", emit: versions + tuple val("${task.process}"), val('coreutils'), val("9.5"), topic: versions, emit: versions_coreutils when: task.ext.when == null || task.ext.when @@ -30,23 +30,11 @@ process CREATE_PEDIGREE_FILE { } """ echo -e "$outfile_text" >${case_name}.ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - create_pedigree_file: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS """ stub: def case_name = samples[0].case_id """ touch ${case_name}.ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - create_pedigree_file: v1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS """ } diff --git a/modules/local/gens/main.nf b/modules/local/gens/main.nf index da1da73aa..c7eb469a7 100644 --- a/modules/local/gens/main.nf +++ b/modules/local/gens/main.nf @@ -12,7 +12,8 @@ process GENS { output: tuple val(meta), path('*.cov.bed') , emit: cov tuple val(meta), path('*.baf.bed') , emit: baf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('generate_gens_data'), eval("generate_gens_data.py --version"), topic: versions, emit: versions_generate_gens_data + tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions, emit: versions_python script: // Exit if running this module with -profile conda / -profile mamba @@ -27,11 +28,6 @@ process GENS { --label $prefix \\ --baf_positions $gnomad_positions \\ --outdir \$PWD - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - generate_gens_data.py: \$(echo \$(generate_gens_data.py --version)) - END_VERSIONS """ stub: @@ -39,10 +35,5 @@ process GENS { """ touch ${prefix}.baf.bed touch ${prefix}.cov.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - generate_gens_data.py: \$(echo \$(generate_gens_data.py --version)) - END_VERSIONS """ } diff --git a/modules/local/get_chrom_sizes/environment.yml b/modules/local/get_chrom_sizes/environment.yml new file mode 100644 index 000000000..7560fdd31 --- /dev/null +++ b/modules/local/get_chrom_sizes/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: +- conda-forge +- bioconda +dependencies: +- conda-forge::coreutils=9.5 \ No newline at end of file diff --git a/modules/local/get_chrom_sizes/main.nf b/modules/local/get_chrom_sizes/main.nf index 1234c9eff..3cad914b8 100644 --- a/modules/local/get_chrom_sizes/main.nf +++ b/modules/local/get_chrom_sizes/main.nf @@ -2,41 +2,29 @@ process GET_CHROM_SIZES { tag "$fai" label 'process_single' - conda "conda-forge::coreutils=8.31" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' : - 'biocontainers/gnu-wget:1.18--h36e9172_9' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(fai) output: path '*.sizes' , emit: sizes - path "versions.yml", emit: versions + tuple val("${task.process}"), val('coreutils'), val("9.5"), topic: versions, emit: versions_coreutils when: task.ext.when == null || task.ext.when script: - def VERSION = "8.31" """ cut -f 1,2 $fai > ${fai}.sizes - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ stub: - def VERSION = "8.31" """ touch ${fai}.sizes - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ } diff --git a/modules/local/mt_deletion_script/environment.yml b/modules/local/mt_deletion_script/environment.yml new file mode 100644 index 000000000..75fca90c9 --- /dev/null +++ b/modules/local/mt_deletion_script/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: +- conda-forge +- bioconda +dependencies: +- bioconda::samtools=1.23 \ No newline at end of file diff --git a/modules/local/mt_deletion_script/main.nf b/modules/local/mt_deletion_script/main.nf index 9ccb56995..c117352e1 100644 --- a/modules/local/mt_deletion_script/main.nf +++ b/modules/local/mt_deletion_script/main.nf @@ -2,9 +2,10 @@ process MT_DELETION { tag "$meta.id" label 'process_single' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b9/b946e2f0e77ec69853787dfc8b312bd7e9d5c65a11a613ce918469a9566992e3/data' : + 'community.wave.seqera.io/library/samtools:1.23--12d9384dd0649f36' }" input: tuple val(meta), path(input), path(input_index) @@ -12,7 +13,8 @@ process MT_DELETION { output: tuple val(meta), path('*.txt'), emit: mt_del_result - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools + tuple val("${task.process}"), val('mitodel'), val("1.0"), topic: versions, emit: versions_mitodel when: task.ext.when == null || task.ext.when @@ -21,28 +23,16 @@ process MT_DELETION { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - """ samtools stats --threads ${task.cpus} $args ${reference} ${input} | \\ grep -E ^IS | \\ awk 'BEGIN {sum=0} (\$2>=1200 && \$2<=15000) {sum=sum+\$3} (\$2<1200 || \$2>15000) {sum_norm=sum_norm+\$3} END \\ {print "intermediate discordant ", sum, "normal ", sum_norm, "ratio ppk", sum*1000/(sum_norm+sum)}' 1> ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mitodel: v1.0 - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/local/rename_align_files/environment.yml b/modules/local/rename_align_files/environment.yml new file mode 100644 index 000000000..7560fdd31 --- /dev/null +++ b/modules/local/rename_align_files/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: +- conda-forge +- bioconda +dependencies: +- conda-forge::coreutils=9.5 \ No newline at end of file diff --git a/modules/local/rename_align_files/main.nf b/modules/local/rename_align_files/main.nf index b450902f0..4f5111c13 100644 --- a/modules/local/rename_align_files/main.nf +++ b/modules/local/rename_align_files/main.nf @@ -2,10 +2,10 @@ process RENAME_ALIGN_FILES { tag "$meta.id" label 'process_single' - conda "conda-forge::coreutils=8.31" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' : - 'biocontainers/gnu-wget:1.18--h36e9172_9' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(input) @@ -13,30 +13,19 @@ process RENAME_ALIGN_FILES { output: tuple val(meta), path("*.{bam,bai}"), emit: output - path "versions.yml", emit: versions + tuple val("${task.process}"), val('coreutils'), val("9.5"), topic: versions, emit: versions_coreutils when: task.ext.when == null || task.ext.when script: - def VERSION = "8.31" """ ln -s $input ${meta.sample}.${extension} - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ stub: - def VERSION = "8.31" """ ln -s $input ${meta.sample}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - coreutils: $VERSION - END_VERSIONS """ } diff --git a/modules/local/replace_spaces_in_vcfinfo/environment.yml b/modules/local/replace_spaces_in_vcfinfo/environment.yml new file mode 100644 index 000000000..c38e0465e --- /dev/null +++ b/modules/local/replace_spaces_in_vcfinfo/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.23 + - conda-forge::python=3.14.3 diff --git a/modules/local/replace_spaces_in_vcfinfo/main.nf b/modules/local/replace_spaces_in_vcfinfo/main.nf index 7027e02df..488a38d79 100644 --- a/modules/local/replace_spaces_in_vcfinfo/main.nf +++ b/modules/local/replace_spaces_in_vcfinfo/main.nf @@ -2,58 +2,29 @@ process REPLACE_SPACES_IN_VCFINFO { tag "$meta.id" label 'process_single' - conda "conda-forge::python=3.8.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2f/2fdb3ffa4bac62e98ec062e991217df2ab96e67bbd45a502bd25ff2effecb96e/data': + 'community.wave.seqera.io/library/htslib_python:d1e4474cbf76f4e9' }" input: tuple val(meta), path(input) output: tuple val(meta), path("*_reformatted.vcf"), emit: vcf - path "versions.yml", emit: versions + tuple val("${task.process}"), val('replace_spaces_in_vcfinfo'), val("1.0"), topic: versions, emit: versions_replace_spaces_in_vcfinfo + tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions, emit: versions_python when: task.ext.when == null || task.ext.when script: """ - python3 < versions.yml - "${task.process}": - replace_spaces_in_vcfinfo: 1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS + replace_space_in_vcfinfo.py --input ${input} """ stub: """ - python3 < versions.yml - "${task.process}": - replace_spaces_in_vcfinfo: 1.0 - python: \$(python --version | sed 's/Python //g') - END_VERSIONS + replace_space_in_vcfinfo.py --input ${input} """ } diff --git a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py new file mode 100644 index 000000000..3bbd9342e --- /dev/null +++ b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python3 + +from pathlib import Path +import argparse + + +def main(): + parser = argparse.ArgumentParser( + description="Reformat VCF by replacing spaces with underscores in INFO field" + ) + parser.add_argument( + "--input", + required=True, + help="Path to input VCF file" + ) + + args = parser.parse_args() + + input_path = Path(args.input) + output_fn = input_path.stem + "_reformatted.vcf" + + with input_path.open() as input_file, open(output_fn, "w") as output: + for line in input_file: + if line.startswith("#"): + output.write(line) + else: + spl = line.rstrip("\n").split("\t") + if len(spl) > 7: + spl[7] = spl[7].replace(" ", "_") + output.write("\t".join(spl) + "\n") + + +if __name__ == "__main__": + main() diff --git a/modules/local/retroseq/call/environment.yml b/modules/local/retroseq/call/environment.yml new file mode 100644 index 000000000..b328db7fa --- /dev/null +++ b/modules/local/retroseq/call/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::perl-retroseq=1.5 diff --git a/modules/local/retroseq/call/main.nf b/modules/local/retroseq/call/main.nf index dd3cc8ca7..0da1012d0 100644 --- a/modules/local/retroseq/call/main.nf +++ b/modules/local/retroseq/call/main.nf @@ -2,9 +2,10 @@ process RETROSEQ_CALL { tag "$meta.id" label 'process_low' - conda "bioconda::perl-retroseq=1.5=pl5321hdfd78af_1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' : 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73188352f5d5762376ee86bb739902750cc7197398f09c1b6a2b8fe3d71e22fc/data': + 'community.wave.seqera.io/library/perl-retroseq:1.5--e825fb294f7eb523' }" input: @@ -14,7 +15,7 @@ process RETROSEQ_CALL { output: tuple val(meta), path("*.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('retroseq'), val("1.5"), topic: versions, emit: versions_retroseq when: task.ext.when == null || task.ext.when @@ -22,8 +23,6 @@ process RETROSEQ_CALL { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.5" - """ retroseq.pl \\ -call \\ @@ -32,22 +31,11 @@ process RETROSEQ_CALL { -input $tab \\ -ref $fasta \\ -output ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - retroseq_call: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.5" """ touch ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - retroseq_call: $VERSION - END_VERSIONS """ } diff --git a/modules/local/retroseq/discover/environment.yml b/modules/local/retroseq/discover/environment.yml new file mode 100644 index 000000000..b328db7fa --- /dev/null +++ b/modules/local/retroseq/discover/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::perl-retroseq=1.5 diff --git a/modules/local/retroseq/discover/main.nf b/modules/local/retroseq/discover/main.nf index 96f84ba3b..02c45dd47 100644 --- a/modules/local/retroseq/discover/main.nf +++ b/modules/local/retroseq/discover/main.nf @@ -2,9 +2,10 @@ process RETROSEQ_DISCOVER { tag "$meta.id" label 'process_low' - conda "bioconda::perl-retroseq=1.5=pl5321hdfd78af_1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' : 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73188352f5d5762376ee86bb739902750cc7197398f09c1b6a2b8fe3d71e22fc/data': + 'community.wave.seqera.io/library/perl-retroseq:1.5--e825fb294f7eb523' }" input: @@ -14,7 +15,7 @@ process RETROSEQ_DISCOVER { output: tuple val(meta), path("*.tab"), emit: tab - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('retroseq'), val("1.5"), topic: versions, emit: versions_retroseq when: task.ext.when == null || task.ext.when @@ -22,8 +23,6 @@ process RETROSEQ_DISCOVER { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.5" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - """ paste <(printf "%s\\n" $me_types | tr -d '[],') <(printf "%s\\n" $me_references) > me_reference_manifest.tsv retroseq.pl \\ @@ -33,22 +32,12 @@ process RETROSEQ_DISCOVER { -refTEs me_reference_manifest.tsv\\ -output ${prefix}.tab - cat <<-END_VERSIONS > versions.yml - "${task.process}": - retroseq_discover: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.5" """ paste <(printf "%s\\n" $me_types | tr -d '[],') <(printf "%s\\n" $me_references) > me_reference_manifest.tsv touch ${prefix}.tab - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - retroseq_discover: $VERSION - END_VERSIONS """ } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 0054b1e54..1f686c410 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -88,12 +88,14 @@ workflow PREPARE_REFERENCES { // Genome indices // if (!val_fai) { - ch_genome_fai = SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[:],[]], false).fai.collect() + SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[:],[]], true) + ch_genome_fai = SAMTOOLS_FAIDX_GENOME.out.fai.collect() + ch_chrom_sizes = SAMTOOLS_FAIDX_GENOME.out.sizes.map {_meta, sizes -> sizes}.collect() } else { - ch_genome_fai = channel.fromPath(val_fai).map {it -> [[id:it.simpleName], it]}.collect() + ch_genome_fai = channel.fromPath(val_fai).map {fai -> [[id:fai.simpleName], fai]}.collect() + ch_chrom_sizes = GET_CHROM_SIZES( ch_genome_fai ).out.sizes.collect() } - GET_CHROM_SIZES( ch_genome_fai ) if (!val_genome_dict) { ch_genome_dict = GATK_SD(ch_genome_fasta).dict.collect() @@ -275,7 +277,7 @@ workflow PREPARE_REFERENCES { genome_bwa_index = ch_bwa // channel:[ val(meta), path(index) ] genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] - genome_chrom_sizes = GET_CHROM_SIZES.out.sizes.collect() // channel:[ path(sizes) ] + genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index c2c47cdb3..75f6da3d8 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -2,7 +2,7 @@ // A subworkflow to create genome interval files necessary for bam/vcf scatter operations. // -include { BUILD_BED } from '../../../modules/local/create_bed_from_fai' +include { GAWK } from '../../../modules/nf-core/gawk' include { GATK4_SPLITINTERVALS } from '../../../modules/nf-core/gatk4/splitintervals/main' workflow SCATTER_GENOME { @@ -13,16 +13,12 @@ workflow SCATTER_GENOME { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] main: - ch_versions = channel.empty() - BUILD_BED (ch_genome_fai) + GAWK (ch_genome_fai, [], false) - GATK4_SPLITINTERVALS(BUILD_BED.out.bed, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) - - ch_versions = ch_versions.mix(BUILD_BED.out.versions) + GATK4_SPLITINTERVALS(GAWK.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) emit: - bed = BUILD_BED.out.bed.collect() // channel: [ val(meta), path(bed) ] + bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 93e51e4d5..8c25c199f 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "genome" }, - "reference.fasta.bed:md5,77b5bd8a06d9f25356c233413bf0318d" + "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], "1": [ @@ -72,16 +72,12 @@ "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] ], - "2": [ - "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", - "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" - ], "bed": [ [ { "id": "genome" }, - "reference.fasta.bed:md5,77b5bd8a06d9f25356c233413bf0318d" + "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], "split_intervals": [ @@ -145,17 +141,13 @@ [ "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] - ], - "versions": [ - "versions.yml:md5,005c9777d9befd3821945bc05709dfc8", - "versions.yml:md5,27694de4c876f5d1aeb42639252e73ea" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-03-31T11:51:27.737317" + "timestamp": "2026-02-09T10:18:23.261854" } } \ No newline at end of file From a9a6cc3a3f685656dfdd7c33260b20e6079ebb36 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 9 Feb 2026 14:21:53 +0100 Subject: [PATCH 309/872] new snapshots from merge --- tests/test_bam.nf.test.snap | 4 +- tests/test_singleton.nf.test.snap | 158 ++++++++++++++++++++++++++++-- 2 files changed, 153 insertions(+), 9 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9ba6e4e05..5a2a421f9 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -243,7 +243,7 @@ "manta": "1.6.0" }, "MARKDUPLICATES": { - "picard": "3.3.0" + "picard": "3.4.0" }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" @@ -1107,6 +1107,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-09T10:07:25.308697516" + "timestamp": "2026-02-09T13:01:02.446698103" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index ce46ab74d..d2fed18ec 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -524,12 +524,34 @@ "annotate_snv", "annotate_snv/genome", "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", - "annotate_snv/genome/earlycasualcaiman_rhocallviz_autozyg_chromograph", - "annotate_snv/genome/hugelymodelbat_chromograph_regions", - "annotate_snv/genome/hugelymodelbat_chromograph_sites", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -559,13 +581,87 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", - "annotate_snv/genome/slowlycivilbuck_rhocallviz_autozyg_chromograph", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -689,7 +785,6 @@ "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/earlycasualcaiman_chromographcov", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", @@ -716,6 +811,31 @@ "qc_bam/earlycasualcaiman_tidditcov.bed", "qc_bam/earlycasualcaiman_tidditcov.bw", "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", @@ -879,7 +999,6 @@ "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/slowlycivilbuck_chromographcov", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", @@ -906,6 +1025,31 @@ "qc_bam/slowlycivilbuck_tidditcov.bed", "qc_bam/slowlycivilbuck_tidditcov.bw", "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", @@ -963,6 +1107,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-09T10:39:58.934868309" + "timestamp": "2026-02-09T14:10:55.531699048" } } \ No newline at end of file From d947bbb97e1f0fbbe14e56974b4035268ab074ca Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 14:50:09 +0100 Subject: [PATCH 310/872] update subwfs --- main.nf | 1 - subworkflows/local/annotate_mt_snvs.nf | 1 - subworkflows/local/call_mobile_elements.nf | 6 ------ subworkflows/local/call_snv.nf | 1 - subworkflows/local/call_snv_deepvariant/main.nf | 1 - subworkflows/local/call_snv_sentieon/main.nf | 5 ----- subworkflows/local/call_structural_variants.nf | 1 - subworkflows/local/call_sv_MT/main.nf | 5 ----- subworkflows/local/gens.nf | 7 ------- subworkflows/local/postprocess_MT_calls/main.nf | 5 ----- subworkflows/local/prepare_references/main.nf | 3 --- subworkflows/local/subsample_mt_frac/main.nf | 6 ------ workflows/raredisease.nf | 4 ---- 13 files changed, 46 deletions(-) diff --git a/main.nf b/main.nf index bd5b3d73b..256b742a5 100644 --- a/main.nf +++ b/main.nf @@ -278,7 +278,6 @@ workflow NFCORE_RAREDISEASE { // Generate pedigree file // ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped - ch_versions = ch_versions.mix(CREATE_PEDIGREE_FILE.out.versions) // Tools skip_eklipse = parseSkipList(val_skip_tools, 'eklipse') diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index d855ebd2d..ee2c04fe8 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -125,7 +125,6 @@ workflow ANNOTATE_MT_SNVS { ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) emit: haplog = ch_haplog // channel: [ val(meta), path(txt) ] diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index b4506c741..45ad5ece7 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -22,8 +22,6 @@ workflow CALL_MOBILE_ELEMENTS { ch_me_references // channel: [mandatory] [path(tsv)] main: - ch_versions = channel.empty() - // Building chromosome channels based on fasta index ch_genome_fai .splitCsv( sep: "\t", elem: 1, limit: 24 ) @@ -121,11 +119,7 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) - ch_versions = ch_versions.mix(RETROSEQ_DISCOVER.out.versions) - ch_versions = ch_versions.mix(RETROSEQ_CALL.out.versions) - emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index e301ef109..4f6acd6c1 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -91,7 +91,6 @@ workflow CALL_SNV { ch_sentieon_tbi = CALL_SNV_SENTIEON.out.tabix ch_sentieon_gvcf = CALL_SNV_SENTIEON.out.gvcf ch_sentieon_gtbi = CALL_SNV_SENTIEON.out.gvcf_tbi - ch_versions = ch_versions.mix(CALL_SNV_SENTIEON.out.versions) } ch_vcf = channel.empty().mix(ch_deepvar_vcf, ch_sentieon_vcf) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 4a9fb1b22..dbec9449b 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -83,7 +83,6 @@ workflow CALL_SNV_DEEPVARIANT { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) ch_versions = ch_versions.mix(GLNEXUS.out.versions) - ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index f14f15413..5c982662b 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -29,8 +29,6 @@ workflow CALL_SNV_SENTIEON { ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] main: - ch_versions = channel.empty() - // Combine bam and intervals bam_bai_intervals = ch_bam_bai.combine(ch_call_interval) .map{ @@ -108,12 +106,9 @@ workflow CALL_SNV_SENTIEON { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - emit: gvcf = SENTIEON_DNASCOPE.out.gvcf // channel: [ val(meta), path(gvcf) ] gvcf_tbi = SENTIEON_DNASCOPE.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi) ] tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 4fe09ca8b..40a3f6768 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -68,7 +68,6 @@ workflow CALL_STRUCTURAL_VARIANTS { if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { CALL_SV_MT (ch_mt_bam_bai, ch_genome_fasta, skip_eklipse) - ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } //merge diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 8fa2d9c52..d72e17fb1 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -12,7 +12,6 @@ workflow CALL_SV_MT { skip_eklipse // boolean main: - ch_versions = channel.empty() ch_eklipse_del = channel.empty() ch_eklipse_genes = channel.empty() ch_eklipse_circos = channel.empty() @@ -22,16 +21,12 @@ workflow CALL_SV_MT { ch_eklipse_del = EKLIPSE.out.deletions ch_eklipse_genes = EKLIPSE.out.genes ch_eklipse_circos = EKLIPSE.out.circos - ch_versions = ch_versions.mix(EKLIPSE.out.versions) } MT_DELETION(ch_bam_bai, ch_fasta) - ch_versions = ch_versions.mix(MT_DELETION.out.versions) - emit: eklipse_del = ch_eklipse_del // channel: [ val(meta), path(csv) ] eklipse_genes = ch_eklipse_genes // channel: [ val(meta), path(csv) ] eklipse_circos = ch_eklipse_circos // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens.nf index e882f64c2..a75b2cbe5 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens.nf @@ -22,8 +22,6 @@ workflow GENS { ch_pon_male // channel: [mandatory] [ path(pon) ] main: - ch_versions = channel.empty() - ch_bam_bai .combine(ch_interval_list) .set { ch_bam_bai_intervals } @@ -65,12 +63,7 @@ workflow GENS { GENS_GENERATE_COV_INDEX (GENS_GENERATE.out.cov) - ch_versions = ch_versions.mix(GENS_GENERATE.out.versions) - ch_versions = ch_versions.mix(GENS_GENERATE_BAF_INDEX.out.versions) - ch_versions = ch_versions.mix(GENS_GENERATE_COV_INDEX.out.versions) - emit: gens_baf_bed_gz = GENS_GENERATE.out.baf // channel: [ val(meta), path(bed) ] gens_cov_bed_gz = GENS_GENERATE.out.cov // channel: [ val(meta), path(bed) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 90e501db7..282d601ad 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -28,8 +28,6 @@ workflow POSTPROCESS_MT_CALLS { ch_mtshift_vcf // channel: [mandatory] [ val(meta), path(vcf) ] main: - ch_versions = channel.empty() - // LIFTOVER SHIFTED VCF TO REFERENCE MT POSITIONS PICARD_LIFTOVERVCF ( ch_mtshift_vcf, @@ -121,10 +119,7 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(ADD_VARCALLER_TO_BED.out.versions) - emit: tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 1f686c410..2b1acf8e7 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -267,9 +267,6 @@ workflow PREPARE_REFERENCES { ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) } - // Gather versions - ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions) - emit: bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 25b64d2b3..798b5ac62 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -14,8 +14,6 @@ workflow SUBSAMPLE_MT_FRAC { val_mt_subsample_seed // channel: [mandatory] [ val(seed) ] main: - ch_versions = channel.empty() - ch_mt_bam_bai.map {meta, bam, _bai -> return [meta, bam, -1]}.set {ch_genomecov_in} BEDTOOLS_GENOMECOV (ch_genomecov_in, [], "genomecov", false) @@ -34,8 +32,4 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') - ch_versions = ch_versions.mix(CALCULATE_SEED_FRACTION.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2a3833dc6..88fe1786b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -327,8 +327,6 @@ workflow RAREDISEASE { if ( val_analysis_type.equals("wgs") && (!skip_smncopynumbercaller || !skip_repeat_calling)) { RENAME_BAM(ch_mapped.genome_marked_bam, "bam") RENAME_BAI(ch_mapped.genome_marked_bai, "bam.bai") - ch_versions = ch_versions.mix(RENAME_BAM.out.versions) - ch_versions = ch_versions.mix(RENAME_BAI.out.versions) } /* @@ -652,7 +650,6 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) - ch_versions = ch_versions.mix(CALL_MOBILE_ELEMENTS.out.versions) if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -773,7 +770,6 @@ workflow RAREDISEASE { ch_gens_pon_female, ch_gens_pon_male ) - ch_versions = ch_versions.mix(GENS.out.versions) } /* From 1a354a6506e5e899a7af2edd0c560892077fa7d1 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 14:59:53 +0100 Subject: [PATCH 311/872] remove out --- subworkflows/local/prepare_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 2b1acf8e7..362f92520 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -93,7 +93,7 @@ workflow PREPARE_REFERENCES { ch_chrom_sizes = SAMTOOLS_FAIDX_GENOME.out.sizes.map {_meta, sizes -> sizes}.collect() } else { ch_genome_fai = channel.fromPath(val_fai).map {fai -> [[id:fai.simpleName], fai]}.collect() - ch_chrom_sizes = GET_CHROM_SIZES( ch_genome_fai ).out.sizes.collect() + ch_chrom_sizes = GET_CHROM_SIZES( ch_genome_fai ).sizes.collect() } From a6d0e0c11f21af5f4ab0c213261aedc030144ad2 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 15:17:45 +0100 Subject: [PATCH 312/872] update retroseq --- .../resources/usr/bin/replace_spaces_in_vcfinfo.py | 5 ++++- modules/local/retroseq/call/environment.yml | 7 ------- modules/local/retroseq/call/main.nf | 6 +----- modules/local/retroseq/discover/environment.yml | 7 ------- modules/local/retroseq/discover/main.nf | 6 +----- 5 files changed, 6 insertions(+), 25 deletions(-) delete mode 100644 modules/local/retroseq/call/environment.yml delete mode 100644 modules/local/retroseq/discover/environment.yml diff --git a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py index 3bbd9342e..23ea6ba63 100644 --- a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py +++ b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py @@ -1,9 +1,12 @@ #!/usr/bin/env python3 + +# Written by Ramprasad Neethiraj and released under the MIT license. +# See git repository (https://github.com/nf-core/raredisease) for full license text. + from pathlib import Path import argparse - def main(): parser = argparse.ArgumentParser( description="Reformat VCF by replacing spaces with underscores in INFO field" diff --git a/modules/local/retroseq/call/environment.yml b/modules/local/retroseq/call/environment.yml deleted file mode 100644 index b328db7fa..000000000 --- a/modules/local/retroseq/call/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::perl-retroseq=1.5 diff --git a/modules/local/retroseq/call/main.nf b/modules/local/retroseq/call/main.nf index 0da1012d0..394744d4b 100644 --- a/modules/local/retroseq/call/main.nf +++ b/modules/local/retroseq/call/main.nf @@ -2,11 +2,7 @@ process RETROSEQ_CALL { tag "$meta.id" label 'process_low' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73188352f5d5762376ee86bb739902750cc7197398f09c1b6a2b8fe3d71e22fc/data': - 'community.wave.seqera.io/library/perl-retroseq:1.5--e825fb294f7eb523' }" - + container 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' input: tuple val(meta), path(tab), path(bam), path(bai) diff --git a/modules/local/retroseq/discover/environment.yml b/modules/local/retroseq/discover/environment.yml deleted file mode 100644 index b328db7fa..000000000 --- a/modules/local/retroseq/discover/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::perl-retroseq=1.5 diff --git a/modules/local/retroseq/discover/main.nf b/modules/local/retroseq/discover/main.nf index 02c45dd47..84ca21d0f 100644 --- a/modules/local/retroseq/discover/main.nf +++ b/modules/local/retroseq/discover/main.nf @@ -2,11 +2,7 @@ process RETROSEQ_DISCOVER { tag "$meta.id" label 'process_low' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73188352f5d5762376ee86bb739902750cc7197398f09c1b6a2b8fe3d71e22fc/data': - 'community.wave.seqera.io/library/perl-retroseq:1.5--e825fb294f7eb523' }" - + container 'docker.io/clinicalgenomics/retroseq:1.5_9d4f3b5-1' input: tuple val(meta), path(bam), path(bai) From 5343599674df185182df336a7ff2566202a44dfa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Feb 2026 23:40:53 +0100 Subject: [PATCH 313/872] update workflow snaps --- .../resources/usr/bin/create_hgncids_file.py | 0 .../local/replace_spaces_in_vcfinfo/main.nf | 4 +-- .../usr/bin/replace_spaces_in_vcfinfo.py | 0 tests/default.nf.test.snap | 34 ++++++++++--------- tests/test_bam.nf.test.snap | 34 ++++++++++--------- tests/test_singleton.nf.test.snap | 34 ++++++++++--------- 6 files changed, 56 insertions(+), 50 deletions(-) mode change 100644 => 100755 modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py mode change 100644 => 100755 modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py diff --git a/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py b/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py old mode 100644 new mode 100755 diff --git a/modules/local/replace_spaces_in_vcfinfo/main.nf b/modules/local/replace_spaces_in_vcfinfo/main.nf index 488a38d79..37dd61141 100644 --- a/modules/local/replace_spaces_in_vcfinfo/main.nf +++ b/modules/local/replace_spaces_in_vcfinfo/main.nf @@ -20,11 +20,11 @@ process REPLACE_SPACES_IN_VCFINFO { script: """ - replace_space_in_vcfinfo.py --input ${input} + replace_spaces_in_vcfinfo.py --input ${input} """ stub: """ - replace_space_in_vcfinfo.py --input ${input} + replace_spaces_in_vcfinfo.py --input ${input} """ } diff --git a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py old mode 100644 new mode 100755 diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 288acbcca..7ff38224b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -3,7 +3,8 @@ "content": [ { "ADD_VARCALLER_TO_BED": { - "tabix": 1.12 + "bgzip": 1.21, + "tabix": 1.21 }, "BCFTOOLS_ANNOTATE": { "bcftools": 1.22 @@ -109,9 +110,12 @@ "CNVNATOR_STAT": { "cnvnator": "0.4.1" }, + "CREATE_HGNCIDS_FILE": { + "create_hgncids_file": 1.0, + "python": "3.14.3" + }, "CREATE_PEDIGREE_FILE": { - "create_pedigree_file": "v1.0", - "python": "3.8.3" + "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { "add_most_severe_consequence": 1.1, @@ -124,9 +128,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -213,7 +214,7 @@ "genmod": "3.10.2" }, "GET_CHROM_SIZES": { - "coreutils": 8.31 + "coreutils": 9.5 }, "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" @@ -248,7 +249,8 @@ "mosdepth": "0.3.11" }, "MT_DELETION": { - "samtools": "1.19.2" + "mitodel": 1.0, + "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { "ngs-bits": 202411 @@ -293,20 +295,20 @@ "picard": "3.4.0" }, "RENAME_BAI": { - "coreutils": 8.31 + "coreutils": 9.5 }, "RENAME_BAM": { - "coreutils": 8.31 + "coreutils": 9.5 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": 1.0, - "python": "3.8.3" + "python": "3.14.3", + "replace_spaces_in_vcfinfo": 1.0 }, "RETROSEQ_CALL": { - "retroseq_call": 1.5 + "retroseq": 1.5 }, "RETROSEQ_DISCOVER": { - "retroseq_discover": 1.5 + "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { "rhocall": "0.5.1" @@ -1098,8 +1100,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-07T11:46:41.611269933" + "timestamp": "2026-02-09T22:34:53.11655695" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 2f175af14..48e8e2792 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -4,7 +4,8 @@ 795, { "ADD_VARCALLER_TO_BED": { - "tabix": 1.12 + "bgzip": 1.21, + "tabix": 1.21 }, "BCFTOOLS_ANNOTATE": { "bcftools": 1.22 @@ -106,9 +107,12 @@ "CNVNATOR_STAT": { "cnvnator": "0.4.1" }, + "CREATE_HGNCIDS_FILE": { + "create_hgncids_file": 1.0, + "python": "3.14.3" + }, "CREATE_PEDIGREE_FILE": { - "create_pedigree_file": "v1.0", - "python": "3.8.3" + "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { "add_most_severe_consequence": 1.1, @@ -121,9 +125,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -204,7 +205,7 @@ "genmod": "3.10.2" }, "GET_CHROM_SIZES": { - "coreutils": 8.31 + "coreutils": 9.5 }, "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" @@ -236,7 +237,8 @@ "mosdepth": "0.3.11" }, "MT_DELETION": { - "samtools": "1.19.2" + "mitodel": 1.0, + "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { "ngs-bits": 202411 @@ -281,20 +283,20 @@ "picard": "3.4.0" }, "RENAME_BAI": { - "coreutils": 8.31 + "coreutils": 9.5 }, "RENAME_BAM": { - "coreutils": 8.31 + "coreutils": 9.5 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": 1.0, - "python": "3.8.3" + "python": "3.14.3", + "replace_spaces_in_vcfinfo": 1.0 }, "RETROSEQ_CALL": { - "retroseq_call": 1.5 + "retroseq": 1.5 }, "RETROSEQ_DISCOVER": { - "retroseq_discover": 1.5 + "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { "rhocall": "0.5.1" @@ -1039,8 +1041,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-07T12:27:20.306676608" + "timestamp": "2026-02-09T23:20:06.096281265" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index ab5180d12..6c009638b 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -4,7 +4,8 @@ 361, { "ADD_VARCALLER_TO_BED": { - "tabix": 1.12 + "bgzip": 1.21, + "tabix": 1.21 }, "BCFTOOLS_ANNOTATE": { "bcftools": 1.22 @@ -101,9 +102,12 @@ "CNVNATOR_STAT": { "cnvnator": "0.4.1" }, + "CREATE_HGNCIDS_FILE": { + "create_hgncids_file": 1.0, + "python": "3.14.3" + }, "CREATE_PEDIGREE_FILE": { - "create_pedigree_file": "v1.0", - "python": "3.8.3" + "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { "add_most_severe_consequence": 1.1, @@ -116,9 +120,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "EKLIPSE": { - "eklipse": 1.8 - }, "ENSEMBLVEP_FILTERVEP": { "ensemblvep": 110.0 }, @@ -205,7 +206,7 @@ "genmod": "3.10.2" }, "GET_CHROM_SIZES": { - "coreutils": 8.31 + "coreutils": 9.5 }, "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" @@ -240,7 +241,8 @@ "mosdepth": "0.3.11" }, "MT_DELETION": { - "samtools": "1.19.2" + "mitodel": 1.0, + "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { "ngs-bits": 202411 @@ -285,20 +287,20 @@ "picard": "3.4.0" }, "RENAME_BAI": { - "coreutils": 8.31 + "coreutils": 9.5 }, "RENAME_BAM": { - "coreutils": 8.31 + "coreutils": 9.5 }, "REPLACE_SPACES_IN_VCFINFO": { - "replace_spaces_in_vcfinfo": 1.0, - "python": "3.8.3" + "python": "3.14.3", + "replace_spaces_in_vcfinfo": 1.0 }, "RETROSEQ_CALL": { - "retroseq_call": 1.5 + "retroseq": 1.5 }, "RETROSEQ_DISCOVER": { - "retroseq_discover": 1.5 + "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { "rhocall": "0.5.1" @@ -713,8 +715,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-07T12:48:58.554399668" + "timestamp": "2026-02-09T23:37:35.658755526" } } \ No newline at end of file From c79448ad06e1509fb9ac269dd832e0a12c5e138b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Feb 2026 00:37:09 +0100 Subject: [PATCH 314/872] update subwf snaps --- .../local/prepare_references/tests/main.nf.test.snap | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 92f305466..62afd11e0 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -388,7 +388,6 @@ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ], @@ -425,7 +424,7 @@ ], "6": [ [ - "reference.fasta.fai.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" + "reference.fasta.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" ] ], "7": [ @@ -506,7 +505,7 @@ ], "genome_chrom_sizes": [ [ - "reference.fasta.fai.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" + "reference.fasta.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" ] ], "genome_dict": [ @@ -898,7 +897,6 @@ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] @@ -906,8 +904,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-06T18:02:00.602808407" + "timestamp": "2026-02-10T00:25:53.797976413" } } \ No newline at end of file From 349edcc4a492a917312068301d4cb1a31c0f56f7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Feb 2026 00:44:45 +0100 Subject: [PATCH 315/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e085629f6..0fb469d40 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1 (homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) +- Topic channels to local modules to caputure versions [#774](https://github.com/nf-core/raredisease/pull/774) ### `Changed` From f2f0e34a0b291884fb5c741571787945b3b50b93 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Feb 2026 00:46:47 +0100 Subject: [PATCH 316/872] pre-commit --- modules/local/create_pedigree_file/environment.yml | 6 +++--- modules/local/get_chrom_sizes/environment.yml | 6 +++--- modules/local/mt_deletion_script/environment.yml | 6 +++--- modules/local/rename_align_files/environment.yml | 6 +++--- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules/local/create_pedigree_file/environment.yml b/modules/local/create_pedigree_file/environment.yml index 7560fdd31..0c4cd9422 100644 --- a/modules/local/create_pedigree_file/environment.yml +++ b/modules/local/create_pedigree_file/environment.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- conda-forge::coreutils=9.5 \ No newline at end of file + - conda-forge::coreutils=9.5 diff --git a/modules/local/get_chrom_sizes/environment.yml b/modules/local/get_chrom_sizes/environment.yml index 7560fdd31..0c4cd9422 100644 --- a/modules/local/get_chrom_sizes/environment.yml +++ b/modules/local/get_chrom_sizes/environment.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- conda-forge::coreutils=9.5 \ No newline at end of file + - conda-forge::coreutils=9.5 diff --git a/modules/local/mt_deletion_script/environment.yml b/modules/local/mt_deletion_script/environment.yml index 75fca90c9..53698527f 100644 --- a/modules/local/mt_deletion_script/environment.yml +++ b/modules/local/mt_deletion_script/environment.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- bioconda::samtools=1.23 \ No newline at end of file + - bioconda::samtools=1.23 diff --git a/modules/local/rename_align_files/environment.yml b/modules/local/rename_align_files/environment.yml index 7560fdd31..0c4cd9422 100644 --- a/modules/local/rename_align_files/environment.yml +++ b/modules/local/rename_align_files/environment.yml @@ -1,7 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- conda-forge::coreutils=9.5 \ No newline at end of file + - conda-forge::coreutils=9.5 From e5a1011204eb76d7613871644bd7c79bffe271b8 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:41:19 +0100 Subject: [PATCH 317/872] update modules --- modules.json | 70 ++-- modules/nf-core/bwa/index/environment.yml | 10 +- modules/nf-core/bwa/index/main.nf | 23 +- modules/nf-core/bwa/index/meta.yml | 44 ++- modules/nf-core/bwa/index/tests/main.nf.test | 26 +- .../nf-core/bwa/index/tests/main.nf.test.snap | 73 +++- modules/nf-core/bwa/index/tests/tags.yml | 2 - modules/nf-core/bwamem2/index/environment.yml | 10 +- modules/nf-core/bwamem2/index/main.nf | 23 +- modules/nf-core/bwamem2/index/meta.yml | 48 ++- .../nf-core/bwamem2/index/tests/main.nf.test | 25 +- .../bwamem2/index/tests/main.nf.test.snap | 75 ++++- modules/nf-core/bwamem2/index/tests/tags.yml | 2 - modules/nf-core/bwamem2/mem/environment.yml | 11 +- modules/nf-core/bwamem2/mem/main.nf | 21 +- modules/nf-core/bwamem2/mem/meta.yml | 75 +++-- .../nf-core/bwamem2/mem/tests/main.nf.test | 8 +- .../bwamem2/mem/tests/main.nf.test.snap | 100 ++++-- modules/nf-core/bwamem2/mem/tests/tags.yml | 2 - .../cnvnator/convert2vcf/tests/main.nf.test | 9 +- .../convert2vcf/tests/main.nf.test.snap | 4 +- .../convert2vcf/tests/nextflow.config | 13 +- .../nf-core/gatk4/collectreadcounts/main.nf | 4 +- .../nf-core/gatk4/collectreadcounts/meta.yml | 17 +- .../collectreadcounts/tests/main.nf.test | 32 +- .../collectreadcounts/tests/main.nf.test.snap | 25 +- .../gatk4/createsequencedictionary/meta.yml | 3 +- .../tests/main.nf.test | 11 +- .../tests/main.nf.test.snap | 8 +- .../nf-core/gatk4/denoisereadcounts/main.nf | 2 +- .../nf-core/gatk4/denoisereadcounts/meta.yml | 1 - .../denoisereadcounts/tests/main.nf.test | 17 +- .../denoisereadcounts/tests/main.nf.test.snap | 2 +- .../determinegermlinecontigploidy/main.nf | 6 +- .../tests/main.nf.test | 9 +- .../tests/main.nf.test.snap | 28 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 12 +- .../filtermutectcalls/tests/main.nf.test | 10 +- .../filtermutectcalls/tests/main.nf.test.snap | 44 +-- .../nf-core/gatk4/germlinecnvcaller/main.nf | 6 +- .../germlinecnvcaller/tests/main.nf.test | 27 +- .../germlinecnvcaller/tests/main.nf.test.snap | 42 +-- .../nf-core/gatk4/intervallisttools/main.nf | 3 - .../intervallisttools/tests/main.nf.test | 7 +- .../intervallisttools/tests/main.nf.test.snap | 8 +- .../nf-core/gatk4/mergebamalignment/main.nf | 2 - .../mergebamalignment/tests/main.nf.test | 26 +- .../mergebamalignment/tests/main.nf.test.snap | 8 +- modules/nf-core/gatk4/mergevcfs/main.nf | 8 +- .../gatk4/mergevcfs/tests/main.nf.test | 46 +-- .../gatk4/mergevcfs/tests/main.nf.test.snap | 30 +- modules/nf-core/gatk4/mutect2/main.nf | 8 +- .../nf-core/gatk4/mutect2/tests/main.nf.test | 166 ++++----- .../gatk4/mutect2/tests/main.nf.test.snap | 40 +-- .../gatk4/postprocessgermlinecnvcalls/main.nf | 18 +- .../tests/main.nf.test | 76 ++--- .../tests/main.nf.test.snap | 24 +- modules/nf-core/gatk4/printreads/main.nf | 4 +- .../gatk4/printreads/tests/main.nf.test | 39 +-- .../gatk4/printreads/tests/main.nf.test.snap | 4 +- .../gatk4/revertsam/tests/main.nf.test | 14 +- .../gatk4/revertsam/tests/main.nf.test.snap | 4 +- .../gatk4/samtofastq/tests/main.nf.test | 16 +- .../gatk4/samtofastq/tests/main.nf.test.snap | 6 +- modules/nf-core/gatk4/selectvariants/main.nf | 12 +- .../gatk4/selectvariants/tests/main.nf.test | 24 +- modules/nf-core/gatk4/shiftfasta/main.nf | 23 +- .../gatk4/shiftfasta/tests/main.nf.test | 9 +- .../gatk4/shiftfasta/tests/main.nf.test.snap | 2 +- .../gatk4/splitintervals/tests/main.nf.test | 36 +- .../splitintervals/tests/main.nf.test.snap | 6 +- .../nf-core/gatk4/variantfiltration/main.nf | 2 +- .../variantfiltration/tests/main.nf.test | 34 +- .../variantfiltration/tests/main.nf.test.snap | 24 +- modules/nf-core/gawk/main.nf | 12 +- modules/nf-core/gawk/meta.yml | 52 ++- modules/nf-core/gawk/tests/main.nf.test | 56 ++-- modules/nf-core/gawk/tests/main.nf.test.snap | 138 +++----- modules/nf-core/haplogrep3/classify/meta.yml | 14 +- modules/nf-core/multiqc/meta.yml | 2 +- modules/nf-core/sambamba/depth/main.nf | 2 +- .../nf-core/sambamba/depth/tests/main.nf.test | 10 +- .../sambamba/depth/tests/main.nf.test.snap | 40 ++- modules/nf-core/samtools/collate/main.nf | 12 +- modules/nf-core/samtools/collate/meta.yml | 26 +- .../samtools/collate/tests/main.nf.test | 47 +-- .../samtools/collate/tests/main.nf.test.snap | 203 ++++++----- .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 16 +- modules/nf-core/samtools/index/meta.yml | 29 +- .../nf-core/samtools/index/tests/main.nf.test | 27 +- .../samtools/index/tests/main.nf.test.snap | 278 +++++---------- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/samtools/view/meta.yml | 4 +- .../nf-core/samtools/view/tests/bam.config | 3 - .../samtools/view/tests/bam_index.config | 3 - .../samtools/view/tests/cram_index.config | 3 - .../nf-core/samtools/view/tests/main.nf.test | 182 +++++----- .../samtools/view/tests/main.nf.test.snap | 225 +++++-------- .../samtools/view/tests/nextflow.config | 5 + modules/nf-core/untar/environment.yml | 5 + modules/nf-core/untar/main.nf | 45 +-- modules/nf-core/untar/meta.yml | 52 ++- modules/nf-core/untar/tests/main.nf.test | 20 +- modules/nf-core/untar/tests/main.nf.test.snap | 176 ++++------ modules/nf-core/untar/tests/tags.yml | 2 - modules/nf-core/upd/environment.yml | 2 + modules/nf-core/upd/main.nf | 18 +- modules/nf-core/upd/meta.yml | 32 +- modules/nf-core/upd/tests/main.nf.test.snap | 40 ++- modules/nf-core/vcf2cytosure/environment.yml | 4 +- modules/nf-core/vcf2cytosure/main.nf | 22 +- modules/nf-core/vcf2cytosure/meta.yml | 44 ++- .../nf-core/vcf2cytosure/tests/main.nf.test | 10 +- .../vcf2cytosure/tests/main.nf.test.snap | 56 ++-- modules/nf-core/vcf2cytosure/tests/tags.yml | 2 - modules/nf-core/vcfanno/environment.yml | 6 +- modules/nf-core/vcfanno/main.nf | 30 +- modules/nf-core/vcfanno/meta.yml | 92 +++-- modules/nf-core/vcfanno/tests/main.nf.test | 6 +- .../nf-core/vcfanno/tests/main.nf.test.snap | 96 +++++- modules/nf-core/vcfanno/tests/nextflow.config | 6 +- modules/nf-core/vcfanno/tests/tags.yml | 2 - .../nf-core/verifybamid/verifybamid2/main.nf | 25 +- .../nf-core/verifybamid/verifybamid2/meta.yml | 50 ++- .../verifybamid2/tests/main.nf.test | 75 ++++- .../verifybamid2/tests/main.nf.test.snap | 317 +++++++++--------- subworkflows/local/align_MT/main.nf | 1 - .../local/align_bwa_bwamem2_bwameme/main.nf | 5 - subworkflows/local/annotate_cadd/main.nf | 2 - subworkflows/local/annotate_genome_snvs.nf | 3 - subworkflows/local/annotate_mt_snvs.nf | 1 - subworkflows/local/generate_cytosure_files.nf | 1 - subworkflows/local/prepare_references/main.nf | 5 - subworkflows/local/qc_bam/main.nf | 2 - subworkflows/local/subsample_mt_reads/main.nf | 7 - workflows/raredisease.nf | 1 - 137 files changed, 2266 insertions(+), 2103 deletions(-) delete mode 100644 modules/nf-core/bwa/index/tests/tags.yml delete mode 100644 modules/nf-core/bwamem2/index/tests/tags.yml delete mode 100644 modules/nf-core/bwamem2/mem/tests/tags.yml delete mode 100644 modules/nf-core/samtools/view/tests/bam.config delete mode 100644 modules/nf-core/samtools/view/tests/bam_index.config delete mode 100644 modules/nf-core/samtools/view/tests/cram_index.config create mode 100644 modules/nf-core/samtools/view/tests/nextflow.config delete mode 100644 modules/nf-core/untar/tests/tags.yml delete mode 100644 modules/nf-core/vcf2cytosure/tests/tags.yml delete mode 100644 modules/nf-core/vcfanno/tests/tags.yml diff --git a/modules.json b/modules.json index 505f5fc66..9939374a9 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ }, "bwa/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", "installed_by": ["modules"] }, "bwa/mem": { @@ -77,12 +77,12 @@ }, "bwamem2/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", "installed_by": ["modules"] }, "bwameme/index": { @@ -117,7 +117,7 @@ }, "cnvnator/convert2vcf": { "branch": "master", - "git_sha": "9d43cc3f4b065a99d62dcd58f10d5f4e9feb4bd8", + "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", "installed_by": ["modules"] }, "custom/addmostsevereconsequence": { @@ -173,97 +173,97 @@ }, "gatk4/collectreadcounts": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/denoisereadcounts": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/mergebamalignment": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "6881702b1f6671b9471e69f4a75ea4e49a0d0349", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/postprocessgermlinecnvcalls": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/printreads": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/revertsam": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/samtofastq": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/selectvariants": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/shiftfasta": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/splitintervals": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", + "git_sha": "76b1f53edcf72798d8515c82f4728ad44b3dd902", "installed_by": ["modules"] }, "genmod/annotate": { @@ -288,7 +288,7 @@ }, "glnexus": { "branch": "master", - "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8", + "git_sha": "9b696bde5b422831751df1a4f2ba728567ec51fd", "installed_by": ["modules"] }, "haplocheck": { @@ -298,7 +298,7 @@ }, "haplogrep3/classify": { "branch": "master", - "git_sha": "c95c60597ce23da23ac21f4e6c5d7c0cdb711b8f", + "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", "installed_by": ["modules"] }, "hmtnote/annotate": { @@ -319,7 +319,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2", + "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b", "installed_by": ["modules"] }, "ngsbits/samplegender": { @@ -399,12 +399,12 @@ }, "sambamba/depth": { "branch": "master", - "git_sha": "b093f74ddc3ada57a84a209f0e4fb3871bacf2ad", + "git_sha": "ca6da11b05740de461b1e2714037345c0f856201", "installed_by": ["modules"] }, "samtools/collate": { "branch": "master", - "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", + "git_sha": "a77125b43fb8973f37c36e2ff137626657de3b21", "installed_by": ["modules"] }, "samtools/faidx": { @@ -414,7 +414,7 @@ }, "samtools/index": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9", "installed_by": ["modules"] }, "samtools/merge": { @@ -434,7 +434,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", + "git_sha": "d2ceed2ec5fccf922638f116a15e02f6458288fb", "installed_by": ["modules"] }, "sentieon/bwaindex": { @@ -534,27 +534,27 @@ }, "untar": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", "installed_by": ["modules"] }, "upd": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index d8789a209..54e679492 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -1,5 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::bwa=0.7.18 + # renovate: datasource=conda depName=bioconda/bwa + - bioconda::bwa=0.7.19 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 2e48b6caa..6be2c43b7 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -1,18 +1,20 @@ process BWA_INDEX { tag "$fasta" - label 'process_single' + // NOTE requires 5.37N memory where N is the size of the database + // source: https://bio-bwa.sourceforge.net/bwa.shtml#8 + memory { 6.B * fasta.size() } conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa:0.7.18--he4a0461_0' : - 'biocontainers/bwa:0.7.18--he4a0461_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data' : + 'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0' }" input: tuple val(meta), path(fasta) output: - tuple val(meta), path(bwa) , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("bwa"), emit: index + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa when: task.ext.when == null || task.ext.when @@ -27,27 +29,16 @@ process BWA_INDEX { $args \\ -p bwa/${prefix} \\ $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${fasta.baseName}" """ mkdir bwa - touch bwa/${prefix}.amb touch bwa/${prefix}.ann touch bwa/${prefix}.bwt touch bwa/${prefix}.pac touch bwa/${prefix}.sa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 4884bca2a..f5bf7f52a 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] - identifier: "" + identifier: "biotools:bwa" input: - - meta: type: map @@ -24,26 +24,48 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: + - edam: "http://edamontology.org/data_2044" # Sequence + - edam: "http://edamontology.org/format_1929" # FASTA output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - bwa: - type: file - description: BWA genome index files + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] pattern: "*.{amb,ann,bwt,pac,sa}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/data_3210" # Genome index + versions_bwa: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@maxulysse" maintainers: - - "@drpatelh" - "@maxulysse" - "@gallvp" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index af33e73ca..f0fba82a1 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -22,8 +22,32 @@ nextflow_process { } then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } + + test("BWA index - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap index 7c8f04657..21a6f73c3 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -1,4 +1,57 @@ { + "BWA index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-23T16:58:59.966558606" + }, "BWA index": { "content": [ { @@ -17,7 +70,11 @@ ] ], "1": [ - "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] ], "index": [ [ @@ -33,15 +90,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-16T11:40:09.925307" + "timestamp": "2026-01-23T16:58:53.330725134" } } \ No newline at end of file diff --git a/modules/nf-core/bwa/index/tests/tags.yml b/modules/nf-core/bwa/index/tests/tags.yml deleted file mode 100644 index 28bb483c4..000000000 --- a/modules/nf-core/bwa/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwa/index: - - modules/nf-core/bwa/index/** diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml index 15cee2387..f3637444a 100644 --- a/modules/nf-core/bwamem2/index/environment.yml +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -1,5 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::bwa-mem2=2.2.1 + # renovate: datasource=conda depName=bioconda/bwa-mem2 + - bwa-mem2=2.3 + # renovate: datasource=conda depName=bioconda/htslib + - htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.22.1 diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index b7688285d..cb2c4bb2f 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -1,18 +1,20 @@ process BWAMEM2_INDEX { tag "$fasta" - label 'process_single' + // NOTE Requires 28N GB memory where N is the size of the reference sequence, floor of 280M + // source: https://github.com/bwa-mem2/bwa-mem2/issues/9 + memory { 280.MB * Math.ceil(fasta.size() / 10000000) * task.attempt } conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : - 'biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : + 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("bwamem2"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions when: task.ext.when == null || task.ext.when @@ -25,12 +27,8 @@ process BWAMEM2_INDEX { bwa-mem2 \\ index \\ $args \\ - $fasta -p bwamem2/${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS + -p bwamem2/${prefix} \\ + $fasta """ stub: @@ -43,10 +41,5 @@ process BWAMEM2_INDEX { touch bwamem2/${prefix}.pac touch bwamem2/${prefix}.amb touch bwamem2/${prefix}.bwt.2bit.64 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index 74f54ef0d..120748601 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -12,8 +12,9 @@ tools: a large reference genome, such as the human genome. homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage - licence: ["MIT"] - identifier: "" + licence: + - "MIT" + identifier: "biotools:bwa-mem2" input: - - meta: type: map @@ -23,22 +24,49 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bwamem2: - type: file + type: string description: BWA genome index files pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/data_3210" + versions_bwamem2: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test index dbf11132c..3ee91048a 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test @@ -8,7 +8,30 @@ nextflow_process { script "../main.nf" process "BWAMEM2_INDEX" - test("BWAMEM2 index") { + test("fasta") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("fasta - stub") { + + options "-stub" when { process { diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap index 69b268ee4..776e87be1 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap @@ -1,5 +1,58 @@ { - "BWAMEM2 index": { + "fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwamem2": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-09T16:19:38.013344" + }, + "fasta": { "content": [ { "0": [ @@ -17,7 +70,11 @@ ] ], "1": [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] ], "index": [ [ @@ -33,15 +90,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" + "versions_bwamem2": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-18T12:59:39.132616" + "timestamp": "2026-02-09T16:19:32.542622" } } \ No newline at end of file diff --git a/modules/nf-core/bwamem2/index/tests/tags.yml b/modules/nf-core/bwamem2/index/tests/tags.yml deleted file mode 100644 index 3953018ee..000000000 --- a/modules/nf-core/bwamem2/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwamem2/index: - - modules/nf-core/bwamem2/index/** diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 7e0b5a347..f3637444a 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,8 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bwa-mem2=2.2.1 - - htslib=1.19.1 - - samtools=1.19.2 + # renovate: datasource=conda depName=bioconda/bwa-mem2 + - bwa-mem2=2.3 + # renovate: datasource=conda depName=bioconda/htslib + - htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.22.1 diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 729428c4e..d1c0ac8f6 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -4,8 +4,8 @@ process BWAMEM2_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' : - 'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : + 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" input: tuple val(meta), path(reads) @@ -19,7 +19,7 @@ process BWAMEM2_MEM { tuple val(meta), path("*.cram") , emit: cram, optional:true tuple val(meta), path("*.crai") , emit: crai, optional:true tuple val(meta), path("*.csi") , emit: csi , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions when: task.ext.when == null || task.ext.when @@ -46,24 +46,15 @@ process BWAMEM2_MEM { \$INDEX \\ $reads \\ | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" def create_index = "" @@ -76,11 +67,5 @@ process BWAMEM2_MEM { """ touch ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index c6333ca17..bcfd006df 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -16,8 +16,9 @@ tools: homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 - licence: ["MIT"] - identifier: "" + licence: + - "MIT" + identifier: "biotools:bwa-mem2" input: - - meta: type: map @@ -29,6 +30,9 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1930" - - meta2: type: map description: | @@ -38,6 +42,8 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" - - meta3: type: map description: | @@ -47,13 +53,16 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fa,fasta,fna}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - sam: - - meta: + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -62,8 +71,10 @@ output: type: file description: Output SAM file containing read alignments pattern: "*.{sam}" - - bam: - - meta: + ontologies: + - edam: "http://edamontology.org/format_2573" + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -72,8 +83,10 @@ output: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: + ontologies: + - edam: "http://edamontology.org/format_2572" + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -82,8 +95,10 @@ output: type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - crai: - - meta: + ontologies: + - edam: "http://edamontology.org/format_3462" + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -92,8 +107,9 @@ output: type: file description: Index file for CRAM file pattern: "*.{crai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -102,11 +118,28 @@ output: type: file description: Index file for BAM file pattern: "*.{csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwamem2: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: The name of the tool + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: The name of the tool + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 9e0ab14ae..20e372545 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -46,7 +46,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -75,7 +75,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -107,7 +107,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -139,7 +139,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index 69bc3612b..74763935c 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -1,17 +1,23 @@ { "sarscov2 - [fastq1, fastq2], index, fasta, false": { "content": [ - "eefa0f44493fd0504e734efd2f1f4a9e", + "e414c2d48e2e44c2c52c20ecd88e8bd8", "57aeef88ed701a8ebc8e2f0a381b2a6", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:37.929675" + "timestamp": "2026-02-09T16:25:00.500092" }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ @@ -44,7 +50,11 @@ ] ], "5": [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] ], "bam": [ [ @@ -73,57 +83,79 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:12:06.693567" + "timestamp": "2026-02-09T16:25:22.004027" }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ - "7aba324f82d5b4e926a5dd7b46029cb4", + "716ed1ef39deaad346ca7cf86e08f959", "af8628d9df18b2d3d4f6fd47ef2bb872", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:53.488374" + "timestamp": "2026-02-09T16:25:14.131056" }, "sarscov2 - fastq, index, fasta, false": { "content": [ - "bc02b41697b3a8f1021b02becec24052", + "283a83f604f3f5338acedfee349dccf4", "798439cbd7fd81cbcc5078022dc5479d", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:05.644682" + "timestamp": "2026-02-09T16:24:34.624533" }, "sarscov2 - fastq, index, fasta, true": { "content": [ - "e41d67320815d29ba5f6e9d1ae21902a", + "ed99048bb552cac58e39923b550b6d5b", "94fcf617f5b994584c4e8d4044e16b4f", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:21.837763" + "timestamp": "2026-02-09T16:24:47.191245" } } \ No newline at end of file diff --git a/modules/nf-core/bwamem2/mem/tests/tags.yml b/modules/nf-core/bwamem2/mem/tests/tags.yml deleted file mode 100644 index 134efb2b3..000000000 --- a/modules/nf-core/bwamem2/mem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwamem2/mem: - - "modules/nf-core/bwamem2/mem/**" diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test index 723a32226..c1d239682 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "rd" """ } } @@ -38,6 +39,7 @@ nextflow_process { input[1] = CNVNATOR_RD.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "his" """ } } @@ -51,6 +53,7 @@ nextflow_process { input[1] = CNVNATOR_HIST.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "stat" """ } } @@ -64,6 +67,7 @@ nextflow_process { input[1] = CNVNATOR_STAT.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "partition" """ } } @@ -77,6 +81,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } @@ -90,7 +95,7 @@ nextflow_process { cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' - cnvnator_call_args = '-call 1000' + cnvnator_args = '-call 1000' } process { """ @@ -118,7 +123,7 @@ nextflow_process { cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' - cnvnator_call_args = '-call 1000' + cnvnator_args = '-call 1000' } process { """ diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap index c8e740009..d51b4befb 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:02:17.740405" + "timestamp": "2026-02-05T13:53:33.545892" }, "test_cnvnator_convert2vcf -- stub": { "content": [ @@ -59,6 +59,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:02:31.268041" + "timestamp": "2026-02-06T13:38:10.965597" } } \ No newline at end of file diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config index f056ed315..9a9f9a920 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config +++ b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config @@ -1,20 +1,21 @@ process { withName: "CNVNATOR_RD" { - ext.args = params.cnvnator_rd_args + ext.args = {params.cnvnator_rd_args} } + withName: "CNVNATOR_HIST" { - ext.args = params.cnvnator_hist_args + ext.args = {params.cnvnator_hist_args} } withName: "CNVNATOR_STAT" { - ext.args = params.cnvnator_stat_args + ext.args = {params.cnvnator_stat_args} } withName: "CNVNATOR_PARTITION" { - ext.args = params.cnvnator_partition_args + ext.args = {params.cnvnator_partition_args} } - withName: "CNVNATOR_CALL" { - ext.args = params.cnvnator_call_args + withName: "CNVNATOR_CNVNATOR" { + ext.args = {params.cnvnator_args} } } diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 750923375..4dbb80169 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -15,7 +15,7 @@ process GATK4_COLLECTREADCOUNTS { output: tuple val(meta), path("*.hdf5"), emit: hdf5, optional: true - tuple val(meta), path("*.tsv"), emit: tsv, optional: true + tuple val(meta), path("*.tsv"), emit: tsv, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -48,7 +48,6 @@ process GATK4_COLLECTREADCOUNTS { ${reference} \\ --tmp-dir . \\ ${args} - """ stub: @@ -61,6 +60,5 @@ process GATK4_COLLECTREADCOUNTS { : "hdf5" """ touch ${prefix}.${extension} - """ } diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index a65f7f065..abd202997 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,7 +1,6 @@ name: "gatk4_collectreadcounts" -description: Collects read counts at specified intervals. The count for each - interval is calculated by counting the number of read starts that lie in the - interval. +description: Collects read counts at specified intervals. The count for each interval + is calculated by counting the number of read starts that lie in the interval. keywords: - collectreadcounts - bam @@ -9,11 +8,11 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences - Platform at the Broad Institute, the toolkit offers a wide variety of - tools with a primary focus on variant discovery and genotyping. Its - powerful processing engine and high-performance computing features make it - capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk @@ -94,7 +93,7 @@ output: description: The read counts in TSV format pattern: "*.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV versions_gatk4: - - ${task.process}: type: string diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test index 0832cf85a..963103ed6 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test @@ -19,26 +19,25 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[],[]] input[2] = [[],[]] input[3] = [[],[]] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( file(process.out.hdf5[0][1]).name, process.out.tsv, - ).match() - } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -52,21 +51,20 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[],[]] input[2] = [[],[]] input[3] = [[],[]] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -81,24 +79,22 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index ca6304c51..d7d3357ba 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -44,22 +44,31 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:04:47.877494" + "timestamp": "2026-01-21T15:57:24.675555145" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ "test.hdf5", [ - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T13:02:48.607644" + "timestamp": "2026-01-21T15:56:53.979162756" }, "test-gatk4-collectreadcounts-tsv": { "content": [ @@ -106,8 +115,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:04:25.535499" + "timestamp": "2026-01-21T15:57:08.386074318" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 9a5c9f235..5fdfcc20a 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -14,8 +14,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: - - "Apache-2.0" + licence: ["Apache-2.0"] identifier: "" input: - - meta: diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test index a8a9c6d2e..076eb0d84 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test @@ -16,18 +16,17 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("sarscov2 - fasta - stub") { @@ -39,18 +38,16 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 497c8cf09..357cd58ee 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -36,9 +36,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:24:16.167358" + "timestamp": "2026-01-21T16:01:50.146061464" }, "sarscov2 - fasta": { "content": [ @@ -77,8 +77,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:24:00.222321" + "timestamp": "2026-01-21T16:01:38.694508582" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 73790c636..c86a6f45a 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -13,7 +13,7 @@ process GATK4_DENOISEREADCOUNTS { output: tuple val(meta), path("*_standardizedCR.tsv"), emit: standardized - tuple val(meta), path("*_denoisedCR.tsv"), emit: denoised + tuple val(meta), path("*_denoisedCR.tsv"), emit: denoised tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/denoisereadcounts/meta.yml b/modules/nf-core/gatk4/denoisereadcounts/meta.yml index 0c7835a7e..cac8142e0 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/meta.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/meta.yml @@ -84,7 +84,6 @@ topics: - gatk --version | sed -n '/GATK.*v/s/.*v//p': type: eval description: The expression to obtain the version of the tool - authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test index 34268f630..9eba43aeb 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test @@ -19,9 +19,9 @@ nextflow_process { script "../../preprocessintervals/main.nf" process { """ - input[0] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[0] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) input[3] = [[],[]] input[4] = [[],[]] """ @@ -32,13 +32,13 @@ nextflow_process { process { """ intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map {meta, list -> list} - input[0] = Channel.of( + input[0] = channel.of( [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)], ) .combine( intervals) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) """ } } @@ -62,8 +62,8 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.standardized, process.out.denoised, @@ -71,6 +71,5 @@ nextflow_process { ).match() } ) } - } } diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index 26892e208..abdeb59b8 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -33,6 +33,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T11:36:00.92882" + "timestamp": "2026-02-05T15:25:28.341041619" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index f23d3ee9d..da9480b60 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -24,10 +24,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" - def exclude = exclude_beds ? exclude_beds.collect { "--exclude-intervals ${it}" }.join(" ") : "" + def exclude = exclude_beds ? exclude_beds.collect { bed_ -> "--exclude-intervals ${bed_}" }.join(" ") : "" def contig_ploidy = contig_ploidy_table ? "--contig-ploidy-priors ${contig_ploidy_table}" : "" def model = ploidy_model ? "--model ${ploidy_model}" : "" - def input_list = counts.collect { "--input ${it}" }.join(" ") + def input_list = counts.collect { count -> "--input ${count}" }.join(" ") def avail_mem = 3072 if (!task.memory) { @@ -53,7 +53,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { ${model} \\ --tmp-dir . \\ ${args} - """ stub: @@ -61,6 +60,5 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ touch ${prefix}-calls touch ${prefix}-model - """ } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index e7187b03c..d89b1f22c 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -60,16 +60,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - bam - stub") { @@ -94,12 +93,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap index 213238f85..8c56e743a 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -1,15 +1,6 @@ { "homo sapiens - bam": { "content": [ - { - "versions_gatk4": [ - [ - "GATK4_DETERMINEGERMLINECONTIGPLOIDY", - "gatk4", - "4.6.2.0" - ] - ] - }, [ "SAMPLE_0", "SAMPLE_1" @@ -23,13 +14,22 @@ "ploidy_config.json", "std_mean_bias_j_interval__.tsv", "std_psi_j_log__.tsv" - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_DETERMINEGERMLINECONTIGPLOIDY", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:46:07.36352943" + "timestamp": "2026-02-05T15:27:49.742708767" }, "homo sapiens - bam - stub": { "content": [ @@ -84,8 +84,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:47:11.516191863" + "timestamp": "2026-02-05T15:27:58.764956454" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index b3fb9116d..cd463b1b4 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -14,8 +14,8 @@ process GATK4_FILTERMUTECTCALLS { tuple val(meta4), path(dict) output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val(meta), path("*.filteringStats.tsv"), emit: stats tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -26,10 +26,10 @@ process GATK4_FILTERMUTECTCALLS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def orientationbias_command = orientationbias ? orientationbias.collect { "--orientation-bias-artifact-priors ${it}" }.join(' ') : '' - def segmentation_command = segmentation ? segmentation.collect { "--tumor-segmentation ${it}" }.join(' ') : '' + def orientationbias_command = orientationbias ? orientationbias.collect { orientationbias_ -> "--orientation-bias-artifact-priors ${orientationbias_}" }.join(' ') : '' + def segmentation_command = segmentation ? segmentation.collect { segmentation_ -> "--tumor-segmentation ${segmentation_}" }.join(' ') : '' def estimate_command = estimate ? " --contamination-estimate ${estimate} " : '' - def table_command = table ? table.collect { "--contamination-table ${it}" }.join(' ') : '' + def table_command = table ? table.collect { table_ -> "--contamination-table ${table_}" }.join(' ') : '' def avail_mem = 3072 if (!task.memory) { @@ -50,7 +50,6 @@ process GATK4_FILTERMUTECTCALLS { ${table_command} \\ --tmp-dir . \\ ${args} - """ stub: @@ -59,6 +58,5 @@ process GATK4_FILTERMUTECTCALLS { echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi touch ${prefix}.vcf.gz.filteringStats.tsv - """ } diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test index f775f3ed2..64007fc1a 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test @@ -47,7 +47,7 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0] - ).match() } + ).match() } ) } @@ -90,10 +90,9 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0..5] - ).match() } + ).match() } ) } - } test("human - vcf - use-val") { @@ -133,10 +132,9 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0] - ).match() } + ).match() } ) } - } test("human - vcf - stub") { @@ -176,7 +174,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 6856af7e7..dee66a039 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -18,19 +18,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:33.782781" - }, - "versions_with-files": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:22:04.77036932" + "timestamp": "2026-02-05T14:24:16.387135961" }, "human - vcf - stub": { "content": [ @@ -103,31 +91,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:52.944908" - }, - "versions_use-val": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:22:18.790658915" - }, - "versions_base": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:21:49.569533374" + "timestamp": "2026-02-05T12:44:42.986778135" }, "human - vcf - with-files": { "content": [ @@ -155,7 +119,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:11.396747" + "timestamp": "2026-02-05T14:24:03.785317232" }, "human - vcf - base": { "content": [ @@ -176,6 +140,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:23:48.108444" + "timestamp": "2026-02-05T14:22:02.165177275" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index c3e6b114e..c7b68ab55 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -13,7 +13,7 @@ process GATK4_GERMLINECNVCALLER { output: tuple val(meta), path("*-cnv-model/*-calls"), emit: cohortcalls, optional: true tuple val(meta), path("*-cnv-model/*-model"), emit: cohortmodel, optional: true - tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true + tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -25,7 +25,7 @@ process GATK4_GERMLINECNVCALLER { def intervals_command = intervals ? "--intervals ${intervals}" : "" def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" def model_command = model ? "--model ${model}" : "" - def input_list = tsv.collect { "--input ${it}" }.join(' ') + def input_list = tsv.collect { tsv_ -> "--input ${tsv_}" }.join(' ') def output_command = model ? "--output ${prefix}-cnv-calls" : "--output ${prefix}-cnv-model" def avail_mem = 3072 @@ -50,7 +50,6 @@ process GATK4_GERMLINECNVCALLER { ${args} \\ ${intervals_command} \\ ${model_command} - """ stub: @@ -59,6 +58,5 @@ process GATK4_GERMLINECNVCALLER { mkdir -p ${prefix}-cnv-calls/${prefix}-calls mkdir -p ${prefix}-cnv-model/${prefix}-model mkdir -p ${prefix}-cnv-model/${prefix}-calls - """ } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index a3bb985ea..640a17d49 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { script "../../collectreadcounts/main.nf" process { """ - input[0] = Channel.of( + input[0] = channel.of( [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), @@ -31,18 +31,19 @@ nextflow_process { file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY") { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + bed = channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv @@ -55,12 +56,13 @@ nextflow_process { """ } } + run("GATK4_BEDTOINTERVALLIST") { script "../../bedtointervallist/main.nf" process { """ - input[0] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[0] = channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } @@ -81,16 +83,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - bam - stub") { @@ -111,16 +112,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index 311076984..aa736b8ed 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -1,15 +1,6 @@ { "homo sapiens - bam": { "content": [ - { - "versions_gatk4": [ - [ - "GATK4_GERMLINECNVCALLER", - "gatk4", - "4.6.2.0" - ] - ] - }, [ "SAMPLE_0", "SAMPLE_1", @@ -32,16 +23,31 @@ "std_ard_u_interval__.tsv", "std_log_mean_bias_t.tsv", "std_psi_t_log__.tsv" - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_GERMLINECNVCALLER", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:09:50.216500599" + "timestamp": "2026-02-05T15:54:16.716891653" }, "homo sapiens - bam - stub": { "content": [ + [ + + ], + [ + + ], { "versions_gatk4": [ [ @@ -50,18 +56,12 @@ "4.6.2.0" ] ] - }, - [ - - ], - [ - - ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:12:05.192665905" + "timestamp": "2026-02-05T15:54:30.034729289" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 2d69d3819..257399cdf 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -29,7 +29,6 @@ process GATK4_INTERVALLISTTOOLS { avail_mem = (task.memory.mega * 0.8).intValue() } """ - mkdir ${prefix}_split gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ @@ -48,7 +47,6 @@ process GATK4_INTERVALLISTTOOLS { newName = os.path.join(directory, str(i + 1) + filename) os.rename(interval, newName) CODE - """ stub: @@ -62,6 +60,5 @@ process GATK4_INTERVALLISTTOOLS { touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list - """ } diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test index 2891bf9e4..19089f485 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test @@ -40,12 +40,11 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() }, ) } - } test("test_gatk4_intervallisttools -stub") { @@ -61,12 +60,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 143136148..100aec5fc 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -46,9 +46,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:44:06.410817008" + "timestamp": "2026-02-05T16:30:27.100653045" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -97,8 +97,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:45:07.987268525" + "timestamp": "2026-02-05T16:30:35.391255689" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 016b275f3..912f585a6 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -39,13 +39,11 @@ process GATK4_MERGEBAMALIGNMENT { --REFERENCE_SEQUENCE ${fasta} \\ --TMP_DIR . \\ ${args} - """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam - """ } diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test index d5878f4de..f12d8dc1f 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test @@ -16,28 +16,26 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -48,26 +46,24 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 2ebca8687..15212afd4 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -36,9 +36,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T19:42:44.250559934" + "timestamp": "2026-02-05T16:39:42.649628142" }, "test-gatk4-mergebamalignment": { "content": [ @@ -55,8 +55,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T19:42:06.516476761" + "timestamp": "2026-02-05T16:39:36.797699941" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 95f1eccc9..93112900a 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -13,7 +13,7 @@ process GATK4_MERGEVCFS { output: tuple val(meta), path('*.vcf.gz'), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -22,7 +22,7 @@ process GATK4_MERGEVCFS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input_list = vcf.collect { "--INPUT ${it}" }.join(' ') + def input_list = vcf.collect { vcf_ -> "--INPUT ${vcf_}" }.join(' ') def reference_command = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" def avail_mem = 3072 @@ -40,14 +40,12 @@ process GATK4_MERGEVCFS { ${reference_command} \\ --TMP_DIR . \\ ${args} - """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - """ } diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index f9765aab5..fd9972b0a 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -20,18 +20,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } test("test_gatk4_mergevcfs_no_dict") { @@ -45,18 +42,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs_no_dict") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } test("test_gatk4_mergevcfs_no_dict_stub") { @@ -73,18 +67,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs_no_dict_stub") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } - } diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 14170940e..38e555502 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,6 +1,8 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -9,18 +11,18 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:51:23.679671657" + "timestamp": "2026-02-05T16:40:17.349813218" }, "test_gatk4_mergevcfs": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -29,18 +31,18 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:49:37.159554677" + "timestamp": "2026-02-05T16:40:03.274024419" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -49,14 +51,12 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:50:41.376990748" + "timestamp": "2026-02-05T16:40:10.948156303" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 269c605f5..828206403 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -20,9 +20,9 @@ process GATK4_MUTECT2 { path panel_of_normals_tbi output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi - tuple val(meta), path("*.stats"), emit: stats + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.stats"), emit: stats tuple val(meta), path("*.f1r2.tar.gz"), emit: f1r2, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -36,7 +36,7 @@ process GATK4_MUTECT2 { def interval_command = intervals ? "--intervals ${intervals}" : "" def pon_command = panel_of_normals ? "--panel-of-normals ${panel_of_normals}" : "" def gr_command = germline_resource ? "--germline-resource ${germline_resource}" : "" - def a_command = alleles ? "--alleles ${alleles}": "" + def a_command = alleles ? "--alleles ${alleles}" : "" def avail_mem = 3072 if (!task.memory) { diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test b/modules/nf-core/gatk4/mutect2/tests/main.nf.test index 8917fd212..3f7afea60 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test @@ -57,17 +57,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -119,17 +117,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2.collect { file(it[1]).getName() }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2.collect { file(it[1]).getName() }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -170,17 +166,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -221,17 +215,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -272,17 +264,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -323,17 +313,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -374,17 +362,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -438,12 +424,11 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("human - bam - tumor_normal_pair - force_call") { @@ -493,17 +478,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -544,19 +527,16 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - } diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index 76db52e05..73ffa9fc3 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -28,9 +28,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:26:03.059145991" + "timestamp": "2026-02-05T16:54:59.699672374" }, "human - bam - tumor_only - force_call": { "content": [ @@ -61,9 +61,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:37:31.740160738" + "timestamp": "2026-02-05T17:02:15.006936591" }, "human - bam - tumor_normal_pair": { "content": [ @@ -96,9 +96,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:10:46.039204223" + "timestamp": "2026-02-05T16:44:25.776848294" }, "human - cram": { "content": [ @@ -129,9 +129,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:22:38.825106184" + "timestamp": "2026-02-05T16:52:48.795368727" }, "mitochondria - bam": { "content": [ @@ -162,9 +162,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:26:44.448416009" + "timestamp": "2026-02-05T16:55:10.945977864" }, "human - bam - tumor_only": { "content": [ @@ -195,9 +195,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:19:10.024181048" + "timestamp": "2026-02-05T16:50:29.074224171" }, "mitochondria - bam - gz_ref": { "content": [ @@ -228,9 +228,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:27:29.464429837" + "timestamp": "2026-02-05T16:55:22.160325012" }, "human - bam - tumor_normal_pair - force_call": { "content": [ @@ -263,9 +263,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:33:21.41092687" + "timestamp": "2026-02-05T16:59:14.299303803" }, "human - bam - tumor_normal_pair_f1r2 - stub": { "content": [ @@ -368,9 +368,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:28:08.170677731" + "timestamp": "2026-02-05T16:55:48.221310078" }, "human - bam - tumor_normal_pair_f1r2": { "content": [ @@ -403,8 +403,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:15:39.798158102" + "timestamp": "2026-02-05T16:47:43.194989668" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index f87511d5f..2c29c87cc 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -12,8 +12,8 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { output: tuple val(meta), path("*_genotyped_intervals.vcf.gz"), emit: intervals, optional: true - tuple val(meta), path("*_genotyped_segments.vcf.gz"), emit: segments, optional: true - tuple val(meta), path("*_denoised.vcf.gz"), emit: denoised, optional: true + tuple val(meta), path("*_genotyped_segments.vcf.gz"), emit: segments, optional: true + tuple val(meta), path("*_denoised.vcf.gz"), emit: denoised, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -22,8 +22,8 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def calls_command = calls ? calls.collect { "--calls-shard-path ${it}" }.join(' ') : "" - def model_command = model ? model.collect { "--model-shard-path ${it}" }.join(' ') : "" + def calls_command = calls ? calls.collect { call -> "--calls-shard-path ${call}" }.join(' ') : "" + def model_command = model ? model.collect { mode -> "--model-shard-path ${mode}" }.join(' ') : "" def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" def avail_mem = 3072 @@ -46,11 +46,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\ --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\ --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -59,10 +54,5 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { echo "" | gzip > ${prefix}_genotyped_intervals.vcf.gz echo "" | gzip > ${prefix}_genotyped_segments.vcf.gz echo "" | gzip > ${prefix}_denoised.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index 00415fd0a..f18e2fb0c 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -21,32 +21,29 @@ nextflow_process { """ intervals = [[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] dict = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] - input = [intervals, dict] """ } } + run("GATK4_COLLECTREADCOUNTS"){ script "../../collectreadcounts/main.nf" process { """ - input_bam = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + input_bam = channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), + ], + [ [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - - fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() - + fasta = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [input_bam, fasta, fai, dict] """ } @@ -55,7 +52,7 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + bed = channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) input = [ GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -68,28 +65,30 @@ nextflow_process { """ } } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_COHORT") { script "../../germlinecnvcaller/main.nf" process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[id:'test'], tsv ] }) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) """ } } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_CASE") { script "../../germlinecnvcaller/main.nf" process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) + .first() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) """ } } @@ -101,25 +100,24 @@ nextflow_process { process { """ input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.intervals[0][1]).name, file(process.out.segments[0][1]).name, file(process.out.denoised[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - counts - stub") { @@ -130,25 +128,23 @@ nextflow_process { process { """ input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.intervals[0][1]).name, file(process.out.segments[0][1]).name, file(process.out.denoised[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap index 15ae1944a..71182fe84 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -1,6 +1,9 @@ { "homo sapiens - counts - stub": { "content": [ + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz", { "versions_gatk4": [ [ @@ -9,19 +12,19 @@ "4.6.2.0" ] ] - }, - "test_genotyped_intervals.vcf.gz", - "test_genotyped_segments.vcf.gz", - "test_denoised.vcf.gz" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T22:29:17.166798377" + "timestamp": "2026-02-05T17:13:11.168329663" }, "homo sapiens - counts": { "content": [ + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz", { "versions_gatk4": [ [ @@ -30,15 +33,12 @@ "4.6.2.0" ] ] - }, - "test_genotyped_intervals.vcf.gz", - "test_genotyped_segments.vcf.gz", - "test_denoised.vcf.gz" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T22:26:44.628515186" + "timestamp": "2026-02-05T17:12:53.53221471" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index 62b771650..66e7f2a6e 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -14,9 +14,9 @@ process GATK4_PRINTREADS { tuple val(meta4), path(dict) output: - tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true - tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test index f86f08a1d..126c780c3 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test @@ -17,36 +17,31 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ] - input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.cram, process.out.sam, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -58,38 +53,32 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) ] - input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.bam, bam(process.out.cram[0][1]).getHeaderMD5(), process.out.sam, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } - } diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index e47cdcae4..26aa18f4e 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:04:26.642559" + "timestamp": "2026-02-05T17:13:29.864614856" }, "test-gatk4-printreads-cram": { "content": [ @@ -47,6 +47,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:04:46.522705" + "timestamp": "2026-02-05T17:13:38.337993548" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test index e06c041f4..a051a9abd 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test @@ -16,21 +16,19 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -41,19 +39,17 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 3858e13bf..e782cdcb2 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:08:17.497786" + "timestamp": "2026-02-05T17:58:02.45058488" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -57,6 +57,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:08:32.702485" + "timestamp": "2026-02-05T17:49:32.744361592" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test index b9af8b189..df9393461 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test @@ -16,16 +16,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( path(process.out.fastq[0][1]).linesGzip[3..7], process.out.findAll { key, val -> key.startsWith("versions") } @@ -41,16 +40,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { path(it).linesGzip[3..7] }, process.out.findAll { key, val -> key.startsWith("versions") } @@ -66,16 +64,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { file(it).name }, process.out.findAll { key, val -> key.startsWith("versions") } @@ -84,5 +81,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index abeb9291f..84f2cc5f7 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:22.128687" + "timestamp": "2026-02-05T17:59:04.980254114" }, "test-gatk4-samtofastq-paired-end-stubs": { "content": [ @@ -45,7 +45,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:53.540133" + "timestamp": "2026-02-05T17:59:18.479857005" }, "test-gatk4-samtofastq-paired-end": { "content": [ @@ -79,6 +79,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:38.875774" + "timestamp": "2026-02-05T17:59:12.509833732" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 9e1d021c2..11ec406b8 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -11,7 +11,7 @@ process GATK4_SELECTVARIANTS { tuple val(meta), path(vcf), path(vcf_idx), path(intervals) output: - tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -38,11 +38,6 @@ process GATK4_SELECTVARIANTS { ${interval} \\ --tmp-dir . \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -50,10 +45,5 @@ process GATK4_SELECTVARIANTS { """ echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test index 3fea99ec1..c9dfee2bb 100644 --- a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test @@ -11,10 +11,6 @@ nextflow_process { test("selectvariants - vcf input") { when { - params { - // define parameters here. Example: - // outdir = "tests/results" - } process { """ input[0] = [ @@ -28,14 +24,14 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - - } test("selectvariants - gz input") { @@ -54,13 +50,13 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 5ccc867ea..797167913 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -13,11 +13,11 @@ process GATK4_SHIFTFASTA { tuple val(meta3), path(dict) output: - tuple val(meta), path("*_shift.fasta"), emit: shift_fa - tuple val(meta), path("*_shift.fasta.fai"), emit: shift_fai - tuple val(meta), path("*_shift.back_chain"), emit: shift_back_chain - tuple val(meta), path("*_shift.dict"), emit: dict, optional: true - tuple val(meta), path("*.intervals"), emit: intervals, optional: true + tuple val(meta), path("*_shift.fasta"), emit: shift_fa + tuple val(meta), path("*_shift.fasta.fai"), emit: shift_fai + tuple val(meta), path("*_shift.back_chain"), emit: shift_back_chain + tuple val(meta), path("*_shift.dict"), emit: dict, optional: true + tuple val(meta), path("*.intervals"), emit: intervals, optional: true tuple val(meta), path("*.shifted.intervals"), emit: shift_intervals, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -48,12 +48,13 @@ process GATK4_SHIFTFASTA { """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" """ - touch test.intervals - touch test_shift.back_chain - touch test_shift.dict - touch test.shifted.intervals - touch test_shift.fasta - touch test_shift.fasta.fai + touch ${prefix}.intervals + touch ${prefix}_shift.back_chain + touch ${prefix}_shift.dict + touch ${prefix}.shifted.intervals + touch ${prefix}_shift.fasta + touch ${prefix}_shift.fasta.fai """ } diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test index d11d144ea..843354e9a 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test @@ -18,15 +18,15 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ @@ -34,11 +34,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap index a465dc485..a4fe7d3af 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap @@ -136,6 +136,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:25:05.997054" + "timestamp": "2026-02-05T17:51:13.969347846" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test index 26c20f88f..41d5c8f4b 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test @@ -17,26 +17,25 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true) + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -49,25 +48,24 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -82,28 +80,26 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap index 092b26007..77cc7afe8 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:38.084533" + "timestamp": "2026-02-05T17:52:08.822076018" }, "test-gatk4-splitintervals-bed": { "content": [ @@ -91,7 +91,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:18.658962" + "timestamp": "2026-02-05T17:52:01.205689288" }, "test-gatk4-splitintervals-intervals-stub": { "content": [ @@ -138,6 +138,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:55.618457" + "timestamp": "2026-02-05T17:52:15.297589219" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index b3c0e340f..6256351b1 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -16,7 +16,7 @@ process GATK4_VARIANTFILTRATION { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test index 65ba4124c..cbb647c47 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test @@ -40,14 +40,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("gatk4_variantfiltration - human - vcf - fasta.gz") { @@ -81,14 +82,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("gatk4_variantfiltration - human - vcf.gz - fasta") { @@ -122,14 +124,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap index 3a621b227..e1a3c785a 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -1,6 +1,8 @@ { "gatk4_variantfiltration - human - vcf - fasta.gz": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -9,18 +11,18 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:33.543304" + "timestamp": "2026-02-05T18:03:01.467326216" }, "gatk4_variantfiltration - human - vcf.gz - fasta": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -29,18 +31,18 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:51.020309" + "timestamp": "2026-02-05T18:03:09.049097033" }, "gatk4_variantfiltration - human - vcf - fasta": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -49,14 +51,12 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:15.367356" + "timestamp": "2026-02-05T18:02:52.913618285" } } \ No newline at end of file diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index da79a0ed3..a76851dff 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -14,7 +14,7 @@ process GAWK { output: tuple val(meta), path("*.${suffix}"), emit: output - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gawk'), eval("awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'"), topic: versions, emit: versions_gawk when: task.ext.when == null || task.ext.when @@ -47,11 +47,6 @@ process GAWK { ${output} ${cleanup} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS """ stub: @@ -61,10 +56,5 @@ process GAWK { """ ${create_cmd} ${prefix}.${suffix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS """ } diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 732e18a97..96cd0c72b 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -15,7 +15,8 @@ tools: homepage: "https://www.gnu.org/software/gawk/" documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -25,22 +26,22 @@ input: e.g. [ id:'test', single_end:false ] - input: type: file - description: The input file - Specify the logic that needs to be executed on - this file on the `ext.args2` or in the program file. If the files have a `.gz` - extension, they will be unzipped using `zcat`. + description: The input file - Specify the logic that needs to be executed + on this file on the `ext.args2` or in the program file. If the files + have a `.gz` extension, they will be unzipped using `zcat`. pattern: "*" ontologies: [] - program_file: type: file - description: Optional file containing logic for awk to execute. If you don't wish - to use a file, you can use `ext.args2` to specify the logic. + description: Optional file containing logic for awk to execute. If you don't + wish to use a file, you can use `ext.args2` to specify the logic. pattern: "*" ontologies: [] - disable_redirect_output: type: boolean - description: Disable the redirection of awk output to a given file. This is useful - if you want to use awk's built-in redirect to write files instead of the shell's - redirect. + description: Disable the redirection of awk output to a given file. This is + useful if you want to use awk's built-in redirect to write files instead + of the shell's redirect. output: output: - - meta: @@ -50,18 +51,33 @@ output: e.g. [ id:'test', single_end:false ] - "*.${suffix}": type: file - description: The output file - if using shell redirection, specify the name - of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, - ensure the awk program produces files with the extension in `ext.suffix`. + description: The output file - if using shell redirection, specify the + name of this file using `ext.prefix` and the extension using + `ext.suffix`. Otherwise, ensure the awk program produces files with + the extension in `ext.suffix`. pattern: "*" ontologies: [] + versions_gawk: + - - ${task.process}: + type: string + description: The name of the process + - gawk: + type: string + description: The name of the tool + - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gawk: + type: string + description: The name of the tool + - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index fc6e240fd..5fa9daf16 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -29,10 +29,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -45,7 +43,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = Channel.of('BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }').collectFile(name:"program.awk") @@ -55,10 +53,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -71,7 +67,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -81,10 +77,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -97,7 +91,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] ] @@ -108,10 +102,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -124,7 +116,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] ] @@ -135,10 +127,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -151,7 +141,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -161,10 +151,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -178,7 +166,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'hello' ], // meta map + [ id:'hello' ], [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] ] @@ -189,10 +177,8 @@ nextflow_process { } then { - assertAll( - { assert process.failed }, - { assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } - ) + assert process.failed + assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } } } diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index d8e8ac755..1444c4688 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "Compress after processing": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -10,32 +10,25 @@ "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-27T17:11:20.054143406" + "timestamp": "2026-02-05T16:42:17.741168488" }, "Convert fasta to bed": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -43,32 +36,25 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T13:14:02.347809811" + "timestamp": "2026-02-05T16:41:46.810784678" }, "Convert fasta to bed with program file": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -76,32 +62,25 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T13:14:11.894616209" + "timestamp": "2026-02-05T16:41:52.884002736" }, "Extract first column from multiple files": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -109,32 +88,25 @@ "test.bed:md5,566c51674bd643227bb2d83e0963376d" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,566c51674bd643227bb2d83e0963376d" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T22:04:47.729300129" + "timestamp": "2026-02-05T16:42:05.455428454" }, "Unzip files before processing": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -142,32 +114,25 @@ "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T22:08:19.533527657" + "timestamp": "2026-02-05T16:42:11.976164295" }, "Convert fasta to bed using awk redirect instead of shell redirect": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -175,26 +140,19 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-03-05T08:31:09.88842854" + "timestamp": "2026-02-05T16:41:58.777371598" } } \ No newline at end of file diff --git a/modules/nf-core/haplogrep3/classify/meta.yml b/modules/nf-core/haplogrep3/classify/meta.yml index 53e40aa64..54b7efdf7 100644 --- a/modules/nf-core/haplogrep3/classify/meta.yml +++ b/modules/nf-core/haplogrep3/classify/meta.yml @@ -42,9 +42,10 @@ output: - haplogrep3: type: string description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': - type: string - description: The command used to generate the version of the tool + - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -53,9 +54,10 @@ topics: - haplogrep3: type: string description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': - type: string - description: The command used to generate the version of the tool + - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 861cd7f76..9fd34f37c 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -71,7 +71,7 @@ output: - "*_plots": type: file description: Plots created by MultiQC - pattern: "*_data" + pattern: "*_plots" ontologies: [] versions: - - ${task.process}: diff --git a/modules/nf-core/sambamba/depth/main.nf b/modules/nf-core/sambamba/depth/main.nf index e1404c7b0..42a1a80a3 100644 --- a/modules/nf-core/sambamba/depth/main.nf +++ b/modules/nf-core/sambamba/depth/main.nf @@ -50,7 +50,7 @@ process SAMBAMBA_DEPTH { cat <<-END_VERSIONS > versions.yml "${task.process}": - sambamba: \$(sambamba --version) + sambamba: \$(echo \$(sambamba --version 2>&1) | awk '{print \$2}' ) END_VERSIONS """ } diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test b/modules/nf-core/sambamba/depth/tests/main.nf.test index 3f5105986..3f6fce50b 100644 --- a/modules/nf-core/sambamba/depth/tests/main.nf.test +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test @@ -30,7 +30,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -85,7 +88,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } ) } } diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap index 7f4951e62..d1eb47aaa 100644 --- a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap @@ -29,10 +29,10 @@ } ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:57:58.097957" + "timestamp": "2025-12-05T12:03:11.190921915" }, "test-sambamba-depth": { "content": [ @@ -61,13 +61,20 @@ "versions": [ "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ] - } + }, + [ + { + "SAMBAMBA_DEPTH": { + "sambamba": "1.0.1" + } + } + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:57:42.031913" + "timestamp": "2025-12-05T12:03:07.689091449" }, "test-sambamba-depth-stub": { "content": [ @@ -82,7 +89,7 @@ ] ], "1": [ - "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ], "bed": [ [ @@ -94,14 +101,21 @@ ] ], "versions": [ - "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ] - } + }, + [ + { + "SAMBAMBA_DEPTH": { + "sambamba": "1.0.1" + } + } + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:58:13.647811" + "timestamp": "2025-12-05T12:03:14.737096819" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index c07cd8a98..b92410cd6 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -15,7 +15,7 @@ process SAMTOOLS_COLLATE { tuple val(meta), path("*.bam"), emit: bam, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.sam"), emit: sam, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -37,11 +37,6 @@ process SAMTOOLS_COLLATE { -@ $task.cpus \\ -o ${prefix}.${extension} \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -53,10 +48,5 @@ process SAMTOOLS_COLLATE { "bam" """ touch ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index 96fdc2fc9..f6069abc4 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -71,13 +71,27 @@ output: description: Sorted SAM pattern: "*.{sam}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test index 2e547c7e8..2918f9e3d 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -14,23 +14,18 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) - ]) + ] input[1] = [ [id:'fasta'], [] ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, - { assert snapshot(process.out.cram).match("bam_cram") }, - { assert snapshot(process.out.sam).match("bam_sam") }, - { assert snapshot(process.out.versions).match("bam_versions") } - ) + assert process.success + assert snapshot(process.out).match() } } @@ -40,26 +35,21 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) - ]) - input[1] = Channel.of([ + ] + input[1] = [ [ id:'fasta'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("cram_fasta_bam") }, - { assert snapshot(process.out.cram).match("cram_fasta_cram") }, - { assert snapshot(process.out.sam).match("cram_fasta_sam") }, - { assert snapshot(process.out.versions).match("cram_fasta_versions") } - ) + assert process.success + assert snapshot(process.out).match() } } @@ -69,23 +59,18 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) - ]) + ] input[1] = [ [id:'fasta'], [] ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out, - path(process.out.versions[0]).yaml - ).match() }, - ) + assert process.success + assert snapshot(process.out).match() } } diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test.snap b/modules/nf-core/samtools/collate/tests/main.nf.test.snap index b0c8f4dce..49c054f96 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collate/tests/main.nf.test.snap @@ -1,52 +1,4 @@ { - "cram_fasta_versions": { - "content": [ - [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T13:02:45.779649" - }, - "bam_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:01.611698" - }, - "cram_fasta_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.325375" - }, - "cram_fasta_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.328907" - }, "sarscov2 - bam -- stub": { "content": [ { @@ -65,7 +17,11 @@ ], "3": [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -81,64 +37,125 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] ] - }, - { - "SAMTOOLS_COLLATE": { - "samtools": "1.22.1" - } } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-10T13:02:50.413313" + "timestamp": "2026-02-04T14:56:50.33210565" }, - "cram_fasta_bam": { + "sarscov2 - bam": { "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.322144" - }, - "bam_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:01.608677" - }, - "bam_sam": { - "content": [ - [ - - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,06aa42b8b8dff9eb8c693dc1a9767e23" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,06aa42b8b8dff9eb8c693dc1a9767e23" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-02-02T16:56:01.613225" + "timestamp": "2026-02-04T14:56:36.179835312" }, - "bam_versions": { + "homo_sapiens - cram + fasta": { "content": [ - [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,aefab9d7e786892bef3fca019494abda" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,aefab9d7e786892bef3fca019494abda" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-10T13:02:39.72811" + "timestamp": "2026-02-04T14:56:44.148216078" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 7019a72e4..e2a0e56da 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input) @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX { tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -27,11 +27,6 @@ process SAMTOOLS_INDEX { -@ ${task.cpus} \\ $args \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -40,10 +35,5 @@ process SAMTOOLS_INDEX { "crai" : args.contains("-c") ? "csi" : "bai" """ touch ${input}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 1bed6bca6..c6d4ce259 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -14,7 +14,8 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:samtools input: - - meta: @@ -60,13 +61,27 @@ output: description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5cd..c96cec860 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -23,7 +23,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -43,7 +46,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -67,7 +73,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.csi[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } @@ -89,7 +95,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -110,7 +119,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -133,7 +145,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.csi, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 72d65e81a..afc8a1ff6 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,250 +1,156 @@ { "csi - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - - ], - "csi": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:25.261127166" + "timestamp": "2026-01-28T17:52:10.030187" }, "crai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:12.653194876" + "timestamp": "2026-01-28T17:51:59.125484" }, "bai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:01.854932651" + "timestamp": "2026-01-28T17:51:47.277042" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", - [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:51.485364222" + "timestamp": "2026-01-28T17:51:35.758735" }, "crai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:40.518873972" + "timestamp": "2026-01-28T17:51:26.561965" }, "bai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:21.184050361" + "timestamp": "2026-01-28T17:51:15.299035" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index aab585ac4..87b3333f6 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -22,7 +22,7 @@ process SAMTOOLS_VIEW { tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true - tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 167206773..215222661 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -147,7 +147,7 @@ output: - samtools: type: string description: Name of the tool - - samtools --version | head -1 | sed -e "s/samtools //": + - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool @@ -159,7 +159,7 @@ topics: - samtools: type: string description: Name of the tool - - samtools --version | head -1 | sed -e "s/samtools //": + - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config deleted file mode 100644 index 83ad29f02..000000000 --- a/modules/nf-core/samtools/view/tests/bam.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt bam" -} diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config deleted file mode 100644 index 60b96d426..000000000 --- a/modules/nf-core/samtools/view/tests/bam_index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt bam --write-index" -} diff --git a/modules/nf-core/samtools/view/tests/cram_index.config b/modules/nf-core/samtools/view/tests/cram_index.config deleted file mode 100644 index ed87c3349..000000000 --- a/modules/nf-core/samtools/view/tests/cram_index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt cram --write-index" -} diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index de57b8e36..74e1c49fd 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process SAMTOOLS_VIEW" script "../main.nf" + config "./nextflow.config" process "SAMTOOLS_VIEW" tag "modules" @@ -10,15 +11,17 @@ nextflow_process { tag "samtools/view" test("bam") { - when { + params { + samtools_args = "" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = [] @@ -35,17 +38,17 @@ nextflow_process { } test("bam_csi_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'csi' @@ -62,17 +65,17 @@ nextflow_process { } test("bam_bai_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'bai' @@ -89,17 +92,17 @@ nextflow_process { } test("bam_bai_index_unselected") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -117,17 +120,17 @@ nextflow_process { } test("cram_crai_index_unselected") { - - config "./cram_index.config" - when { + params { + samtools_args = "--output-fmt cram --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -145,19 +148,21 @@ nextflow_process { } test("cram") { - when { + params { + samtools_args = "" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -173,21 +178,21 @@ nextflow_process { } test("cram_to_bam") { - - config "./bam.config" - when { + params { + samtools_args = "--output-fmt bam" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -203,21 +208,21 @@ nextflow_process { } test("cram_to_bam_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -233,22 +238,23 @@ nextflow_process { } test("cram_to_bam_index_qname") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) - input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) + ] + input[2] = Channel.of("testN:2817", "testN:2814") + .collectFile(name: "readnames.list", newLine: true) input[3] = [] """ } @@ -265,16 +271,18 @@ nextflow_process { test("bam_stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = [] @@ -293,16 +301,18 @@ nextflow_process { test("bam_csi_index - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'csi' @@ -321,16 +331,18 @@ nextflow_process { test("bam_bai_index - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'bai' @@ -349,16 +361,18 @@ nextflow_process { test("bam_bai_index_uselected - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -378,16 +392,18 @@ nextflow_process { test("cram_crai_index_unselected - stub") { options "-stub" - config "./cram_index.config" when { + params { + samtools_args = "--output-fmt cram --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6ee160cd4..95205e56f 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -8,8 +8,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -23,8 +22,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -48,10 +46,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:48.952660444" + "timestamp": "2026-02-03T16:49:14.82588493" }, "bam_csi_index - stub": { "content": [ @@ -59,8 +57,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -77,8 +74,7 @@ "4": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -105,8 +101,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -120,8 +115,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -145,10 +139,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:14.881335093" + "timestamp": "2026-02-03T16:49:31.409368544" }, "bam_csi_index": { "content": [ @@ -159,8 +153,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -174,8 +167,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -199,10 +191,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:40:50.701779393" + "timestamp": "2026-02-03T16:48:46.36824035" }, "cram_to_bam_index_qname": { "content": [ @@ -213,8 +205,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -228,8 +219,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,15d725bced7ececd45b4312b2af99a6b" ] @@ -240,8 +230,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam" ] @@ -249,8 +238,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi" ] @@ -265,10 +253,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:58.085628072" + "timestamp": "2026-02-03T16:49:20.747636525" }, "bam_bai_index_unselected": { "content": [ @@ -276,8 +264,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai" ] @@ -285,8 +272,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -306,8 +292,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam" ] @@ -315,8 +300,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi" ] @@ -331,10 +315,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:10.249194373" + "timestamp": "2026-02-03T16:48:57.713608154" }, "cram_crai_index_unselected - stub": { "content": [ @@ -345,8 +329,7 @@ "1": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -363,8 +346,7 @@ "5": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -372,8 +354,7 @@ "6": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -381,8 +362,7 @@ "7": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -403,8 +383,7 @@ "crai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -412,8 +391,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -427,8 +405,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -436,8 +413,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -452,10 +428,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:39.3240134" + "timestamp": "2026-02-03T16:49:48.092654899" }, "bam": { "content": [ @@ -466,8 +442,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -500,10 +475,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:40:42.829284764" + "timestamp": "2026-02-03T16:48:27.608944526" }, "bam_bai_index": { "content": [ @@ -511,8 +486,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai" ] @@ -520,8 +494,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -554,10 +527,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:00.734899949" + "timestamp": "2026-02-03T16:48:52.047178732" }, "cram_to_bam": { "content": [ @@ -568,8 +541,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -602,10 +574,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:40.148480065" + "timestamp": "2026-02-03T16:50:41.727031999" }, "bam_bai_index - stub": { "content": [ @@ -613,8 +585,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -628,8 +599,7 @@ "3": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -656,8 +626,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -665,8 +634,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -699,10 +667,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:22.748940869" + "timestamp": "2026-02-03T16:49:36.783381688" }, "cram": { "content": [ @@ -719,8 +687,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram" ] @@ -747,10 +714,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:30.602610389" + "timestamp": "2026-02-03T16:49:09.393102901" }, "bam_bai_index_uselected - stub": { "content": [ @@ -758,8 +725,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -773,8 +739,7 @@ "3": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -788,8 +753,7 @@ "6": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -797,8 +761,7 @@ "7": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -813,8 +776,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -822,8 +784,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -843,8 +804,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -852,8 +812,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -868,10 +827,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:31.1133801" + "timestamp": "2026-02-03T16:49:42.344755528" }, "cram_crai_index_unselected": { "content": [ @@ -885,8 +844,7 @@ "crai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai" ] @@ -894,8 +852,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,9b6eeca8f6b4b744297ae7cc87c031a4" ] @@ -909,8 +866,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram" ] @@ -918,8 +874,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai" ] @@ -934,10 +889,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:49:09.738258028" + "timestamp": "2026-02-03T16:49:03.431621547" }, "bam_stub": { "content": [ @@ -948,8 +903,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -963,8 +917,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -988,9 +941,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:06.108061867" + "timestamp": "2026-02-03T16:49:26.152824543" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/nextflow.config b/modules/nf-core/samtools/view/tests/nextflow.config new file mode 100644 index 000000000..37c564396 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SAMTOOLS_VIEW { + ext.args = params.samtools_args + } +} diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index c7794856d..9b926b1ff 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,7 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 9bd8f5546..b9c324dac 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -1,56 +1,52 @@ process UNTAR { - tag "$archive" + tag "${archive}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : - 'nf-core/ubuntu:22.04' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(archive) output: - tuple val(meta), path("$prefix"), emit: untar - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}"), emit: untar + tuple val("${task.process}"), val('untar'), eval('tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//"'), emit: versions_untar, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) """ - mkdir $prefix + mkdir ${prefix} ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ - -C $prefix --strip-components 1 \\ + -C ${prefix} --strip-components 1 \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} else tar \\ - -C $prefix \\ + -C ${prefix} \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} fi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ stub: - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ mkdir ${prefix} ## Dry-run untaring the archive to get the files and place all in prefix @@ -75,10 +71,5 @@ process UNTAR { fi done fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index 290346b3f..571d8078a 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -1,5 +1,5 @@ name: untar -description: Extract files. +description: Extract files from tar, tar.gz, tar.bz2, tar.xz archives keywords: - untar - uncompress @@ -7,7 +7,7 @@ keywords: tools: - untar: description: | - Extract tar.gz files. + Extract tar, tar.gz, tar.bz2, tar.xz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] identifier: "" @@ -19,24 +19,48 @@ input: e.g. [ id:'test', single_end:false ] - archive: type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + description: File to be untarred + pattern: "*.{tar,tar.gz,tar.bz2,tar.xz}" + ontologies: + - edam: http://edamontology.org/format_3981 # TAR format + - edam: http://edamontology.org/format_3989 # GZIP format output: - - untar: - - meta: + untar: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*/" + - ${prefix}: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - $prefix: - type: directory - description: Directory containing contents of archive pattern: "*/" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_untar: + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index c957517aa..fde8db16a 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -20,7 +20,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -38,7 +41,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -58,7 +64,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -78,7 +87,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index ceb91b792..51a414dd4 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,158 +1,118 @@ { "test_untar_onlyfiles": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:28.231047" + "timestamp": "2026-01-28T17:49:32.000491" }, "test_untar_onlyfiles - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:45.773103" + "timestamp": "2026-01-28T17:49:58.812479" }, "test_untar - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:36.777441" + "timestamp": "2026-01-28T17:49:48.119456" }, "test_untar": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:19.377674" + "timestamp": "2026-01-28T17:49:17.252494" } } \ No newline at end of file diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml deleted file mode 100644 index feb6f15c0..000000000 --- a/modules/nf-core/untar/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -untar: - - modules/nf-core/untar/** diff --git a/modules/nf-core/upd/environment.yml b/modules/nf-core/upd/environment.yml index 307f13b37..a45a25cd9 100644 --- a/modules/nf-core/upd/environment.yml +++ b/modules/nf-core/upd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/upd/main.nf b/modules/nf-core/upd/main.nf index c4bcaf175..1196a03c8 100644 --- a/modules/nf-core/upd/main.nf +++ b/modules/nf-core/upd/main.nf @@ -9,14 +9,14 @@ process UPD { 'biocontainers/upd:0.1.1--pyhdfd78af_0' }" input: - tuple val(meta), path(vcf) + tuple val(meta), path(vcf) output: - tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: versions + tuple val(meta), path("*.bed"), emit: bed + tuple val("${task.process}"), val('upd'), eval("upd --version 2>&1 | sed 's/upd, version //'"), topic: versions, emit: versions_upd when: - task.ext.when == null || task.ext.when + task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' @@ -26,22 +26,12 @@ process UPD { --vcf $vcf \\ $args \\ | sort -k 1,1 -k 2,2n >${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - upd: \$( upd --version 2>&1 | sed 's/upd, version //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - upd: \$( upd --version 2>&1 | sed 's/upd, version //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/upd/meta.yml b/modules/nf-core/upd/meta.yml index a0e900632..650cf217d 100644 --- a/modules/nf-core/upd/meta.yml +++ b/modules/nf-core/upd/meta.yml @@ -24,9 +24,10 @@ input: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] output: - - bed: - - meta: + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -35,11 +36,28 @@ output: type: file description: BED file pattern: "*.{bed}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_upd: + - - ${task.process}: + type: string + description: The name of the process + - upd: + type: string + description: The name of the tool + - upd --version 2>&1 | sed 's/upd, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - upd: + type: string + description: The name of the tool + - upd --version 2>&1 | sed 's/upd, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@hrydbeck" maintainers: diff --git a/modules/nf-core/upd/tests/main.nf.test.snap b/modules/nf-core/upd/tests/main.nf.test.snap index 866792f11..d6af9ef77 100644 --- a/modules/nf-core/upd/tests/main.nf.test.snap +++ b/modules/nf-core/upd/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + [ + "UPD", + "upd", + "0.1" + ] ], "bed": [ [ @@ -23,16 +27,20 @@ "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + "versions_upd": [ + [ + "UPD", + "upd", + "0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T11:51:33.816939" + "timestamp": "2026-02-04T15:38:45.859374" }, "test-upd": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + [ + "UPD", + "upd", + "0.1" + ] ], "bed": [ [ @@ -58,15 +70,19 @@ "test.bed:md5,beea3890636075d5c99db1b0d74f9ff5" ] ], - "versions": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + "versions_upd": [ + [ + "UPD", + "upd", + "0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T11:51:29.35452" + "timestamp": "2026-02-04T15:38:42.052606" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml index d078bfaed..32517278a 100644 --- a/modules/nf-core/vcf2cytosure/environment.yml +++ b/modules/nf-core/vcf2cytosure/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::vcf2cytosure=0.9.1 + - bioconda::vcf2cytosure=0.9.3 diff --git a/modules/nf-core/vcf2cytosure/main.nf b/modules/nf-core/vcf2cytosure/main.nf index 92351337a..f356456b3 100644 --- a/modules/nf-core/vcf2cytosure/main.nf +++ b/modules/nf-core/vcf2cytosure/main.nf @@ -4,8 +4,8 @@ process VCF2CYTOSURE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vcf2cytosure:0.9.1--pyh7cba7a3_1': - 'biocontainers/vcf2cytosure:0.9.1--pyh7cba7a3_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/584cf1de62ed0d65a064456ec0d052d6b657b3245c8f10c626bca7131884c0fc/data': + 'community.wave.seqera.io/library/pip_vcf2cytosure:6852c55eb4c9d406' }" input: tuple val(meta), path(sv_vcf) @@ -16,7 +16,7 @@ process VCF2CYTOSURE { output: tuple val(meta), path("*.cgh"), emit: cgh - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('vcf2cytosure'), eval("vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'"), topic: versions, emit: versions_vcf2cytosure when: task.ext.when == null || task.ext.when @@ -40,27 +40,11 @@ process VCF2CYTOSURE { $snv \\ $blacklist \\ $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2cytosure: \$(echo \$(vcf2cytosure --version 2>&1) | sed 's/^.* cytosure //' ) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def coverage = coverage_bed ? "--coverage ${coverage_bed}" : '' - def cnvkit = cns ? ( coverage_bed ? '' : "--cn ${cns}" ) : '' - def snv = snv_vcf ? ( coverage_bed ? '' : "--snv ${snv_vcf}" ) : '' - def blacklist = blacklist_bed ? "--blacklist ${blacklist_bed}" : '' def prefix = task.ext.prefix ?: "${meta.id}" - """ touch ${prefix}.cgh - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2cytosure: \$(echo \$(vcf2cytosure --version 2>&1) | sed 's/^.* cytosure //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml index 0c38d9c8d..517f80fdd 100644 --- a/modules/nf-core/vcf2cytosure/meta.yml +++ b/modules/nf-core/vcf2cytosure/meta.yml @@ -25,6 +25,7 @@ input: type: file description: VCF file with structural variants pattern: "*.{vcf,vcf.gz}" + ontologies: [] - - meta2: type: map description: | @@ -34,6 +35,7 @@ input: type: file description: Bed file with coverage data pattern: "*.bed" + ontologies: [] - - meta3: type: map description: | @@ -42,6 +44,7 @@ input: - cns: type: file description: CN file from CNVkit, not compatible with coverage_bed file + ontologies: [] - - meta4: type: map description: | @@ -53,13 +56,15 @@ input: VCF file with SNVs to calculate probe coverage, not compatible with coverage_bed pattern: "*.{vcf,vcf.gz}" - - - blacklist_bed: - type: file - description: Bed file with regions to exclude - pattern: "*.bed" + ontologies: [] + - blacklist_bed: + type: file + description: Bed file with regions to exclude + pattern: "*.bed" + ontologies: [] output: - - cgh: - - meta: + cgh: + - - meta: type: map description: | Groovy Map containing sample information @@ -68,10 +73,27 @@ output: type: file description: SV:s in CytoSure format pattern: "*.cgh" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_vcf2cytosure: + - - ${task.process}: + type: string + description: The name of the process + - vcf2cytosure: + type: string + description: The name of the tool + - vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - vcf2cytosure: + type: string + description: The name of the tool + - vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p': + type: eval + description: The expression to obtain the version of the tool authors: - "@jemten" diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test b/modules/nf-core/vcf2cytosure/tests/main.nf.test index edd3063d6..a6d4bcd34 100644 --- a/modules/nf-core/vcf2cytosure/tests/main.nf.test +++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test @@ -31,8 +31,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.cgh).match("cgh") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.cgh, + process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -63,8 +64,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.cgh).match("cgh - stub") }, - { assert snapshot(process.out.versions).match("versions - stub") } + { assert snapshot( + process.out.cgh, + process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap index 0a0fae292..d0e0b8135 100644 --- a/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap +++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap @@ -1,26 +1,31 @@ { - "cgh": { + "homo sapiens - vcf - bed": { "content": [ [ [ { "id": "test" }, - "test.cgh:md5,fc3f1ffac5b797881d992994d5d56550" + "test.cgh:md5,c9bcda3fafe67359e353bedf02d041e8" ] - ] - ], - "timestamp": "2023-12-21T18:33:25.202806" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb" - ] + ], + { + "versions_vcf2cytosure": [ + [ + "VCF2CYTOSURE", + "vcf2cytosure", + "0.9.3" + ] + ] + } ], - "timestamp": "2023-12-21T18:33:25.205826" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:29:44.501025" }, - "cgh - stub": { + "homo sapiens - vcf - bed - stub": { "content": [ [ [ @@ -29,16 +34,21 @@ }, "test.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ] - ], - "timestamp": "2023-12-21T18:38:06.660655" - }, - "versions - stub": { - "content": [ - [ - "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb" - ] + ], + { + "versions_vcf2cytosure": [ + [ + "VCF2CYTOSURE", + "vcf2cytosure", + "0.9.3" + ] + ] + } ], - "timestamp": "2023-12-21T18:38:06.663571" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:29:50.263249" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2cytosure/tests/tags.yml b/modules/nf-core/vcf2cytosure/tests/tags.yml deleted file mode 100644 index 88ff60385..000000000 --- a/modules/nf-core/vcf2cytosure/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -vcf2cytosure: - - "modules/nf-core/vcf2cytosure/**" diff --git a/modules/nf-core/vcfanno/environment.yml b/modules/nf-core/vcfanno/environment.yml index 32c48b15b..a625e831c 100644 --- a/modules/nf-core/vcfanno/environment.yml +++ b/modules/nf-core/vcfanno/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::vcfanno=0.3.5 + - bioconda::htslib=1.23 + - bioconda::vcfanno=0.3.7 diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 25c131b1d..8c5e466f4 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -4,8 +4,8 @@ process VCFANNO { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.5--h9ee0642_0': - 'biocontainers/vcfanno:0.3.5--h9ee0642_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b23fffa38d9740616e3b414df24e44c22fbc0510264f79b5062b3eecd619393f/data': + 'community.wave.seqera.io/library/htslib_vcfanno:c88d6077509197fe' }" input: tuple val(meta), path(vcf), path(tbi), path(specific_resources) @@ -14,15 +14,18 @@ process VCFANNO { path resources output: - tuple val(meta), path("*.vcf") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + tuple val("${task.process}"), val('vcfanno'), eval("vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'"), topic: versions, emit: versions_vcfanno when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def lua_cmd = lua ? "--lua ${lua}" : "" """ vcfanno \\ @@ -31,22 +34,17 @@ process VCFANNO { ${lua_cmd} \\ ${toml} \\ ${vcf} \\ - > ${prefix}.vcf + | bgzip ${args2} --threads ${task.cpus} \\ + > ${prefix}.vcf.gz \\ + && tabix ${args3} ${prefix}.vcf.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) - END_VERSIONS """ } diff --git a/modules/nf-core/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml index 18d27127c..70d5e4f7e 100644 --- a/modules/nf-core/vcfanno/meta.yml +++ b/modules/nf-core/vcfanno/meta.yml @@ -1,6 +1,6 @@ name: vcfanno -description: quickly annotate your VCF with any number of INFO fields from any number - of VCFs or BED files +description: quickly annotate your VCF with any number of INFO fields from any + number of VCFs or BED files keywords: - vcf - bed @@ -26,45 +26,83 @@ input: type: file description: query VCF file pattern: "*.{vcf, vcf.gz}" + ontologies: [] - tbi: type: file description: tabix index file for the query VCF pattern: "*.tbi" + ontologies: [] - specific_resources: type: map - description: A list of sample specific reference files defined in toml config, - must also include indices if bgzipped. - - - toml: - type: file - description: configuration file with reference file basenames - pattern: "*.toml" - - - lua: - type: file - description: Lua file for custom annotations - pattern: "*.lua" - - - resources: - type: map - description: List of reference files defined in toml config, must also include - indices if bgzipped. + description: A list of sample specific reference files defined in toml + config, must also include indices if bgzipped. + - toml: + type: file + description: configuration file with reference file basenames + pattern: "*.toml" + ontologies: [] + - lua: + type: file + description: Lua file for custom annotations + pattern: "*.lua" + ontologies: [] + - resources: + type: map + description: List of reference files defined in toml config, must also + include indices if bgzipped. output: - - vcf: - - meta: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + - "*.vcf.gz.tbi": type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.vcf": - type: file - description: Annotated VCF file - pattern: "*.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + pattern: "*.vcf.gz.tbi" + versions_vcfanno: + - - ${task.process}: + type: string + description: The name of the process + - vcfanno: + type: string + description: The name of the tool + - vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - vcfanno: + type: string + description: The name of the tool + - vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@projectoriented" - "@matthdsm" + - "@nvnieuwk" maintainers: - "@projectoriented" - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test index 8bbcfd894..ef6eb4b5d 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test +++ b/modules/nf-core/vcfanno/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } @@ -54,7 +54,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } @@ -86,7 +86,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } diff --git a/modules/nf-core/vcfanno/tests/main.nf.test.snap b/modules/nf-core/vcfanno/tests/main.nf.test.snap index 7e5f737c5..731848b5d 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test.snap +++ b/modules/nf-core/vcfanno/tests/main.nf.test.snap @@ -1,12 +1,14 @@ { "sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi] - stub": { "content": [ - "test_compressed.vcf", - [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" - ] + "test_compressed.vcf.gz", + null ], - "timestamp": "2023-12-06T12:18:25.69588598" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T13:57:00.201785" }, "sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi]": { "content": [ @@ -17,11 +19,33 @@ "id": "test_compressed", "single_end": false }, - "test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_compressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], "1": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + [ + { + "id": "test_compressed", + "single_end": false + }, + "test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] + ], + "2": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] + ], + "tbi": [ + [ + { + "id": "test_compressed", + "single_end": false + }, + "test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] ], "vcf": [ [ @@ -29,15 +53,23 @@ "id": "test_compressed", "single_end": false }, - "test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_compressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], - "versions": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + "versions_vcfanno": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] ] } ], - "timestamp": "2023-12-06T12:21:13.209704154" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:57:31.157631" }, "sarscov2 - [vcf, [], vcf], [], toml, [vcf, tbi]": { "content": [ @@ -48,11 +80,33 @@ "id": "test_uncompressed", "single_end": false }, - "test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_uncompressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], "1": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + [ + { + "id": "test_uncompressed", + "single_end": false + }, + "test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] + ], + "2": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] + ], + "tbi": [ + [ + { + "id": "test_uncompressed", + "single_end": false + }, + "test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] ], "vcf": [ [ @@ -60,14 +114,22 @@ "id": "test_uncompressed", "single_end": false }, - "test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_uncompressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], - "versions": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + "versions_vcfanno": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] ] } ], - "timestamp": "2023-12-06T12:21:19.255212216" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:57:35.91459" } } \ No newline at end of file diff --git a/modules/nf-core/vcfanno/tests/nextflow.config b/modules/nf-core/vcfanno/tests/nextflow.config index af28ad82e..b22599fc2 100644 --- a/modules/nf-core/vcfanno/tests/nextflow.config +++ b/modules/nf-core/vcfanno/tests/nextflow.config @@ -1,4 +1,4 @@ process { - - -} \ No newline at end of file + + +} diff --git a/modules/nf-core/vcfanno/tests/tags.yml b/modules/nf-core/vcfanno/tests/tags.yml deleted file mode 100644 index e861bd53e..000000000 --- a/modules/nf-core/vcfanno/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -vcfanno: - - "modules/nf-core/vcfanno/**" diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 9568fee95..7bf68ce98 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,9 +3,9 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : - 'biocontainers/verifybamid2:2.0.1--h19d48f6_8' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/9700eb810dc7a72011c9149b8ab6cc7fa9d273795632ddd00af019ab32816811/data' + : 'community.wave.seqera.io/library/verifybamid2:2.0.1--166cf392bec584ce'}" input: tuple val(meta), path(bam), path(bai) @@ -20,7 +20,7 @@ process VERIFYBAMID_VERIFYBAMID2 { tuple val(meta), path("*.mu") , optional:true, emit: mu tuple val(meta), path("*.selfSM") , optional:true, emit: self_sm tuple val(meta), path("*.Ancestry") , optional:true, emit: ancestry - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('verifybamid2'), eval("verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'"), topic: versions, emit: versions_verifybamid2 when: task.ext.when == null || task.ext.when @@ -36,23 +36,19 @@ process VERIFYBAMID_VERIFYBAMID2 { "--SVDPrefix ${svd_ud.baseName}" : "--UDPath ${svd_ud} --MeanPath ${svd_mu} --BedPath ${svd_bed}" def refvcf_args = "${refvcf}".endsWith(".vcf") ? "--RefVCF ${refvcf}" : "" - def reference_args = ("$references".endsWith('.fasta')) ? - "--Reference ${references}" : '' + def reference_args = "${references}".matches(/.+((fasta)|(fa)|(fna))(\.gz)*$/) + ? "--Reference ${references}" + : '' """ verifybamid2 \\ - --NumThread $task.cpus \\ + --NumThread ${task.cpus} \\ ${svd_args} \\ ${bam_file} \\ ${refvcf_args} \\ ${reference_args} \\ ${args_list.join(' ')} \\ > ${prefix}.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - verifybamid: \$(echo \$(verifybamid2 --help 2>&1 | sed -e '3p;d' | sed -e 's/ Version://')) - END_VERSIONS """ stub: @@ -64,10 +60,5 @@ process VERIFYBAMID_VERIFYBAMID2 { touch ${prefix}.mu touch ${prefix}.selfSM touch ${prefix}.Ancestry - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - verifybamid: \$(echo \$(verifybamid2 --help 2>&1 | sed -e '3p;d' | sed -e 's/ Version://')) - END_VERSIONS """ } diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index 8b6f2bdf8..210e1e852 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -1,7 +1,7 @@ name: "VERIFYBAMID_VERIFYBAMID2" -description: Detecting and estimating inter-sample DNA contamination became a crucial - quality assessment step to ensure high quality sequence reads and reliable downstream - analysis. +description: Detecting and estimating inter-sample DNA contamination became a + crucial quality assessment step to ensure high quality sequence reads and + reliable downstream analysis. keywords: - contamination - bam @@ -15,7 +15,8 @@ tools: documentation: "http://griffan.github.io/VerifyBamID" tool_dev_url: "https://github.com/Griffan/VerifyBamID" doi: "10.1101/gr.246934.118" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:verifybamid input: - - meta: @@ -45,13 +46,14 @@ input: ontologies: [] - svd_bed: type: file - description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] + description: .Bed file for markers used in this + analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] pattern: "*.bed" ontologies: [] - refvcf: type: file - description: Reference panel VCF with genotype information, for generation of - .UD .mu .bed files [Optional] + description: Reference panel VCF with genotype information, for generation + of .UD .mu .bed files [Optional] pattern: "*.vcf" ontologies: [] - references: @@ -101,8 +103,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.mu": type: file - description: .mu matrix file of genotype matrix from customized reference - vcf input + description: .mu matrix file of genotype matrix from customized + reference vcf input pattern: "*.mu" ontologies: [] self_sm: @@ -113,8 +115,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.selfSM": type: file - description: Shares the same format as legacy VB1 and the key information - FREEMIX indicates the estimated contamination level. + description: Shares the same format as legacy VB1 and the key + information FREEMIX indicates the estimated contamination level. pattern: "*.selfSM" ontologies: [] ancestry: @@ -128,13 +130,27 @@ output: description: Ancestry information pattern: "*.Ancestry" ontologies: [] + versions_verifybamid2: + - - ${task.process}: + type: string + description: The name of the process + - verifybamid2: + type: string + description: The name of the tool + - verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - verifybamid2: + type: string + description: The name of the tool + - verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p': + type: eval + description: The expression to obtain the version of the tool authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test index 99acd6844..e9f2e0101 100644 --- a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test +++ b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test @@ -60,13 +60,14 @@ nextflow_process { process.out.mu, process.out.self_sm, process.out.ancestry, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.ud[0][1]).name ).match() } ) } } + test("Should run with panel input") { config "./nextflow.config" @@ -90,7 +91,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.log[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -119,7 +120,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } @@ -145,7 +147,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } @@ -173,8 +176,68 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } + ) + } + } + + test("Should run with alternative .fa reference input -stub") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ] + input[1] = [ [], [], [] ] + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf') + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log[0][1]).name, + process.out.bed, + process.out.mu, + process.out.self_sm, + process.out.ancestry, + process.out.findAll { key, val -> key.startsWith("versions") }, + file(process.out.ud[0][1]).name + ).match() } + ) + } + } + + test("Should run with alternative .fa reference input") { + config "./nextflow.config" + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ] + input[1] = [ [], [], [] ] + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf') + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap index 9bc0853a4..31316fe0a 100644 --- a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap +++ b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap @@ -1,78 +1,77 @@ { - "Should run with panel input": { + "Should run with alternative .fa reference input -stub": { "content": [ "test.log", [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ] + [ + { + "id": "test", + "single_end": false + }, + "test.genome.vcf.bed:md5,47106c764019ee359b1936410e2efa1e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.genome.vcf.mu:md5,0810db02af2a176fa5ddc0f404911b66" + ] + ], + [ + + ], + [ + + ], + { + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + }, + "test.genome.vcf.UD" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-22T13:02:25.962766167" + "timestamp": "2026-02-04T15:06:31.079305" }, - "Should run with panel input - stub": { + "Should run with panel input": { "content": [ + "test.log", { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ + "versions_verifybamid2": [ [ - { - "id": "test", - "single_end": false - }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:06:11.925134" + }, + "Should run with panel input - stub": { + "content": [ + { "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -81,7 +80,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -90,7 +89,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -99,7 +98,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -108,84 +107,103 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:46:04.375799563" + "timestamp": "2026-02-04T15:12:24.048732" }, "Should run with RefVCF input - stub": { "content": [ { - "0": [ + "ancestry": [ [ { "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], - "1": [ - - ], - "2": [ + "bed": [ [ { "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], - "3": [ + "log": [ [ { "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], - "4": [ + "mu": [ [ { "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], - "5": [ + "self_sm": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "ud": [ + ], + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:12:19.940733" + }, + "Should run with alternative .fa reference input": { + "content": [ + { "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -194,7 +212,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -203,7 +221,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -212,7 +230,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -221,22 +239,26 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:45:57.687144464" + "timestamp": "2026-02-04T15:12:37.072815" }, "Should run with SVD input": { "content": [ @@ -278,7 +300,11 @@ ] ], "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ], "ancestry": [ [ @@ -316,16 +342,20 @@ "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-05T20:51:39.853534509" + "timestamp": "2026-02-04T15:00:42.110941" }, "Should run with RefVCF input": { "content": [ @@ -354,78 +384,33 @@ [ ], - [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], + { + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + }, "test.genome.vcf.UD" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-20T13:43:20.984216864" + "timestamp": "2026-02-04T15:06:07.266104" }, "Should run with SVD input - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -434,7 +419,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -443,7 +428,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -452,7 +437,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -461,21 +446,25 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:40:02.231564621" + "timestamp": "2026-02-04T15:12:16.230109" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 5a1dbbf4f..da40874e9 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -27,7 +27,6 @@ workflow ALIGN_MT { if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) ch_align = BWAMEM2_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions) } else if (val_mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 0c95d6ef1..b0284b4b9 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -43,7 +43,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions) } SAMTOOLS_INDEX_ALIGN ( ch_align ) @@ -76,16 +75,12 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions) } // Marking duplicates MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) - emit: marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index fb7828b92..0d571e48b 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -28,10 +28,8 @@ workflow ANNOTATE_CADD { if (val_genome.equals('GRCh38')) { REFERENCE_TO_CADD_CHRNAMES ( ch_fai , [], false ) - ch_versions = ch_versions.mix(REFERENCE_TO_CADD_CHRNAMES.out.versions) CADD_TO_REFERENCE_CHRNAMES ( ch_fai , [], false ) - ch_versions = ch_versions.mix(CADD_TO_REFERENCE_CHRNAMES.out.versions) CADD_TO_REFERENCE_CHRNAMES.out.output.map { _meta, txt -> txt } .set { ch_rename_chrs } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 1f2bd6953..e0f30eb91 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -195,9 +195,6 @@ workflow ANNOTATE_GENOME_SNVS { ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(VCFANNO.out.versions) - ch_versions = ch_versions.mix(UPD_SITES.out.versions) - ch_versions = ch_versions.mix(UPD_REGIONS.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) emit: diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index d855ebd2d..d31278c57 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -123,7 +123,6 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } - ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) ch_versions = ch_versions.mix(REPLACE_SPACES_IN_VCFINFO.out.versions) diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index fd8600298..4a72744eb 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -89,7 +89,6 @@ workflow GENERATE_CYTOSURE_FILES { ) ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) - ch_versions = ch_versions.mix(VCF2CYTOSURE.out.versions) emit: versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 0054b1e54..3cb05515d 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -106,7 +106,6 @@ workflow PREPARE_REFERENCES { if (!val_bwa) { if (!val_aligner.equals("sentieon") || val_mtaligner.equals("bwa")) { ch_bwa = BWA_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWA_INDEX_GENOME.out.versions) } if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { ch_bwa = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() @@ -117,7 +116,6 @@ workflow PREPARE_REFERENCES { if (!val_bwamem2 && (val_aligner.equals("bwamem2") || val_mtaligner.equals("bwamem2"))) { ch_genome_bwamem2_index = BWAMEM2_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) } else if (val_bwamem2) { ch_genome_bwamem2_index = channel.fromPath(val_bwamem2).map {it -> [[id:it.simpleName], it]}.collect() } @@ -166,12 +164,10 @@ workflow PREPARE_REFERENCES { if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwamem2")) { ch_mt_bwamem2_index = BWAMEM2_INDEX_MT(ch_mt_fasta).index.collect() ch_mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions, BWAMEM2_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwa")) { ch_mt_bwa_index = BWA_INDEX_MT(ch_mt_fasta).index.collect() ch_mtshift_bwa_index = BWA_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() - ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions, BWA_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("sentieon")) { ch_mt_bwa_index = SENTIEON_BWAINDEX_MT(ch_mt_fasta).index.collect() @@ -250,7 +246,6 @@ workflow PREPARE_REFERENCES { if (val_vep_cache) { if (val_vep_cache.endsWith("tar.gz")) { ch_vep_resources = UNTAR_VEP_CACHE (channel.fromPath(val_vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()).untar.map{ _meta, files -> [files]}.collect() - ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) } else { ch_vep_resources = channel.fromPath(val_vep_cache).collect() } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 8b755908b..89aceb143 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -101,8 +101,6 @@ workflow QC_BAM { ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) - ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) - ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions) emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index e7663da39..52ae75a9a 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -14,8 +14,6 @@ workflow SUBSAMPLE_MT_READS { ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] main: - ch_versions = channel.empty() - SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) @@ -28,9 +26,4 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') - ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) - ch_versions = ch_versions.mix(GAWK.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2a3833dc6..f61792943 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -288,7 +288,6 @@ workflow RAREDISEASE { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, ) - ch_versions = ch_versions.mix(SUBSAMPLE_MT_READS.out.versions) } } From 353563599dd21aebe7242ca68472184fb421b171 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 11 Feb 2026 08:51:31 +0100 Subject: [PATCH 318/872] update snaps --- tests/default.nf.test.snap | 8 ++++---- tests/test_bam.nf.test.snap | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1d5b71922..d0efa35e8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -315,10 +315,10 @@ "retroseq_discover": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -1104,8 +1104,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-09T09:41:15.778427811" + "timestamp": "2026-02-11T05:27:37.311350676" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 5a2a421f9..943c308b3 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -319,7 +319,7 @@ "rhocall": "0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -377,7 +377,7 @@ "tabix": 1.23 }, "SVDB_MERGE": { - "bcftools": 1.23, + "bcftools": null, "svdb": "2.8.3" }, "SVDB_MERGE_CNVNATOR": { @@ -1105,8 +1105,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-09T13:01:02.446698103" + "timestamp": "2026-02-11T04:38:31.369480108" } } \ No newline at end of file From 9b1586356074efacad453809ed2f3ecdd0e79c07 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 15 Feb 2026 18:05:10 +0100 Subject: [PATCH 319/872] update snaps --- tests/test_bam.nf.test.snap | 78 +----- tests/test_singleton.nf.test.snap | 412 +----------------------------- 2 files changed, 17 insertions(+), 473 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 943c308b3..6001b2cdc 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 823, + 795, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -66,10 +66,6 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -144,12 +140,6 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, - "FASTP": { - "fastp": "1.0.1" - }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -242,15 +232,9 @@ "MANTA": { "manta": "1.6.0" }, - "MARKDUPLICATES": { - "picard": "3.4.0" - }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, - "MITOSALT": { - "mitosalt": "1.1.1" - }, "MOSDEPTH": { "mosdepth": "0.3.11" }, @@ -330,30 +314,18 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 - }, - "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, - "SEQTK_SAMPLE": { - "seqtk": "1.4-r122" - }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -369,15 +341,12 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 }, "SVDB_MERGE": { - "bcftools": null, + "bcftools": 1.23, "svdb": "2.8.3" }, "SVDB_MERGE_CNVNATOR": { @@ -503,19 +472,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -687,25 +647,9 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -1081,22 +1025,6 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -1107,6 +1035,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-11T04:38:31.369480108" + "timestamp": "2026-02-11T15:35:13.393755104" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index d2fed18ec..d1afd078a 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 823, + 365, { "ADD_VARCALLER_TO_BED": { "tabix": 1.12 @@ -15,9 +15,6 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.22 - }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -86,12 +83,6 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -369,9 +360,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -464,12 +452,6 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -501,21 +483,11 @@ }, [ "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -523,35 +495,6 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -581,87 +524,8 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -687,38 +551,22 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -731,113 +579,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - 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"qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/earlycasualcaiman/qualimapReport.html", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.summary.txt", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/earlycasualcaiman_tidditcov.bed", - "qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", "qc_bam/hugelymodelbat/css", "qc_bam/hugelymodelbat/css/agogo.css", @@ -945,113 +686,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck", - "qc_bam/slowlycivilbuck/css", - "qc_bam/slowlycivilbuck/css/agogo.css", - "qc_bam/slowlycivilbuck/css/ajax-loader.gif", - "qc_bam/slowlycivilbuck/css/basic.css", - "qc_bam/slowlycivilbuck/css/bgfooter.png", - "qc_bam/slowlycivilbuck/css/bgtop.png", - "qc_bam/slowlycivilbuck/css/comment-bright.png", - "qc_bam/slowlycivilbuck/css/comment-close.png", - "qc_bam/slowlycivilbuck/css/comment.png", - "qc_bam/slowlycivilbuck/css/doctools.js", - "qc_bam/slowlycivilbuck/css/down-pressed.png", - "qc_bam/slowlycivilbuck/css/down.png", - "qc_bam/slowlycivilbuck/css/file.png", - "qc_bam/slowlycivilbuck/css/jquery.js", - "qc_bam/slowlycivilbuck/css/minus.png", - "qc_bam/slowlycivilbuck/css/plus.png", - "qc_bam/slowlycivilbuck/css/pygments.css", - "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", - "qc_bam/slowlycivilbuck/css/report.css", - "qc_bam/slowlycivilbuck/css/searchtools.js", - "qc_bam/slowlycivilbuck/css/underscore.js", - "qc_bam/slowlycivilbuck/css/up-pressed.png", - "qc_bam/slowlycivilbuck/css/up.png", - "qc_bam/slowlycivilbuck/css/websupport.js", - "qc_bam/slowlycivilbuck/genome_results.txt", - "qc_bam/slowlycivilbuck/images_qualimapReport", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/slowlycivilbuck/qualimapReport.html", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -1066,47 +700,29 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/earlycasualcaiman.cgh", - "vcf2cytosure/hugelymodelbat.cgh", - "vcf2cytosure/slowlycivilbuck.cgh" + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-09T14:10:55.531699048" + "timestamp": "2026-02-11T19:08:15.435078959" } } \ No newline at end of file From 0bd314e8f54399ed80d23db347f43272ad214a33 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Feb 2026 22:31:41 +0100 Subject: [PATCH 320/872] update snap --- tests/test_bam.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 6001b2cdc..463ca48a9 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -303,7 +303,7 @@ "rhocall": "0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -1035,6 +1035,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-11T15:35:13.393755104" + "timestamp": "2026-02-16T22:08:02.449482922" } } \ No newline at end of file From b9f344183289343c8011e2124fa696fddcb7c03e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Feb 2026 06:01:10 +0100 Subject: [PATCH 321/872] update prepref snap --- .../tests/main.nf.test.snap | 158 +++++++++++++----- 1 file changed, 114 insertions(+), 44 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 92f305466..f48fdad6b 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -16,12 +16,20 @@ ] ], "10": [ + [ + { + "id": "reference" + }, + "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + ] + ], + "11": [ [ "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ], - "11": [ + "12": [ [ { "id": "reference" @@ -35,10 +43,10 @@ ] ] ], - "12": [ + "13": [ ], - "13": [ + "14": [ [ { "id": "reference" @@ -46,7 +54,7 @@ "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" ] ], - "14": [ + "15": [ [ { "id": "reference" @@ -54,7 +62,7 @@ "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], - "15": [ + "16": [ [ { "id": "reference" @@ -62,12 +70,28 @@ "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" ] ], - "16": [ + "17": [ [ "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ], - "17": [ + "18": [ + [ + { + "id": "reference" + }, + [ + "reference.bck:md5,cb2ea69e38f2f48b0e9fd86511f00efa", + "reference.des:md5,d9189e49407ad59a8d15e527a5262d88", + "reference.prj:md5,afb6ee4759a4ccd9edb52fdb8e5a3a26", + "reference.sds:md5,503e83c0d24f5ea38d9d6c013d9777d1", + "reference.ssp:md5,5c62ddb0bd75481784efb7120045bf42", + "reference.suf:md5,b2180a9a2d85be97f896808c05b0e38c", + "reference.tis:md5,c4167c6aebb2139c3dc9b07a65830c3d" + ] + ] + ], + "19": [ [ { "id": "reference" @@ -75,7 +99,15 @@ "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ], - "18": [ + "2": [ + [ + { + "id": "dbsnp_-138-" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + ] + ], + "20": [ [ { "id": "reference" @@ -89,18 +121,10 @@ ] ] ], - "19": [ + "21": [ ], - "2": [ - [ - { - "id": "dbsnp_-138-" - }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" - ] - ], - "20": [ + "22": [ [ { "id": "reference" @@ -108,7 +132,7 @@ "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" ] ], - "21": [ + "23": [ [ { "id": "reference" @@ -116,7 +140,7 @@ "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" ] ], - "22": [ + "24": [ [ { "id": "reference" @@ -124,15 +148,15 @@ "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" ] ], - "23": [ + "25": [ [ "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" ] ], - "24": [ + "26": [ ], - "25": [ + "27": [ [ { "id": "target" @@ -141,19 +165,33 @@ "target_pad100.bed.gz.tbi:md5,dc41277c9c9be1203643b9192260f9ac" ] ], - "26": [ + "28": [ [ "target_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" ] ], - "27": [ + "29": [ [ [ ] ] ], - "28": [ + "3": [ + [ + { + "id": "reference" + }, + [ + "reference.amb:md5,0a85644af00f9a856d874381d24e7803", + "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", + "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", + "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", + "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" + ] + ] + ], + "30": [ [ [ "LoFtool_scores.txt:md5,d9abd640ef22c790583b4b15d144ea6f", @@ -384,28 +422,16 @@ ] ] ], - "29": [ + "31": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", + "versions.yml:md5,1b3327823f65f68efc82043fc802a384", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", + "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ], - "3": [ - [ - { - "id": "reference" - }, - [ - "reference.amb:md5,0a85644af00f9a856d874381d24e7803", - "reference.ann:md5,8fdb46970ca95a4ef54f5f1a02d233cd", - "reference.bwt:md5,0d1ba8d4e0229df6abb869a69f621dc8", - "reference.pac:md5,96b449e1316067fdfba91b1399687bc2", - "reference.sa:md5,c5c99cdc7a3cb6224841131b4b4285fe" - ] - ] - ], "4": [ [ { @@ -449,7 +475,16 @@ { "id": "reference" }, - "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + [ + "reference.1.ht2:md5,f1f1779341ba9a0ab7078e358f6efdde", + "reference.2.ht2:md5,09f0021a3a29a0e4aee96083ea4d4020", + "reference.3.ht2:md5,3b641d6168aa70fe864844bb02ef39f2", + "reference.4.ht2:md5,2dd52cfb372404a3619c0f9367fc4012", + "reference.5.ht2:md5,999891dff8303f7c576f5a1ad4be5036", + "reference.6.ht2:md5,e1a25310dabfaeb7f0fa200785bad49f", + "reference.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "reference.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" + ] ] ], "bait_intervals": [ @@ -533,6 +568,23 @@ "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ], + "genome_hisat2_index": [ + [ + { + "id": "reference" + }, + [ + "reference.1.ht2:md5,f1f1779341ba9a0ab7078e358f6efdde", + "reference.2.ht2:md5,09f0021a3a29a0e4aee96083ea4d4020", + "reference.3.ht2:md5,3b641d6168aa70fe864844bb02ef39f2", + "reference.4.ht2:md5,2dd52cfb372404a3619c0f9367fc4012", + "reference.5.ht2:md5,999891dff8303f7c576f5a1ad4be5036", + "reference.6.ht2:md5,e1a25310dabfaeb7f0fa200785bad49f", + "reference.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "reference.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" + ] + ] + ], "gnomad_af_idx": [ [ "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", @@ -585,6 +637,22 @@ "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ], + "mt_last_index": [ + [ + { + "id": "reference" + }, + [ + "reference.bck:md5,cb2ea69e38f2f48b0e9fd86511f00efa", + "reference.des:md5,d9189e49407ad59a8d15e527a5262d88", + "reference.prj:md5,afb6ee4759a4ccd9edb52fdb8e5a3a26", + "reference.sds:md5,503e83c0d24f5ea38d9d6c013d9777d1", + "reference.ssp:md5,5c62ddb0bd75481784efb7120045bf42", + "reference.suf:md5,b2180a9a2d85be97f896808c05b0e38c", + "reference.tis:md5,c4167c6aebb2139c3dc9b07a65830c3d" + ] + ] + ], "mtshift_backchain": [ [ { @@ -896,18 +964,20 @@ ], "versions": [ "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", + "versions.yml:md5,1b3327823f65f68efc82043fc802a384", "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", "versions.yml:md5,7ac7b6cf323372066f60eea4bcdf2a56", "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", + "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-06T18:02:00.602808407" + "timestamp": "2026-02-16T23:13:28.796983269" } } \ No newline at end of file From 8665c22a380a2b12f34020e6e8bb6b15060123c8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Feb 2026 06:28:39 +0100 Subject: [PATCH 322/872] update default snap --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d0efa35e8..60f5f9516 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -315,10 +315,10 @@ "retroseq_discover": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" From 74283ef68c6900b0c345548f3dca69b6b184c9df Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Feb 2026 07:02:39 +0100 Subject: [PATCH 323/872] update changelog --- CHANGELOG.md | 4 ++++ modules/local/mitosalt/main.nf | 14 +------------- subworkflows/local/call_sv_MT/main.nf | 1 - 3 files changed, 5 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e085629f6..4ae5c5997 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A helper function channelFromPathWithMeta to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A helper function channelFromSamplesheet to create channels in a readable fashion in main.nf [#767](https://github.com/nf-core/raredisease/pull/767) - A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1 (homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) +- MitoSalt to detect mitochondrial deletions [#743](https://github.com/nf-core/raredisease/pull/743) ### `Changed` @@ -27,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update gens-preproc script [#747](https://github.com/nf-core/raredisease/pull/747) - Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763) - Sambamba depth now filters on not duplicates and not failed_quality_control [#768](https://github.com/nf-core/raredisease/pull/768) +- Removed eKLIPse [#743](https://github.com/nf-core/raredisease/pull/743) ### `Fixed` @@ -66,6 +68,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | | deepvariant | 1.8.0 | 1.9.0 | +| MitoSalt | | 1.1.1 | +| eKLIPse | 1.8 | | ## 2.6.0 - Cacofonix [2025-06-25] diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index d0ed62b98..caf939c44 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -21,10 +21,9 @@ process MITOSALT { output: tuple val(meta), path("*breakpoint") , emit: breakpoint tuple val(meta), path("*cluster") , emit: cluster - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('mitosalt'), val("1.1.1"), topic: versions, emit: versions_mitosalt script: - def VERSION = "1.1.1" // from perl script, unlikely to be updated def prefix = task.ext.prefix ?: "${meta.id}" """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} @@ -32,25 +31,14 @@ process MITOSALT { mitosalt new-${msconfig} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint mv indel/*.cluster ${prefix}.cluster - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mitosalt: $VERSION - END_VERSIONS """ stub: - def VERSION = "1.1.1" def prefix = task.ext.prefix ?: "${meta.id}" """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} touch ${prefix}.breakpoint touch ${prefix}.cluster - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mitosalt: $VERSION - END_VERSIONS """ } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 14131b335..40080feac 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -78,7 +78,6 @@ workflow CALL_SV_MT { ch_mt_lastdb ) - ch_versions = ch_versions.mix(MITOSALT.out.versions) ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) From af93253576f3aa4c121e5e91f6ff14926bea46e9 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Feb 2026 10:43:03 +0100 Subject: [PATCH 324/872] update modules draft --- modules.json | 42 +-- modules/nf-core/bwameme/index/environment.yml | 6 +- modules/nf-core/bwameme/index/main.nf | 19 +- modules/nf-core/bwameme/index/meta.yml | 32 +- .../bwameme/index/tests/main.nf.test.snap | 40 ++- modules/nf-core/bwameme/index/tests/tags.yml | 2 - modules/nf-core/bwameme/mem/environment.yml | 6 +- modules/nf-core/bwameme/mem/main.nf | 24 +- modules/nf-core/bwameme/mem/meta.yml | 93 ++++-- .../nf-core/bwameme/mem/tests/main.nf.test | 2 +- .../bwameme/mem/tests/main.nf.test.snap | 90 ++--- modules/nf-core/bwameme/mem/tests/tags.yml | 2 - .../addmostsevereconsequence/environment.yml | 7 + .../custom/addmostsevereconsequence/main.nf | 20 +- .../custom/addmostsevereconsequence/meta.yml | 55 +++- .../usr/bin/add_most_severe_consequence.py | 2 +- .../tests/main.nf.test | 146 ++++++++ .../tests/main.nf.test.snap | 112 +++++++ .../tests/nextflow.config | 1 + .../custom/addmostseverepli/environment.yml | 7 + .../nf-core/custom/addmostseverepli/main.nf | 20 +- .../nf-core/custom/addmostseverepli/meta.yml | 55 +++- .../resources/usr/bin/add_most_severe_pli.py | 2 +- .../addmostseverepli/tests/main.nf.test | 60 ++++ .../addmostseverepli/tests/main.nf.test.snap | 112 +++++++ .../addmostseverepli/tests/nextflow.config | 1 + modules/nf-core/glnexus/environment.yml | 3 + modules/nf-core/glnexus/main.nf | 20 +- modules/nf-core/glnexus/meta.yml | 44 ++- modules/nf-core/glnexus/tests/main.nf.test | 126 +++++++ .../nf-core/glnexus/tests/main.nf.test.snap | 166 ++++++++++ modules/nf-core/hisat2/build/main.nf | 12 +- modules/nf-core/hisat2/build/meta.yml | 28 +- .../nf-core/hisat2/build/tests/main.nf.test | 10 +- .../hisat2/build/tests/main.nf.test.snap | 96 ++---- modules/nf-core/last/lastdb/main.nf | 12 +- modules/nf-core/last/lastdb/meta.yml | 28 +- .../last/lastdb/tests/main.nf.test.snap | 54 ++- .../ngsbits/samplegender/environment.yml | 3 +- modules/nf-core/ngsbits/samplegender/main.nf | 16 +- modules/nf-core/ngsbits/samplegender/meta.yml | 41 ++- .../samplegender/tests/main.nf.test.snap | 20 +- modules/nf-core/qualimap/bamqc/main.nf | 16 +- modules/nf-core/qualimap/bamqc/meta.yml | 26 +- .../nf-core/qualimap/bamqc/tests/main.nf.test | 4 +- .../qualimap/bamqc/tests/main.nf.test.snap | 38 ++- .../nf-core/rtgtools/format/environment.yml | 4 +- modules/nf-core/rtgtools/format/main.nf | 16 +- modules/nf-core/rtgtools/format/meta.yml | 56 +++- .../rtgtools/format/tests/fastq.config | 3 + .../rtgtools/format/tests/main.nf.test | 138 ++++++++ .../rtgtools/format/tests/main.nf.test.snap | 144 ++++++++ .../nf-core/rtgtools/format/tests/sam.config | 3 + .../nf-core/rtgtools/vcfeval/environment.yml | 4 +- modules/nf-core/rtgtools/vcfeval/main.nf | 17 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 136 +++++--- .../rtgtools/vcfeval/tests/main.nf.test.snap | 90 +++-- modules/nf-core/samtools/collate/main.nf | 2 +- modules/nf-core/samtools/collate/meta.yml | 13 +- .../samtools/collate/tests/main.nf.test | 7 +- modules/nf-core/samtools/faidx/main.nf | 3 +- modules/nf-core/samtools/faidx/meta.yml | 17 +- .../nf-core/samtools/faidx/tests/main.nf.test | 118 +++---- .../samtools/faidx/tests/main.nf.test.snap | 311 ++---------------- modules/nf-core/samtools/merge/main.nf | 4 +- modules/nf-core/samtools/merge/meta.yml | 10 - .../nf-core/samtools/merge/tests/main.nf.test | 35 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/samtools/view/meta.yml | 13 +- .../nf-core/samtools/view/tests/main.nf.test | 32 +- modules/nf-core/seqtk/sample/main.nf | 12 +- modules/nf-core/seqtk/sample/meta.yml | 30 +- .../seqtk/sample/tests/main.nf.test.snap | 80 ++++- .../seqtk/sample/tests/standard.config | 2 +- .../smncopynumbercaller/environment.yml | 2 + modules/nf-core/smncopynumbercaller/main.nf | 15 +- modules/nf-core/smncopynumbercaller/meta.yml | 40 ++- .../tests/main.nf.test.snap | 40 ++- modules/nf-core/spring/decompress/main.nf | 20 +- modules/nf-core/spring/decompress/meta.yml | 42 ++- .../spring/decompress/tests/main.nf.test | 2 +- .../spring/decompress/tests/main.nf.test.snap | 160 ++++----- .../spring/decompress/tests/nextflow.config | 4 +- modules/nf-core/tiddit/cov/environment.yml | 2 +- modules/nf-core/tiddit/cov/main.nf | 40 +-- modules/nf-core/tiddit/cov/meta.yml | 39 ++- modules/nf-core/tiddit/cov/tests/main.nf.test | 32 +- .../tiddit/cov/tests/main.nf.test.snap | 159 ++++++--- modules/nf-core/tiddit/sv/environment.yml | 4 +- modules/nf-core/tiddit/sv/main.nf | 38 +-- modules/nf-core/tiddit/sv/meta.yml | 47 ++- modules/nf-core/tiddit/sv/tests/main.nf.test | 24 +- .../nf-core/tiddit/sv/tests/main.nf.test.snap | 132 +++++--- modules/nf-core/tiddit/sv/tests/tags.yml | 2 - .../nf-core/ucsc/wigtobigwig/environment.yml | 2 +- modules/nf-core/ucsc/wigtobigwig/main.nf | 25 +- modules/nf-core/ucsc/wigtobigwig/meta.yml | 31 +- .../ucsc/wigtobigwig/tests/main.nf.test.snap | 44 ++- subworkflows/local/align/main.nf | 2 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 5 +- subworkflows/local/align_sentieon/main.nf | 2 +- .../local/annotate_consequence_pli.nf | 6 - .../local/annotate_rhocallviz/main.nf | 1 - subworkflows/local/call_mobile_elements.nf | 2 +- .../local/call_snv_deepvariant/main.nf | 2 - .../local/call_structural_variants.nf | 1 - subworkflows/local/call_sv_MT/main.nf | 1 - subworkflows/local/call_sv_tiddit/main.nf | 3 - subworkflows/local/generate_cytosure_files.nf | 6 - subworkflows/local/prepare_references/main.nf | 10 +- subworkflows/local/qc_bam/main.nf | 7 - subworkflows/local/subsample_mt_frac/main.nf | 2 +- subworkflows/local/subsample_mt_reads/main.nf | 6 +- subworkflows/local/variant_evaluation.nf | 7 - workflows/raredisease.nf | 12 - 115 files changed, 2574 insertions(+), 1470 deletions(-) delete mode 100644 modules/nf-core/bwameme/index/tests/tags.yml delete mode 100644 modules/nf-core/bwameme/mem/tests/tags.yml create mode 100644 modules/nf-core/custom/addmostsevereconsequence/environment.yml create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config create mode 100644 modules/nf-core/custom/addmostseverepli/environment.yml create mode 100644 modules/nf-core/custom/addmostseverepli/tests/main.nf.test create mode 100644 modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/addmostseverepli/tests/nextflow.config create mode 100644 modules/nf-core/glnexus/tests/main.nf.test create mode 100644 modules/nf-core/glnexus/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/format/tests/fastq.config create mode 100644 modules/nf-core/rtgtools/format/tests/main.nf.test create mode 100644 modules/nf-core/rtgtools/format/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/format/tests/sam.config delete mode 100644 modules/nf-core/tiddit/sv/tests/tags.yml diff --git a/modules.json b/modules.json index 9d9709457..01c0bca4e 100644 --- a/modules.json +++ b/modules.json @@ -87,12 +87,12 @@ }, "bwameme/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", "installed_by": ["modules"] }, "bwameme/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", "installed_by": ["modules"] }, "cadd": { @@ -122,12 +122,12 @@ }, "custom/addmostsevereconsequence": { "branch": "master", - "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "custom/addmostseverepli": { "branch": "master", - "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "deepvariant/rundeepvariant": { @@ -283,7 +283,7 @@ }, "glnexus": { "branch": "master", - "git_sha": "9b696bde5b422831751df1a4f2ba728567ec51fd", + "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, "haplocheck": { @@ -298,7 +298,7 @@ }, "hisat2/build": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c", "installed_by": ["modules"] }, "hmtnote/annotate": { @@ -309,7 +309,7 @@ }, "last/lastdb": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d92ad4055433d66d3e3eb4fd8d729d6ae9f75693", "installed_by": ["modules"] }, "manta/germline": { @@ -329,7 +329,7 @@ }, "ngsbits/samplegender": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "54c18191be1e99d78832cb62dc6fb9513ed97eae", "installed_by": ["modules"] }, "peddy": { @@ -379,7 +379,7 @@ }, "qualimap/bamqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "aa50b51492f79e0bf3ca9ca6e34640e3435b60ba", "installed_by": ["modules"] }, "rhocall/annotate": { @@ -394,12 +394,12 @@ }, "rtgtools/format": { "branch": "master", - "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", - "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "sambamba/depth": { @@ -409,12 +409,12 @@ }, "samtools/collate": { "branch": "master", - "git_sha": "a77125b43fb8973f37c36e2ff137626657de3b21", + "git_sha": "18ef126d5c91f6f4ad94fe6b939647771d5bc7b0", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "samtools/index": { @@ -424,7 +424,7 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "samtools/sort": { @@ -439,7 +439,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "d2ceed2ec5fccf922638f116a15e02f6458288fb", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "sentieon/bwaindex": { @@ -484,17 +484,17 @@ }, "seqtk/sample": { "branch": "master", - "git_sha": "af2861c63a6db77168f039ac265d84cfecd9efc2", + "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33", "installed_by": ["modules"] }, "smncopynumbercaller": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "spring/decompress": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "stranger": { @@ -529,17 +529,17 @@ }, "tiddit/cov": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/bwameme/index/environment.yml b/modules/nf-core/bwameme/index/environment.yml index f209d62e8..21fb9c42f 100644 --- a/modules/nf-core/bwameme/index/environment.yml +++ b/modules/nf-core/bwameme/index/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" + - bioconda::bwa-meme=1.0.6 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwameme/index/main.nf b/modules/nf-core/bwameme/index/main.nf index 870f494cc..ca13f8971 100644 --- a/modules/nf-core/bwameme/index/main.nf +++ b/modules/nf-core/bwameme/index/main.nf @@ -4,15 +4,16 @@ process BWAMEME_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa-meme:1.0.6--hdcf5f25_2': - 'biocontainers/bwa-meme:1.0.6--hdcf5f25_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9ddd41b93c5e182db9d643ca266dd1677e59593a9cb49904b982ff45ad5aa8c3/data': + 'community.wave.seqera.io/library/bwa-meme_mbuffer_samtools:03f3f60b6c289776' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("bwameme"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwameme'), val('1.0.6'), topic: versions, emit: versions_bwameme + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -20,7 +21,6 @@ process BWAMEME_INDEX { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${fasta}" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ mkdir bwameme @@ -31,16 +31,10 @@ process BWAMEME_INDEX { $fasta build_rmis_dna.sh bwameme/$prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${fasta}" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ mkdir bwameme touch bwameme/${prefix}.0123 @@ -52,10 +46,5 @@ process BWAMEME_INDEX { touch bwameme/${prefix}.suffixarray_uint64_L0_PARAMETERS touch bwameme/${prefix}.suffixarray_uint64_L1_PARAMETERS touch bwameme/${prefix}.suffixarray_uint64_L2_PARAMETERS - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/bwameme/index/meta.yml b/modules/nf-core/bwameme/index/meta.yml index e0cb04a63..b89af8713 100644 --- a/modules/nf-core/bwameme/index/meta.yml +++ b/modules/nf-core/bwameme/index/meta.yml @@ -23,9 +23,10 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: [] output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,11 +35,28 @@ output: type: file description: BWA-MEME genome index files pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwameme: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/index/tests/main.nf.test.snap b/modules/nf-core/bwameme/index/tests/main.nf.test.snap index e608af8b9..282e2e7f3 100644 --- a/modules/nf-core/bwameme/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwameme/index/tests/main.nf.test.snap @@ -21,7 +21,11 @@ ] ], "1": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ], "index": [ [ @@ -41,16 +45,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + "versions_bwameme": [ + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T13:44:38.551252246" + "timestamp": "2026-02-13T18:49:37.030181" }, "BWAMEME index": { "content": [ @@ -74,7 +82,11 @@ ] ], "1": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ], "index": [ [ @@ -94,15 +106,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + "versions_bwameme": [ + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T13:44:25.040725565" + "timestamp": "2026-02-13T18:49:29.151239" } } \ No newline at end of file diff --git a/modules/nf-core/bwameme/index/tests/tags.yml b/modules/nf-core/bwameme/index/tests/tags.yml deleted file mode 100644 index ddbcab044..000000000 --- a/modules/nf-core/bwameme/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwameme/index: - - "modules/nf-core/bwameme/index/**" diff --git a/modules/nf-core/bwameme/mem/environment.yml b/modules/nf-core/bwameme/mem/environment.yml index cad794404..21fb9c42f 100644 --- a/modules/nf-core/bwameme/mem/environment.yml +++ b/modules/nf-core/bwameme/mem/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" - - "bioconda::mbuffer=20160228" - - "bioconda::samtools=1.20" + - bioconda::bwa-meme=1.0.6 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwameme/mem/main.nf b/modules/nf-core/bwameme/mem/main.nf index 2efc8c0fa..14421453b 100644 --- a/modules/nf-core/bwameme/mem/main.nf +++ b/modules/nf-core/bwameme/mem/main.nf @@ -4,8 +4,8 @@ process BWAMEME_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-ed29b84fa94419f5a7bf6a841ddbcb964768825b:139b5e403886ad278b9ad139174967441c1c6ff3-0': - 'biocontainers/mulled-v2-ed29b84fa94419f5a7bf6a841ddbcb964768825b:139b5e403886ad278b9ad139174967441c1c6ff3-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9ddd41b93c5e182db9d643ca266dd1677e59593a9cb49904b982ff45ad5aa8c3/data': + 'community.wave.seqera.io/library/bwa-meme_mbuffer_samtools:03f3f60b6c289776' }" input: tuple val(meta), path(reads) @@ -21,7 +21,8 @@ process BWAMEME_MEM { tuple val(meta), path("*.cram") , emit: cram, optional:true tuple val(meta), path("*.crai") , emit: crai, optional:true tuple val(meta), path("*.csi") , emit: csi , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwameme'), val('1.0.6'), topic: versions, emit: versions_bwameme + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), topic: versions, emit: versions_samtools // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -50,7 +51,6 @@ process BWAMEME_MEM { def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` @@ -62,24 +62,15 @@ process BWAMEME_MEM { $reads \\ $mbuffer_command \\ | samtools $samtools_command $args2 $mem_per_thread -@ $threads ${reference} -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" def create_index = "" @@ -88,15 +79,8 @@ process BWAMEME_MEM { } else if (extension == "bam") { create_index = "touch ${prefix}.csi" } - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ touch ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml index 070aefebf..324d96245 100644 --- a/modules/nf-core/bwameme/mem/meta.yml +++ b/modules/nf-core/bwameme/mem/meta.yml @@ -31,6 +31,7 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] - - meta2: type: map description: | @@ -40,6 +41,7 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + ontologies: [] - - meta3: type: map description: | @@ -49,19 +51,20 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fa,fasta,fna}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" - - - mbuffer: - type: integer - description: memory for mbuffer in megabytes (default 3072) - - - samtools_threads: - type: integer - description: number of threads for samtools (default 2) + ontologies: [] + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" + - mbuffer: + type: integer + description: memory for mbuffer in megabytes (default 3072) + - samtools_threads: + type: integer + description: number of threads for samtools (default 2) output: - - sam: - - meta: + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -70,8 +73,9 @@ output: type: file description: Output SAM file containing read alignments pattern: "*.{sam}" - - bam: - - meta: + ontologies: [] + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -80,8 +84,9 @@ output: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -90,8 +95,9 @@ output: type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -100,8 +106,9 @@ output: type: file description: Index file for CRAM file pattern: "*.{crai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -110,11 +117,47 @@ output: type: file description: Index file for BAM file pattern: "*.{csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwameme: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test b/modules/nf-core/bwameme/mem/tests/main.nf.test index 6d93fd6eb..fd378c0b3 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test @@ -187,4 +187,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap index bc845155c..5c6487e75 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap @@ -1,59 +1,51 @@ { "sarscov2 - [fastq1, fastq2], index, fasta, false, 0, 4": { "content": [ - "640e6a53bedb535837cc35cc1c145dcb", + "b537f2936bcb8c120127251ab44d917b", "57aeef88ed701a8ebc8e2f0a381b2a6", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:25:03.99184" + "timestamp": "2026-02-13T19:51:39.510097" }, - "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''": { + "sarscov2 - fastq, index, fasta, true, 2048, 4": { "content": [ - "7af5d6b93d3f8bd4f53d4f9ace7ee981", - "af8628d9df18b2d3d4f6fd47ef2bb872", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + "91c0b36a7aa238cca2acbce1997d94e8", + "94fcf617f5b994584c4e8d4044e16b4f", + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:26:17.237557" + "timestamp": "2026-02-13T19:51:19.196468" }, - "sarscov2 - fastq, index, fasta, true, 2048, 4": { + "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''": { "content": [ - "4ccda5ce5d3b09b697786589b3753825", - "94fcf617f5b994584c4e8d4044e16b4f", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + "ffc18373a0992612ccb5df41a245947b", + "af8628d9df18b2d3d4f6fd47ef2bb872", + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:24:07.289865" + "timestamp": "2026-02-13T19:52:00.628046" }, "sarscov2 - fastq, index, fasta, false, 0, 4": { "content": [ - "a58fa4a997be7d13a3dc62c9c9eb83d2", + "585cc3d6cdff0dce2e30b6e8c1542669", "798439cbd7fd81cbcc5078022dc5479d", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:17.201419" + "timestamp": "2026-02-13T19:50:58.198221" }, "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, 4 - stub": { "content": [ @@ -86,7 +78,18 @@ ] ], "5": [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "6": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] ], "bam": [ [ @@ -115,15 +118,26 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:31:46.777111" + "timestamp": "2026-02-13T19:52:05.913267" } } \ No newline at end of file diff --git a/modules/nf-core/bwameme/mem/tests/tags.yml b/modules/nf-core/bwameme/mem/tests/tags.yml deleted file mode 100644 index 9e3a26cfe..000000000 --- a/modules/nf-core/bwameme/mem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwameme/mem: - - "modules/nf-core/bwameme/mem/**" diff --git a/modules/nf-core/custom/addmostsevereconsequence/environment.yml b/modules/nf-core/custom/addmostsevereconsequence/environment.yml new file mode 100644 index 000000000..315b7489e --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.21 + - conda-forge::python=3.13.2 diff --git a/modules/nf-core/custom/addmostsevereconsequence/main.nf b/modules/nf-core/custom/addmostsevereconsequence/main.nf index c4dacf3e9..5dfbd8798 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/main.nf +++ b/modules/nf-core/custom/addmostsevereconsequence/main.nf @@ -14,7 +14,8 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('addmostsevereconsequence'), val("1.1"), topic: versions, emit: versions_addmostsevereconsequence + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -23,8 +24,6 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. - """ add_most_severe_consequence.py \\ $args \\ @@ -36,26 +35,11 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { $args2 \\ --threads ${task.cpus} \\ ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. """ echo | gzip > ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ } diff --git a/modules/nf-core/custom/addmostsevereconsequence/meta.yml b/modules/nf-core/custom/addmostsevereconsequence/meta.yml index 07f69da7e..3f4e97af1 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/meta.yml +++ b/modules/nf-core/custom/addmostsevereconsequence/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_addmostsevereconsequence" description: Annotate a VEP annotated VCF with the most severe consequence field keywords: @@ -11,9 +10,9 @@ tools: description: "Custom module to annotate a VEP annotated VCF with the most severe consequence field" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostsevereconsequence/main.nf" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map @@ -34,7 +33,6 @@ input: type: file description: File with VEP variant consequences, one per line. pattern: "*" - ontologies: [] output: vcf: @@ -47,17 +45,48 @@ output: type: file description: Annotated VCF file pattern: "*.vcf.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 + versions_addmostsevereconsequence: + - - ${task.process}: + type: string + description: The name of the process + - addmostsevereconsequence: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - addmostsevereconsequence: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" - "@fellen31" diff --git a/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py index b3aa22a0c..a3902c062 100755 --- a/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py +++ b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py @@ -7,7 +7,7 @@ import gzip import sys from pathlib import Path -from typing import Tuple, TextIO +from typing import TextIO, Tuple def parse_vep_csq_transcripts( diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test new file mode 100644 index 000000000..4664c198b --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test @@ -0,0 +1,146 @@ +// nf-core modules test custom/addmostsevereconsequence +nextflow_process { + + name "Test Process CUSTOM_ADDMOSTSEVERECONSEQUENCE" + script "../main.nf" + process "CUSTOM_ADDMOSTSEVERECONSEQUENCE" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/addmostsevereconsequence" + config "./nextflow.config" + + test("vcf") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + input[1] = Channel.of([ + "transcript_ablation", + "splice_acceptor_variant", + "splice_donor_variant", + "stop_gained", + "frameshift_variant", + "stop_lost", + "start_lost", + "transcript_amplification", + "feature_elongation", + "feature_truncation", + "inframe_insertion", + "inframe_deletion", + "missense_variant", + "protein_altering_variant", + "splice_donor_5th_base_variant", + "splice_region_variant", + "splice_donor_region_variant", + "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", + "start_retained_variant", + "stop_retained_variant", + "synonymous_variant", + "coding_sequence_variant", + "mature_miRNA_variant", + "5_prime_UTR_variant", + "3_prime_UTR_variant", + "non_coding_transcript_exon_variant", + "intron_variant", + "NMD_transcript_variant", + "non_coding_transcript_variant", + "coding_transcript_variant", + "upstream_gene_variant", + "downstream_gene_variant", + "TFBS_ablation", + "TFBS_amplification", + "TF_binding_site_variant", + "regulatory_region_ablation", + "regulatory_region_amplification", + "regulatory_region_variant", + "intergenic_variant", + "sequence_variant" + ]).collectFile(name: 'variant_consequences.txt', newLine:true).map { file -> [ [ id: file.simpleName ], file ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + input[1] = Channel.of([ + "transcript_ablation", + "splice_acceptor_variant", + "splice_donor_variant", + "stop_gained", + "frameshift_variant", + "stop_lost", + "start_lost", + "transcript_amplification", + "feature_elongation", + "feature_truncation", + "inframe_insertion", + "inframe_deletion", + "missense_variant", + "protein_altering_variant", + "splice_donor_5th_base_variant", + "splice_region_variant", + "splice_donor_region_variant", + "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", + "start_retained_variant", + "stop_retained_variant", + "synonymous_variant", + "coding_sequence_variant", + "mature_miRNA_variant", + "5_prime_UTR_variant", + "3_prime_UTR_variant", + "non_coding_transcript_exon_variant", + "intron_variant", + "NMD_transcript_variant", + "non_coding_transcript_variant", + "coding_transcript_variant", + "upstream_gene_variant", + "downstream_gene_variant", + "TFBS_ablation", + "TFBS_amplification", + "TF_binding_site_variant", + "regulatory_region_ablation", + "regulatory_region_amplification", + "regulatory_region_variant", + "intergenic_variant", + "sequence_variant" + ]).collectFile(name: 'variant_consequences.txt', newLine:true).map { file -> [ [ id: file.simpleName ], file ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap new file mode 100644 index 000000000..5fad697fd --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap @@ -0,0 +1,112 @@ +{ + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d82db60282f5c594c105c010b3a76639" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d82db60282f5c594c105c010b3a76639" + ] + ], + "versions_addmostsevereconsequence": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:54:09.581706", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_addmostsevereconsequence": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:54:14.314711", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config b/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config new file mode 100644 index 000000000..651f0b86a --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config @@ -0,0 +1 @@ +nextflow.enable.moduleBinaries = true diff --git a/modules/nf-core/custom/addmostseverepli/environment.yml b/modules/nf-core/custom/addmostseverepli/environment.yml new file mode 100644 index 000000000..315b7489e --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.21 + - conda-forge::python=3.13.2 diff --git a/modules/nf-core/custom/addmostseverepli/main.nf b/modules/nf-core/custom/addmostseverepli/main.nf index 0d252c046..f3fd3122c 100644 --- a/modules/nf-core/custom/addmostseverepli/main.nf +++ b/modules/nf-core/custom/addmostseverepli/main.nf @@ -12,7 +12,8 @@ process CUSTOM_ADDMOSTSEVEREPLI { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('addmostseverepli'), val("1.1"), topic: versions, emit: versions_addmostseverepli + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -21,8 +22,6 @@ process CUSTOM_ADDMOSTSEVEREPLI { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. - """ add_most_severe_pli.py \\ $args \\ @@ -33,26 +32,11 @@ process CUSTOM_ADDMOSTSEVEREPLI { $args2 \\ --threads ${task.cpus} \\ ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. """ echo | gzip > ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ } diff --git a/modules/nf-core/custom/addmostseverepli/meta.yml b/modules/nf-core/custom/addmostseverepli/meta.yml index f69423822..e17225229 100644 --- a/modules/nf-core/custom/addmostseverepli/meta.yml +++ b/modules/nf-core/custom/addmostseverepli/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_addmostseverepli" description: Annotate a VEP annotated VCF with the most severe pLi field keywords: @@ -11,9 +10,9 @@ tools: description: "Custom module to annotate a VEP annotated VCF with the most severe pLi field" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostseverepli/main.nf" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: VEP annotated VCF file pattern: "*.{vcf,vcf.gz}" - ontologies: [] output: vcf: @@ -37,17 +35,48 @@ output: type: file description: Annotated VCF file pattern: "*.vcf.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 + versions_addmostseverepli: + - - ${task.process}: + type: string + description: The name of the process + - addmostseverepli: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - addmostseverepli: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" - "@fellen31" diff --git a/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py index 6ef40515a..8c0b3d00d 100755 --- a/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py +++ b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py @@ -57,7 +57,7 @@ def construct_most_severe_pli_info(line: str, pli_ind: int) -> list: except ValueError: pli_max = "" if pli_max: - columns[7] += ";most_severe_pli={:.2f}".format(float(pli_max)) + columns[7] += f";most_severe_pli={float(pli_max):.2f}" return columns diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test new file mode 100644 index 000000000..5263f5c5c --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test @@ -0,0 +1,60 @@ +// nf-core modules test custom/addmostseverepli +nextflow_process { + + name "Test Process CUSTOM_ADDMOSTSEVEREPLI" + script "../main.nf" + process "CUSTOM_ADDMOSTSEVEREPLI" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/addmostseverepli" + config "./nextflow.config" + + test("vcf") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap new file mode 100644 index 000000000..d492bb3ce --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap @@ -0,0 +1,112 @@ +{ + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d29918951676cc028d980aaab161db21" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d29918951676cc028d980aaab161db21" + ] + ], + "versions_addmostseverepli": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:53:27.215565", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_addmostseverepli": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:53:31.072965", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/addmostseverepli/tests/nextflow.config b/modules/nf-core/custom/addmostseverepli/tests/nextflow.config new file mode 100644 index 000000000..651f0b86a --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/nextflow.config @@ -0,0 +1 @@ +nextflow.enable.moduleBinaries = true diff --git a/modules/nf-core/glnexus/environment.yml b/modules/nf-core/glnexus/environment.yml index 9190508a9..c9e4703dc 100644 --- a/modules/nf-core/glnexus/environment.yml +++ b/modules/nf-core/glnexus/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + - bioconda::bcftools=1.21 - bioconda::glnexus=1.4.1 diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 191f04995..65180995e 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -4,16 +4,16 @@ process GLNEXUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : - 'biocontainers/glnexus:1.4.1--h40d77a6_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6cf504ad8e4ebda286609fa3c1a5f9af68dbca9ec06bb4428e219e84754bd140/data' : + 'community.wave.seqera.io/library/bcftools_glnexus:cf380f1a6410f606' }" input: - tuple val(meta), path(gvcfs) + tuple val(meta), path(gvcfs), path(custom_config) tuple val(meta2), path(bed) output: tuple val(meta), path("*.bcf"), emit: bcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('glnexus'), eval("glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'"), topic: versions, emit: versions_glnexus when: task.ext.when == null || task.ext.when @@ -24,7 +24,7 @@ process GLNEXUS { def regions = bed ? "--bed ${bed}" : "" // Make list of GVCFs to merge - def input = gvcfs.collect { it.toString() } + def input = gvcfs.collect {vcf -> vcf.toString() } def avail_mem = 3 if (!task.memory) { log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -39,21 +39,11 @@ process GLNEXUS { $args \\ ${input.join(' ')} \\ > ${prefix}.bcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index 8f18bf3f8..cacfa5c90 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -23,6 +23,12 @@ input: type: list description: Input genomic vcf files pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + - custom_config: + type: file + description: Custom YML config for additional profiles + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML - - meta2: type: map description: | @@ -33,20 +39,38 @@ input: description: Input BED file pattern: "*.bed" output: - - bcf: - - meta: - type: file - description: merged BCF file - pattern: "*.bcf" + bcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] - "*.bcf": type: file description: merged BCF file pattern: "*.bcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_glnexus: + - - ${task.process}: + type: string + description: The name of the process + - glnexus: + type: string + description: The name of the tool + - glnexus_cli 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - glnexus: + type: string + description: The name of the tool + - glnexus_cli 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/glnexus/tests/main.nf.test b/modules/nf-core/glnexus/tests/main.nf.test new file mode 100644 index 000000000..647373559 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test @@ -0,0 +1,126 @@ +nextflow_process { + + name "Test Process GLNEXUS" + script "../main.nf" + process "GLNEXUS" + + tag "modules" + tag "modules_nfcore" + tag "glnexus" + + test("vcfs, []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, [], custom_config") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + file(params.modules_testdata_base_path + '/delete_me/glnexus/gatk.yml', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/glnexus/tests/main.nf.test.snap b/modules/nf-core/glnexus/tests/main.nf.test.snap new file mode 100644 index 000000000..00426dd67 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test.snap @@ -0,0 +1,166 @@ +{ + "vcfs, bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:43:16.499731323" + }, + "vcfs, [], custom_config": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:39:47.593781473" + }, + "vcfs, bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:41:26.083883984" + }, + "vcfs, []": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:36:50.552668413" + } +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 1d9370107..906d36fe5 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -15,7 +15,7 @@ process HISAT2_BUILD { output: tuple val(meta), path("hisat2"), emit: index - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hisat2'), eval("hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'"), emit: versions_hisat2, topic: versions when: task.ext.when == null || task.ext.when @@ -55,20 +55,10 @@ process HISAT2_BUILD { ${args} \\ ${fasta} \\ hisat2/${fasta.baseName} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) - END_VERSIONS """ stub: """ mkdir hisat2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) - END_VERSIONS """ } diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index ede99d0cc..805804910 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -59,13 +59,29 @@ output: description: HISAT2 genome index file pattern: "*.ht2" ontologies: [] + versions_hisat2: + - - ${task.process}: + type: string + description: The name of the process + - hisat2: + type: string + description: The name of the tool + - "hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - hisat2: + type: string + description: The name of the tool + - "hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'": + type: eval + description: The expression to obtain the version of the tool + authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index 948f98eae..9bee5f676 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -46,7 +46,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -91,7 +94,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index 68fc7ffba..99b33cb2c 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,90 +1,54 @@ { "Should run without failures - stub": { "content": [ + [ + [ + { + "id": "genome" + }, + "hisat2" + ] + ], { - "0": [ - [ - { - "id": "genome" - }, - [ - - ] - ] - ], - "1": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ], - "index": [ + "versions_hisat2": [ [ - { - "id": "genome" - }, - [ - - ] + "HISAT2_BUILD", + "hisat2", + "2.2.1" ] - ], - "versions": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-06-20T18:18:08.896422" + "timestamp": "2026-02-02T15:53:37.611420605" }, "Should run without failures": { "content": [ + [ + [ + { + "id": "genome" + }, + "hisat2" + ] + ], { - "0": [ - [ - { - "id": "genome" - }, - [ - "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", - "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", - "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", - "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" - ] - ] - ], - "1": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ], - "index": [ + "versions_hisat2": [ [ - { - "id": "genome" - }, - [ - "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", - "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", - "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", - "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" - ] + "HISAT2_BUILD", + "hisat2", + "2.2.1" ] - ], - "versions": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2023-10-16T14:42:22.381609786" + "timestamp": "2026-02-02T15:53:31.34596606" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index ae1df8b42..43d84750b 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -12,7 +12,8 @@ process LAST_LASTDB { output: tuple val(meta), path("lastdb"), emit: index - path "versions.yml" , emit: versions + // last-dotplot has no --version option so let's use lastal from the same suite + tuple val("${task.process}"), val('last'), eval("lastal --version | sed 's/lastal //'"), emit: versions_last, topic: versions when: task.ext.when == null || task.ext.when @@ -27,11 +28,6 @@ process LAST_LASTDB { -P $task.cpus \\ lastdb/${prefix} \\ $fastx - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - last: \$(lastdb --version 2>&1 | sed 's/lastdb //') - END_VERSIONS """ stub: @@ -47,9 +43,5 @@ process LAST_LASTDB { touch lastdb/${prefix}.suf touch lastdb/${prefix}.tis - cat <<-END_VERSIONS > versions.yml - "${task.process}": - last: \$(lastdb --version 2>&1 | sed 's/lastdb //') - END_VERSIONS """ } diff --git a/modules/nf-core/last/lastdb/meta.yml b/modules/nf-core/last/lastdb/meta.yml index 9a5bcbb0a..4c041d211 100644 --- a/modules/nf-core/last/lastdb/meta.yml +++ b/modules/nf-core/last/lastdb/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +cd# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastdb" description: Prepare sequences for subsequent alignment with lastal. keywords: @@ -38,13 +38,27 @@ output: type: directory description: directory containing the files of the LAST index pattern: "lastdb/" + versions_last: + - - "${task.process}": + type: string + description: The name of the process + - last: + type: string + description: The name of the tool + - "lastal --version | sed 's/lastal //'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - "${task.process}": + type: string + description: The name of the process + - last: + type: string + description: The name of the tool + - "lastal --version | sed 's/lastal //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap index 382b364ba..e54777878 100644 --- a/modules/nf-core/last/lastdb/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -37,16 +41,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:34.761783" + "timestamp": "2026-01-13T10:40:55.31640271" }, "sarscov2 - fastq gzipped": { "content": [ @@ -68,7 +76,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -86,16 +98,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:20.038195" + "timestamp": "2026-01-13T10:40:49.204117613" }, "sarscov2 - fasta": { "content": [ @@ -117,7 +133,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -135,15 +155,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:04.861781" + "timestamp": "2026-01-13T10:40:42.992657054" } } \ No newline at end of file diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml index 906277c5d..b8793f52a 100644 --- a/modules/nf-core/ngsbits/samplegender/environment.yml +++ b/modules/nf-core/ngsbits/samplegender/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ngs-bits=2024_11 + # renovate: datasource=conda depName=bioconda/ngs-bits + - bioconda::ngs-bits=2025_12 diff --git a/modules/nf-core/ngsbits/samplegender/main.nf b/modules/nf-core/ngsbits/samplegender/main.nf index 655149084..39ab69b4c 100644 --- a/modules/nf-core/ngsbits/samplegender/main.nf +++ b/modules/nf-core/ngsbits/samplegender/main.nf @@ -4,8 +4,8 @@ process NGSBITS_SAMPLEGENDER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ngs-bits:2024_11--py312hd80e9a6_0': - 'biocontainers/ngs-bits:2024_11--py312hd80e9a6_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data': + 'community.wave.seqera.io/library/ngs-bits:2025_12--958625b0e620100a' }" input: tuple val(meta), path(bam), path(bai) @@ -15,7 +15,7 @@ process NGSBITS_SAMPLEGENDER { output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('ngsbits'), eval("SampleGender --version 2>&1 | sed 's/SampleGender //'"), topic: versions, emit: versions_ngsbits when: task.ext.when == null || task.ext.when @@ -31,21 +31,11 @@ process NGSBITS_SAMPLEGENDER { -out ${prefix}.tsv \\ ${ref} \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ngs-bits: \$(echo \$(SampleGender --version 2>&1) | sed 's/SampleGender //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ngs-bits: \$(echo \$(SampleGender --version 2>&1) | sed 's/SampleGender //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml index 4b79dfca3..8d4773efe 100644 --- a/modules/nf-core/ngsbits/samplegender/meta.yml +++ b/modules/nf-core/ngsbits/samplegender/meta.yml @@ -11,7 +11,8 @@ tools: homepage: "https://github.com/imgag/ngs-bits" documentation: "https://github.com/imgag/ngs-bits" tool_dev_url: "https://github.com/imgag/ngs-bits" - licence: ["MIT"] + licence: + - "MIT" identifier: "" input: - - meta: @@ -36,7 +37,8 @@ input: e.g. [ id:'test' ] - fasta: type: file - description: The reference FASTA to use (mandatory when CRAM files are used) + description: The reference FASTA to use (mandatory when CRAM files are + used) pattern: "*.{fasta,fa,fna}" ontologies: [] - - meta3: @@ -51,8 +53,8 @@ input: ontologies: [] - method: type: string - description: The method to use to define the gender (possibilities are 'xy', 'hetx' - and 'sry') + description: The method to use to define the gender (possibilities are 'xy', + 'hetx' and 'sry') pattern: "(xy|hetx|sry)" output: tsv: @@ -63,17 +65,32 @@ output: e.g. [ id:'test', single_end:false ] - "*.tsv": type: file - description: An output TSV file containing the results of the gender prediction + description: An output TSV file containing the results of the gender + prediction pattern: "*.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 + versions_ngsbits: + - - ${task.process}: + type: string + description: The name of the process + - ngsbits: + type: string + description: The name of the tool + - SampleGender --version 2>&1 | sed 's/SampleGender //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - ngsbits: + type: string + description: The name of the tool + - SampleGender --version 2>&1 | sed 's/SampleGender //': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap index cb493a2c2..f6343474d 100644 --- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap +++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" + [ + "NGSBITS_SAMPLEGENDER", + "ngsbits", + "2025_12" + ] ], "tsv": [ [ @@ -21,15 +25,19 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" + "versions_ngsbits": [ + [ + "NGSBITS_SAMPLEGENDER", + "ngsbits", + "2025_12" + ] ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-12-10T13:36:08.650020628" + "timestamp": "2026-02-16T09:21:42.78314623" } } \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 8140e143e..5d7109bed 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -4,8 +4,8 @@ process QUALIMAP_BAMQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' : - 'biocontainers/qualimap:2.3--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b795495fdae4cb3319d19ed4a694302366aa574ba15a0613b85c602f0de4911/data' : + 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' }" input: tuple val(meta), path(bam) @@ -13,7 +13,7 @@ process QUALIMAP_BAMQC { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap when: task.ext.when == null || task.ext.when @@ -46,11 +46,6 @@ process QUALIMAP_BAMQC { $collect_pairs \\ -outdir $prefix \\ -nt $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS """ stub: @@ -114,10 +109,5 @@ process QUALIMAP_BAMQC { touch genome_results.txt touch qualimapReport.html cd ../ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 6a563fa4c..e93a99137 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -43,13 +43,27 @@ output: type: directory description: Qualimap results dir pattern: "*/*" + versions_qualimap: + - - ${task.process}: + type: string + description: The name of the process + - qualimap: + type: string + description: The name of the tool + - qualimap -h | sed -n 's/^QualiMap v.//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - qualimap: + type: string + description: The name of the tool + - qualimap -h | sed -n 's/^QualiMap v.//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@phue" maintainers: diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test index eec1a41a1..7deb086dd 100644 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test @@ -29,7 +29,7 @@ nextflow_process { { assert snapshot( file("${process.out.results[0][1]}/qualimapReport.html").name, path("${process.out.results[0][1]}/genome_results.txt"), - process.out.versions) + process.out.findAll {key, value -> key.startsWith("versions")}) .match() } ) } @@ -58,4 +58,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap index fb6e23e49..0f67dee18 100644 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap @@ -69,7 +69,11 @@ ] ], "1": [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] ], "results": [ [ @@ -137,29 +141,39 @@ ] ] ], - "versions": [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" + "versions_qualimap": [ + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-22T12:27:15.04081" + "timestamp": "2026-02-13T22:03:27.280522" }, "homo_sapiens [bam]": { "content": [ "qualimapReport.html", "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3", - [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" - ] + { + "versions_qualimap": [ + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-22T11:21:02.541915" + "timestamp": "2026-02-13T22:12:46.38879" } } \ No newline at end of file diff --git a/modules/nf-core/rtgtools/format/environment.yml b/modules/nf-core/rtgtools/format/environment.yml index 8aa83cdc4..27597a220 100644 --- a/modules/nf-core/rtgtools/format/environment.yml +++ b/modules/nf-core/rtgtools/format/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::rtg-tools=3.12.1 + - bioconda::rtg-tools=3.13 diff --git a/modules/nf-core/rtgtools/format/main.nf b/modules/nf-core/rtgtools/format/main.nf index 9cae7f99c..ffbbbdfb9 100644 --- a/modules/nf-core/rtgtools/format/main.nf +++ b/modules/nf-core/rtgtools/format/main.nf @@ -4,15 +4,15 @@ process RTGTOOLS_FORMAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dca5ba13b7ec38bf7cacf00a33517b9080067bea638745c05d50a4957c75fc2e/data': + 'community.wave.seqera.io/library/rtg-tools:3.13--3465421f1b0be0ce' }" input: tuple val(meta), path(input1), path(input2), path(sam_rg) output: tuple val(meta), path("*.sdf"), emit: sdf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('rtgtools'), eval("rtg version | head -n 1 | sed 's/Product: RTG Tools //'"), topic: versions, emit: versions_rtgtools when: task.ext.when == null || task.ext.when @@ -38,11 +38,6 @@ process RTGTOOLS_FORMAT { ${rg} \\ --output ${prefix}.sdf \\ ${input} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ stub: @@ -56,10 +51,5 @@ process RTGTOOLS_FORMAT { } """ touch ${prefix}.sdf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ } diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index e09aff3af..309a9ffb0 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -1,6 +1,6 @@ name: "rtgtools_format" -description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into - the RTG Sequence Data File (SDF) format. +description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) + into the RTG Sequence Data File (SDF) format. keywords: - rtg - fasta @@ -12,9 +12,10 @@ tools: description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" - documentation: "https://github.com/RealTimeGenomics/rtg-tools" + documentation: "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: ["BSD"] + licence: + - "BSD" identifier: "" input: - - meta: @@ -24,34 +25,57 @@ input: e.g. [ id:'test', single_end:false ] - input1: type: file - description: FASTA, FASTQ, BAM or SAM file. This should be the left input file - when using paired end FASTQ/FASTA data + description: FASTA, FASTQ, BAM or SAM file. This should be the left input + file when using paired end FASTQ/FASTA data pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ - input2: type: file description: The right input file when using paired end FASTQ/FASTA data pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ - sam_rg: type: file - description: A file containing a single readgroup header as a SAM header. This - can also be supplied as a string in `task.ext.args` as `--sam-rg `. + description: A file containing a single readgroup header as a SAM header. + This can also be supplied as a string in `task.ext.args` as `--sam-rg + `. pattern: "*.{txt,sam}" + ontologies: [] output: - - sdf: - - meta: + sdf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.sdf": type: directory - description: The sequence dictionary format folder created from the input file(s) + description: The sequence dictionary format folder created from the + input file(s) pattern: "*.sdf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_rtgtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/format/tests/fastq.config b/modules/nf-core/rtgtools/format/tests/fastq.config new file mode 100644 index 000000000..24540986e --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/fastq.config @@ -0,0 +1,3 @@ +process { + ext.args = "--format fastq" +} diff --git a/modules/nf-core/rtgtools/format/tests/main.nf.test b/modules/nf-core/rtgtools/format/tests/main.nf.test new file mode 100644 index 000000000..d768da7d8 --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/main.nf.test @@ -0,0 +1,138 @@ +nextflow_process { + + name "Test Process RTGTOOLS_FORMAT" + script "../main.nf" + process "RTGTOOLS_FORMAT" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/format" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - fastqs") { + + config "./fastq.config" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - bam, rg") { + + config "./sam.config" + + when { + process { + """ + def rg = Channel.of("@RG\tID:READGROUP1\tSM:SAMPLE\tPL:ILLUMINA") + .collectFile(name:'sam_rg.txt') + + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + [] + ]).combine(rg) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/rtgtools/format/tests/main.nf.test.snap b/modules/nf-core/rtgtools/format/tests/main.nf.test.snap new file mode 100644 index 000000000..437afa7af --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/main.nf.test.snap @@ -0,0 +1,144 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.sdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ], + "sdf": [ + [ + { + "id": "test" + }, + "test.sdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:42.538436462", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - fasta": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "suffixIndex0", + "suffixdata0", + "suffixpointer0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:07.354438336", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - fastqs": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "qualitydata0", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "suffixIndex0", + "suffixdata0", + "suffixpointer0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:19.613328433", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - bam, rg": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "qualitydata0", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:31.66811346", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/format/tests/sam.config b/modules/nf-core/rtgtools/format/tests/sam.config new file mode 100644 index 000000000..5ccfdb27b --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/sam.config @@ -0,0 +1,3 @@ +process { + ext.args = "--format sam-se" +} diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index 8aa83cdc4..27597a220 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::rtg-tools=3.12.1 + - bioconda::rtg-tools=3.13 diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 330a1f3d9..82477eb11 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -4,8 +4,8 @@ process RTGTOOLS_VCFEVAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dca5ba13b7ec38bf7cacf00a33517b9080067bea638745c05d50a4957c75fc2e/data': + 'community.wave.seqera.io/library/rtg-tools:3.13--3465421f1b0be0ce' }" input: tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(regions_bed) @@ -25,7 +25,8 @@ process RTGTOOLS_VCFEVAL { tuple val(meta), path("*.weighted_roc.tsv.gz") , emit: weighted_roc tuple val(meta), path("*.summary.txt") , emit: summary tuple val(meta), path("*.phasing.txt") , emit: phasing - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('rtgtools'), eval("rtg version | sed 's/Product: RTG Tools //; q'"), topic: versions, emit: versions_rtgtools + when: task.ext.when == null || task.ext.when @@ -57,11 +58,6 @@ process RTGTOOLS_VCFEVAL { mv done progress .. for f in * ; do mv "\$f" "../${prefix}.\$f" ; done cd .. - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ stub: @@ -81,10 +77,5 @@ process RTGTOOLS_VCFEVAL { echo | gzip > ${prefix}.weighted_roc.tsv.gz touch ${prefix}.summary.txt touch ${prefix}.phasing.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ } diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 4c59bab52..bfe06aa94 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -1,6 +1,6 @@ name: "rtgtools_vcfeval" -description: The VCFeval tool of RTG tools. It is used to evaluate called variants - for agreement with a baseline variant set +description: The VCFeval tool of RTG tools. It is used to evaluate called + variants for agreement with a baseline variant set keywords: - benchmarking - vcf @@ -10,9 +10,10 @@ tools: description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" - documentation: "https://github.com/RealTimeGenomics/rtg-tools" + documentation: "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: ["BSD"] + licence: + - "BSD" identifier: "" input: - - meta: @@ -24,30 +25,37 @@ input: type: file description: A VCF with called variants to benchmark against the standard pattern: "*.{vcf,vcf.gz}" + ontologies: [] - query_vcf_tbi: type: file - description: The index of the VCF file with called variants to benchmark against the standard + description: The index of the VCF file with called variants to benchmark + against the standard pattern: "*.{vcf.gz.tbi, vcf.tbi}" + ontologies: [] - truth_vcf: type: file description: A standard VCF to compare against pattern: "*.{vcf,vcf.gz}" + ontologies: [] - truth_vcf_tbi: type: file description: The index of the standard VCF to compare against pattern: "*.{vcf.gz.tbi, vcf.tbi}" + ontologies: [] - truth_bed: type: file - description: A BED file containining the strict regions where VCFeval should - only evaluate the fully overlapping variants (optional) - This input should be used to provide the golden truth BED files. + description: A BED file containing the strict regions where VCFeval should + only evaluate the fully overlapping variants (optional) This input + should be used to provide the golden truth BED files. pattern: "*.bed" + ontologies: [] - regions_bed: type: file - description: A BED file containing the regions where VCFeval will evaluate every - fully and partially overlapping variant (optional) - This input should be used to provide the regions used by the analysis + description: A BED file containing the regions where VCFeval will evaluate + every fully and partially overlapping variant (optional) This input + should be used to provide the regions used by the analysis pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -55,10 +63,12 @@ input: e.g. [ id:'test', single_end:false ] - sdf: type: file - description: The SDF (RTG Sequence Data File) folder of the reference genome + description: The SDF (RTG Sequence Data File) folder of the reference + genome + ontologies: [] output: - - tp_vcf: - - meta: + tp_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +77,10 @@ output: type: file description: A VCF file for the true positive variants pattern: "*.tp.vcf.gz" - - tp_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tp_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,8 +89,9 @@ output: type: file description: The index of the VCF file for the true positive variants pattern: "*.tp.vcf.gz.tbi" - - fn_vcf: - - meta: + ontologies: [] + fn_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -87,8 +100,10 @@ output: type: file description: A VCF file for the false negative variants pattern: "*.fn.vcf.gz" - - fn_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + fn_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -97,8 +112,9 @@ output: type: file description: The index of the VCF file for the false negative variants pattern: "*.fn.vcf.gz.tbi" - - fp_vcf: - - meta: + ontologies: [] + fp_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -107,8 +123,10 @@ output: type: file description: A VCF file for the false positive variants pattern: "*.fp.vcf.gz" - - fp_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + fp_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -117,8 +135,9 @@ output: type: file description: The index of the VCF file for the false positive variants pattern: "*.fp.vcf.gz.tbi" - - baseline_vcf: - - meta: + ontologies: [] + baseline_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -127,19 +146,22 @@ output: type: file description: A VCF file for the true positive variants from the baseline pattern: "*.tp-baseline.vcf.gz" - - baseline_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + baseline_tbi: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.tp-baseline.vcf.gz.tbi": type: file - description: The index of the VCF file for the true positive variants from the - baseline + description: The index of the VCF file for the true positive variants + from the baseline pattern: "*.tp-baseline.vcf.gz.tbi" - - snp_roc: - - meta: + ontologies: [] + snp_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -148,8 +170,10 @@ output: type: file description: TSV files containing ROC data for the SNPs pattern: "*.snp_roc.tsv.gz" - - non_snp_roc: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + non_snp_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -158,8 +182,10 @@ output: type: file description: TSV files containing ROC data for all variants except SNPs pattern: "*.non_snp_roc.tsv.gz" - - weighted_roc: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + weighted_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -168,8 +194,10 @@ output: type: file description: TSV files containing weighted ROC data for all variants pattern: "*.weighted_snp_roc.tsv.gz" - - summary: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + summary: + - - meta: type: map description: | Groovy Map containing sample information @@ -178,8 +206,9 @@ output: type: file description: A TXT file containing the summary of the evaluation pattern: "*.summary.txt" - - phasing: - - meta: + ontologies: [] + phasing: + - - meta: type: map description: | Groovy Map containing sample information @@ -188,11 +217,28 @@ output: type: file description: A TXT file containing the data on the phasing pattern: "*.phasing.txt" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rtgtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | sed 's/Product: RTG Tools //; q'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | sed 's/Product: RTG Tools //; q'": + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap index 4f39e2d46..f85d503e5 100644 --- a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap @@ -23,7 +23,7 @@ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + "test.weighted_roc.tsv.gz:md5,c0155caab6b8a314c303ca1b481ba1af" ] ], "11": [ @@ -43,7 +43,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -98,7 +102,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + "test.snp_roc.tsv.gz:md5,6c8977c744a08c90123a21f22c0f4e54" ] ], "9": [ @@ -106,7 +110,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + "test.non_snp_roc.tsv.gz:md5,574afefc756c4102bb3aefb0cde19dff" ] ], "baseline_tbi": [ @@ -162,7 +166,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + "test.non_snp_roc.tsv.gz:md5,574afefc756c4102bb3aefb0cde19dff" ] ], "phasing": [ @@ -178,7 +182,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + "test.snp_roc.tsv.gz:md5,6c8977c744a08c90123a21f22c0f4e54" ] ], "summary": [ @@ -205,24 +209,28 @@ "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + "test.weighted_roc.tsv.gz:md5,c0155caab6b8a314c303ca1b481ba1af" ] ] } ], + "timestamp": "2026-02-12T13:43:20.930061214", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:17:31.564974666" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } }, "homo_sapiens - [vcf, [], truth, [], [], []], sdf": { "content": [ @@ -248,7 +256,7 @@ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + "test.weighted_roc.tsv.gz:md5,599331bcba15312abc402bdffc8d2e30" ] ], "11": [ @@ -268,7 +276,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -323,7 +335,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + "test.snp_roc.tsv.gz:md5,7906ac0bdf54d34ac9b52bfd101cddfd" ] ], "9": [ @@ -331,7 +343,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + "test.non_snp_roc.tsv.gz:md5,0917d6986ae90818f431c316b1cbea27" ] ], "baseline_tbi": [ @@ -387,7 +399,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + "test.non_snp_roc.tsv.gz:md5,0917d6986ae90818f431c316b1cbea27" ] ], "phasing": [ @@ -403,7 +415,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + "test.snp_roc.tsv.gz:md5,7906ac0bdf54d34ac9b52bfd101cddfd" ] ], "summary": [ @@ -430,24 +442,28 @@ "test.tp.vcf.gz:md5,5125ee41457c9d93f46b19e32788edb4" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + "test.weighted_roc.tsv.gz:md5,599331bcba15312abc402bdffc8d2e30" ] ] } ], + "timestamp": "2026-02-12T13:43:44.651308348", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:18:04.344989466" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } }, "homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub": { "content": [ @@ -493,7 +509,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -655,8 +675,12 @@ "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ @@ -668,10 +692,10 @@ ] } ], + "timestamp": "2026-02-12T13:44:03.078796934", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:23:21.165461388" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index b92410cd6..a81622ba2 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_COLLATE { input: tuple val(meta), path(input) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) output: tuple val(meta), path("*.bam"), emit: bam, optional: true diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index f6069abc4..5e4c71548 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -29,12 +29,17 @@ input: - - meta2: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file - description: FASTA ref file - pattern: "*.fasta" + description: Reference genome file + pattern: "*.{fa,fasta}" + ontologies: [] + - fai: + type: file + description: Reference genome index file + pattern: "*.fai" ontologies: [] output: #Only when we have meta diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test index 2918f9e3d..b2dedc717 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - input[1] = [ [id:'fasta'], [] ] + input[1] = [ [id:'fasta'], [], [] ] """ } } @@ -41,7 +41,8 @@ nextflow_process { ] input[1] = [ [ id:'fasta'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + [] ] """ } @@ -63,7 +64,7 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - input[1] = [ [id:'fasta'], [] ] + input[1] = [ [id:'fasta'], [], [] ] """ } } diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 57a03497f..97bfb578f 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -8,8 +8,7 @@ process SAMTOOLS_FAIDX { 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: - tuple val(meta), path(fasta) - tuple val(meta2), path(fai) + tuple val(meta), path(fasta), path(fai) val get_sizes output: diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 163c30151..80aae1dae 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -1,5 +1,6 @@ name: samtools_faidx -description: Index FASTA file, and optionally generate a file of chromosome sizes +description: Index FASTA file, and optionally generate a file of chromosome + sizes keywords: - index - fasta @@ -14,7 +15,8 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:samtools input: - - meta: @@ -27,11 +29,6 @@ input: description: FASTA file pattern: "*.{fa,fasta}" ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - fai: type: file description: FASTA index file @@ -40,7 +37,6 @@ input: - get_sizes: type: boolean description: use cut to get the sizes of the index (true) or not (false) - output: fa: - - meta: @@ -94,9 +90,8 @@ output: type: string description: The tool name - "samtools version | sed '1!d;s/.* //'": - type: string + type: eval description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -106,7 +101,7 @@ topics: type: string description: The tool name - "samtools version | sed '1!d;s/.* //'": - type: string + type: eval description: The command used to generate the version of the tool authors: - "@drpatelh" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 02ba5040c..9a86db862 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -18,10 +18,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -29,7 +31,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -42,10 +44,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -53,7 +57,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -66,11 +70,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = false """ } } @@ -78,7 +83,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -92,11 +97,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = false """ } } @@ -104,7 +110,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -118,10 +124,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -129,7 +137,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -142,12 +150,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -155,7 +163,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -168,12 +176,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -181,7 +189,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -196,12 +204,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -209,7 +217,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -224,12 +232,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -237,7 +245,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 565d20e71..416974442 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -2,39 +2,13 @@ "test_samtools_faidx": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] @@ -56,47 +30,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:02:40.159309157" + "timestamp": "2026-02-10T15:39:12.541649151" }, "test_samtools_faidx_get_sizes_bgzip - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -135,42 +75,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:39.550619177" + "timestamp": "2026-02-10T15:41:44.040426987" }, "test_samtools_faidx_get_sizes": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -204,52 +115,20 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:16.844965756" + "timestamp": "2026-02-10T15:47:03.653912015" }, "test_samtools_faidx_bgzip": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] @@ -257,8 +136,7 @@ "gzi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" ] @@ -277,43 +155,17 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:02:47.301476131" + "timestamp": "2026-02-10T15:50:04.023566795" }, "test_samtools_faidx_fasta": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" ] @@ -338,42 +190,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T09:44:40.559583279" + "timestamp": "2026-02-10T15:39:23.529404162" }, "test_samtools_faidx_get_sizes - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -407,43 +230,17 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:31.989929281" + "timestamp": "2026-02-10T15:41:39.039834304" }, "test_samtools_faidx_stub_fasta": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -468,46 +265,20 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T09:44:48.295693103" + "timestamp": "2026-02-10T15:39:28.961701609" }, "test_samtools_faidx_stub_fai": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -529,47 +300,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:09.784289542" + "timestamp": "2026-02-10T15:39:34.471028474" }, "test_samtools_faidx_get_sizes_bgzip": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -608,8 +345,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:24.814967939" + "timestamp": "2026-02-10T15:39:45.439016495" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 6785f22e8..87ebc5014 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -9,9 +9,7 @@ process SAMTOOLS_MERGE { input: tuple val(meta), path(input_files, stageAs: "?/*") - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(gzi) + tuple val(meta2), path(fasta), path(fai), path(gzi) output: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 4237ce74e..31cc576bc 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -37,21 +37,11 @@ input: description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - fai: type: file description: Index of the reference file the CRAM was created with (optional) pattern: "*.fai" ontologies: [] - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - gzi: type: file description: Index of the compressed reference file the CRAM was created with diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index 08ef26945..a784c8367 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -24,9 +24,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -61,13 +59,10 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true), + [] ] - input[2] = [ - [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [[],[]] """ } } @@ -103,14 +98,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) - ] - input[2] = [ - [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) - ] - input[3] = [ - [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) ] """ @@ -145,9 +134,7 @@ nextflow_process { [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -183,9 +170,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -214,9 +199,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 87b3333f6..b189b5ba4 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_VIEW { input: tuple val(meta), path(input), path(index) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) path qname val index_format diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 215222661..23a1af338 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -36,12 +36,19 @@ input: type: map description: | Groovy Map containing reference information - e.g. [ id:'test' ] + e.g. [ id:'genome' ] - fasta: type: file - description: Reference file the CRAM was created with (optional) + description: Fasta reference file pattern: "*.{fasta,fa}" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_1929 # FASTA + - fai: + type: file + description: Fasta reference file index + pattern: "*.{fai}" + ontologies: + - edam: http://edamontology.org/format_3326 # Index - qname: type: file description: Optional file with read names to output only select alignments diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 74e1c49fd..8d8f292fb 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = [] """ @@ -49,7 +49,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'csi' """ @@ -76,7 +76,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'bai' """ @@ -103,7 +103,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'bai' @@ -131,7 +131,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'crai' @@ -161,7 +161,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -191,7 +192,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -221,7 +223,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -251,7 +254,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = Channel.of("testN:2817", "testN:2814") .collectFile(name: "readnames.list", newLine: true) @@ -283,7 +287,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = [] """ @@ -313,7 +317,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'csi' """ @@ -343,7 +347,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'bai' """ @@ -373,7 +377,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'bai' @@ -404,7 +408,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'crai' diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 0c2aaeda2..1a5d8cd72 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -12,7 +12,7 @@ process SEQTK_SAMPLE { output: tuple val(meta), path("*.fastq.gz"), emit: reads - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('seqtk'), eval("seqtk 2>&1 | sed -n 's/^Version: //p'"), emit: versions_seqtk, topic: versions when: task.ext.when == null || task.ext.when @@ -36,11 +36,6 @@ process SEQTK_SAMPLE { $sample_size \\ | gzip --no-name > ${prefix}_\$(basename \$f) done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -48,11 +43,6 @@ process SEQTK_SAMPLE { """ echo "" | gzip > ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml index ed1f3325c..9574c705c 100644 --- a/modules/nf-core/seqtk/sample/meta.yml +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -6,8 +6,8 @@ keywords: - reads tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in - the FASTA or FASTQ format. Seqtk sample command subsamples sequences. + description: Seqtk is a fast and lightweight tool for processing sequences + in the FASTA or FASTQ format. Seqtk sample command subsamples sequences. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk @@ -39,13 +39,27 @@ output: description: Subsampled FastQ files pattern: "*.{fastq.gz}" ontologies: [] + versions_seqtk: + - - ${task.process}: + type: string + description: The name of the process + - seqtk: + type: string + description: The name of the tool + - "seqtk 2>&1 | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - seqtk: + type: string + description: The name of the tool + - "seqtk 2>&1 | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@kaurravneet4123" - "@sidorov-si" diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap index aa6991e6c..c770b22e1 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -23,12 +27,20 @@ "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:45.902956" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:11.92830069" }, "sarscov2_sample_pairedend_fqgz": { "content": [ @@ -43,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -54,12 +70,20 @@ "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:37.679954" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:00.582612488" }, "sarscov2_sample_singleend_fqgz": { "content": [ @@ -74,7 +98,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -85,12 +113,20 @@ "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:29.474491" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:28:47.676166475" }, "sarscov2_sample_singleend_frac": { "content": [ @@ -105,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -116,11 +156,19 @@ "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2025-07-15T09:48:30.275951" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:23.3474291" } } \ No newline at end of file diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config index b2dd4b9f9..8d1db62fd 100644 --- a/modules/nf-core/seqtk/sample/tests/standard.config +++ b/modules/nf-core/seqtk/sample/tests/standard.config @@ -3,4 +3,4 @@ process { ext.args = '-s100' ext.prefix = { "${meta.id}.sampled" } } -} \ No newline at end of file +} diff --git a/modules/nf-core/smncopynumbercaller/environment.yml b/modules/nf-core/smncopynumbercaller/environment.yml index afbc40076..6102e6333 100644 --- a/modules/nf-core/smncopynumbercaller/environment.yml +++ b/modules/nf-core/smncopynumbercaller/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/smncopynumbercaller/main.nf b/modules/nf-core/smncopynumbercaller/main.nf index efe0a639e..6fa8811f0 100644 --- a/modules/nf-core/smncopynumbercaller/main.nf +++ b/modules/nf-core/smncopynumbercaller/main.nf @@ -13,7 +13,8 @@ process SMNCOPYNUMBERCALLER { output: tuple val(meta), path("out/*.tsv"), emit: smncopynumber tuple val(meta), path("out/*.json"), emit: run_metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('smncopynumbercaller'), val('1.1.2'), topic: versions, emit: versions_smncopynumbercaller + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -21,7 +22,6 @@ process SMNCOPYNUMBERCALLER { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.1.2" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. """ echo $bam | tr ' ' ' ' > manifest.txt @@ -31,24 +31,13 @@ process SMNCOPYNUMBERCALLER { --prefix $prefix \\ --outDir "out" \\ --threads $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - SMNCopyNumberCaller: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.1.2" """ mkdir out touch out/${prefix}.tsv touch out/${prefix}.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - SMNCopyNumberCaller: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/smncopynumbercaller/meta.yml b/modules/nf-core/smncopynumbercaller/meta.yml index 9d91fc096..c0f4078bf 100644 --- a/modules/nf-core/smncopynumbercaller/meta.yml +++ b/modules/nf-core/smncopynumbercaller/meta.yml @@ -27,13 +27,15 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - bai: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" + ontologies: [] output: - - smncopynumber: - - meta: + smncopynumber: + - - meta: type: map description: | Groovy Map containing sample information @@ -42,8 +44,10 @@ output: type: file description: File containing the output of SMNCopyNumberCaller pattern: "*.{tsv}" - - run_metrics: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + run_metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -52,11 +56,29 @@ output: type: file description: File containing run parameters of SMNCopyNumberCaller pattern: "*.{json}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + versions_smncopynumbercaller: + - - ${task.process}: + type: string + description: The name of the process + - smncopynumbercaller: + type: string + description: The name of the tool + - 1.1.2: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - smncopynumbercaller: + type: string + description: The name of the tool + - 1.1.2: + type: string + description: The expression to obtain the version of the tool authors: - "@peterpru" maintainers: diff --git a/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap b/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap index 834fe67b9..22c1f1fc8 100644 --- a/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap +++ b/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "2": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ], "run_metrics": [ [ @@ -37,16 +41,20 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + "versions_smncopynumbercaller": [ + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T12:54:27.295453" + "timestamp": "2026-02-11T21:26:46.783248" }, "test-smncopynumbercaller": { "content": [ @@ -68,7 +76,11 @@ ] ], "2": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ], "run_metrics": [ [ @@ -86,15 +98,19 @@ "test.tsv:md5,0de62f196972c17e1701aa8cea0849f9" ] ], - "versions": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + "versions_smncopynumbercaller": [ + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T12:54:21.71312" + "timestamp": "2026-02-11T21:26:43.145754" } } \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/main.nf b/modules/nf-core/spring/decompress/main.nf index 86ced2690..316080482 100644 --- a/modules/nf-core/spring/decompress/main.nf +++ b/modules/nf-core/spring/decompress/main.nf @@ -4,8 +4,8 @@ process SPRING_DECOMPRESS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/spring:1.1.1--h4ac6f70_2' : - 'biocontainers/spring:1.1.1--h4ac6f70_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f6/f67f27c8cb2d1a149564f1a10f5f2b7a6acfa87ef3d3d27d2d8752dbe95e6acf/data' : + 'community.wave.seqera.io/library/spring:1.1.1--911a17b4ccfb85ee' }" input: tuple val(meta), path(spring) @@ -13,7 +13,8 @@ process SPRING_DECOMPRESS { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('spring'), val('1.1.1'), topic: versions, emit: versions_spring + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when @@ -21,9 +22,7 @@ process SPRING_DECOMPRESS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def output = write_one_fastq_gz ? "-o ${prefix}.fastq.gz" : "-o ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz" - """ spring \\ -d \\ @@ -32,23 +31,12 @@ process SPRING_DECOMPRESS { $args \\ -i ${spring} \\ ${output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - spring: ${VERSION} - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def output = write_one_fastq_gz ? "echo '' | gzip > ${prefix}.fastq.gz" : "echo '' | gzip > ${prefix}_R1.fastq.gz; echo '' | gzip > ${prefix}_R2.fastq.gz" """ ${output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - spring: ${VERSION} - END_VERSIONS """ } diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml index 72b72b75d..e41c4bf90 100644 --- a/modules/nf-core/spring/decompress/meta.yml +++ b/modules/nf-core/spring/decompress/meta.yml @@ -24,14 +24,15 @@ input: type: file description: Spring file to decompress. pattern: "*.{spring}" - - - write_one_fastq_gz: - type: boolean - description: | - Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions - pattern: "true or false" + ontologies: [] + - write_one_fastq_gz: + type: boolean + description: | + Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions + pattern: "true or false" output: - - fastq: - - meta: + fastq: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,11 +41,28 @@ output: type: file description: Decompressed FASTQ file(s). pattern: "*.{fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_spring: + - - ${task.process}: + type: string + description: The name of the process + - spring: + type: string + description: The name of the tool + - 1.1.1: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - spring: + type: string + description: The name of the tool + - 1.1.1: + type: string + description: The expression to obtain the version of the tool authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/spring/decompress/tests/main.nf.test b/modules/nf-core/spring/decompress/tests/main.nf.test index c7ac2b1f3..f960b0d5b 100644 --- a/modules/nf-core/spring/decompress/tests/main.nf.test +++ b/modules/nf-core/spring/decompress/tests/main.nf.test @@ -151,4 +151,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/spring/decompress/tests/main.nf.test.snap b/modules/nf-core/spring/decompress/tests/main.nf.test.snap index 7dcadbab6..dd6cc252d 100644 --- a/modules/nf-core/spring/decompress/tests/main.nf.test.snap +++ b/modules/nf-core/spring/decompress/tests/main.nf.test.snap @@ -1,76 +1,4 @@ { - "Write-One-File stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" - ] - ], - "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ], - "fastq": [ - [ - { - "id": "test" - }, - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" - ] - ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T10:03:50.626223289" - }, - "Write-Two-Files stub": { - "content": [ - { - "0": [ - [ - { - "id": "test2" - }, - [ - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" - ] - ] - ], - "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ], - "fastq": [ - [ - { - "id": "test2" - }, - [ - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" - ] - ] - ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T10:03:57.417015606" - }, "Write-Two-Files": { "content": [ { @@ -86,7 +14,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -99,16 +31,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:00.074323", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T13:41:46.090761471" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-One-File": { "content": [ @@ -122,7 +58,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -132,16 +72,20 @@ "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:15:54.633046", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T13:02:07.466039653" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-One-File-stub": { "content": [ @@ -155,7 +99,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -165,16 +113,20 @@ "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:04.953817", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T13:55:53.594615215" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-Two-Files-stub": { "content": [ @@ -191,7 +143,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -204,15 +160,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:09.98067", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T13:56:01.212228909" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/tests/nextflow.config b/modules/nf-core/spring/decompress/tests/nextflow.config index 50f50a7a3..8730f1c4b 100644 --- a/modules/nf-core/spring/decompress/tests/nextflow.config +++ b/modules/nf-core/spring/decompress/tests/nextflow.config @@ -1,5 +1,5 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file + +} diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index a33b14c85..df74ec81e 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.6.1 + - bioconda::tiddit=3.9.4 diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 20d4720e7..690a8b62b 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -4,48 +4,38 @@ process TIDDIT_COV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' : - 'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" input: - tuple val(meta), path(input) + tuple val(meta), path(input), path(index) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bed"), optional: true, emit: cov - tuple val(meta), path("*.wig"), optional: true, emit: wig - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bed"), optional: true, emit: cov + tuple val(meta), path("${prefix}.wig"), optional: true, emit: wig + tuple val("${task.process}"), val('tiddit'), eval("tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'"), topic: versions, emit: versions_tiddit when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--ref $fasta" : "" + prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--ref ${fasta}" : "" """ tiddit \\ --cov \\ - -o $prefix \\ - $args \\ - --bam $input \\ - $reference - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + -o ${prefix} \\ + ${args} \\ + --bam ${input} \\ + ${reference} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.wig - touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + echo "" > ${prefix}.wig + echo "" > ${prefix}.bed """ } diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml index 71bbf7864..0f28625d9 100644 --- a/modules/nf-core/tiddit/cov/meta.yml +++ b/modules/nf-core/tiddit/cov/meta.yml @@ -11,7 +11,8 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: "10.12688/f1000research.11168.1" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:tiddit input: - - meta: @@ -24,6 +25,12 @@ input: description: BAM/CRAM file pattern: "*.{bam,cram}" ontologies: [] + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai,csi}" + ontologies: + - edam: http://edamontology.org/format_3327 - - meta2: type: map description: | @@ -43,7 +50,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.bed": + - ${prefix}.bed: type: file description: The coverage of different regions in bed format. Optional. pattern: "*.bed" @@ -54,18 +61,32 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.wig": + - ${prefix}.wig: type: file description: The coverage of different regions in WIG format. Optional. pattern: "*.wig" ontologies: [] + versions_tiddit: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test b/modules/nf-core/tiddit/cov/tests/main.nf.test index 24c273d86..97d386460 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test @@ -16,7 +16,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -33,7 +34,7 @@ nextflow_process { { assert process.out.cov[0][1] ==~ ".*/test.bed" }, { assert snapshot( process.out.cov, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -48,7 +49,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] ] input[1] = [ [:], [] ] """ @@ -61,7 +63,7 @@ nextflow_process { { assert process.out.cov[0][1] ==~ ".*/test.bed" }, { assert snapshot( process.out.cov, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -78,7 +80,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -95,7 +98,7 @@ nextflow_process { { assert process.out.wig[0][1] ==~ ".*/test.wig" }, { assert snapshot( process.out.wig, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -112,7 +115,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] ] input[1] = [ [:], [] ] @@ -126,7 +130,7 @@ nextflow_process { { assert process.out.wig[0][1] ==~ ".*/test.wig" }, { assert snapshot( process.out.wig, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -145,7 +149,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -159,14 +164,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.cov[0][1] ==~ ".*/test.bed" }, - { assert process.out.wig[0][1] ==~ ".*/test.wig" }, - { assert snapshot( - process.out.cov, - process.out.wig, - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap index 5067886d6..977b8c768 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap @@ -10,15 +10,21 @@ "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:36:08.358493", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:07.66262" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - cram - wig": { "content": [ @@ -31,45 +37,82 @@ "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:36:03.766699", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:01.397993" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wig:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "2": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ], + "cov": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ], + "wig": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wig:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] - ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + } ], + "timestamp": "2026-02-16T11:40:15.064301", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:12.873466" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens - bam - bed": { "content": [ @@ -82,15 +125,21 @@ "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:35:59.061703", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:43:54.542951" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - cram - bed": { "content": [ @@ -103,14 +152,20 @@ "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:35:54.066148", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:43:47.441318" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index 2fd01cfd4..df74ec81e 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.6.1 + - bioconda::tiddit=3.9.4 diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index f350e3144..c3808ed3d 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -4,8 +4,8 @@ process TIDDIT_SV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' : - 'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" input: tuple val(meta), path(input), path(input_index) @@ -13,44 +13,34 @@ process TIDDIT_SV { tuple val(meta3), path(bwa_index) output: - tuple val(meta), path("*.vcf") , emit: vcf - tuple val(meta), path("*.ploidies.tab"), emit: ploidy - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf") , emit: vcf + tuple val(meta), path("${prefix}.ploidies.tab"), emit: ploidy + tuple val("${task.process}"), val('tiddit'), eval("tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'"), topic: versions, emit: versions_tiddit when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def bwa_command = bwa_index ? "[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! \"\$i\" =~ .*\"$fasta.\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : "" + prefix = task.ext.prefix ?: "${meta.id}" + def bwa_command = bwa_index ? "[[ -d ${bwa_index} ]] && for i in ${bwa_index}/*; do [[ -f ${fasta} && ! \"\$i\" =~ .*\"${fasta}.\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : "" """ $bwa_command tiddit \\ --sv \\ - $args \\ + ${args} \\ --threads $task.cpus \\ - --bam $input \\ - --ref $fasta \\ - -o $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + --bam ${input} \\ + --ref ${fasta} \\ + -o ${prefix} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf - touch ${prefix}.ploidies.tab - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + echo "" > ${prefix}.vcf + echo "" > ${prefix}.ploidies.tab """ } diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index 21527baf1..b27987926 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -10,7 +10,8 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:tiddit input: - - meta: @@ -22,10 +23,12 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - input_index: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +38,7 @@ input: type: file description: Input FASTA file pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -44,32 +48,51 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.vcf": + - "${prefix}.vcf": type: file description: vcf pattern: "*.{vcf}" - - ploidy: - - meta: + ontologies: [] + ploidy: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.ploidies.tab": + - "${prefix}.ploidies.tab": type: file description: tab pattern: "*.{ploidies.tab}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_tiddit: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test b/modules/nf-core/tiddit/sv/tests/main.nf.test index 6e32b9e1c..090175ee4 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test @@ -46,9 +46,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("bam_bwa_version") } + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -78,9 +77,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("bam_version") } + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -122,11 +120,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("cram_bwa_version") }) + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } + ) } - } test("human - cram - no_bwa") { @@ -153,11 +150,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("cram_version") }) + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } + ) } - } test("sarscov2 - bam - stub") { diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap index 541c48bbd..6927d6916 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap @@ -1,28 +1,4 @@ { - "cram_bwa_version": { - "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-22T10:33:01.300519" - }, - "cram_version": { - "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-22T10:27:12.52902" - }, "sarscov2 - bam - stub": { "content": [ { @@ -31,7 +7,7 @@ { "id": "test" }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.vcf:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -39,18 +15,22 @@ { "id": "test" }, - "test.ploidies.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ploidies.tab:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "2": [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] ], "ploidy": [ [ { "id": "test" }, - "test.ploidies.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ploidies.tab:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "vcf": [ @@ -58,42 +38,98 @@ { "id": "test" }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.vcf:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-11T13:40:16.597914" + }, + "sarscov2 - bam - bwa": { + "content": [ + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-11T21:38:47.040361" + }, + "human - cram - bwa": { + "content": [ + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:21:51.950503" + "timestamp": "2026-02-11T21:37:13.220785" }, - "bam_bwa_version": { + "sarscov2 - bam - no_bwa": { "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:31:40.918479" + "timestamp": "2026-02-11T21:38:54.658816" }, - "bam_version": { + "human - cram - no_bwa": { "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:21:38.449053" + "timestamp": "2026-02-11T21:39:11.028105" } } \ No newline at end of file diff --git a/modules/nf-core/tiddit/sv/tests/tags.yml b/modules/nf-core/tiddit/sv/tests/tags.yml deleted file mode 100644 index aac5351ec..000000000 --- a/modules/nf-core/tiddit/sv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tiddit/sv: - - "modules/nf-core/tiddit/sv/**" diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml index e80eb6d09..6bd9f2509 100644 --- a/modules/nf-core/ucsc/wigtobigwig/environment.yml +++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-wigtobigwig=447 + - bioconda::ucsc-wigtobigwig=482 diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 4b7adb62f..e7c4c6cb8 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -5,46 +5,35 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:447--h2a80c09_1' : - 'biocontainers/ucsc-wigtobigwig:447--h2a80c09_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0394161be68e8dd5b30a47f0b19ffa00cb3226bb2e6c9fe3ec89e571a50b871d/data' : + 'community.wave.seqera.io/library/ucsc-wigtobigwig:482--7b910cc21c32327e' }" input: tuple val(meta), path(wig) path sizes output: - tuple val(meta), path("*.bw"), emit: bw - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bw"), emit: bw + tuple val("${task.process}"), val('ucsc'), val('482'), topic: versions, emit: versions_ucsc + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ wigToBigWig \\ $args \\ $wig \\ $sizes \\ ${prefix}.bw - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ucsc: $VERSION - END_VERSIONS """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bw - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ucsc: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml index bc82734da..3bbd3e312 100644 --- a/modules/nf-core/ucsc/wigtobigwig/meta.yml +++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml @@ -10,7 +10,8 @@ tools: Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format homepage: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html - licence: ["varies; see http://genome.ucsc.edu/license"] + licence: + - "varies; see http://genome.ucsc.edu/license" identifier: "" input: - - meta: @@ -34,18 +35,32 @@ output: description: bigwig file pattern: "*.{bw}" ontologies: [] - - "*.bw": + - ${prefix}.bw: type: file description: bigwig file pattern: "*.{bw}" ontologies: [] + versions_ucsc: + - - ${task.process}: + type: string + description: The name of the process + - ucsc: + type: string + description: The name of the tool + - "482": + type: string + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - ucsc: + type: string + description: The name of the tool + - "482": + type: string + description: The expression to obtain the version of the tool authors: - "@jianhong" - "@projectoriented" diff --git a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap index acc59555c..ee8704437 100644 --- a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ], "bw": [ [ @@ -23,16 +27,20 @@ "test.bw:md5,b64af7003665dc51fae958216b06ed95" ] ], - "versions": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + "versions_ucsc": [ + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ] } ], + "timestamp": "2026-02-16T09:50:37.235738", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-27T11:54:03.735102" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-ucsc-wigtobigwig-stub": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ], "bw": [ [ @@ -58,15 +70,19 @@ "test.bw:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + "versions_ucsc": [ + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ] } ], + "timestamp": "2026-02-16T09:50:41.464164", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-27T11:54:07.924401" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 88895ccdb..c946c1d18 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -156,7 +156,7 @@ workflow ALIGN { } if (val_save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) + SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) } emit: diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index b0284b4b9..42a19c489 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -39,7 +39,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions) } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam @@ -66,14 +65,14 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta, ch_genome_fai, [[:], []] ) + SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return[meta,fasta,fai,[]]}) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) - EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') + EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta.join(ch_genome_fai), [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 498c1b64f..31d3541ad 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -40,7 +40,7 @@ workflow ALIGN_SENTIEON { // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { - EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') + EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai), [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) } diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index af57747d9..72b88487d 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -13,8 +13,6 @@ workflow ANNOTATE_CSQ_PLI { val_index // bool main: - ch_versions = channel.empty() - CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) CUSTOM_ADDMOSTSEVEREPLI (CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.vcf) @@ -23,10 +21,6 @@ workflow ANNOTATE_CSQ_PLI { TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) } - ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.versions) - ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVEREPLI.out.versions) - emit: vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index ac5db5cc8..120f36013 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -55,7 +55,6 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 45ad5ece7..8719eca4e 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -40,7 +40,7 @@ workflow CALL_MOBILE_ELEMENTS { .set { ch_genome_bam_bai_interval } // Split bam file on chromosome and index - ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], []], [], 'bai' ) + ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], [], []], [], 'bai' ) ME_SPLIT_ALIGNMENT.out.bam .join( ME_SPLIT_ALIGNMENT.out.bai, failOnMismatch: true, failOnDuplicate: true ) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index dbec9449b..96c8ec4f7 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -82,8 +82,6 @@ workflow CALL_SNV_DEEPVARIANT { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(GLNEXUS.out.versions) - emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index e7c0bb5c2..f7ff6b90a 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -47,7 +47,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .vcf .collect{ _meta, vcf -> vcf } .set { tiddit_vcf } - ch_versions = ch_versions.mix(CALL_SV_TIDDIT.out.versions) CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6bc1ccbba..8733edab0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -78,7 +78,6 @@ workflow CALL_SV_MT { ch_mt_lastdb ) - ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index fc3b79817..ac3d457fd 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -29,9 +29,6 @@ workflow CALL_SV_TIDDIT { SVDB_MERGE_TIDDIT ( merge_input_vcfs, [], true ) - ch_versions = TIDDIT_SV.out.versions - emit: vcf = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 4a72744eb..d0f1a472b 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -17,7 +17,6 @@ workflow GENERATE_CYTOSURE_FILES { val_sample_id_map // string: path to sample_id_map file main: - ch_versions = channel.empty() ch_reheader_out = channel.empty() TIDDIT_COV_VCF2CYTOSURE (ch_bam, [[],[]]) @@ -87,9 +86,4 @@ workflow GENERATE_CYTOSURE_FILES { [[:], []], [[:], []], ch_blacklist ) - - ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) - - emit: - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index ac06731a5..ebfb7b3c1 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -92,7 +92,7 @@ workflow PREPARE_REFERENCES { // Genome indices // if (!val_fai) { - SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[:],[]], true) + SAMTOOLS_FAIDX_GENOME(ch_genome_fasta.map{meta, fasta -> return [meta,fasta,[]]}, true) ch_genome_fai = SAMTOOLS_FAIDX_GENOME.out.fai.collect() ch_chrom_sizes = SAMTOOLS_FAIDX_GENOME.out.sizes.map {_meta, sizes -> sizes}.collect() } else { @@ -128,7 +128,6 @@ workflow PREPARE_REFERENCES { if (!val_bwamem2 && val_aligner.equals("bwameme")) { ch_genome_bwameme_index = BWAMEME_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) } else if (val_bwameme) { ch_genome_bwameme_index = channel.fromPath(val_bwameme).map {it -> [[id:it.simpleName], it]}.collect() } @@ -137,12 +136,12 @@ workflow PREPARE_REFERENCES { // if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { if (!val_mtfasta) { - ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_genome_fai, false).fa.collect() + ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta.join(ch_genome_fai), false).fa.collect() } else { ch_mt_fasta = channel.fromPath(val_mtfasta).map { it -> [[id:it.simpleName], it] }.collect() } - ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[:],[]], false).fai.collect() + ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta.map{meta, fasta -> return [meta, fasta,[]]}, false).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).index.collect() @@ -166,8 +165,6 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix (HISAT2_INDEX_GENOME.out.versions, - LAST_INDEX_MT.out.versions) } // // MT alignment indices @@ -268,7 +265,6 @@ workflow PREPARE_REFERENCES { ch_genome_fasta.map { meta, fasta -> return [meta, fasta, [], [] ] } .set {ch_rtgformat_in} ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf - ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) } emit: diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 89aceb143..1484b0f76 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -43,7 +43,6 @@ workflow QC_BAM { main: ch_cov = channel.empty() ch_cov_y = channel.empty() - ch_versions = channel.empty() ch_hsmetrics = channel.empty() ch_qualimap = channel.empty() ch_ngsbits = channel.empty() @@ -60,7 +59,6 @@ workflow QC_BAM { } if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results - ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions) } TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input @@ -93,15 +91,11 @@ workflow QC_BAM { if (!skip_ngsbits) { NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_ngsbits_method) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv - ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions) } // Check contamination ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) - ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) - emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] @@ -114,5 +108,4 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 798b5ac62..6ac7c6c98 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -30,6 +30,6 @@ workflow SUBSAMPLE_MT_FRAC { } .set { ch_subsample_in } - SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') + SAMTOOLS_VIEW(ch_subsample_in, [[:],[],[]], [], 'bai') } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 52ae75a9a..e141eaea3 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -14,15 +14,15 @@ workflow SUBSAMPLE_MT_READS { ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] main: - SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[],[]], [], '') - SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) + SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[],[]]) GAWK(SAMTOOLS_COLLATE.out.sam, [], false) GAWK.out.output.map {meta, sam -> return [meta, sam, []] }.set {ch_convert_to_bam} - SAM_TO_BAM(ch_convert_to_bam, [[:],[]], [], '') + SAM_TO_BAM(ch_convert_to_bam, [[:],[],[]], [], '') SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index f4f0e4027..5aa8f526b 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -14,8 +14,6 @@ workflow VARIANT_EVALUATION { ch_snv_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: - ch_versions = channel.empty() - ch_rtg_truthvcfs .splitCsv ( header:true ) .map { row -> @@ -42,9 +40,4 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) - ch_versions = ch_versions.mix(TABIX_TRUTHVCF.out.versions) - ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 007dea3bf..f0e1cd12b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -220,14 +220,11 @@ workflow RAREDISEASE { // Just one fastq.gz.spring-file with both R1 and R2 ch_one_fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(ch_input_by_sample_type.interleaved_spring, false).fastq - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_FQ_PAIR.out.versions) // Two fastq.gz.spring-files - one for R1 and one for R2 ch_r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[0] ]}, true).fastq ch_r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[1] ]}, true).fastq ch_two_fastq_gz_from_spring = ch_r1_fastq_gz_from_spring.join(ch_r2_fastq_gz_from_spring).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]} - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R1_FQ.out.versions) - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R2_FQ.out.versions) ch_input_fastqs = ch_input_by_sample_type.fastq_gz.mix(ch_one_fastq_gz_pair_from_spring).mix(ch_two_fastq_gz_from_spring) @@ -318,8 +315,6 @@ workflow RAREDISEASE { skip_ngsbits, skip_qualimap ) - ch_versions = ch_versions.mix(QC_BAM.out.versions) - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -448,7 +443,6 @@ workflow RAREDISEASE { ch_ann_csq_snv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) ANN_CSQ_PLI_SNV.out.vcf_ann .filter { meta, _vcf -> @@ -520,7 +514,6 @@ workflow RAREDISEASE { ch_ann_csq_mtsnv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions) ANN_CSQ_PLI_MT.out.vcf_ann .filter { meta, _vcf -> @@ -615,7 +608,6 @@ workflow RAREDISEASE { ch_ann_csq_sv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions) ANN_CSQ_PLI_SV.out.vcf_ann .filter { meta, _vcf -> @@ -725,7 +717,6 @@ workflow RAREDISEASE { ch_ann_csq_me_in, true ) - ch_versions = ch_versions.mix( ANN_CSQ_PLI_ME.out.versions ) } } @@ -756,7 +747,6 @@ workflow RAREDISEASE { SMNCOPYNUMBERCALLER ( ch_bams_bais ) - ch_versions = ch_versions.mix(SMNCOPYNUMBERCALLER.out.versions) } /* @@ -786,7 +776,6 @@ workflow RAREDISEASE { ch_sv_annotate.vcf_ann, val_sample_id_map ) - ch_versions = ch_versions.mix(GENERATE_CYTOSURE_FILES.out.versions) } /* @@ -820,7 +809,6 @@ workflow RAREDISEASE { ch_sdf, CALL_SNV.out.genome_vcf_tabix ) - ch_versions = ch_versions.mix(VARIANT_EVALUATION.out.versions) } /* From 914f03e92cc09c93758a140c574f8e1ac4a67b7a Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Feb 2026 16:53:15 +0100 Subject: [PATCH 325/872] update more modules --- modules.json | 16 +- modules/nf-core/bwa/mem/environment.yml | 11 +- modules/nf-core/bwa/mem/main.nf | 21 +- modules/nf-core/bwa/mem/meta.yml | 108 +++-- modules/nf-core/bwa/mem/tests/main.nf.test | 15 +- .../nf-core/bwa/mem/tests/main.nf.test.snap | 212 +++++++--- modules/nf-core/bwa/mem/tests/tags.yml | 3 - modules/nf-core/cat/cat/main.nf | 4 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/last/lastdb/main.nf | 1 - modules/nf-core/peddy/environment.yml | 2 + modules/nf-core/peddy/main.nf | 52 +-- modules/nf-core/peddy/meta.yml | 195 +++++++-- modules/nf-core/peddy/tests/main.nf.test | 84 +++- modules/nf-core/peddy/tests/main.nf.test.snap | 377 ++++++++++++++++-- modules/nf-core/peddy/tests/nextflow.config | 5 + modules/nf-core/peddy/tests/tags.yml | 2 - .../nf-core/rhocall/annotate/environment.yml | 2 + modules/nf-core/rhocall/annotate/main.nf | 20 +- modules/nf-core/rhocall/annotate/meta.yml | 46 ++- .../rhocall/annotate/tests/main.nf.test | 87 ++++ .../rhocall/annotate/tests/main.nf.test.snap | 62 +++ modules/nf-core/rhocall/viz/environment.yml | 4 +- modules/nf-core/rhocall/viz/main.nf | 16 +- modules/nf-core/rhocall/viz/meta.yml | 42 +- .../rhocall/viz/tests/main.nf.test.snap | 20 +- modules/nf-core/rhocall/viz/tests/tags.yml | 2 - modules/nf-core/svdb/merge/main.nf | 8 +- subworkflows/local/align/main.nf | 6 - subworkflows/local/align_MT/main.nf | 3 - .../local/align_bwa_bwamem2_bwameme/main.nf | 4 - subworkflows/local/annotate_genome_snvs.nf | 3 - .../local/annotate_rhocallviz/main.nf | 6 - workflows/raredisease.nf | 2 - 34 files changed, 1139 insertions(+), 304 deletions(-) delete mode 100644 modules/nf-core/bwa/mem/tests/tags.yml create mode 100644 modules/nf-core/peddy/tests/nextflow.config delete mode 100644 modules/nf-core/peddy/tests/tags.yml create mode 100644 modules/nf-core/rhocall/annotate/tests/main.nf.test create mode 100644 modules/nf-core/rhocall/annotate/tests/main.nf.test.snap delete mode 100644 modules/nf-core/rhocall/viz/tests/tags.yml diff --git a/modules.json b/modules.json index 01c0bca4e..9c46403dd 100644 --- a/modules.json +++ b/modules.json @@ -72,7 +72,7 @@ }, "bwa/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", "installed_by": ["modules"] }, "bwamem2/index": { @@ -102,7 +102,7 @@ }, "cat/cat": { "branch": "master", - "git_sha": "69614d4579a6bd9b8a2ecffb35959809d9c36559", + "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a", "installed_by": ["modules"] }, "chromograph": { @@ -158,7 +158,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "5bdb098216aaf5df9c3b6343e6204cd932503c16", + "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { @@ -309,7 +309,7 @@ }, "last/lastdb": { "branch": "master", - "git_sha": "d92ad4055433d66d3e3eb4fd8d729d6ae9f75693", + "git_sha": "a54953d05812af249d40ffaccb5b8ee371a75866", "installed_by": ["modules"] }, "manta/germline": { @@ -334,7 +334,7 @@ }, "peddy": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { @@ -384,12 +384,12 @@ }, "rhocall/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "rhocall/viz": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "rtgtools/format": { @@ -504,7 +504,7 @@ }, "svdb/merge": { "branch": "master", - "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", + "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", "installed_by": ["modules"] }, "svdb/query": { diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index ef7b966c0..54e679492 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,8 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bwa=0.7.18 - - htslib=1.20.0 - - samtools=1.20 + # renovate: datasource=conda depName=bioconda/bwa + - bioconda::bwa=0.7.19 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 9c815f0c8..e3732673e 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -4,8 +4,8 @@ process BWA_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0' : - 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data' : + 'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0' }" input: tuple val(meta) , path(reads) @@ -18,7 +18,8 @@ process BWA_MEM { tuple val(meta), path("*.cram") , emit: cram, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true tuple val(meta), path("*.crai") , emit: crai, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -44,19 +45,11 @@ process BWA_MEM { \$INDEX \\ $reads \\ | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension = args2.contains("--output-fmt sam") ? "sam" : args2.contains("--output-fmt cram") ? "cram": sort_bam && args2.contains("-O cram")? "cram": @@ -66,11 +59,5 @@ process BWA_MEM { touch ${prefix}.${extension} touch ${prefix}.csi touch ${prefix}.crai - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index 37467d291..450a3fe99 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -16,8 +16,9 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 - licence: ["GPL-3.0-or-later"] - identifier: "" + licence: + - "GPL-3.0-or-later" + identifier: "biotools:bwa" input: - - meta: type: map @@ -29,6 +30,9 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1930" - - meta2: type: map description: | @@ -38,6 +42,8 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + ontologies: + - edam: "http://edamontology.org/data_3210" - - meta3: type: map description: | @@ -47,52 +53,92 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fasta,fa}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - bam: - - meta: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + bam: + - - meta: + type: map + description: Groovy Map containing sample information - "*.bam": type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + ontologies: + - edam: "http://edamontology.org/format_2572" + cram: + - - meta: + type: map + description: Groovy Map containing sample information - "*.cram": type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - csi: - - meta: - type: file - description: Optional index file for BAM file - pattern: "*.{csi}" + ontologies: + - edam: "http://edamontology.org/format_3462" + csi: + - - meta: + type: map + description: Groovy Map containing sample information - "*.csi": type: file description: Optional index file for BAM file pattern: "*.{csi}" - - crai: - - meta: - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + ontologies: [] + crai: + - - meta: + type: map + description: Groovy Map containing sample information - "*.crai": type: file description: Optional index file for CRAM file pattern: "*.{crai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwa: + - - ${task.process}: + type: string + description: The name of the process + - bwa: + type: string + description: The name of the tool + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: eval + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwa: + type: string + description: The name of the tool + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index 5de2c2f45..6486ab000 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -48,8 +48,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -83,8 +82,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -119,8 +117,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -155,8 +152,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -191,8 +187,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap index 2079ea224..8aca4b234 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -10,17 +10,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "b6d9cb250261a4c125413c5d867d87a7", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "798439cbd7fd81cbcc5078022dc5479d" ], + "timestamp": "2026-02-18T12:42:52.901827", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:28.051598" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Single-End Sort": { "content": [ @@ -33,17 +45,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "848434ae4b79cfdcb2281c60b33663ce", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "94fcf617f5b994584c4e8d4044e16b4f" ], + "timestamp": "2026-02-18T12:43:01.149915", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:39.671154" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End": { "content": [ @@ -56,17 +80,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "5b34d31be84478761f789e3e2e805e31", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], + "timestamp": "2026-02-18T12:43:09.528042", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:51.919479" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End Sort": { "content": [ @@ -79,17 +115,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "69003376d9a8952622d8587b39c3eaae", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "af8628d9df18b2d3d4f6fd47ef2bb872" ], + "timestamp": "2026-02-18T12:43:17.876121", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:23:00.833562" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Single-end - stub": { "content": [ @@ -125,7 +173,18 @@ ] ], "4": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "5": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -157,16 +216,27 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-18T12:43:33.853248", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:31:29.46282" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End - no fasta": { "content": [ @@ -179,17 +249,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "5b34d31be84478761f789e3e2e805e31", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], + "timestamp": "2026-02-18T12:43:26.121474", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:23:09.942545" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-end - stub": { "content": [ @@ -225,7 +307,18 @@ ] ], "4": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "5": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -257,15 +350,26 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-18T12:43:42.119907", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:31:37.757037" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/bwa/mem/tests/tags.yml b/modules/nf-core/bwa/mem/tests/tags.yml deleted file mode 100644 index 82992d1f0..000000000 --- a/modules/nf-core/bwa/mem/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -bwa/mem: - - modules/nf-core/bwa/index/** - - modules/nf-core/bwa/mem/** diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index aa72fc4d9..15274c4ce 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -20,7 +20,7 @@ process CAT_CAT { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def file_list = files_in.collect { it.toString() } + def file_list = files_in.collect { file -> file.toString() } // choose appropriate concatenation tool depending on input and output format @@ -55,7 +55,7 @@ process CAT_CAT { """ stub: - def file_list = files_in.collect { it.toString() } + def file_list = files_in.collect { file -> file.toString() } prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" if(file_list.contains(prefix.trim())) { error "The name of the input file can't be the same as for the output prefix in the " + diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 4b3041dc5..f5629527d 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -1,6 +1,6 @@ process FASTQC { tag "${meta.id}" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 43d84750b..8f5b5c27e 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -31,7 +31,6 @@ process LAST_LASTDB { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir lastdb diff --git a/modules/nf-core/peddy/environment.yml b/modules/nf-core/peddy/environment.yml index 8d7fa2b6a..2bb1deb8e 100644 --- a/modules/nf-core/peddy/environment.yml +++ b/modules/nf-core/peddy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 0e533ec3b..0090f4e28 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -4,26 +4,35 @@ process PEDDY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : - 'biocontainers/peddy:0.4.8--pyh5e36f6f_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a1f7f39ed4c0e429d5a5805cdfa5251cbe56d4f2cf9cf4257172db1a56ab6bf/data' : + 'community.wave.seqera.io/library/peddy:0.4.8--e3cef30bae621593' }" input: tuple val(meta), path(vcf), path(vcf_tbi) - path ped + tuple val(meta2), path(ped) + tuple val(meta3), path(sites) output: - tuple val(meta), path("*.html") , emit: html - tuple val(meta), path("*.csv") , emit: csv - tuple val(meta), path("*.peddy.ped"), emit: ped - tuple val(meta), path("*.png") , optional: true, emit: png - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vs.html") , emit: vs_html + tuple val(meta), path("${prefix}.html") , emit: html + tuple val(meta), path("${prefix}.peddy.ped") , emit: ped + tuple val(meta), path("${prefix}.het_check.png") , optional: true, emit: het_check_png + tuple val(meta), path("${prefix}.ped_check.png") , optional: true, emit: ped_check_png + tuple val(meta), path("${prefix}.sex_check.png") , optional: true, emit: sex_check_png + tuple val(meta), path("${prefix}.het_check.csv") , optional: true, emit: het_check_csv + tuple val(meta), path("${prefix}.ped_check.csv") , optional: true, emit: ped_check_csv + tuple val(meta), path("${prefix}.sex_check.csv") , optional: true, emit: sex_check_csv + tuple val(meta), path("${prefix}.ped_check.rel-difference.csv") , optional: true, emit: ped_check_rel_difference_csv + tuple val("${task.process}"), val("peddy"), eval("peddy --version | sed 's/peddy, version //'"), topic: versions, emit: versions_peddy when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def sites_arg = sites ? "--sites $sites" : '' + if (sites && args.contains('--sites')) error "Double definition of --sites (in sites channel and in ext.args)" """ peddy \\ $args \\ @@ -31,27 +40,24 @@ process PEDDY { --plot \\ -p $task.cpus \\ $vcf \\ + $sites_arg \\ $ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' ) - END_VERSIONS """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + if (sites && args.contains('--sites')) error "Double definition of --sites (in sites channel and in ext.args)" """ - touch ${prefix}.ped_check.csv touch ${prefix}.vs.html + touch ${prefix}.html + touch ${prefix}.peddy.ped touch ${prefix}.het_check.csv + touch ${prefix}.ped_check.csv touch ${prefix}.sex_check.csv - touch ${prefix}.peddy.ped - touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' ) - END_VERSIONS + touch ${prefix}.het_check.png + touch ${prefix}.ped_check.png + touch ${prefix}.sex_check.png + touch ${prefix}.ped_check.rel-difference.csv """ } diff --git a/modules/nf-core/peddy/meta.yml b/modules/nf-core/peddy/meta.yml index 6b6b7347d..b503b76b9 100644 --- a/modules/nf-core/peddy/meta.yml +++ b/modules/nf-core/peddy/meta.yml @@ -6,13 +6,14 @@ keywords: - family tools: - peddy: - description: genotype, ped correspondence check, ancestry check, sex check. directly, - quickly on VCF + description: genotype, ped correspondence check, ancestry check, sex check. + directly, quickly on VCF homepage: https://github.com/brentp/peddy documentation: https://peddy.readthedocs.io/en/latest/ tool_dev_url: https://github.com/brentp/peddy doi: "10.1016/j.ajhg.2017.01.017" - licence: ["MIT"] + licence: + - "MIT" identifier: "" input: - - meta: @@ -23,61 +24,195 @@ input: - vcf: type: file description: VCF file - pattern: "*.{vcf.gz}" + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 - vcf_tbi: type: file description: TBI file - pattern: "*.{vcf.gz.tbi}" - - - ped: + pattern: "*.vcf.gz.tbi" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ped: type: file description: PED/FAM file pattern: "*.{ped,fam}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: sites file. By defaults peddy uses hg19/GRCh37, "--sites + hg38" can be specified in the process argument or a custom file + following syntax + https://github.com/brentp/peddy/blob/master/peddy/GRCH37.sites can be + provided + pattern: "*.sites" + ontologies: [] output: - - html: - - meta: + vs_html: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.html": + - ${prefix}.vs.html: type: file - description: HTML file - pattern: "*.{html}" - - csv: - - meta: + description: HTML file comparison between reported and inferred sex + pattern: "*.vs.html" + ontologies: [] + html: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.csv": + - ${prefix}.html: type: file - description: CSV file - pattern: "*.{csv}" - - ped: - - meta: + description: HTML report + pattern: "*.html" + ontologies: [] + ped: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.peddy.ped": + - ${prefix}.peddy.ped: type: file - description: PED/FAM file - pattern: "*.peddy.{ped}" - - png: - - meta: + description: Inferred PED file + pattern: "*.peddy.ped" + ontologies: [] + het_check_png: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.png": + - ${prefix}.het_check.png: type: file - description: PNG file - pattern: "*.{png}" - - versions: - - versions.yml: + description: | + PNG file containing heterozygosity check. + Rate of het calls, allele-balance at het calls, + mean and median depth, and a PCA projection onto thousand + genomes. + pattern: "*.het_check.png" + ontologies: [] + ped_check_png: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.png: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + PNG file containing pedigree check between reported + and inferred sex + pattern: "*.het_check.png" + ontologies: [] + sex_check_png: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sex_check.png: + type: file + description: | + PNG file with sex check performs a comparison + between the sex reported in the ped file and that + inferred from the genotypes on the non-PAR regions + of the X chromosome. + pattern: "*.sex_check.png" + ontologies: [] + het_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.het_check.csv: + type: file + description: | + CSV file containing heterozygosity check. + Rate of het calls, allele-balance at het calls, + mean and median depth, and a PCA projection onto thousand + genomes. + pattern: "*.het_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + ped_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.csv: + type: file + description: | + CSV file containing pedigree check between reported + and inferred sex + pattern: "*.het_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + sex_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sex_check.csv: + type: file + description: | + CSV file with sex check performs a comparison + between the sex reported in the ped file and that + inferred from the genotypes on the non-PAR regions + of the X chromosome. + pattern: "*.sex_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + ped_check_rel_difference_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.rel-difference.csv: + type: file + description: | + CSV file with the comparison between inferred and given relatedness + pattern: "*.ped_check.rel-difference.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + versions_peddy: + - - ${task.process}: + type: string + description: The name of the process + - peddy: + type: string + description: The name of the tool + - peddy --version | sed 's/peddy, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - peddy: + type: string + description: The name of the tool + - peddy --version | sed 's/peddy, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@rannick" maintainers: diff --git a/modules/nf-core/peddy/tests/main.nf.test b/modules/nf-core/peddy/tests/main.nf.test index 21ff538d1..f52d22919 100644 --- a/modules/nf-core/peddy/tests/main.nf.test +++ b/modules/nf-core/peddy/tests/main.nf.test @@ -8,6 +8,70 @@ nextflow_process { tag "modules_nfcore" tag "peddy" + test("test - peddy") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + + ) + } + + } + + test("test - peddy - double_sites") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert !process.success }, + { assert process.exitStatus != 0 } + ) + } + } + test("test - peddy - stub") { options "-stub" @@ -17,19 +81,27 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) ] - input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) """ } } then { - assert process.success - assert snapshot(process.out).match() + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) } } - } diff --git a/modules/nf-core/peddy/tests/main.nf.test.snap b/modules/nf-core/peddy/tests/main.nf.test.snap index 5de593f1d..c122208ad 100644 --- a/modules/nf-core/peddy/tests/main.nf.test.snap +++ b/modules/nf-core/peddy/tests/main.nf.test.snap @@ -8,10 +8,7 @@ "id": "test", "single_end": false }, - [ - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -20,11 +17,14 @@ "id": "test", "single_end": false }, - [ - "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + "PEDDY", + "peddy", + "0.4.8" ] ], "2": [ @@ -37,22 +37,84 @@ ] ], "3": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "4": [ - "versions.yml:md5,d3587e67aded68bcf24c47542efe012f" + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], - "csv": [ + "5": [ [ { "id": "test", "single_end": false }, - [ - "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sex_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "het_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "het_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "html": [ @@ -61,10 +123,7 @@ "id": "test", "single_end": false }, - [ - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "ped": [ @@ -76,18 +135,278 @@ "test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "png": [ - + "ped_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ped_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ped_check_rel_difference_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sex_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sex_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_peddy": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "vs_html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-02-18T10:39:07.038845862", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test - peddy": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,a749380edef4653dade663534ddcfbd6" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,e3af87096747a19966222a74242943b6" + ] + ], + "10": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.peddy.ped:md5,8378f6599ee4ad6a9db42bfe226968a6" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,ce21f5e727cc6b4346d407d2963b0442" + ] ], - "versions": [ - "versions.yml:md5,d3587e67aded68bcf24c47542efe012f" + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,861d8b204d78a22a59b0cedafd8d4a16" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,b2ff9afe9f596dee5a22431ba920980c" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,b8623fa750218dade5468542d459fafe" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,21dded6c03dab39859d2936d4820c426" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,763950d0eff48b64da29a6a883d6b11c" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,b59f50df00b5b3af6e71e774d8b99103" + ] + ], + "het_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,b8623fa750218dade5468542d459fafe" + ] + ], + "het_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,ce21f5e727cc6b4346d407d2963b0442" + ] + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,e3af87096747a19966222a74242943b6" + ] + ], + "ped": [ + [ + { + "id": "test", + "single_end": false + }, + "test.peddy.ped:md5,8378f6599ee4ad6a9db42bfe226968a6" + ] + ], + "ped_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,21dded6c03dab39859d2936d4820c426" + ] + ], + "ped_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,861d8b204d78a22a59b0cedafd8d4a16" + ] + ], + "ped_check_rel_difference_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,b59f50df00b5b3af6e71e774d8b99103" + ] + ], + "sex_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,763950d0eff48b64da29a6a883d6b11c" + ] + ], + "sex_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,b2ff9afe9f596dee5a22431ba920980c" + ] + ], + "versions_peddy": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "vs_html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,a749380edef4653dade663534ddcfbd6" + ] ] } ], + "timestamp": "2026-02-18T10:44:20.669530641", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T09:28:05.418978589" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/peddy/tests/nextflow.config b/modules/nf-core/peddy/tests/nextflow.config new file mode 100644 index 000000000..bca49c052 --- /dev/null +++ b/modules/nf-core/peddy/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'PEDDY' { + ext.args = '--sites --hg38' + } +} diff --git a/modules/nf-core/peddy/tests/tags.yml b/modules/nf-core/peddy/tests/tags.yml deleted file mode 100644 index d8324a74c..000000000 --- a/modules/nf-core/peddy/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mosdepth: - - "modules/nf-core/peddy/**" diff --git a/modules/nf-core/rhocall/annotate/environment.yml b/modules/nf-core/rhocall/annotate/environment.yml index ba95c3cbe..8a0fe435e 100644 --- a/modules/nf-core/rhocall/annotate/environment.yml +++ b/modules/nf-core/rhocall/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 78de45c18..070d37c1c 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -4,8 +4,8 @@ process RHOCALL_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - 'biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7d/7dbf7021085cfea72a20cafffe57fcf47392706d9a433f1143f1e60b389b85ae/data': + 'community.wave.seqera.io/library/rhocall:0.5.1--a7eced77e39d2b82' }" input: tuple val(meta), path(vcf), path(tbi) @@ -14,7 +14,7 @@ process RHOCALL_ANNOTATE { output: tuple val(meta), path("*_rhocall.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("rhocall"), eval("rhocall --version | sed 's/rhocall, version //'"), topic: versions, emit: versions_rhocall when: task.ext.when == null || task.ext.when @@ -24,6 +24,8 @@ process RHOCALL_ANNOTATE { def prefix = task.ext.prefix ?: "${meta.id}" def az_bed = bed ? "-b ${bed}" : '' """ + export MPLCONFIGDIR=\$PWD + rhocall \\ annotate \\ $args \\ @@ -31,21 +33,13 @@ process RHOCALL_ANNOTATE { -r $roh \\ -o ${prefix}_rhocall.vcf \\ $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_rhocall.vcf + export MPLCONFIGDIR=\$PWD - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS + touch ${prefix}_rhocall.vcf """ } diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml index fb041cae8..4df7c6d6e 100644 --- a/modules/nf-core/rhocall/annotate/meta.yml +++ b/modules/nf-core/rhocall/annotate/meta.yml @@ -10,7 +10,8 @@ tools: homepage: "https://github.com/dnil/rhocall" documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -22,10 +23,12 @@ input: type: file description: vcf file pattern: "*.{vcf,vcf.gz}" + ontologies: [] - tbi: type: file description: vcf index file pattern: "*.{tbi}" + ontologies: [] - - meta2: type: map description: | @@ -35,13 +38,15 @@ input: type: file description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL pattern: "*.{roh}" - - - bed: - type: file - description: BED file with AZ windows. - pattern: "*.{bed}" + ontologies: [] + - bed: + type: file + description: BED file with AZ windows. + pattern: "*.{bed}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,11 +55,28 @@ output: type: file description: vcf file pattern: "*.{vcf,vcf.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rhocall: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/annotate/tests/main.nf.test b/modules/nf-core/rhocall/annotate/tests/main.nf.test new file mode 100644 index 000000000..fafd3826d --- /dev/null +++ b/modules/nf-core/rhocall/annotate/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process RHOCALL_ANNOTATE" + + script "../main.nf" + process "RHOCALL_ANNOTATE" + + tag "modules" + tag "modules_nfcore" + tag "rhocall" + tag "rhocall/annotate" + tag "bcftools" + tag "bcftools/roh" + + setup { + run("BCFTOOLS_ROH") { + script "../../../bcftools/roh/main.nf" + + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true) + ] + input[1] = [[],[]] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + } + + test("sarscov2") { + + when { + params { + module_args = '' + } + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true) + ] + input[1] = BCFTOOLS_ROH.out.roh + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.findAll {key, value -> key.startsWith("versions")} + ).match() } + ) + } + } + + test("sarscov2 - stub") { + options '-stub' + when { + params { + module_args = '' + } + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true)] + input[1] = BCFTOOLS_ROH.out.roh + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap b/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap new file mode 100644 index 000000000..44987e7fd --- /dev/null +++ b/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "sarscov2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_rhocall.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_rhocall.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rhocall": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ] + } + ], + "timestamp": "2026-02-18T10:11:48.513471", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2": { + "content": [ + "bc7bf3ee9e8430e064c539eb81e59bf9", + { + "versions_rhocall": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ] + } + ], + "timestamp": "2026-02-18T10:14:26.928869", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rhocall/viz/environment.yml b/modules/nf-core/rhocall/viz/environment.yml index 538db5092..8a0fe435e 100644 --- a/modules/nf-core/rhocall/viz/environment.yml +++ b/modules/nf-core/rhocall/viz/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::rhocall=0.5.1" + - bioconda::rhocall=0.5.1 diff --git a/modules/nf-core/rhocall/viz/main.nf b/modules/nf-core/rhocall/viz/main.nf index 4191ef3bc..78c048ede 100644 --- a/modules/nf-core/rhocall/viz/main.nf +++ b/modules/nf-core/rhocall/viz/main.nf @@ -4,8 +4,8 @@ process RHOCALL_VIZ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - 'biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7d/7dbf7021085cfea72a20cafffe57fcf47392706d9a433f1143f1e60b389b85ae/data': + 'community.wave.seqera.io/library/rhocall:0.5.1--a7eced77e39d2b82' }" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process RHOCALL_VIZ { output: tuple val(meta), path("${prefix}/${prefix}.bed"), emit: bed tuple val(meta), path("${prefix}/${prefix}.wig"), emit: wig - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("rhocall"), eval("rhocall --version | sed 's/rhocall, version //'"), topic: versions, emit: versions_rhocall when: task.ext.when == null || task.ext.when @@ -32,11 +32,6 @@ process RHOCALL_VIZ { mv ${prefix}/output.bed ${prefix}/${prefix}.bed mv ${prefix}/output.wig ${prefix}/${prefix}.wig - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ stub: @@ -45,10 +40,5 @@ process RHOCALL_VIZ { mkdir ${prefix} touch ${prefix}/${prefix}.bed touch ${prefix}/${prefix}.wig - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/rhocall/viz/meta.yml b/modules/nf-core/rhocall/viz/meta.yml index 7efcab02a..5911cae46 100644 --- a/modules/nf-core/rhocall/viz/meta.yml +++ b/modules/nf-core/rhocall/viz/meta.yml @@ -10,9 +10,9 @@ tools: homepage: "https://github.com/dnil/rhocall" documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - input: - - meta: type: map @@ -23,6 +23,7 @@ input: type: file description: VCF file pattern: "*.{vcf}" + ontologies: [] - - meta2: type: map description: | @@ -32,9 +33,10 @@ input: type: file description: Input RHO file produced from rhocall pattern: "*.{roh}" + ontologies: [] output: - - bed: - - meta: + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -43,8 +45,9 @@ output: type: file description: Bed file containing roh calls pattern: "*.{bed}" - - wig: - - meta: + ontologies: [] + wig: + - - meta: type: map description: | Groovy Map containing sample information @@ -53,11 +56,28 @@ output: type: file description: Wig file containing roh calls pattern: "*.{wig}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rhocall: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/viz/tests/main.nf.test.snap b/modules/nf-core/rhocall/viz/tests/main.nf.test.snap index cba4067f2..c7c75a230 100644 --- a/modules/nf-core/rhocall/viz/tests/main.nf.test.snap +++ b/modules/nf-core/rhocall/viz/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "2": [ - "versions.yml:md5,079291120b14dd6b9368dd1cff72518e" + [ + "RHOCALL_VIZ", + "rhocall", + "0.5.1" + ] ], "bed": [ [ @@ -29,8 +33,12 @@ "test.bed:md5,4579710bbd8e1e4449274d261c439891" ] ], - "versions": [ - "versions.yml:md5,079291120b14dd6b9368dd1cff72518e" + "versions_rhocall": [ + [ + "RHOCALL_VIZ", + "rhocall", + "0.5.1" + ] ], "wig": [ [ @@ -42,6 +50,10 @@ ] } ], - "timestamp": "2024-02-05T17:57:24.70125206" + "timestamp": "2026-02-18T10:11:58.070955", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/rhocall/viz/tests/tags.yml b/modules/nf-core/rhocall/viz/tests/tags.yml deleted file mode 100644 index bc2d74a70..000000000 --- a/modules/nf-core/rhocall/viz/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rhocall/viz: - - "modules/nf-core/rhocall/viz/**" diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 8779a2ce4..88002c962 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -37,10 +37,10 @@ process SVDB_MERGE { if (input_priority) { if (vcfs.collect().size() > 1 && sort_inputs) { // make vcf-priority pairs and sort on VCF name, so priority is also sorted the same - def pairs = vcfs.indices.collect { [vcfs[it], input_priority[it]] } + def pairs = vcfs.indices.collect { index -> [vcfs[index], input_priority[index]] } pairs = pairs.sort { a, b -> a[0].name <=> b[0].name } - vcfs = pairs.collect { it[0] } - priority = pairs.collect { it[1] } + vcfs = pairs.collect { vcf -> vcf[0] } + priority = pairs.collect { pair -> pair[1] } } else { priority = input_priority } @@ -54,7 +54,7 @@ process SVDB_MERGE { } else { // if there's no priority input just sort the vcfs by name if possible - input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { it.name } : vcfs + input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { vcf_file -> vcf_file.name } : vcfs } def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" : diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index c946c1d18..cc9cf0b9f 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -51,7 +51,6 @@ workflow ALIGN { ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() - ch_versions = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) @@ -95,7 +94,6 @@ workflow ALIGN { ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics - ch_versions = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions) } else if (val_aligner.equals("sentieon")) { ALIGN_SENTIEON ( ch_genome_bwaindex, @@ -107,7 +105,6 @@ workflow ALIGN { ) ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai - ch_versions = ch_versions.mix(ALIGN_SENTIEON.out.versions) } ch_genome_marked_bam = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) @@ -151,8 +148,6 @@ workflow ALIGN { .join(ALIGN_MT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling ch_mtshift_bam_bai_gatksubwf = ALIGN_MT_SHIFT.out.marked_bam .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling - ch_versions = ch_versions - .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions) } if (val_save_mapped_as_cram) { @@ -168,5 +163,4 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index da40874e9..17de7f7c1 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -22,7 +22,6 @@ workflow ALIGN_MT { val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' main: - ch_versions = channel.empty() if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) @@ -33,7 +32,6 @@ workflow ALIGN_MT { } else if (val_mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) ch_align = BWA_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions) } ch_align .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true) @@ -50,5 +48,4 @@ workflow ALIGN_MT { emit: marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 42a19c489..65e7b1256 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -29,13 +29,10 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { val_sort_threads // integer: [mandatory] default: 4 main: - ch_versions = channel.empty() - // Map, sort, and index if (val_aligner.equals("bwa")) { BWA ( ch_input_reads, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam - ch_versions = ch_versions.mix(BWA.out.versions) } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam @@ -85,5 +82,4 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index e0f30eb91..f5a1ef3e9 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -194,9 +194,6 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) - ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) - emit: tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 120f36013..d2a2a52da 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -18,8 +18,6 @@ workflow ANNOTATE_RHOCALLVIZ { ch_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: - ch_versions = channel.empty() - ch_vcf_tbi .combine(ch_samples) .map {_meta, vcf, tbi, meta2 -> return [meta2,vcf,tbi]} @@ -54,8 +52,4 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index f0e1cd12b..43c907b6a 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -274,7 +274,6 @@ workflow RAREDISEASE { val_save_mapped_as_cram ) .set { ch_mapped } - ch_versions = ch_versions.mix(ALIGN.out.versions) if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { if (val_mt_subsample_approach.equals("fraction")) { @@ -759,7 +758,6 @@ workflow RAREDISEASE { CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), ch_pedfile ) - ch_versions = ch_versions.mix(PEDDY.out.versions) } /* From 15ff99177cd7eea10f6ce0c98d1bbe1b7f800f4e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 19:34:10 +0100 Subject: [PATCH 326/872] update subworkflows and snapshots --- CHANGELOG.md | 27 +- main.nf | 1 - miss | 0 subworkflows/local/align/main.nf | 1 - subworkflows/local/align/tests/main.nf.test | 8 +- .../local/align/tests/main.nf.test.snap | 69 +- .../local/align_MT/tests/main.nf.test.snap | 20 +- .../tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 32 +- .../align_sentieon/tests/main.nf.test.snap | 4 +- .../local/annotate_structural_variants.nf | 3 - .../tests/main.nf.test.snap | 4 +- subworkflows/local/call_snv.nf | 1 - .../local/call_snv_deepvariant/main.nf | 3 +- subworkflows/local/call_sv_MT/main.nf | 2 - subworkflows/local/generate_cytosure_files.nf | 8 +- subworkflows/local/prepare_references/main.nf | 3 - .../tests/main.nf.test.snap | 26 +- subworkflows/local/qc_bam/main.nf | 2 +- .../local/qc_bam/tests/main.nf.test.snap | 16 +- subworkflows/local/rank_variants.nf | 3 - .../scatter_genome/tests/main.nf.test.snap | 4 +- test.sh | 2 + tests/default.nf.test.snap | 51 +- tests/test_bam.nf.test.snap | 40 +- tests/test_singleton.nf.test.snap | 47 +- wflog1 | 6024 +++++++++ wflog2 | 10617 ++++++++++++++++ workflows/raredisease.nf | 7 +- 29 files changed, 16790 insertions(+), 241 deletions(-) create mode 100644 miss create mode 100644 test.sh create mode 100644 wflog1 create mode 100644 wflog2 diff --git a/CHANGELOG.md b/CHANGELOG.md index 3309acd15..35f2d8ba0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -53,24 +53,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | --------------------- | ----------- | ----------- | | bcftools | 1.20 | 1.21 | -| htslib | 1.20 | 1.21 | -| mosdepth | 0.3.8 | 0.3.11 | -| ngs-bits | 2023_02 | 2024_11 | -| gatk4 | 4.5.0.0 | 4.6.2.0 | -| gens-preproc | 1.0.11 | 1.1.2 | -| pigz | 2.3.4 | 2.8 | -| samtools | 1.21 | 1.22.1 | -| sambamba | | 1.0.1 | +| bwa | 0.7.18 | 0.7.19 | +| deepvariant | 1.8.0 | 1.9.0 | +| eKLIPse | 1.8 | | | ensemblverp/filtervep | 113 | 115.2 | | fastp | 0.23.4 | 1.0.1 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | | genmod | 3.9 | 3.10.2 | +| gens-preproc | 1.0.11 | 1.1.2 | +| htslib | 1.20 | 1.21 | +| MitoSalt | | 1.1.1 | +| mosdepth | 0.3.8 | 0.3.11 | | multiqc | 1.32 | 1.33 | +| ngsbits | 202411 | 202512 | | picard | 3.3.0 | 3.4.0 | +| pigz | 2.3.4 | 2.8 | +| sambamba | | 1.0.1 | +| samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | -| deepvariant | 1.8.0 | 1.9.0 | -| MitoSalt | | 1.1.1 | -| eKLIPse | 1.8 | | +| tiddit | 3.6.1 | 3.9.4 | +| ucsc | 447 | 482 | +| vcfanno | 0.3.5 | 0.3.7 | +| vcf2cytosure | 0.9.1 | 0.9.3 | ## 2.6.0 - Cacofonix [2025-06-25] diff --git a/main.nf b/main.nf index c1c42455f..5346dbd30 100644 --- a/main.nf +++ b/main.nf @@ -183,7 +183,6 @@ workflow NFCORE_RAREDISEASE { ch_target_intervals = ch_references.target_intervals ch_vcfanno_extra = ch_references.vcfanno_extra ch_vep_cache = ch_references.vep_resources - ch_versions = ch_versions.mix(ch_references.versions) // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) ch_cadd_resources = channelFromPath(val_cadd_resources, true) diff --git a/miss b/miss new file mode 100644 index 000000000..e69de29bb diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index c946c1d18..327ade6e6 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -107,7 +107,6 @@ workflow ALIGN { ) ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai - ch_versions = ch_versions.mix(ALIGN_SENTIEON.out.versions) } ch_genome_marked_bam = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 32c053815..dce17b191 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -123,8 +123,7 @@ nextflow_workflow { workflow.out.mt_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } ) @@ -224,7 +223,7 @@ nextflow_workflow { workflow.out.mt_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, ).match() } ) @@ -314,8 +313,7 @@ nextflow_workflow { workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } ) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 07d7157f9..ceb34df54 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -236,30 +236,13 @@ "427b5e476d84c5277d2d24210800ad60", "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" ] - ], - [ - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T14:52:33.087126495", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T16:47:38.865548433" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwameme - wgs": { "content": [ @@ -383,30 +366,13 @@ ], [ - ], - [ - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T15:06:13.790400908", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:31:32.266454329" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwamem2 - wes": { "content": [ @@ -477,23 +443,12 @@ ], [ - ], - [ - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T14:53:17.634008549", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T16:48:59.035282254" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 7537c0bd6..2108f323f 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -103,9 +103,7 @@ ] ], "2": [ - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" + ], "marked_bai": [ [ @@ -208,17 +206,15 @@ ] ], "versions": [ - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" + ] } ], + "timestamp": "2026-02-17T11:24:25.300014158", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:37:55.606130634" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align mt - bwa": { "content": [ @@ -435,10 +431,10 @@ ] } ], + "timestamp": "2026-02-06T17:44:37.818378883", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:44:37.818378883" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index a9d3a12f1..cdde33d3e 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -56,8 +56,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, - workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, - workflow.out.versions + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() } ) @@ -113,8 +112,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, - workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, - workflow.out.versions + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() } ) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 3b33ea9a7..d73f1f5fe 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "da588ff12491da491e3059326ffef0de" + "24b5799be5403926a272596963f9683f" ] ], [ @@ -30,19 +30,13 @@ }, "af8628d9df18b2d3d4f6fd47ef2bb872" ] - ], - [ - "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", - "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], + "timestamp": "2026-02-17T15:13:51.33678644", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:47:53.965738943" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwameme": { "content": [ @@ -58,7 +52,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "91efdc668b5f6e075743e414c7afd0f8" + "b9b01b7ac356afa64bc411d6f10e741" ] ], [ @@ -75,18 +69,12 @@ }, "af8628d9df18b2d3d4f6fd47ef2bb872" ] - ], - [ - "versions.yml:md5,390a09ae83280da84de93856149cc3a1", - "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], + "timestamp": "2026-02-17T15:14:44.637382457", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:50:27.94216545" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 61e2f2be2..79a96bf5a 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -244,10 +244,10 @@ ] } ], + "timestamp": "2026-01-26T23:22:09.03170299", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-26T23:22:09.03170299" + } } } \ No newline at end of file diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 63cd40b07..aa29499df 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -25,8 +25,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { val_vep_cache_version // string: [mandatory] default: 107 main: - ch_versions = channel.empty() - if (val_svdb_query_dbs) { ch_svdb_dbs .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> @@ -101,5 +99,4 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { emit: tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index da37ecae6..685492b45 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -4,10 +4,10 @@ "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], + "timestamp": "2025-10-14T14:06:58.984015651", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-14T14:06:58.984015651" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 4f6acd6c1..126d4f6e8 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -72,7 +72,6 @@ workflow CALL_SNV { ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix - ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 96c8ec4f7..897cc7373 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -25,7 +25,6 @@ workflow CALL_SNV_DEEPVARIANT { val_analysis_type // boolean main: - ch_versions = channel.empty() if (val_analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) @@ -48,6 +47,7 @@ workflow CALL_SNV_DEEPVARIANT { ch_case_info .combine(ch_file_list) + .map {meta, gvcf -> return [meta, gvcf, []]} .set { ch_gvcfs } GLNEXUS ( ch_gvcfs, [[:],[]] ) @@ -87,5 +87,4 @@ workflow CALL_SNV_DEEPVARIANT { gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] tabix = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 8733edab0..f24d752fc 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -36,7 +36,6 @@ workflow CALL_SV_MT { val_split_length // string: [mandatory] mitosalt_split_length main: - ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -85,5 +84,4 @@ workflow CALL_SV_MT { mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index d0f1a472b..18f6ed80a 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -9,7 +9,7 @@ include { VCF2CYTOSURE } from '../../modules/nf workflow GENERATE_CYTOSURE_FILES { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_blacklist // channel: [optional] [path(blacklist)] ch_sample_id_map // channel: [optional] [val(id), val(id)] ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] @@ -19,15 +19,15 @@ workflow GENERATE_CYTOSURE_FILES { main: ch_reheader_out = channel.empty() - TIDDIT_COV_VCF2CYTOSURE (ch_bam, [[],[]]) + TIDDIT_COV_VCF2CYTOSURE (ch_bam_bai, [[],[]]) // Build channel: [val(sample_meta), path(vcf), path(vcf_index)] ch_vcf.join( ch_tbi, failOnMismatch: true ) .set { ch_vcf_tbi } - ch_bam.combine(ch_vcf_tbi) + ch_bam_bai.combine(ch_vcf_tbi) .map { - meta_sample, _bam, _meta_case, vcf, tbi -> + meta_sample, _bam, _bai, _meta_case, vcf, tbi -> def id_meta = ['id':meta_sample.sample] def sex_meta = ['sex':meta_sample.sex] return [ id_meta, sex_meta, vcf, tbi ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index ebfb7b3c1..096e644d9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -59,7 +59,6 @@ workflow PREPARE_REFERENCES { main: - ch_versions = channel.empty() ch_bait_intervals = channel.empty() ch_bwa = channel.empty() ch_genome_bwameme_index = channel.empty() @@ -299,6 +298,4 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] - versions = ch_versions // channel:[ path(versions.yml) ] - } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 0a020cfba..ccd669709 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -422,15 +422,6 @@ ] ] ], - "31": [ - "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,1b3327823f65f68efc82043fc802a384", - "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", - "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" - ], "4": [ [ { @@ -960,22 +951,13 @@ "spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi:md5,3fab1357156412ca02b2bdf075e97382" ] ] - ], - "versions": [ - "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,1b3327823f65f68efc82043fc802a384", - "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", - "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] } ], + "timestamp": "2026-02-17T15:18:47.287844356", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-16T23:13:28.796983269" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 1484b0f76..d2edb0da1 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -61,7 +61,7 @@ workflow QC_BAM { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results } - TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input + TIDDIT_COV (ch_bam_bai, [[],[]]) // 2nd pos. arg is req. only for cram input UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_genome_chrsizes) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index b1d3ef2cf..aa697e3ef 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -72,11 +72,11 @@ ] ] ], + "timestamp": "2026-02-17T15:20:57.570426841", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-27T10:15:41.947673274" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "QC_BAM - test, sentieon": { "content": [ @@ -151,10 +151,10 @@ ] ] ], + "timestamp": "2026-02-17T15:21:49.953972761", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-27T10:17:32.616739257" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 7dc4589b7..92fc42819 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -19,8 +19,6 @@ workflow RANK_VARIANTS { process_with_sort // Boolean main: - ch_versions = channel.empty() - GENMOD_ANNOTATE(ch_vcf) ch_models_in = GENMOD_ANNOTATE.out.vcf.combine(ch_pedfile) @@ -41,5 +39,4 @@ workflow RANK_VARIANTS { emit: vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 8c25c199f..0e41bad3f 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -144,10 +144,10 @@ ] } ], + "timestamp": "2026-02-09T10:18:23.261854", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T10:18:23.261854" + } } } \ No newline at end of file diff --git a/test.sh b/test.sh new file mode 100644 index 000000000..c76b0b687 --- /dev/null +++ b/test.sh @@ -0,0 +1,2 @@ +nf-test test subworkflows/local/ --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >wflog 2>&1 +nf-test test tests --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >>wflog 2>&1 diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bf8774f4c..dee909d0d 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -67,15 +67,13 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -118,11 +116,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -217,7 +215,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOCHECK_MT": { "haplocheck": "1.3.3" @@ -262,7 +260,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -320,10 +318,10 @@ "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -335,10 +333,13 @@ "samtools": "1.22.1" }, "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" }, "SAMTOOLS_SORT": { "samtools": "1.22.1" @@ -359,7 +360,7 @@ "seqtk": "1.4-r122" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -454,16 +455,16 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 @@ -475,13 +476,13 @@ "upd": 0.1 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -1107,10 +1108,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-02-19T10:01:20.665806391", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T05:27:37.311350676" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 70af846c2..0b94ca3c2 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -68,11 +68,10 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -115,11 +114,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -208,7 +207,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOCHECK_MT": { "haplocheck": "1.3.3" @@ -247,7 +246,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -319,6 +318,9 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, @@ -332,7 +334,7 @@ "samtools": "1.22.1" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -424,16 +426,16 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 @@ -445,13 +447,13 @@ "upd": 0.1 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -1036,10 +1038,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-02-19T15:08:50.558312851", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-16T22:08:02.449482922" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index da510cdc4..9b4a21e11 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -65,15 +65,13 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -110,11 +108,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -209,7 +207,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOCHECK_MT": { "haplocheck": "1.3.3" @@ -254,7 +252,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -327,10 +325,13 @@ "samtools": "1.22.1" }, "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" }, "SAMTOOLS_SORT": { "samtools": "1.22.1" @@ -351,7 +352,7 @@ "seqtk": "1.4-r122" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -443,28 +444,28 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -724,10 +725,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], + "timestamp": "2026-02-19T18:45:40.125652788", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T19:08:15.435078959" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/wflog1 b/wflog1 new file mode 100644 index 000000000..d4a1be1a7 --- /dev/null +++ b/wflog1 @@ -0,0 +1,6024 @@ +Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp + +🚀 nf-test 0.9.4 +https://www.nf-test.com +(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr + +Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar +Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar +Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar +Warning: every snapshot that fails during this test run is re-recorded. + +Test Workflow ALIGN + + Test [9e55951e] 'align bwamem2 - wgs' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 76951fb0df + [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e0/2e14cf254f7fbb4dc949380310a337/earlycasualcaiman.fastp.json" + ], + [ + { + "id": "hugelymodelbat", + "sample": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": 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"mt_bam_bai_gatksubwf": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/38/908410bfc3d6b21a01178d2fff1ae4/earlycasualcaiman_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/38/908410bfc3d6b21a01178d2fff1ae4/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/83a7b2f1f57b0d1ca7ae28dde0fa2c/hugelymodelbat_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/83a7b2f1f57b0d1ca7ae28dde0fa2c/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/a1/caaca66e607db2356b239ec7eac182/slowlycivilbuck_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/a1/caaca66e607db2356b239ec7eac182/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "mtshift_bam_bai_gatksubwf": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ae/1bd8a1f66e7867f907762839b1e897/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ae/1bd8a1f66e7867f907762839b1e897/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] + ], + "versions": [ + + ] + } +PASSED (5684.323s) + Test [59260ec0] 'align bwamem2 - wes' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: db2dc4c6c7 + [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/b8/4d574f613662456c74c71fbcd5c43a/earlycasualcaiman.fastp.json" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/51/29cdff1116f2d5e95019c51dfab7ad/hugelymodelbat.fastp.json" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/41/6ea3afbfecf3264f36467ff22e97cd/slowlycivilbuck.fastp.json" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "5": [ + + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "fastp_json": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/b8/4d574f613662456c74c71fbcd5c43a/earlycasualcaiman.fastp.json" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/51/29cdff1116f2d5e95019c51dfab7ad/hugelymodelbat.fastp.json" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/41/6ea3afbfecf3264f36467ff22e97cd/slowlycivilbuck.fastp.json" + ] + ], + "genome_marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "genome_marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam" + ] + ], + "genome_marked_bam_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "markdup_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "mt_bam_bai": [ + + ], + "mt_bam_bai_gatksubwf": [ + + ], + "mtshift_bam_bai_gatksubwf": [ + + ], + "versions": [ + + ] + } +PASSED (422.715s) + Test [412be509] 'align bwameme - wgs' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 615692c6bf + [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/86/bd7aff1284232cbe15e2675b533a8b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/14/875b8f9dc9717693a954a75ae4724f/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "markdup_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "mt_bam_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/a4/7b57bc11845f5bc4733ece4b94487c/earlycasualcaiman.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/8f/07d888a3a1a96250875143512851fc/earlycasualcaiman.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6e/1e98c80a7f7f86de7f7ad0079d83c4/hugelymodelbat.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/06/a0bcb0d96d10dd4846aa48058420ad/hugelymodelbat.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/b6/94d26985a363ee0238ddaf899e2567/slowlycivilbuck.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/7a/e1e0a559087a8c8d70f19682163a1d/slowlycivilbuck.bam.bai" + ] + ], + "mt_bam_bai_gatksubwf": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "mtshift_bam_bai_gatksubwf": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] + ], + "versions": [ + + ] + } +PASSED (4812.56s) + +Test Workflow ALIGN_MT + + Test [b23715c6] 'align mt - bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: b10847aa0f + [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "2": [ + + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "versions": [ + + ] + } +PASSED (1439.157s) + Test [846f97b8] 'align mt - bwa' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: f6ad620135 + [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "2": [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "versions": [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" + ] + } +PASSED (1343.021s) + +Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME + + Test [dfe67d65] 'align bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 399b5fe8cb + [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" + ] + ], + "4": [ + + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" + ] + ], + "versions": [ + + ] + } +PASSED (296.275s) + Test [6b77a48f] 'align bwameme' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 9f7b282f72 + [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" + ] + ], + "4": [ + + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" + ] + ], + "versions": [ + + ] + } +PASSED (321.442s) + +Test Workflow ALIGN_SENTIEON + + Test [b3f3ddb4] 'align sentieon' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 2840f9cc33 + [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" + ] + ], + "6": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" + ] + ], + "7": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" + ] + ], + "aln_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" + ] + ], + "gc_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" + ] + ], + "gc_summary": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" + ] + ], + "is_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" + ] + ], + "mq_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" + ] + ], + "qd_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" + ] + ] + } +PASSED (340.075s) + +Test Workflow CALL_REPEAT_EXPANSIONS + + Test [9ebd2699] 'CALL_REPEAT_EXPANSIONS' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value + > WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value + WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 5dde73596c + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" + ] + ] + } +PASSED (518.242s) + +Test Workflow PREPARE_REFERENCES + + Test [8ce0dfef] 'Should run without failures' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 + > [HISAT2 index build] Available memory: 15 GB + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 + [HISAT2 index build] Available memory: 15 GB + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 458de812a0 + [HISAT2 index build] Available memory: 15 GB + [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" + ] + ], + "1": [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ], + "10": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" + ] + ], + "11": [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" + ] + ], + "12": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" + ] + ], + "13": [ + + ], + "14": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" + ] + ], + "15": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" + ] + ], + "16": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" + ] + ], + "17": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" + ] + ], + "18": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" + ] + ], + "19": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" + ] + ], + "2": [ + [ + { + "id": "dbsnp_-138-" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" + ] + ], + "20": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" + ] + ], + "21": [ + + ], + "22": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" + ] + ], + "23": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" + ] + ], + "24": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" + ] + ], + "25": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" + ] + ], + "26": [ + + ], + "27": [ + [ + { + "id": "target" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" + ] + ], + "28": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" + ] + ], + "29": [ + [ + [ + + ] + ] + ], + "3": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" + ] + ], + "30": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" + ] + ], + "4": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" + ] + ], + "5": [ + + ], + "6": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" + ] + ], + "7": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" + ] + ], + "8": [ + [ + { + "id": "reference" + }, + "/nf-core/test-datasets/raredisease/reference/reference.fasta" + ] + ], + "9": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" + ] + ], + "bait_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" + ] + ], + "dbsnp": [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ], + "dbsnp_tbi": [ + [ + { + "id": "dbsnp_-138-" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" + ] + ], + "genome_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" + ] + ], + "genome_bwamem2_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" + ] + ], + "genome_bwameme_index": [ + + ], + "genome_chrom_sizes": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" + ] + ], + "genome_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" + ] + ], + "genome_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" + ] + ], + "genome_fasta": [ + [ + { + "id": "reference" + }, + "/nf-core/test-datasets/raredisease/reference/reference.fasta" + ] + ], + "genome_hisat2_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" + ] + ], + "gnomad_af_idx": [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" + ] + ], + "mt_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" + ] + ], + "mt_bwamem2_index": [ + + ], + "mt_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" + ] + ], + "mt_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" + ] + ], + "mt_fasta": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" + ] + ], + "mt_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" + ] + ], + "mt_last_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" + ] + ], + "mtshift_backchain": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" + ] + ], + "mtshift_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" + ] + ], + "mtshift_bwamem2_index": [ + + ], + "mtshift_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" + ] + ], + "mtshift_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" + ] + ], + "mtshift_fasta": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" + ] + ], + "mtshift_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" + ] + ], + "sdf": [ + + ], + "target_bed": [ + [ + { + "id": "target" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" + ] + ], + "target_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" + ] + ], + "vcfanno_extra": [ + [ + [ + + ] + ] + ], + "vep_resources": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" + ] + ] + } +PASSED (1793.716s) + +Test Workflow QC_BAM + + Test [afc7bf7a] 'QC_BAM - test, bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: ad4f64ff7c + [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "10": [ + + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" + ] + ], + "4": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" + ] + ], + "5": [ + + ], + "6": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "bigwig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" + ] + ], + "cov": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "cov_y": [ + + ], + "d4": [ + + ], + "global_dist": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "hs_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "multiple_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "qualimap_results": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" + ] + ], + "self_sm": [ + + ], + "sex_check": [ + + ], + "tiddit_wig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" + ] + ] + } +PASSED (291.083s) + Test [f2c7c2bb] 'QC_BAM - test, sentieon' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 60d4a16c8e + [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "10": [ + + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" + ] + ], + "4": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" + ] + ], + "5": [ + + ], + "6": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" + ] + ], + "bigwig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" + ] + ], + "cov": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" + ] + ], + "cov_y": [ + + ], + "d4": [ + + ], + "global_dist": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "hs_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "multiple_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "qualimap_results": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" + ] + ], + "self_sm": [ + + ], + "sex_check": [ + + ], + "tiddit_wig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" + ] + ] + } +PASSED (214.248s) + +Test Workflow SCATTER_GENOME + + Test [ad40db63] 'Should run without failures' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 5c5d631253 + [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) + [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "genome" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" + ] + ], + "1": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" + ] + ], + "bed": [ + [ + { + "id": "genome" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" + ] + ], + "split_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" + ] + ] + } +PASSED (512.277s) + + +SUCCESS: Executed 13 tests in 17995.327s + diff --git a/wflog2 b/wflog2 new file mode 100644 index 000000000..4f05bdf51 --- /dev/null +++ b/wflog2 @@ -0,0 +1,10617 @@ +Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp + +🚀 nf-test 0.9.4 +https://www.nf-test.com +(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr + +Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar +Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar +Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar +Warning: every snapshot that fails during this test run is re-recorded. + +Test pipeline + + Test [6304aa7b] '-profile test' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - default + > config_profile_description : Minimal test dataset to check pipeline function + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_00-58-31 + > + > Core Nextflow options + > runName : zen_franklin + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - default + config_profile_description : Minimal test dataset to check pipeline function + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_00-58-31 + + Core Nextflow options + runName : zen_franklin + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (32575.636s) + Snapshots: + 1 updated [-profile test] + +Test pipeline + + Test [df780376] '-profile test_bam' + + Profiles: [test_bam, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/params.json -ansi-log false -profile test_bam,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > ngsbits_samplegender_method : sry + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - bam + > config_profile_description : Minimal test dataset to check pipeline function + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_10-01-37 + > + > Core Nextflow options + > runName : gloomy_newton + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test_bam,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + ngsbits_samplegender_method : sry + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - bam + config_profile_description : Minimal test dataset to check pipeline function + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_10-01-37 + + Core Nextflow options + runName : gloomy_newton + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test_bam,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (18448.933s) + Snapshots: + 1 updated [-profile test_bam] + +Test pipeline + + Test [577d1960] '-profile test_singleton' + + Profiles: [test_singleton, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/params.json -ansi-log false -profile test_singleton,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - singleton + > config_profile_description : Minimal test dataset to check pipeline function using a single sample + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_15-09-08 + > + > Core Nextflow options + > runName : zen_hugle + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test_singleton,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - singleton + config_profile_description : Minimal test dataset to check pipeline function using a single sample + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_15-09-08 + + Core Nextflow options + runName : zen_hugle + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test_singleton,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (13011.306s) + Snapshots: + 1 updated [-profile test_singleton] + + +Snapshot Summary: + 3 updated + +SUCCESS: Executed 3 tests in 64038.604s + diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index f0e1cd12b..cff53f4f9 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -460,7 +460,6 @@ workflow RAREDISEASE { ch_ranksnv_nuclear_in, false ) - ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) } // @@ -531,7 +530,6 @@ workflow RAREDISEASE { ch_ranksnv_mt_in, false ) - ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions) } } @@ -580,7 +578,6 @@ workflow RAREDISEASE { val_genome, val_vep_cache_version ).set { ch_sv_annotate } - ch_versions = ch_versions.mix(ch_sv_annotate.versions) ch_sv_annotate.vcf_ann .multiMap { meta, vcf -> @@ -625,7 +622,6 @@ workflow RAREDISEASE { ch_ranksnv_sv_in, true ) - ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) } } /* @@ -661,7 +657,6 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) - ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } /* @@ -769,7 +764,7 @@ workflow RAREDISEASE { */ if (!skip_vcf2cytosure && val_analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { GENERATE_CYTOSURE_FILES ( - ch_mapped.genome_marked_bam, + ch_mapped.genome_marked_bam_bai, ch_vcf2cytosure_blacklist, ch_sample_id_map, ch_sv_annotate.tbi, From ff3b29e2c4a65955ecbe2b57766bf3a50fe517e7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 19:35:20 +0100 Subject: [PATCH 327/872] remove logs --- miss | 0 test.sh | 2 - wflog1 | 6024 ------------------------------- wflog2 | 10617 ------------------------------------------------------ 4 files changed, 16643 deletions(-) delete mode 100644 miss delete mode 100644 test.sh delete mode 100644 wflog1 delete mode 100644 wflog2 diff --git a/miss b/miss deleted file mode 100644 index e69de29bb..000000000 diff --git a/test.sh b/test.sh deleted file mode 100644 index c76b0b687..000000000 --- a/test.sh +++ /dev/null @@ -1,2 +0,0 @@ -nf-test test subworkflows/local/ --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >wflog 2>&1 -nf-test test tests --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >>wflog 2>&1 diff --git a/wflog1 b/wflog1 deleted file mode 100644 index d4a1be1a7..000000000 --- a/wflog1 +++ /dev/null @@ -1,6024 +0,0 @@ -Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp - -🚀 nf-test 0.9.4 -https://www.nf-test.com -(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr - -Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar -Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar -Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar -Warning: every snapshot that fails during this test run is re-recorded. - -Test Workflow ALIGN - - Test [9e55951e] 'align bwamem2 - wgs' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 76951fb0df - [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e0/2e14cf254f7fbb4dc949380310a337/earlycasualcaiman.fastp.json" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/98/26e65c7abf446866ff37cbbd541717/hugelymodelbat.fastp.json" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/f5/98f07ad89689da1a3f1100da58ed14/slowlycivilbuck.fastp.json" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/bf/df3174d0c94ba9bcfdf3f79ac94aff/earlycasualcaiman.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/24/2893d5535a534aa7039df0a5261eea/earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/c4c15846708fac2faff4a670b81503/hugelymodelbat.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/12/26927042b8031768ba14d2a75910f5/hugelymodelbat.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/9b/c35b8bf43ad637c89a38893c11055e/slowlycivilbuck.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/8c/d4a49d10b0869d21d9186339b356b8/slowlycivilbuck.bam.bai" - ] - ], - "6": [ - [ - { - 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"id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] - ], - "versions": [ - - ] - } -PASSED (5684.323s) - Test [59260ec0] 'align bwamem2 - wes' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: db2dc4c6c7 - [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/b8/4d574f613662456c74c71fbcd5c43a/earlycasualcaiman.fastp.json" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/51/29cdff1116f2d5e95019c51dfab7ad/hugelymodelbat.fastp.json" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/41/6ea3afbfecf3264f36467ff22e97cd/slowlycivilbuck.fastp.json" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": 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1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam" - ] - ], - "genome_marked_bam_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "markdup_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "mt_bam_bai": [ - - ], - "mt_bam_bai_gatksubwf": [ - - ], - "mtshift_bam_bai_gatksubwf": [ - - ], - "versions": [ - - ] - } -PASSED (422.715s) - Test [412be509] 'align bwameme - wgs' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 615692c6bf - [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/8f/07d888a3a1a96250875143512851fc/earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6e/1e98c80a7f7f86de7f7ad0079d83c4/hugelymodelbat.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/06/a0bcb0d96d10dd4846aa48058420ad/hugelymodelbat.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/b6/94d26985a363ee0238ddaf899e2567/slowlycivilbuck.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/7a/e1e0a559087a8c8d70f19682163a1d/slowlycivilbuck.bam.bai" - ] - ], - "mt_bam_bai_gatksubwf": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "mtshift_bam_bai_gatksubwf": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] - ], - "versions": [ - - ] - } -PASSED (4812.56s) - -Test Workflow ALIGN_MT - - Test [b23715c6] 'align mt - bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: b10847aa0f - [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "2": [ - - ], - "marked_bai": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "versions": [ - - ] - } -PASSED (1439.157s) - Test [846f97b8] 'align mt - bwa' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: f6ad620135 - [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "2": [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" - ], - "marked_bai": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "versions": [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" - ] - } -PASSED (1343.021s) - -Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME - - Test [dfe67d65] 'align bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 399b5fe8cb - [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "3": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" - ] - ], - "4": [ - - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" - ] - ], - "metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "stats": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" - ] - ], - "versions": [ - - ] - } -PASSED (296.275s) - Test [6b77a48f] 'align bwameme' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 9f7b282f72 - [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "3": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" - ] - ], - "4": [ - - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" - ] - ], - "metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "stats": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" - ] - ], - "versions": [ - - ] - } -PASSED (321.442s) - -Test Workflow ALIGN_SENTIEON - - Test [b3f3ddb4] 'align sentieon' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 2840f9cc33 - [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" - ] - ] - } -PASSED (340.075s) - -Test Workflow CALL_REPEAT_EXPANSIONS - - Test [9ebd2699] 'CALL_REPEAT_EXPANSIONS' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value - > WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value - WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 5dde73596c - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" - ] - ], - "vcf": [ - [ - { - "id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" - ] - ] - } -PASSED (518.242s) - -Test Workflow PREPARE_REFERENCES - - Test [8ce0dfef] 'Should run without failures' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 - > [HISAT2 index build] Available memory: 15 GB - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 - [HISAT2 index build] Available memory: 15 GB - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 458de812a0 - [HISAT2 index build] Available memory: 15 GB - [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" - ] - ], - "1": [ - [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" - ] - ], - "10": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" - ] - ], - "11": [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" - ] - ], - "12": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" - ] - ], - "13": [ - - ], - "14": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" - ] - ], - "15": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" - ] - ], - "16": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" - ] - ], - "17": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" - ] - ], - "18": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" - ] - ], - "19": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" - ] - ], - "2": [ - [ - { - "id": "dbsnp_-138-" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" - ] - ], - "20": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" - ] - ], - "21": [ - - ], - "22": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" - ] - ], - "23": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" - ] - ], - "24": [ - [ - { - "id": "reference" - }, - 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" - ] - ], - "genome_bwamem2_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" - ] - ], - "genome_bwameme_index": [ - - ], - "genome_chrom_sizes": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" - ] - ], - "genome_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" - ] - ], - "genome_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" - ] - ], - "genome_fasta": [ - [ - { - "id": "reference" - }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" - ] - ], - "genome_hisat2_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" - ] - ], - "gnomad_af_idx": [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" - ] - ], - "mt_bwa_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" - ] - ], - "mt_bwamem2_index": [ - - ], - "mt_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" - ] - ], - "mt_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" - ] - ], - "mt_fasta": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" - ] - ], - "mt_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" - ] - ], - "mt_last_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" - ] - ], - "mtshift_backchain": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" - ] - ], - "mtshift_bwa_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" - ] - ], - "mtshift_bwamem2_index": [ - - ], - "mtshift_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" - ] - ], - "mtshift_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" - ] - ], - "mtshift_fasta": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" - ] - ], - "mtshift_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" - ] - ], - "sdf": [ - - ], - "target_bed": [ - [ - { - "id": "target" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" - ] - ], - "target_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" - ] - ], - "vcfanno_extra": [ - [ - [ - - ] - ] - ], - "vep_resources": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" - ] - ] - } -PASSED (1793.716s) - -Test Workflow QC_BAM - - Test [afc7bf7a] 'QC_BAM - test, bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: ad4f64ff7c - [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "10": [ - - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" - ] - ], - "3": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" - ] - ], - "4": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" - ] - ], - "5": [ - - ], - "6": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" - ] - ], - "bigwig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" - ] - ], - "cov": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" - ] - ], - "cov_y": [ - - ], - "d4": [ - - ], - "global_dist": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "hs_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "multiple_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "qualimap_results": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" - ] - ] - } -PASSED (291.083s) - Test [f2c7c2bb] 'QC_BAM - test, sentieon' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 60d4a16c8e - [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "10": [ - - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" - ] - ], - "3": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" - ] - ], - "4": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" - ] - ], - "5": [ - - ], - "6": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" - ] - ], - "bigwig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" - ] - ], - "cov": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" - ] - ], - "cov_y": [ - - ], - "d4": [ - - ], - "global_dist": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "hs_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "multiple_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "qualimap_results": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" - ] - ] - } -PASSED (214.248s) - -Test Workflow SCATTER_GENOME - - Test [ad40db63] 'Should run without failures' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 5c5d631253 - [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "genome" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" - ] - ], - "1": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" - ] - ], - "bed": [ - [ - { - "id": "genome" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" - ] - ], - "split_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" - ] - ] - } -PASSED (512.277s) - - -SUCCESS: Executed 13 tests in 17995.327s - diff --git a/wflog2 b/wflog2 deleted file mode 100644 index 4f05bdf51..000000000 --- a/wflog2 +++ /dev/null @@ -1,10617 +0,0 @@ -Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp - -🚀 nf-test 0.9.4 -https://www.nf-test.com -(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr - -Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar -Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar -Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar -Warning: every snapshot that fails during this test run is re-recorded. - -Test pipeline - - Test [6304aa7b] '-profile test' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - default - > config_profile_description : Minimal test dataset to check pipeline function - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_00-58-31 - > - > Core Nextflow options - > runName : zen_franklin - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - default - config_profile_description : Minimal test dataset to check pipeline function - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_00-58-31 - - Core Nextflow options - runName : zen_franklin - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (32575.636s) - Snapshots: - 1 updated [-profile test] - -Test pipeline - - Test [df780376] '-profile test_bam' - - Profiles: [test_bam, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/params.json -ansi-log false -profile test_bam,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > ngsbits_samplegender_method : sry - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - bam - > config_profile_description : Minimal test dataset to check pipeline function - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_10-01-37 - > - > Core Nextflow options - > runName : gloomy_newton - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test_bam,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - ngsbits_samplegender_method : sry - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - bam - config_profile_description : Minimal test dataset to check pipeline function - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_10-01-37 - - Core Nextflow options - runName : gloomy_newton - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test_bam,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (18448.933s) - Snapshots: - 1 updated [-profile test_bam] - -Test pipeline - - Test [577d1960] '-profile test_singleton' - - Profiles: [test_singleton, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/params.json -ansi-log false -profile test_singleton,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - singleton - > config_profile_description : Minimal test dataset to check pipeline function using a single sample - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_15-09-08 - > - > Core Nextflow options - > runName : zen_hugle - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test_singleton,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - singleton - config_profile_description : Minimal test dataset to check pipeline function using a single sample - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_15-09-08 - - Core Nextflow options - runName : zen_hugle - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test_singleton,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (13011.306s) - Snapshots: - 1 updated [-profile test_singleton] - - -Snapshot Summary: - 3 updated - -SUCCESS: Executed 3 tests in 64038.604s - From 4d023ecdcbc4adc96693cafc260af3e408a15fcd Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 20:27:24 +0100 Subject: [PATCH 328/872] update modules --- modules.json | 6 +- modules/nf-core/bwamem2/mem/main.nf | 49 ++++---- modules/nf-core/bwamem2/mem/meta.yml | 19 +++ .../nf-core/bwamem2/mem/tests/main.nf.test | 8 +- .../bwamem2/mem/tests/main.nf.test.snap | 109 +++++++++--------- .../ensemblvep/filtervep/environment.yml | 4 +- modules/nf-core/ensemblvep/filtervep/main.nf | 5 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 37 ++++-- .../filtervep/tests/main.nf.test.snap | 14 +++ .../vcf_filter_bcftools_ensemblvep/main.nf | 1 - 10 files changed, 152 insertions(+), 100 deletions(-) diff --git a/modules.json b/modules.json index 9c46403dd..d0dbd21bc 100644 --- a/modules.json +++ b/modules.json @@ -82,7 +82,7 @@ }, "bwamem2/mem": { "branch": "master", - "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", + "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a", "installed_by": ["modules"] }, "bwameme/index": { @@ -137,7 +137,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2", + "git_sha": "09ea5d9fcd6eda714f148e0f3b6a4920b2091f41", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { @@ -588,7 +588,7 @@ }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", - "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", + "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index d1c0ac8f6..b8ac263b5 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -1,25 +1,26 @@ process BWAMEM2_MEM { - tag "$meta.id" + tag "${meta.id}" label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : - 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' + : 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113'}" input: tuple val(meta), path(reads) tuple val(meta2), path(index) tuple val(meta3), path(fasta) - val sort_bam + val sort_bam output: - tuple val(meta), path("*.sam") , emit: sam , optional:true - tuple val(meta), path("*.bam") , emit: bam , optional:true - tuple val(meta), path("*.cram") , emit: cram, optional:true - tuple val(meta), path("*.crai") , emit: crai, optional:true - tuple val(meta), path("*.csi") , emit: csi , optional:true + tuple val(meta), path("*.sam"), emit: sam, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -31,39 +32,41 @@ process BWAMEM2_MEM { def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" - if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" - + def reference = fasta && extension == "cram" ? "--reference ${fasta}" : "" + if (!fasta && extension == "cram") { + error("Fasta reference is required for CRAM output") + } """ INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` bwa-mem2 \\ mem \\ - $args \\ - -t $task.cpus \\ + ${args} \\ + -t ${task.cpus} \\ \$INDEX \\ - $reads \\ - | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} - + ${reads} \\ + | samtools ${samtools_command} ${args2} -@ ${task.cpus} ${reference} -o ${prefix}.${extension} - """ stub: - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" + if (!fasta && extension == "cram") { + error("Fasta reference is required for CRAM output") + } def create_index = "" if (extension == "cram") { create_index = "touch ${prefix}.crai" - } else if (extension == "bam") { + } + else if (extension == "bam") { create_index = "touch ${prefix}.csi" } - """ touch ${prefix}.${extension} ${create_index} diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index bcfd006df..a60d67889 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -129,6 +129,16 @@ output: - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": type: eval description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -140,6 +150,15 @@ topics: - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": type: eval description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 20e372545..be33a3a7e 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -50,7 +50,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - fastq, index, fasta, true") { @@ -79,7 +78,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, false") { @@ -111,7 +109,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, true") { @@ -143,7 +140,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") { @@ -170,10 +166,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index 74763935c..06d854b00 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -10,52 +10,25 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:27.481278728", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:00.500092" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - "BWAMEM2_MEM", - "bwamem2", - "2.2.1" - ] - ], "bam": [ [ { @@ -89,14 +62,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:54:06.902806102", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:22.004027" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ @@ -109,14 +89,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:40.483217643", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:14.131056" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq, index, fasta, false": { "content": [ @@ -129,14 +116,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:02.459481643", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:24:34.624533" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq, index, fasta, true": { "content": [ @@ -149,13 +143,20 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:15.170720681", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:24:47.191245" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index d9ed9b6bd..7e60f7f95 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/ensembl-vep - - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 + - bioconda::ensembl-vep=115.2 + - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index dcf0148ef..ed561b023 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' - : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" input: tuple val(meta), path(input) @@ -14,6 +14,7 @@ process ENSEMBLVEP_FILTERVEP { output: tuple val(meta), path("*.${extension}"), emit: output tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index 68928cfc8..6c6641597 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_filtervep -description: Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations. +description: Filter variants based on Ensembl Variant Effect Predictor (VEP) + annotations. keywords: - annotation - vcf @@ -12,7 +13,8 @@ tools: or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html - licence: ["Apache-2.0"] + licence: + - "Apache-2.0" identifier: "" input: - - meta: @@ -25,11 +27,11 @@ input: description: VCF/TAB file annotated with vep pattern: "*.{vcf,tab,tsv,txt}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 - feature_file: type: file - description: File containing features on separate lines. To be used with --filter - option. + description: File containing features on separate lines. To be used with + --filter option. ontologies: [] output: output: @@ -43,7 +45,7 @@ output: description: VCF/TAB file pattern: "*.{vcf,tab,txt,tsv}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_ensemblvep: - - ${task.process}: type: string @@ -52,8 +54,18 @@ output: type: string description: The tool name - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string + type: eval description: The command used to generate the version of the tool + versions_perlmathcdf: + - - ${task.process}: + type: string + description: The process the versions were collected from + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -63,8 +75,17 @@ topics: type: string description: The tool name - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string + type: eval description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 1559d7e79..0bd02680e 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -8,6 +8,13 @@ "ensemblvep", "115.2" ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_FILTERVEP", + "perl-math-cdf", + "" + ] ] } ], @@ -26,6 +33,13 @@ "ensemblvep", "115.2" ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_FILTERVEP", + "perl-math-cdf", + "" + ] ] } ], diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 33b4d9a8d..00c752502 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -11,7 +11,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { filter_with_filter_vep // bool: should filter_vep be run main: - ch_versions = channel.empty() ch_tbi = channel.empty() // Since bcftools is likely much faster than filter_vep, From a2426c8fd350bc8e8bc99a8a296669999c114f8d Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 20:57:44 +0100 Subject: [PATCH 329/872] update vep --- modules.json | 471 +++++++++++++----- .../ensemblvep/vep/ensemblvep-vep.diff | 61 +-- .../nf-core/ensemblvep/vep/environment.yml | 8 + modules/nf-core/ensemblvep/vep/main.nf | 69 +-- modules/nf-core/ensemblvep/vep/meta.yml | 227 +++++++-- .../nf-core/ensemblvep/vep/tests/main.nf.test | 89 ++++ .../ensemblvep/vep/tests/main.nf.test.snap | 69 +++ .../ensemblvep/vep/tests/nextflow.config | 5 + .../ensemblvep/vep/tests/tab.gz.config | 5 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + 10 files changed, 770 insertions(+), 239 deletions(-) create mode 100644 modules/nf-core/ensemblvep/vep/environment.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config diff --git a/modules.json b/modules.json index d0dbd21bc..4d01e7c44 100644 --- a/modules.json +++ b/modules.json @@ -8,564 +8,791 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/sample": { "branch": "master", "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -574,25 +801,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index f141ba410..b94671e36 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -1,51 +1,34 @@ Changes in component 'nf-core/ensemblvep/vep' +Changes in 'ensemblvep/vep/environment.yml': +--- modules/nf-core/ensemblvep/vep/environment.yml ++++ modules/nf-core/ensemblvep/vep/environment.yml +@@ -4,5 +4,5 @@ + - conda-forge + - bioconda + dependencies: +- - bioconda::ensembl-vep=115.2 ++ - bioconda::ensembl-vep=110.1 + - bioconda::perl-math-cdf=0.1 + 'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf +++ modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ - conda "bioconda::ensembl-vep=110.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : -- 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : -+ 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container +- ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' +- : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" ++ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' ++ : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" input: tuple val(meta), path(vcf), path(custom_extra_files) -@@ -20,8 +20,8 @@ - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json -- path "*.summary.html" , emit: report -- path "versions.yml" , emit: versions -+ tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true -+ tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - - when: - task.ext.when == null || task.ext.when -@@ -48,11 +48,6 @@ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ - -- -- cat <<-END_VERSIONS > versions.yml -- "${task.process}": -- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') -- END_VERSIONS - """ - - stub: -@@ -63,9 +58,5 @@ - touch ${prefix}.json.gz - touch ${prefix}.summary.html - -- cat <<-END_VERSIONS > versions.yml -- "${task.process}": -- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') -- END_VERSIONS - """ - } +'modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap' is unchanged +'modules/nf-core/ensemblvep/vep/tests/tab.gz.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/vcf.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/nextflow.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml new file mode 100644 index 000000000..744ccc71c --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::ensembl-vep=110.1 + - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 61da45d06..2e79210f3 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,62 +1,67 @@ process ENSEMBLVEP_VEP { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' - conda "bioconda::ensembl-vep=110.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : - 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" input: tuple val(meta), path(vcf), path(custom_extra_files) - val genome - val species - val cache_version - path cache + val genome + val species + val cache_version + path cache tuple val(meta2), path(fasta) - path extra_files + path extra_files output: - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json + tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.tab.gz"), emit: tab, optional: true + tuple val(meta), path("${prefix}.json.gz"), emit: json, optional: true tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \\\$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' + def args2 = task.ext.args2 ?: '' + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" - def reference = fasta ? "--fasta $fasta" : "" + def reference = fasta ? "--fasta ${fasta}" : "" + def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : "" """ vep \\ - -i $vcf \\ + -i ${vcf} \\ -o ${prefix}.${file_extension}.gz \\ - $args \\ - $compress_cmd \\ - $reference \\ - --assembly $genome \\ - --species $species \\ + ${args} \\ + ${compress_cmd} \\ + ${reference} \\ + --assembly ${genome} \\ + --species ${species} \\ --cache \\ - --cache_version $cache_version \\ - --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --cache_version ${cache_version} \\ + --dir_cache ${dir_cache} \\ + --fork ${task.cpus} + ${create_index} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' + def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : "" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz - touch ${prefix}.summary.html - + echo "" | gzip > ${prefix}.${file_extension}.gz + ${create_index} + touch ${prefix}_summary.html """ } diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847dc..48f025495 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ -name: ENSEMBLVEP_VEP -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +name: ensemblvep_vep +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is + controlled through `task.ext.args`. keywords: - annotation - vcf @@ -12,22 +13,26 @@ tools: or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html - licence: ["Apache-2.0"] + licence: + - "Apache-2.0" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + ontologies: [] + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + ontologies: [] - genome: type: string description: | @@ -44,45 +49,167 @@ input: type: file description: | path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + ontologies: [] - extra_files: type: file description: | path to file(s) needed for plugins (optional) + ontologies: [] output: - - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" - - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" - - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" - - report: - type: file - description: VEP report file - pattern: "*.html" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + vcf: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.vcf.gz: + type: file + description: | + annotated vcf (optional) + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + tbi: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.vcf.gz.tbi: + type: file + description: | + annotated vcf index (optional) + pattern: "*.vcf.gz.tbi" + ontologies: [] + tab: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.tab.gz: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + json: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.json.gz: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + report: + - - meta: + type: map + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions_ensemblvep: + - - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: eval + description: The command used to generate the version of the tool + versions_tabix: + - - ${task.process}: + type: string + description: The process + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + versions_perlmathcdf: + - - ${task.process}: + type: string + description: The process + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool +topics: + multiqc_files: + - - meta: + type: string + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: eval + description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The process + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 000000000..374f840cf --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + + test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") { + config "./vcf.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.vcf[0][1]).name + ",variantsMD5:" + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.tab[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") + }).match() }, + { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 000000000..96c18d9cd --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + "test.tab.gz", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_VEP", + "perl-math-cdf", + "0.1" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-06T12:47:57.03116265" + }, + "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { + "content": [ + "test.vcf.gz,variantsMD5:d41d8cd98f00b204e9800998ecf8427e", + "test.vcf.gz.tbi", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_VEP", + "perl-math-cdf", + "0.1" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-06T12:47:34.421995264" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 000000000..8e68fe24a --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,5 @@ +params { + vep_cache_version = "115" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 000000000..40eb03e59 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 000000000..ad8955a37 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} From 761a6b5a28ae05fd7e35878b18c42bf03fd0a8cb Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 21:00:20 +0100 Subject: [PATCH 330/872] Update modules.json --- modules.json | 469 +++++++++++++-------------------------------------- 1 file changed, 117 insertions(+), 352 deletions(-) diff --git a/modules.json b/modules.json index 4d01e7c44..6e017be96 100644 --- a/modules.json +++ b/modules.json @@ -8,791 +8,564 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - 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"installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upd": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -801,33 +574,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 70d2d5656b7717bfb94fdb8a79d04fe1f814507a Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 20 Feb 2026 13:51:03 +0100 Subject: [PATCH 331/872] removed haplocheck --- CITATIONS.md | 4 - assets/multiqc_config.yml | 3 - conf/modules/call_snv_MT.config | 14 +-- docs/output.md | 13 --- modules.json | 5 - modules/nf-core/haplocheck/environment.yml | 5 - modules/nf-core/haplocheck/main.nf | 44 -------- modules/nf-core/haplocheck/meta.yml | 60 ----------- modules/nf-core/haplocheck/tests/main.nf.test | 56 ---------- .../haplocheck/tests/main.nf.test.snap | 100 ------------------ subworkflows/local/call_snv_MT/main.nf | 6 -- 11 files changed, 1 insertion(+), 309 deletions(-) delete mode 100644 modules/nf-core/haplocheck/environment.yml delete mode 100644 modules/nf-core/haplocheck/main.nf delete mode 100644 modules/nf-core/haplocheck/meta.yml delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test.snap diff --git a/CITATIONS.md b/CITATIONS.md index bd5c97d4f..7c25c42cf 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -76,10 +76,6 @@ > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081 -- [Haplocheck](https://genome.cshlp.org/content/31/2/309.long) - - > Weissensteiner H, Forer L, Fendt L, et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 2021;31(2):309-316. doi:10.1101/gr.256545.119 - - [HaploGrep 2](https://academic.oup.com/nar/article/44/W1/W58/2499296) > Weissensteiner H, Pacher D, Kloss-Brandstätter A, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58-W63. doi:10.1093/nar/gkw233 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 0fa4b51ef..2e69f6a3d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -20,7 +20,6 @@ export_plots: true run_modules: - fastqc - fastp - - haplocheck - qualimap - picard - mosdepth @@ -42,8 +41,6 @@ module_order: name: "fastp" - mosdepth: name: "Mosdepth" - - haplocheck: - name: "haplocheck" - ngsbits: name: "ngsbits" - peddy: diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config index f77d2f6b1..f6a49bf50 100644 --- a/conf/modules/call_snv_MT.config +++ b/conf/modules/call_snv_MT.config @@ -26,14 +26,6 @@ process { ext.prefix = { "${meta.id}_filtered" } } - withName: '.*CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT' { - publishDir = [ - path: { "${params.outdir}/haplocheck" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.endsWith(".txt") ? filename : null } - ] - } - } // @@ -51,8 +43,4 @@ process { ext.prefix = { "${meta.id}_filtered_shifted" } } - withName: '.*CALL_SNV_MT_SHIFT:HAPLOCHECK_MT' { - ext.when = false - } - -} +} \ No newline at end of file diff --git a/docs/output.md b/docs/output.md index 5c5d0401a..1a9ff5a9e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -59,7 +59,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [SVDB query](#svdb-query) - [VEP](#vep-1) - [Mitochondrial analysis](#mitochondrial-analysis) - - [Haplocheck](#haplocheck) - [Alignment and variant calling](#alignment-and-variant-calling) - [MT deletion script](#mt-deletion-script) - [eKLIPse](#eklipse) @@ -461,18 +460,6 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e Mitochondrial analysis is run by default. If you want to turn off annotations set `--skip_subworkflows mt_annotation`. -#### Haplocheck - -[Haplocheck](https://github.com/genepi/haplocheck/) analyses the mitochondrial content to detect contamination in samples. The results are displayed in MultiQC. - -
    -Output files - -- `{outputdir}/haplocheck/` - - `.raw.txt`: haplocheck raw output. Read more about the file content [here](https://mitoverse.readthedocs.io/haplocheck/haplocheck/#textual-report-file-raw). - -
    - #### Alignment and variant calling [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-) The mitochondrial genome poses several challenges to the identification and understanding of somatic variants. The circularity of the mitochondrial genome means that the breakpoint in the reference genome is at an arbitrary position in the non-coding control region, creating a challenge in analyzing variation. Additionally, insertions of mitochondrial DNA into the nuclear genome (NuMTs) complicate the mapping of the mitochondrial genome and the distinction between NuMTs and the mitochondrial contig of interest. Lastly, mitochondrial variants often have very low heteroplasmy. Such low allele fraction (AF) variants can thus be mistaken for inherent sequencer noise. diff --git a/modules.json b/modules.json index 12ce80fb0..1849a5759 100644 --- a/modules.json +++ b/modules.json @@ -286,11 +286,6 @@ "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8", "installed_by": ["modules"] }, - "haplocheck": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "haplogrep3/classify": { "branch": "master", "git_sha": "c95c60597ce23da23ac21f4e6c5d7c0cdb711b8f", diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml deleted file mode 100644 index 4fb40238b..000000000 --- a/modules/nf-core/haplocheck/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf deleted file mode 100644 index 0d26c449e..000000000 --- a/modules/nf-core/haplocheck/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process HAPLOCHECK { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - 'biocontainers/haplocheck:1.3.3--h4a94de4_0' }" - - input: - tuple val(meta), path(vcf) - - output: - tuple val(meta), path("*.txt") , emit: txt - tuple val(meta), path("*.html"), emit: html - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - haplocheck --raw --out $prefix $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.raw.txt - touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml deleted file mode 100644 index 25e6127a7..000000000 --- a/modules/nf-core/haplocheck/meta.yml +++ /dev/null @@ -1,60 +0,0 @@ -name: "haplocheck" -description: | - Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing - the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides - users a graphical report to investigate the contamination further. Internally, it uses the - Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. -keywords: - - mitochondrial - - mtDNA - - contamination -tools: - - "haplocheck": - description: "Detects in-sample contamination in mtDNA or WGS sequencing studies - by analyzing the mitochondrial content." - homepage: "https://github.com/genepi/haplocheck" - documentation: "https://github.com/genepi/haplocheck" - tool_dev_url: "https://github.com/genepi/haplocheck" - doi: 10.1101/gr.256545.119 - licence: ["MIT"] - identifier: biotools:haplocheck -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" -output: - - txt: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.txt": - type: file - description: Raw report in txt format - pattern: "*.{txt}" - - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: Haplocheck HTML report - pattern: "*.{html}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@lmtani" -maintainers: - - "@lmtani" diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test deleted file mode 100644 index 8957d02e2..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test +++ /dev/null @@ -1,56 +0,0 @@ - -nextflow_process { - - name "Test Process HAPLOCHECK" - script "../main.nf" - process "HAPLOCHECK" - - tag "modules" - tag "modules_nfcore" - tag "haplocheck" - - test("test-haplocheck") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test-haplocheck-stub") { - options '-stub' - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} diff --git a/modules/nf-core/haplocheck/tests/main.nf.test.snap b/modules/nf-core/haplocheck/tests/main.nf.test.snap deleted file mode 100644 index abe1eab56..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test.snap +++ /dev/null @@ -1,100 +0,0 @@ -{ - "test-haplocheck-stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:41:40.703528" - }, - "test-haplocheck": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:43:05.761086" - } -} \ No newline at end of file diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 353e96e0e..14c4c4701 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -2,7 +2,6 @@ // Call SNV MT // -include { HAPLOCHECK as HAPLOCHECK_MT } from '../../../modules/nf-core/haplocheck/main' include { GATK4_MUTECT2 as GATK4_MUTECT2_MT } from '../../../modules/nf-core/gatk4/mutect2/main' include { GATK4_FILTERMUTECTCALLS as GATK4_FILTERMUTECTCALLS_MT } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' @@ -21,9 +20,6 @@ workflow CALL_SNV_MT { GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) - HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf) - ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions) - // Filter Mutect2 calls ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) ch_mutect_out = ch_mutect_vcf.join(GATK4_MUTECT2_MT.out.stats, failOnMismatch:true, failOnDuplicate:true) @@ -36,10 +32,8 @@ workflow CALL_SNV_MT { emit: filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] - html = HAPLOCHECK_MT.out.html // channel: [ val(meta), path(html) ] stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] - txt = HAPLOCHECK_MT.out.txt // channel: [ val(meta), path(txt) ] vcf = GATK4_FILTERMUTECTCALLS_MT.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } From e2903c3a0de7071a507193af859a111622ff600d Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 20 Feb 2026 15:02:03 +0100 Subject: [PATCH 332/872] remove references to haplocheck txt --- subworkflows/local/call_snv.nf | 3 --- workflows/raredisease.nf | 3 --- 2 files changed, 6 deletions(-) diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 4f6acd6c1..1e0fc8047 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -50,7 +50,6 @@ workflow CALL_SNV { ch_mt_vcf = channel.empty() ch_mt_tabix = channel.empty() ch_mt_vcf_tabix = channel.empty() - ch_mt_txt = channel.empty() ch_sentieon_vcf = channel.empty() ch_sentieon_tbi = channel.empty() ch_sentieon_gvcf = channel.empty() @@ -139,7 +138,6 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_mt_txt = CALL_SNV_MT.out.txt ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions) ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions) } @@ -159,6 +157,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - mt_txt = ch_mt_txt // channel: [ val(meta), path(txt) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3dd3ace7c..dcfe3487c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -206,7 +206,6 @@ workflow RAREDISEASE { main: ch_multiqc_files = channel.empty() - ch_mt_txt = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -394,7 +393,6 @@ workflow RAREDISEASE { val_variant_caller ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) - ch_mt_txt = CALL_SNV.out.mt_txt // // ANNOTATE GENOME SNVs @@ -894,7 +892,6 @@ workflow RAREDISEASE { if (!skip_fastqc) { ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{_meta, reports -> reports}.ifEmpty([])) } - ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) From 04ea65c1b1f4ecca2884bb0b150ea81b6c1375d8 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 24 Feb 2026 11:48:34 +0100 Subject: [PATCH 333/872] add saltshaker modules and run mitosalt from bin --- conf/modules/call_sv_MT.config | 22 ++++ modules/local/mitosalt/main.nf | 7 +- .../resources/usr/bin/MitoSAlt1.1.1.pl | 120 +++++++++--------- modules/local/prep_mitosalt/main.nf | 1 + modules/local/saltshaker/call/main.nf | 63 +++++++++ modules/local/saltshaker/classify/main.nf | 57 +++++++++ modules/local/saltshaker/plot/main.nf | 44 +++++++ subworkflows/local/call_sv_MT/main.nf | 54 +++++++- workflows/raredisease.nf | 10 ++ 9 files changed, 305 insertions(+), 73 deletions(-) create mode 100644 modules/local/saltshaker/call/main.nf create mode 100644 modules/local/saltshaker/classify/main.nf create mode 100644 modules/local/saltshaker/plot/main.nf diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index deedd506d..35cda22dd 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -35,4 +35,26 @@ process { ] } + withName: '.*CALL_SV_MT:SALTSHAKER_CALL' { + ext.args = '--blacklist' + } + + withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' { + ext.args = '--blacklist' + publishDir = [ + path: { "${params.outdir}/call_sv/mitochondria" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { + ext.args = '--blacklist --genes' + publishDir = [ + path: { "${params.outdir}/call_sv/mitochondria" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + } diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index caf939c44..c2e03464b 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -4,9 +4,8 @@ process MITOSALT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc2631dac526622d28ea1109b0f714d536606d0e5b3b85fe24407c8206e7e6b6/data': - 'community.wave.seqera.io/library/mitosalt:1.1.1--5fd87ac48a683358' }" - + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': + 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" input: tuple val(meta), path(reads) @@ -28,7 +27,7 @@ process MITOSALT { """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} mkdir -p log indel bam tab bw plot - mitosalt new-${msconfig} $reads $prefix + MitoSAlt1.1.1.pl new-${msconfig} $reads $prefix mv indel/*.breakpoint ${prefix}.breakpoint mv indel/*.cluster ${prefix}.cluster """ diff --git a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl index 5c6739daf..c0a0be0e6 100755 --- a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl +++ b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl @@ -4,20 +4,12 @@ use List::Util qw(first min max sum); use Data::Dumper; -#INPUT +#INPUT my $config_file = $ARGV[0]; my $p1 = $ARGV[1]; my $p2 = $ARGV[2]; my $tag = $ARGV[3]; -#CREATE DIRECTORIES -- added by ID -mkdir "log" unless -d "log"; -mkdir "indel" unless -d "indel"; -mkdir "bam" unless -d "bam"; -mkdir "tab" unless -d "tab"; -mkdir "bw" unless -d "bw"; -mkdir "plot" unless -d "plot"; - #LOG open (STDOUT, "| tee -ai log/$tag.log"); @@ -44,7 +36,7 @@ $User_Preferences->{$var} = $value; my $line = $_; print $line."\n"; -} +} #PROGRAMS my $hisat2 = $User_Preferences->{hisat2}; @@ -124,7 +116,7 @@ #EXTRACT READS print scalar(localtime).": Extract reads\n"; - system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); + system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); system("$samtools index tmp_$tag.bam"); system("$samtools idxstats tmp_$tag.bam > indel/$tag.count.txt"); system("$samtools view -u -@ $threads -f 12 tmp_$tag.bam > tmp1_$tag.bam"); #flag to extract unmapped reads with mate also unmapped @@ -158,7 +150,7 @@ if($nu_mt eq 'no' && $o_mt eq 'yes' && $enriched eq 'yes'){ #REMAP ON MT GENOME print scalar(localtime).": Map to MT genome\n"; - system("$reformat in=$p1 in2=$p2 out=tmp_$tag.fq overwrite=true addslash=t trimreaddescription=t spaceslash=f -Xmx100g"); #2>> log/$tag.log"); + system("$reformat in=$p1 in2=$p2 out=tmp_$tag.fq overwrite=true addslash=t trimreaddescription=t spaceslash=f -Xmx100g 2>> log/$tag.log"); system("$lastal -Q1 -e80 -P$threads $lastindex tmp_$tag.fq|$lastsp > tmp_$tag.maf"); system("$mfcv sam -d tmp_$tag.maf|$samtools view -@ $threads -bt $mtfaindex -|$samtools sort -@ $threads -o bam/$tag.bam -"); system("$samtools index bam/$tag.bam"); @@ -187,7 +179,7 @@ my $bedfile = "indel/$tag.bed"; my $breakpointfile = "indel/$tag.breakpoint"; my $clusterfile = "indel/$tag.cluster"; - + my $check_paired = &check_paired($infile); print scalar(localtime).": Build split read hash\n"; $hash = &build_hash($infile,$check_paired); @@ -264,7 +256,7 @@ sub build_hash{ } elsif($check_paired == 1){ my @name = split(/\//,$elements[6]); $id = $name[0]; - $mate = $name[1]; + $mate = $name[1]; } my $strand = $elements[9]; @@ -273,12 +265,12 @@ sub build_hash{ next if exists $check_hash->{$id}->{$start.$length}; $check_hash->{$id}->{$start.$length}++; $mate = 2 if $mate > 1; - #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; + #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; #FILTER BY SCORE AND MAP EVALUE next if $score < $score_threshold; next if $evalue > $evalue_threshold; - + push(@{$hash->{$id}->{$mate}->{starts}},$start); push(@{$hash->{$id}->{$mate}->{ends}},$end); push(@{$hash->{$id}->{$mate}->{rstarts}},$read_start); @@ -324,7 +316,7 @@ sub remove_duplicates{ my @signatures = ($signature1,$signature2); @signatures = sort @signatures; - my $signature = join("",@signatures); + my $signature = join("",@signatures); if(exists $check_duplicates->{$signature} && $count1>0 && $count2>0){ @@ -345,17 +337,17 @@ sub print_bed{ open(ABED,">$filename"); for my $id (keys %{$hash}){ #print $id."\n"; - + for my $read(keys %{$hash->{$id}}){ my $name = $id."_".$read; #CHECK IF READ IS SPLIT ALIGNED my $count = @{$hash->{$id}->{$read}->{starts}}; next if $count > 1; - my $start = @{$hash->{$id}->{$read}->{starts}}[0]; + my $start = @{$hash->{$id}->{$read}->{starts}}[0]; my $end = @{$hash->{$id}->{$read}->{ends}}[0]; - print ABED "$refchr\t$start\t$end\t$name\n"; - } + print ABED "$refchr\t$start\t$end\t$name\n"; + } } system("sort -k2,2n $filename -o $filename"); close(ABED); @@ -385,7 +377,7 @@ sub process_hash{ next unless $min_len >= $split_length; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -397,11 +389,11 @@ sub process_hash{ elsif($read_starts[0]>$read_starts[1] && $read_local_starts[0]<$read_local_starts[1]){$read_check = 'yes';} elsif($read_starts[0]<=$read_starts[1] && $read_local_starts[0]<$read_local_starts[1] && $read_starts[1]<$read_ends[0] ){$read_check = 'yes';} elsif($read_starts[0]>=$read_starts[1] && $read_local_starts[0]>$read_local_starts[1] && $read_ends[1]>$read_starts[0] ){$read_check = 'yes';} - + #CHECK IF THE SPLIT READ FRAGMENTS SPAN THE DLOOP - my $min_start = min @{$hash->{$id}->{$read}->{starts}}; + my $min_start = min @{$hash->{$id}->{$read}->{starts}}; my $max_end = max @{$hash->{$id}->{$read}->{ends}}; - next if $min_start <= $dloop1 && $max_end >= $dloop2; + next if $min_start <= $dloop1 && $max_end >= $dloop2; my ($size,$start,$end) = &get_frag_distance(\@read_starts,\@read_ends,$read_check,$msize); next if $size < $deletion_threshold_min; @@ -410,7 +402,7 @@ sub process_hash{ #print "$name\t$start\t$end\t$size\n"; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #CHECK IF PAIRED READ EXISTS AND ITS ALIGNMENT POSITION SUPPORTS THE SPLIT READ my $pair = 1 if $read == 2; @@ -435,7 +427,7 @@ sub process_hash{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + $start = $len[2]; $end = $len[3]; $size = $len[4]; @@ -463,7 +455,7 @@ sub process_hash1{ my $bpe = shift; my $delhash; - + open(BP,">$breakpointfile"); open(BED,">$bedfile"); open(BPS,">$bps"); @@ -478,7 +470,7 @@ sub process_hash1{ next unless $count == 3; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -548,7 +540,7 @@ sub process_hash1{ #CHECK IF THE SPLIT READ FRAGMENTS ARE ABOVE LENGTH THRESHOLD my $min_len = min @read_lengthsN; next unless $min_len >= $split_length; - + #LOOK FOR SPLIT READS WHICH MAP INVERSELY SPANNING THE D'LOOP my $read_check = 'no'; @@ -566,7 +558,7 @@ sub process_hash1{ $paired_support = 'yes' if $distance_paired_support <= $paired_distance; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #LOOK FOR SPLIT READS WITH LARGE UNMAPPED AREA my ($split_distance) = &get_split_distance(\@read_local_startsN,\@read_lengthsN); @@ -582,7 +574,7 @@ sub process_hash1{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + #$start = $len[2]; #$end = $len[3]; #$size = $len[4]; @@ -611,10 +603,10 @@ sub paired_support{ my $distance1 = 0; my $distance2=0; - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; - - my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; + + my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; my $pair_end = @{$hash->{$id}->{$pair}->{ends}}[0]; $distance1 = $read_starts[0] - $pair_end if $read_starts[0] > $pair_end; @@ -640,10 +632,10 @@ sub get_frag_distance{ my $frag1_end = @{$ends}[0]; my $frag2_end = @{$ends}[1]; - + if($read_check eq 'no'){ if($frag1_start > $frag2_end){ - my $size = $frag1_start - $frag2_end; + my $size = $frag1_start - $frag2_end; @res = ($size,$frag2_end,$frag1_start); } elsif($frag2_start > $frag1_end){ @@ -670,7 +662,7 @@ sub get_frag_distance{ if($read_check eq 'yes'){ if($frag1_start > $frag2_end){ - my $size = ($msize -$frag1_end) + $frag2_start; + my $size = ($msize -$frag1_end) + $frag2_start; @res = ($size,$frag2_start,$frag1_end); } elsif($frag2_start > $frag1_end){ @@ -708,7 +700,7 @@ sub get_split_distance{ my $local1_length = @{$lengths}[0]; my $local2_length = @{$lengths}[1]; - + if($local1_start>$local2_start){ my $distance = $local1_start - $local2_start - $local2_length; @res = ($distance); @@ -716,7 +708,7 @@ sub get_split_distance{ if($local2_start>$local1_start){ my $distance = $local2_start - $local1_start - $local1_length; @res = ($distance); - } + } return @res; } @@ -729,7 +721,7 @@ sub generate_bed{ my $lengths = shift; my $scores = shift; my $strand = shift; - + my $size = shift; my $bstart = shift; my $bend = shift; @@ -759,7 +751,7 @@ sub generate_bed{ $size = $frag1_start - $frag2_end; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag1_start > $frag2_end && $strand eq '+'){ @@ -770,53 +762,53 @@ sub generate_bed{ $size = 1 + $msize- $frag1_end + $frag2_start; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_end; $bend = $frag2_start; $size = $frag2_start - $frag1_end; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '-'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_start; $bend = $frag2_end; $size = 1 + $msize - $frag2_end + $frag1_start; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag2_start < $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag2_start; - $bend = $frag1_end; + $bend = $frag1_end; $size = $msize - $frag1_end + $frag2_start; my $block_start=$frag1_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } elsif($frag1_start < $frag2_end && $strand eq '-'){ $start = $frag2_start; - $end = $frag1_end; + $end = $frag1_end; $bstart = $frag1_start; - $bend = $frag2_end; + $bend = $frag2_end; $size = $msize - $frag2_end + $frag1_start; my $block_start=$frag2_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } return @len; } @@ -852,14 +844,14 @@ sub generate_bed1{ $start = $frag2_start; $end = $frag1_end; my $block_start=$frag1_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length); } elsif($frag2_start > $frag1_end){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; my $block_start=$frag2_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length); } return @len; @@ -901,7 +893,7 @@ sub get_cluster{ $bpe_hash->{$readid} = $clusterid; } close(BPE); - + for my $readid(keys %{$delhash}){ next unless exists $bps_hash->{$readid}; next unless exists $bpe_hash->{$readid}; @@ -920,17 +912,17 @@ sub build_results{ my $refchr = shift; my $cluster_read_count_threshold = shift; my $tag = shift; - my $clustercount; + my $clustercount; my $nosplitbed_file = "tmp_".$tag."_nosplit.bed";; for my $clusterid (keys %{$clusterhash}){ - my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; - next if $cluster_read_count < $cluster_read_count_threshold; + my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; + next if $cluster_read_count < $cluster_read_count_threshold; print "Check $clusterid\n"; my $clustercheck; $clustercount->{$clusterid}->{wt} = 0; - $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; + $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; my $splitbed_fileS = "tmp_".$tag.".split.start.bed"; my $splitbed_fileE = "tmp_".$tag.".split.end.bed"; @@ -1041,3 +1033,5 @@ sub print_result{ } close(CF); } + + diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf index 41b0caa4f..83455fd3c 100644 --- a/modules/local/prep_mitosalt/main.nf +++ b/modules/local/prep_mitosalt/main.nf @@ -53,6 +53,7 @@ process PREP_MITOSALT { echo "MT_fasta = ${mtfasta}" >> mitosalt_config.txt echo "threads = 1" >> mitosalt_config.txt echo "refchr = ${mito_name}" >> mitosalt_config.txt + echo "msize = 16569" >> mitosalt_config.txt echo "exclude = ${exclude}" >> mitosalt_config.txt echo "orihs = 16081" >> mitosalt_config.txt echo "orihe = 407" >> mitosalt_config.txt diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf new file mode 100644 index 000000000..072ae75c6 --- /dev/null +++ b/modules/local/saltshaker/call/main.nf @@ -0,0 +1,63 @@ +process SALTSHAKER_CALL { + tag "$meta.id" + label "process_low" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': + 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + + input: + tuple val(meta), path(breakpoint) + tuple val(meta), path(cluster) + tuple val(meta2), path(mtfasta) + val flank + val hplimit + val mito_length + val ori_h_start + val ori_h_end + val ori_l_start + val ori_l_end + + output: + tuple val(meta), path("*_call_metadata.tsv"), emit: call + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + saltshaker call \\ + --prefix $prefix \\ + --output-dir . \\ + -r $mtfasta \\ + -c $cluster \\ + -p $breakpoint \\ + -f $flank \\ + -H $hplimit \\ + -g $mito_length \\ + --ori-h-start $ori_h_start \\ + --ori-h-end $ori_h_end \\ + --ori-l-start $ori_l_start \\ + --ori-l-end $ori_l_end \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_call: \$(echo \$(saltshaker call 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}_call_metadata.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_call: \$(echo \$(saltshaker call 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + +} diff --git a/modules/local/saltshaker/classify/main.nf b/modules/local/saltshaker/classify/main.nf new file mode 100644 index 000000000..d5dbc81de --- /dev/null +++ b/modules/local/saltshaker/classify/main.nf @@ -0,0 +1,57 @@ +process SALTSHAKER_CLASSIFY { + tag "$meta.id" + label "process_low" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': + 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + + input: + tuple val(meta), path(call) + val dom_frac + val group_radius + val high_het + val mult_thresh + val noise_thresh + + output: + tuple val(meta), path("*_classify_metadata.tsv"), emit: classify + tuple val(meta), path("*saltshaker.vcf") , emit: vcf + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + saltshaker classify \\ + --prefix $prefix \\ + --input-dir . \\ + --vcf \\ + --dominant-fraction $dom_frac \\ + --radius $group_radius \\ + --high-het $high_het \\ + --multiple-threshold $mult_thresh \\ + --noise $noise_thresh \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_classify: \$(echo \$(saltshaker classify 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.vcf + touch ${prefix}_call_metadata.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_classify: \$(echo \$(saltshaker classify 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + +} diff --git a/modules/local/saltshaker/plot/main.nf b/modules/local/saltshaker/plot/main.nf new file mode 100644 index 000000000..98e80ab38 --- /dev/null +++ b/modules/local/saltshaker/plot/main.nf @@ -0,0 +1,44 @@ +process SALTSHAKER_PLOT { + tag "$meta.id" + label "process_low" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': + 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + + input: + tuple val(meta), path(classify) + + output: + tuple val(meta), path("*saltshaker.png"), emit: plot + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + saltshaker plot \\ + --prefix $prefix \\ + --input-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_plot: \$(echo \$(saltshaker plot 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.png + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + saltshaker_plot: \$(echo \$(saltshaker plot 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ + +} diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 40080feac..495205985 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -2,10 +2,13 @@ // Call SV MT // -include { MT_DELETION } from '../../../modules/local/mt_deletion_script' -include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { MT_DELETION } from '../../../modules/local/mt_deletion_script' +include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' +include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { SALTSHAKER_CALL } from '../../../modules/local/saltshaker/call/main' +include { SALTSHAKER_CLASSIFY } from '../../../modules/local/saltshaker/classify/main' +include { SALTSHAKER_PLOT } from '../../../modules/local/saltshaker/plot/main' workflow CALL_SV_MT { take: @@ -24,11 +27,21 @@ workflow CALL_SV_MT { val_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold val_deletion_threshold_max // string: [mandatory] mitosalt_del_threshold_max val_deletion_threshold_min // string: [mandatory] mitosalt_del_threshold_min + val_dom_frac // string: [mandatory] saltshaker_dominant_fraction val_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold val_exclude // string: [mandatory] mitosalt_exclude val_flank // string: [mandatory] mitosalt_flank + val_group_radius // string: [mandatory] saltshaker_group_radius + val_high_het // string: [mandatory] saltshaker_high_heteroplasmy val_hplimit // string: [mandatory] mitosalt_hp_limit + val_mito_length // string: [mandatory] mito_length val_mito_name // string: [mandatory] mito_name + val_mult_thresh // string: [mandatory] saltshaker_multi_threshold + val_noise_thresh // string: [mandatory] saltshaker_noise_threshold + val_ori_h_start // string: [mandatory] mito_ori_h_start + val_ori_h_end // string: [mandatory] mito_ori_h_end + val_ori_l_start // string: [mandatory] mito_ori_l_start + val_ori_l_end // string: [mandatory] mito_ori_l_end val_paired_distance // string: [mandatory] mitosalt_paired_distance val_score_threshold // string: [mandatory] mitosalt_score_threshold val_sizelimit // string: [mandatory] mitosalt_size_limit @@ -78,6 +91,35 @@ workflow CALL_SV_MT { ch_mt_lastdb ) + SALTSHAKER_CALL( + MITOSALT.out.breakpoint, + MITOSALT.out.cluster, + ch_mt_fasta, + val_flank, + val_hplimit, + val_mito_length, + val_ori_h_start, + val_ori_h_end, + val_ori_l_start, + val_ori_l_end + ) + + SALTSHAKER_CLASSIFY( + SALTSHAKER_CALL.out.call, + val_dom_frac, + val_group_radius, + val_high_het, + val_mult_thresh, + val_noise_thresh + ) + ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify + + SALTSHAKER_PLOT( + SALTSHAKER_CLASSIFY.out.classify + ) + ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot + + ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) @@ -85,8 +127,8 @@ workflow CALL_SV_MT { ch_versions = ch_versions.mix(MT_DELETION.out.versions) emit: - mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] - mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] + mitosalt_vcf = ch_mitosalt_vcf // channel: [ val(meta), path(vcf) ] + mitosalt_plot = ch_mitosalt_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index c94c5d6c3..4504a57b6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -661,11 +661,21 @@ workflow RAREDISEASE { params.cluster_threshold, params.deletion_threshold_max, params.deletion_threshold_min, + params.dom_frac, params.evalue_threshold, params.exclude, params.flank, + params.group_radius, + params.high_het, params.hplimit, + params.mito_length, params.mito_name, + params.mult_thresh, + params.noise_thresh, + params.ori_h_start, + params.ori_h_end, + params.ori_l_start, + params.ori_l_end, params.paired_distance, params.score_threshold, params.sizelimit, From 8cc51b19df283fff9c61a64e381a42058f508df1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 11:51:15 +0100 Subject: [PATCH 334/872] update snapshots --- conf/test.config | 6 --- conf/test_bam.config | 6 --- conf/test_full.config | 6 --- conf/test_sentieon.config | 6 --- conf/test_singleton.config | 6 --- modules.json | 2 +- modules/nf-core/ensemblvep/filtervep/main.nf | 2 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 4 +- .../filtervep/tests/main.nf.test.snap | 20 ++++----- .../ensemblvep/filtervep/tests/tab.gz.config | 2 +- .../ensemblvep/filtervep/tests/vcf.config | 2 +- .../local/align_MT/tests/main.nf.test.snap | 24 ++--------- tests/default.nf.test.snap | 41 ++++++++++++------- tests/test_bam.nf.test.snap | 34 ++++++++++----- tests/test_singleton.nf.test.snap | 37 +++++++++++------ workflows/raredisease.nf | 7 +++- 16 files changed, 100 insertions(+), 105 deletions(-) diff --git a/conf/test.config b/conf/test.config index dc6dd262e..ee863b84e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '2.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_bam.config b/conf/test_bam.config index 0173ea483..8e90c1a5b 100644 --- a/conf/test_bam.config +++ b/conf/test_bam.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_full.config b/conf/test_full.config index cca2a2463..ff2c306c8 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config index e34a7f9c1..330be5a04 100644 --- a/conf/test_sentieon.config +++ b/conf/test_sentieon.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_singleton.config b/conf/test_singleton.config index 180bfc0a1..559e1d6da 100644 --- a/conf/test_singleton.config +++ b/conf/test_singleton.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/modules.json b/modules.json index 6e017be96..9ae2f6592 100644 --- a/modules.json +++ b/modules.json @@ -137,7 +137,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "09ea5d9fcd6eda714f148e0f3b6a4920b2091f41", + "git_sha": "2e751c119b5e6e9c7ecda7a682e157aabb57a812", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index ed561b023..d9deff488 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -14,7 +14,7 @@ process ENSEMBLVEP_FILTERVEP { output: tuple val(meta), path("*.${extension}"), emit: output tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \\\$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index 6c6641597..20239ba91 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -63,7 +63,7 @@ output: - perl-math-cdf: type: string description: The tool name - - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': type: eval description: The expression to obtain the version of the tool topics: @@ -83,7 +83,7 @@ topics: - perl-math-cdf: type: string description: The tool name - - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': type: eval description: The expression to obtain the version of the tool authors: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 0bd02680e..6ed6da27b 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -13,16 +13,16 @@ [ "ENSEMBLVEP_FILTERVEP", "perl-math-cdf", - "" + "0.1" ] ] } ], + "timestamp": "2026-02-25T10:48:08.943902", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-07T17:41:53.157363596" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test_ensemblvep_filtervep_tab_gz": { "content": [ @@ -38,15 +38,15 @@ [ "ENSEMBLVEP_FILTERVEP", "perl-math-cdf", - "" + "0.1" ] ] } ], + "timestamp": "2026-02-25T10:48:20.24913", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-07T17:42:10.309756999" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index f1eb11d65..ace089baa 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -7,7 +7,7 @@ process { withName: ENSEMBLVEP_VEP { - ext.args = '--tab' + ext.args = '--tab --offline' ext.prefix = { "${meta.id}_vep" } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index a737274ef..9f34e2a90 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -7,7 +7,7 @@ process { withName: ENSEMBLVEP_VEP { - ext.args = '--vcf' + ext.args = '--vcf --offline' ext.prefix = { "${meta.id}_vep" } } diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 2108f323f..978d90592 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -101,9 +101,6 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] - ], - "2": [ - ], "marked_bai": [ [ @@ -204,13 +201,10 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-02-17T11:24:25.300014158", + "timestamp": "2026-02-20T00:15:07.330482228", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -319,11 +313,6 @@ "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] ], - "2": [ - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" - ], "marked_bai": [ [ { @@ -423,18 +412,13 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] - ], - "versions": [ - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" ] } ], - "timestamp": "2026-02-06T17:44:37.818378883", + "timestamp": "2026-02-20T00:32:17.118099572", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dee909d0d..5cfbd8886 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -67,10 +67,12 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -127,19 +129,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -318,10 +329,10 @@ "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -672,11 +683,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -726,10 +735,14 @@ "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -1108,10 +1121,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-19T10:01:20.665806391", + "timestamp": "2026-02-24T17:18:24.169571113", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 0b94ca3c2..d0235fb4c 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -68,7 +68,8 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -125,19 +126,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -634,11 +644,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -672,10 +680,14 @@ "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -1038,10 +1050,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-19T15:08:50.558312851", + "timestamp": "2026-02-24T23:58:33.320173721", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 9b4a21e11..6a9f197b0 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -65,10 +65,12 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -119,19 +121,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -537,11 +548,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -575,10 +584,14 @@ "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -725,10 +738,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-02-19T18:45:40.125652788", + "timestamp": "2026-02-25T02:33:23.251038469", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 037a8630e..d4c2b0503 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -751,7 +751,8 @@ workflow RAREDISEASE { if (!skip_peddy) { PEDDY ( CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), - ch_pedfile + ch_pedfile.map{ped -> return[[id:"pedigree"], ped]}, + [[:],[]] ) } @@ -887,7 +888,9 @@ workflow RAREDISEASE { if (!skip_peddy) { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.het_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.sex_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) } MULTIQC ( From 0672da50e8b8b99b86a6abbbccacab1f36db1abc Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:11:33 +0100 Subject: [PATCH 335/872] update modules --- modules.json | 25 +-- modules/nf-core/cadd/environment.yml | 2 + modules/nf-core/cadd/main.nf | 46 ++--- modules/nf-core/cadd/meta.yml | 59 ++++-- modules/nf-core/cadd/tests/main.nf.test | 37 ++++ modules/nf-core/cadd/tests/main.nf.test.snap | 48 +++++ modules/nf-core/haplocheck/environment.yml | 5 - modules/nf-core/haplocheck/main.nf | 44 ---- modules/nf-core/haplocheck/meta.yml | 60 ------ modules/nf-core/haplocheck/tests/main.nf.test | 56 ------ .../haplocheck/tests/main.nf.test.snap | 100 --------- .../picard/addorreplacereadgroups/main.nf | 3 - .../picard/addorreplacereadgroups/meta.yml | 1 - .../addorreplacereadgroups/tests/bam.config | 1 - .../addorreplacereadgroups/tests/cram.config | 1 - .../addorreplacereadgroups/tests/main.nf.test | 23 +-- .../tests/main.nf.test.snap | 37 +--- .../nf-core/picard/collecthsmetrics/main.nf | 43 ++-- .../nf-core/picard/collecthsmetrics/meta.yml | 4 +- .../collecthsmetrics/tests/main.nf.test | 25 +-- .../collecthsmetrics/tests/main.nf.test.snap | 44 ++-- .../picard/collectmultiplemetrics/main.nf | 29 ++- .../picard/collectmultiplemetrics/meta.yml | 4 +- .../collectmultiplemetrics/tests/main.nf.test | 144 +++++++++---- .../tests/main.nf.test.snap | 156 ++++++++++++++- .../nf-core/picard/collectwgsmetrics/main.nf | 33 ++- .../nf-core/picard/collectwgsmetrics/meta.yml | 5 +- .../collectwgsmetrics/tests/main.nf.test | 119 ++++++++--- .../collectwgsmetrics/tests/main.nf.test.snap | 74 ++++++- modules/nf-core/picard/liftovervcf/main.nf | 29 ++- modules/nf-core/picard/liftovervcf/meta.yml | 6 +- .../picard/liftovervcf/tests/main.nf.test | 65 +++--- .../liftovervcf/tests/main.nf.test.snap | 32 ++- modules/nf-core/picard/markduplicates/main.nf | 46 +++-- .../nf-core/picard/markduplicates/meta.yml | 6 +- .../picard/markduplicates/tests/main.nf.test | 6 +- .../markduplicates/tests/main.nf.test.snap | 189 ++++-------------- .../markduplicates/tests/nextflow.config | 2 +- .../nf-core/picard/renamesampleinvcf/main.nf | 26 ++- .../nf-core/picard/renamesampleinvcf/meta.yml | 6 +- .../renamesampleinvcf/tests/main.nf.test | 29 ++- .../renamesampleinvcf/tests/main.nf.test.snap | 30 ++- modules/nf-core/picard/sortvcf/main.nf | 32 +-- modules/nf-core/picard/sortvcf/meta.yml | 5 +- .../nf-core/picard/sortvcf/tests/main.nf.test | 47 +++-- .../picard/sortvcf/tests/main.nf.test.snap | 30 ++- tests/default.nf.test.snap | 7 - tests/test_bam.nf.test.snap | 7 - tests/test_singleton.nf.test.snap | 5 - 49 files changed, 947 insertions(+), 886 deletions(-) create mode 100644 modules/nf-core/cadd/tests/main.nf.test create mode 100644 modules/nf-core/cadd/tests/main.nf.test.snap delete mode 100644 modules/nf-core/haplocheck/environment.yml delete mode 100644 modules/nf-core/haplocheck/main.nf delete mode 100644 modules/nf-core/haplocheck/meta.yml delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index 9ae2f6592..dcf570b57 100644 --- a/modules.json +++ b/modules.json @@ -97,7 +97,7 @@ }, "cadd": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "1d40acd9f567cea7ccdd4b6211310d4e94356357", "installed_by": ["modules"] }, "cat/cat": { @@ -286,11 +286,6 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, - "haplocheck": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", @@ -303,7 +298,7 @@ }, "hmtnote/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"], "patch": "modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff" }, @@ -339,42 +334,42 @@ }, "picard/addorreplacereadgroups": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collecthsmetrics": { "branch": "master", - "git_sha": "976ed20e328a92cb24ab6c63a8983ed31bf48469", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/renamesampleinvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "qualimap/bamqc": { diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml index 4477e16e5..d98de6522 100644 --- a/modules/nf-core/cadd/environment.yml +++ b/modules/nf-core/cadd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf index 0af87f6e5..94aa19796 100644 --- a/modules/nf-core/cadd/main.nf +++ b/modules/nf-core/cadd/main.nf @@ -1,53 +1,47 @@ process CADD { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1' - containerOptions { - (workflow.containerEngine == 'singularity') ? + containerOptions "${ prescored_dir ? + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? + "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -B ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : + "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -v ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" : - "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" - } + "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" }" input: tuple val(meta), path(vcf) - path(annotation_dir) + tuple val(meta2), path(annotation_dir) + tuple val(meta3), path(prescored_dir) output: - tuple val(meta), path("*.tsv.gz"), emit: tsv - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.tsv.gz"), emit: tsv + tuple val("${task.process}"), val("cadd"), val("1.6.post1"), emit: versions_cadd, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ + export XDG_CACHE_HOME=\$PWD/snakemake_cache + mkdir -p \$XDG_CACHE_HOME + cadd.sh \\ -o ${prefix}.tsv.gz \\ - $args \\ - $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cadd: $VERSION - END_VERSIONS + ${args} \\ + ${vcf} """ stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.tsv.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cadd: $VERSION - END_VERSIONS + echo "" | gzip > ${prefix}.tsv.gz """ } diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml index 751bea454..b70cb7d9c 100644 --- a/modules/nf-core/cadd/meta.yml +++ b/modules/nf-core/cadd/meta.yml @@ -1,6 +1,6 @@ name: "cadd" -description: CADD is a tool for scoring the deleteriousness of single nucleotide variants - as well as insertion/deletions variants in the human genome. +description: CADD is a tool for scoring the deleteriousness of single nucleotide + variants as well as insertion/deletions variants in the human genome. keywords: - cadd - annotate @@ -25,28 +25,61 @@ input: type: file description: Input file for annotation in vcf or vcf.gz format pattern: "*.{vcf,vcf.gz}" - - - annotation_dir: - type: file + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - annotation_dir: + type: directory description: | Path to folder containing the vcf files with precomputed CADD scores. This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. - pattern: "*.{vcf,vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - prescored_dir: + type: directory + description: | + Path to folder containing prescored files. + This folder contains the uncompressed files that would otherwise be in data/prescored/${GENOME_BUILD}_${VERSION}/ folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. output: - - tsv: - - meta: + tsv: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tsv.gz": + - ${prefix}.tsv.gz: type: file description: Annotated tsv file pattern: "*.{tsv,tsv.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 + versions_cadd: + - - ${task.process}: + type: string + description: The name of the process + - cadd: + type: string + description: The name of the tool + - 1.6.post1: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - cadd: + type: string + description: The name of the tool + - 1.6.post1: + type: string + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cadd/tests/main.nf.test b/modules/nf-core/cadd/tests/main.nf.test new file mode 100644 index 000000000..cc36d0cdd --- /dev/null +++ b/modules/nf-core/cadd/tests/main.nf.test @@ -0,0 +1,37 @@ +nextflow_process { + + name "Test Process CADD" + + script "../main.nf" + process "CADD" + + tag "modules" + tag "modules_nfcore" + tag "cadd" + + test("test_cadd - stub") { + options '-stub' + when { + + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf',checkIfExists:true) + ] + input[1] = Channel.from("\$PWD").map { dir -> [ [ id: dir ], dir ] } + input[2] = Channel.from("/").map { dir -> [ [ id: dir ], dir ] } + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } + ) + } + } +} diff --git a/modules/nf-core/cadd/tests/main.nf.test.snap b/modules/nf-core/cadd/tests/main.nf.test.snap new file mode 100644 index 000000000..de4c6dc7c --- /dev/null +++ b/modules/nf-core/cadd/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test_cadd - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CADD", + "cadd", + "1.6.post1" + ] + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_cadd": [ + [ + "CADD", + "cadd", + "1.6.post1" + ] + ] + }, + [ + + ] + ], + "timestamp": "2026-02-19T20:06:20.885977", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml deleted file mode 100644 index 4fb40238b..000000000 --- a/modules/nf-core/haplocheck/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf deleted file mode 100644 index 0d26c449e..000000000 --- a/modules/nf-core/haplocheck/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process HAPLOCHECK { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - 'biocontainers/haplocheck:1.3.3--h4a94de4_0' }" - - input: - tuple val(meta), path(vcf) - - output: - tuple val(meta), path("*.txt") , emit: txt - tuple val(meta), path("*.html"), emit: html - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - haplocheck --raw --out $prefix $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.raw.txt - touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml deleted file mode 100644 index 25e6127a7..000000000 --- a/modules/nf-core/haplocheck/meta.yml +++ /dev/null @@ -1,60 +0,0 @@ -name: "haplocheck" -description: | - Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing - the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides - users a graphical report to investigate the contamination further. Internally, it uses the - Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. -keywords: - - mitochondrial - - mtDNA - - contamination -tools: - - "haplocheck": - description: "Detects in-sample contamination in mtDNA or WGS sequencing studies - by analyzing the mitochondrial content." - homepage: "https://github.com/genepi/haplocheck" - documentation: "https://github.com/genepi/haplocheck" - tool_dev_url: "https://github.com/genepi/haplocheck" - doi: 10.1101/gr.256545.119 - licence: ["MIT"] - identifier: biotools:haplocheck -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" -output: - - txt: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.txt": - type: file - description: Raw report in txt format - pattern: "*.{txt}" - - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: Haplocheck HTML report - pattern: "*.{html}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@lmtani" -maintainers: - - "@lmtani" diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test deleted file mode 100644 index 8957d02e2..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test +++ /dev/null @@ -1,56 +0,0 @@ - -nextflow_process { - - name "Test Process HAPLOCHECK" - script "../main.nf" - process "HAPLOCHECK" - - tag "modules" - tag "modules_nfcore" - tag "haplocheck" - - test("test-haplocheck") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test-haplocheck-stub") { - options '-stub' - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} diff --git a/modules/nf-core/haplocheck/tests/main.nf.test.snap b/modules/nf-core/haplocheck/tests/main.nf.test.snap deleted file mode 100644 index abe1eab56..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test.snap +++ /dev/null @@ -1,100 +0,0 @@ -{ - "test-haplocheck-stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:41:40.703528" - }, - "test-haplocheck": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:43:05.761086" - } -} \ No newline at end of file diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 5ef3b7d8e..7261dc8e2 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -34,7 +34,6 @@ process PICARD_ADDORREPLACEREADGROUPS { } if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ picard \\ -Xmx${avail_mem}M \\ @@ -43,7 +42,6 @@ process PICARD_ADDORREPLACEREADGROUPS { $reference \\ --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} - """ stub: @@ -52,6 +50,5 @@ process PICARD_ADDORREPLACEREADGROUPS { if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.${suffix} - """ } diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index 6c3ed7599..b26a1c508 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -90,7 +90,6 @@ output: - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config index 3f37c2fd9..132cc0f7c 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config @@ -9,5 +9,4 @@ process { "-SM ${meta.id}" ].join(' ').trim()} } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config index 966c14d79..be92e72bb 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config @@ -9,5 +9,4 @@ process { ].join(' ').trim()} ext.suffix = { "cram" } } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 45729f3b5..5586ab469 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -27,14 +27,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.bai[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.bam[0][1]).name, + file(process.out.bai[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("homo_sapiens - cram") { @@ -58,19 +56,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.cram[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.cram[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("sarscov2 - bam - stub") { config "./bam.config" options "-stub" - when { process { """ @@ -84,10 +79,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index d2a99ee27..7ec99fbb5 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -12,36 +12,15 @@ ] } ], + "timestamp": "2026-02-02T09:36:16.966842212", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:16.966842212" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - - }, - "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - "PICARD_ADDORREPLACEREADGROUPS", - "picard", - "3.4.0" - ] - ], "bai": [ ], @@ -65,11 +44,11 @@ ] } ], + "timestamp": "2026-02-19T17:34:40.3572859", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:29.861163004" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam": { "content": [ @@ -85,10 +64,10 @@ ] } ], + "timestamp": "2026-02-02T09:36:00.935196996", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:00.935196996" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index b13871f8c..96045b5dd 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -1,22 +1,22 @@ process PICARD_COLLECTHSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') tuple val(meta2), path(ref) tuple val(meta3), path(ref_fai) tuple val(meta4), path(ref_dict) - tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped + tuple val(meta5), path(ref_gzi) output: - tuple val(meta), path("*_metrics") , emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*_metrics"), emit: metrics + tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -28,41 +28,38 @@ process PICARD_COLLECTHSMETRICS { def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } def bait_interval_list = bait_intervals def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/){ + if (bait_intervals =~ /.(bed|bed.gz)$/) { bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } def target_interval_list = target_intervals def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/){ + if (target_intervals =~ /.(bed|bed.gz)$/) { target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } - - """ - - $bait_intervallist_cmd - $target_intervallist_cmd + ${bait_intervallist_cmd} + ${target_intervallist_cmd} picard \\ -Xmx${avail_mem}M \\ CollectHsMetrics \\ - $args \\ - $reference \\ - --BAIT_INTERVALS $bait_interval_list \\ - --TARGET_INTERVALS $target_interval_list \\ - --INPUT $bam \\ + ${args} \\ + ${reference} \\ + --BAIT_INTERVALS ${bait_interval_list} \\ + --TARGET_INTERVALS ${target_interval_list} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics - """ stub: diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index a21aa6ecd..89bc502c9 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -106,7 +106,7 @@ output: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -118,7 +118,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 07a9ccf42..d73661111 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -40,11 +40,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - gzippedfa") { @@ -78,17 +76,13 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - stub") { - options "-stub" - when { process { """ @@ -110,10 +104,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2 - bam - nofasta") { @@ -147,11 +140,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - bed") { @@ -186,11 +177,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - samebed") { @@ -225,10 +214,8 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } } diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 74d9441fa..43385314a 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -115,31 +115,15 @@ ] } ], + "timestamp": "2026-01-05T17:03:29.566021877", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:29.566021877" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ], "metrics": [ [ { @@ -158,11 +142,11 @@ ] } ], + "timestamp": "2026-02-19T17:36:03.822502867", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:13.333276975" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam - gzippedfa": { "content": [ @@ -280,11 +264,11 @@ ] } ], + "timestamp": "2026-01-05T17:03:04.382110367", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:04.382110367" + } }, "sarscov2 - bam - samebed": { "content": [ @@ -402,11 +386,11 @@ ] } ], + "timestamp": "2026-01-05T17:13:22.872920293", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:22.872920293" + } }, "sarscov2 - bam": { "content": [ @@ -524,11 +508,11 @@ ] } ], + "timestamp": "2026-01-05T17:02:47.615784738", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:02:47.615784738" + } }, "sarscov2 - bam - bed": { "content": [ @@ -646,10 +630,10 @@ ] } ], + "timestamp": "2026-01-05T17:13:02.812282052", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:02.812282052" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 3c6152e5f..9de927e69 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -1,21 +1,21 @@ process PICARD_COLLECTMULTIPLEMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: - tuple val(meta) , path(bam), path(bai) + tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val(meta), path("*.pdf") , emit: pdf, optional: true - tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*.pdf"), emit: pdf, optional: true + tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,19 +26,19 @@ process PICARD_COLLECTMULTIPLEMETRICS { def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectMultipleMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectMultipleMetrics \\ - $reference - + ${reference} """ stub: @@ -54,6 +54,5 @@ process PICARD_COLLECTMULTIPLEMETRICS { touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - """ } diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 1ea47244c..213d600be 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -81,7 +81,7 @@ output: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -93,7 +93,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test index 08456941b..0037acab6 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -16,16 +16,15 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] """ } } @@ -37,8 +36,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -49,13 +47,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] input[2] = [[id:'genome'],[]] - """ } } @@ -67,8 +64,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -79,19 +75,18 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] """ } } @@ -103,10 +98,89 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} + ) + } + } + + test("test-picard-collectmultiplemetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectmultiplemetrics-nofasta - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } + test("test-picard-collectmultiplemetrics-cram - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index 1acf37765..393ed1003 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -25,11 +25,107 @@ ] } ], + "timestamp": "2026-02-02T10:22:21.230301646", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:22:21.230301646" + } + }, + "test-picard-collectmultiplemetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:38.701455244", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectmultiplemetrics-nofasta - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:48.923918624", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -57,11 +153,11 @@ ] } ], + "timestamp": "2026-02-02T10:23:52.23446844", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:52.23446844" + } }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -89,10 +185,58 @@ ] } ], + "timestamp": "2026-02-02T10:23:27.387621193", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:27.387621193" + } + }, + "test-picard-collectmultiplemetrics-cram - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:57.11686549", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index aa77100c7..a5db512c0 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -1,51 +1,50 @@ process PICARD_COLLECTWGSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) - path intervallist + path intervallist output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 - def interval = intervallist ? "--INTERVALS ${intervallist}" : '' + def interval = intervallist ? "--INTERVALS ${intervallist}" : '' if (!task.memory) { - log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectWgsMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --REFERENCE_SEQUENCE ${fasta} \\ - $interval - + ${interval} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.CollectWgsMetrics.coverage_metrics - """ } diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index c59811d58..c5afe2e7c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -76,10 +76,9 @@ output: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -88,7 +87,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test index d6a60e6bf..1bda5980a 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test @@ -16,19 +16,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] """ } } @@ -37,10 +36,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -51,19 +49,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) """ } } @@ -72,12 +69,70 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-collectwgsmetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectwgsmetrics-with-interval - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index 375c2ef9d..79f1145ff 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -1,7 +1,34 @@ { + "test-picard-collectwgsmetrics-with-interval - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:35:04.636691319", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-collectwgsmetrics-with-interval": { "content": [ - true, + false, { "versions_picard": [ [ @@ -12,15 +39,42 @@ ] } ], + "timestamp": "2026-02-20T10:34:45.059411647", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectwgsmetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:34:54.347278951", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:55.091876466" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectwgsmetrics": { "content": [ - true, + false, { "versions_picard": [ [ @@ -31,10 +85,10 @@ ] } ], + "timestamp": "2026-02-20T10:34:25.744978033", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:11.334274481" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 186afc50f..da025c9b6 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -1,11 +1,11 @@ process PICARD_LIFTOVERVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(input_vcf) @@ -14,9 +14,9 @@ process PICARD_LIFTOVERVCF { tuple val(meta4), path(chain) output: - tuple val(meta), path("*.lifted.vcf.gz") , emit: vcf_lifted + tuple val(meta), path("*.lifted.vcf.gz"), emit: vcf_lifted tuple val(meta), path("*.unlifted.vcf.gz"), emit: vcf_unlifted - tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,21 +26,21 @@ process PICARD_LIFTOVERVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ LiftoverVcf \\ - $args \\ - --INPUT $input_vcf \\ + ${args} \\ + --INPUT ${input_vcf} \\ --OUTPUT ${prefix}.lifted.vcf.gz \\ - --CHAIN $chain \\ + --CHAIN ${chain} \\ --REJECT ${prefix}.unlifted.vcf.gz \\ - --REFERENCE_SEQUENCE $fasta - + --REFERENCE_SEQUENCE ${fasta} """ stub: @@ -48,6 +48,5 @@ process PICARD_LIFTOVERVCF { """ echo | gzip > ${prefix}.lifted.vcf.gz echo | gzip > ${prefix}.unlifted.vcf.gz - """ } diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index bc4baf2da..24253b41f 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -79,10 +79,9 @@ output: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -91,10 +90,9 @@ topics: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test index d0e35b45d..8317403ca 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -17,18 +17,17 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -37,33 +36,31 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf_lifted[0][1]).vcf.summary, - path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, + path(process.out.vcf_lifted[0][1]).vcf.summary, + path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } - test("test-picard-liftovervcf-stubs") { - options '-stub' + test("test-picard-liftovervcf - stub") { + options "-stub" when { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -71,14 +68,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.vcf_lifted[0][1]).name, - file(process.out.vcf_unlifted[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } - } diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index 9bb324bbe..c17b69349 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -1,9 +1,23 @@ { - "test-picard-liftovervcf-stubs": { + "test-picard-liftovervcf - stub": { "content": [ - "test.lifted.vcf.gz", - "test.unlifted.vcf.gz", { + "vcf_lifted": [ + [ + { + "id": "test" + }, + "test.lifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_unlifted": [ + [ + { + "id": "test" + }, + "test.unlifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], "versions_picard": [ [ "PICARD_LIFTOVERVCF", @@ -13,11 +27,11 @@ ] } ], + "timestamp": "2026-02-20T10:38:09.430447871", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:41:30.546426132" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-liftovervcf": { "content": [ @@ -33,10 +47,10 @@ ] } ], + "timestamp": "2026-02-02T11:40:19.064084452", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:40:19.064084452" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 10621e019..17bcf27ba 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -1,11 +1,11 @@ process PICARD_MARKDUPLICATES { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(reads) @@ -13,11 +13,11 @@ process PICARD_MARKDUPLICATES { tuple val(meta3), path(fai) output: - tuple val(meta), path("*.bam") , emit: bam, optional: true - tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.metrics.txt"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -25,37 +25,39 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ picard \\ -Xmx${avail_mem}M \\ MarkDuplicates \\ - $args \\ - --INPUT $reads \\ + ${args} \\ + --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} \\ - $reference \\ - --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - + ${reference} \\ + --METRICS_FILE ${prefix}.metrics.txt """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ touch ${prefix}.${suffix} touch ${prefix}.${suffix}.bai - touch ${prefix}.MarkDuplicates.metrics.txt - + touch ${prefix}.metrics.txt """ } diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 0ec99c7f1..aa0ddbdba 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -100,10 +100,9 @@ output: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -112,10 +111,9 @@ topics: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index e18723be0..4d0064531 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -114,7 +114,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -137,7 +137,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 848013849..4ea479a32 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -2,50 +2,13 @@ "sarscov2 [sorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -54,7 +17,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -66,7 +29,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -78,59 +41,22 @@ ] } ], + "timestamp": "2026-02-19T17:43:13.544887277", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:02.077382134" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -139,7 +65,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -151,7 +77,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -163,18 +89,18 @@ ] } ], + "timestamp": "2026-02-19T17:43:06.193033248", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:49.985589186" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -187,18 +113,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:40.574463587", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:42:49.704752548" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [sorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -211,18 +137,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:49.374645492", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:44:17.407572621" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram]": { "content": [ - "test.marked.cram", + "test.md.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.md.cram --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -235,59 +161,22 @@ ] } ], + "timestamp": "2026-02-19T17:42:59.07843756", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:33.412603893" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram] - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -299,7 +188,7 @@ "id": "test", "single_end": false }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metrics": [ @@ -308,7 +197,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -320,10 +209,10 @@ ] } ], + "timestamp": "2026-02-19T17:43:20.676018462", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:18.599127485" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config index 02818dd6e..f8dd0f1ca 100644 --- a/modules/nf-core/picard/markduplicates/tests/nextflow.config +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -1,6 +1,6 @@ process { withName: PICARD_MARKDUPLICATES { - ext.prefix = { "${meta.id}.marked" } + ext.prefix = { "${meta.id}.md" } ext.args = '--ASSUME_SORT_ORDER queryname' } } diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 6b02886bf..801ed9f26 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -1,19 +1,18 @@ - process PICARD_RENAMESAMPLEINVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -24,19 +23,18 @@ process PICARD_RENAMESAMPLEINVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - RenameSampleInVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ + RenameSampleInVcf \\ + --INPUT ${vcf} \\ --OUTPUT ${prefix}_renam.vcf.gz \\ - $extended_args - + ${extended_args} """ stub: diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 762780bd0..2b757b19d 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -44,10 +44,9 @@ output: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -56,10 +55,9 @@ topics: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test index 42e127a01..3e59c23bc 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -16,9 +16,8 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] """ } } @@ -27,12 +26,30 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.vcf[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-renamesampleinvcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index 86626ce81..2b6367ae7 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -12,10 +12,36 @@ ] } ], + "timestamp": "2026-02-02T15:51:56.010473", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T15:51:56.010473" + } + }, + "test-picard-renamesampleinvcf - stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_renam.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_RENAMESAMPLEINVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:39:17.132250662", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 782deba2b..92286e8a7 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -1,11 +1,11 @@ process PICARD_SORTVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process PICARD_SORTVCF { output: tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -22,23 +22,23 @@ process PICARD_SORTVCF { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def seq_dict = dict ? "--SEQUENCE_DICTIONARY $dict" : "" - def reference = fasta ? "--REFERENCE_SEQUENCE $fasta" : "" + def seq_dict = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - SortVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ - $args \\ - $seq_dict \\ - $reference \\ + SortVcf \\ + --INPUT ${vcf} \\ + ${args} \\ + ${seq_dict} \\ + ${reference} \\ --OUTPUT ${prefix}_sorted.vcf.gz """ diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index f6e327ff9..6cbe6b724 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -62,10 +62,9 @@ output: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -74,7 +73,7 @@ topics: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test index e8ef67501..a594b011b 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -16,15 +16,14 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] """ } } @@ -33,12 +32,36 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).linesGzip[3..7], + path(process.out.vcf[0][1]).linesGzip[3..7], process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-sortvcf stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index 9db773653..25dcb7ef6 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -1,4 +1,30 @@ { + "test-picard-sortvcf stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_SORTVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:40:26.218029661", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-sortvcf": { "content": [ [ @@ -18,10 +44,10 @@ ] } ], + "timestamp": "2026-02-02T11:47:50.61817621", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:47:50.61817621" + } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5cfbd8886..0b1d006a7 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -228,9 +228,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -720,10 +717,6 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index d0235fb4c..7f9221f2d 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -219,9 +219,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -665,10 +662,6 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 6a9f197b0..75dbcd61f 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -220,9 +220,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -573,8 +570,6 @@ "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", - "haplocheck", - "haplocheck/hugelymodelbat.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", From abd5bc6f6435e1aeb8a69828db98acd1c2a5cbfc Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:25:04 +0100 Subject: [PATCH 336/872] update modules --- modules.json | 23 +-- .../picard/addorreplacereadgroups/main.nf | 3 - .../picard/addorreplacereadgroups/meta.yml | 1 - .../addorreplacereadgroups/tests/bam.config | 1 - .../addorreplacereadgroups/tests/cram.config | 1 - .../addorreplacereadgroups/tests/main.nf.test | 23 +-- .../tests/main.nf.test.snap | 37 +--- .../nf-core/picard/collecthsmetrics/main.nf | 43 ++-- .../nf-core/picard/collecthsmetrics/meta.yml | 4 +- .../collecthsmetrics/tests/main.nf.test | 25 +-- .../collecthsmetrics/tests/main.nf.test.snap | 44 ++-- .../picard/collectmultiplemetrics/main.nf | 29 ++- .../picard/collectmultiplemetrics/meta.yml | 4 +- .../collectmultiplemetrics/tests/main.nf.test | 144 +++++++++---- .../tests/main.nf.test.snap | 156 ++++++++++++++- .../nf-core/picard/collectwgsmetrics/main.nf | 33 ++- .../nf-core/picard/collectwgsmetrics/meta.yml | 5 +- .../collectwgsmetrics/tests/main.nf.test | 119 ++++++++--- .../collectwgsmetrics/tests/main.nf.test.snap | 74 ++++++- modules/nf-core/picard/liftovervcf/main.nf | 29 ++- modules/nf-core/picard/liftovervcf/meta.yml | 6 +- .../picard/liftovervcf/tests/main.nf.test | 65 +++--- .../liftovervcf/tests/main.nf.test.snap | 32 ++- modules/nf-core/picard/markduplicates/main.nf | 46 +++-- .../nf-core/picard/markduplicates/meta.yml | 6 +- .../picard/markduplicates/tests/main.nf.test | 6 +- .../markduplicates/tests/main.nf.test.snap | 189 ++++-------------- .../markduplicates/tests/nextflow.config | 2 +- .../nf-core/picard/renamesampleinvcf/main.nf | 26 ++- .../nf-core/picard/renamesampleinvcf/meta.yml | 6 +- .../renamesampleinvcf/tests/main.nf.test | 29 ++- .../renamesampleinvcf/tests/main.nf.test.snap | 30 ++- modules/nf-core/picard/sortvcf/main.nf | 32 +-- modules/nf-core/picard/sortvcf/meta.yml | 5 +- .../nf-core/picard/sortvcf/tests/main.nf.test | 47 +++-- .../picard/sortvcf/tests/main.nf.test.snap | 30 ++- 36 files changed, 793 insertions(+), 562 deletions(-) diff --git a/modules.json b/modules.json index 9ae2f6592..d90a2bf82 100644 --- a/modules.json +++ b/modules.json @@ -286,11 +286,6 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, - "haplocheck": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", @@ -303,7 +298,7 @@ }, "hmtnote/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"], "patch": "modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff" }, @@ -339,42 +334,42 @@ }, "picard/addorreplacereadgroups": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collecthsmetrics": { "branch": "master", - "git_sha": "976ed20e328a92cb24ab6c63a8983ed31bf48469", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/renamesampleinvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "qualimap/bamqc": { diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 5ef3b7d8e..7261dc8e2 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -34,7 +34,6 @@ process PICARD_ADDORREPLACEREADGROUPS { } if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ picard \\ -Xmx${avail_mem}M \\ @@ -43,7 +42,6 @@ process PICARD_ADDORREPLACEREADGROUPS { $reference \\ --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} - """ stub: @@ -52,6 +50,5 @@ process PICARD_ADDORREPLACEREADGROUPS { if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.${suffix} - """ } diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index 6c3ed7599..b26a1c508 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -90,7 +90,6 @@ output: - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config index 3f37c2fd9..132cc0f7c 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config @@ -9,5 +9,4 @@ process { "-SM ${meta.id}" ].join(' ').trim()} } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config index 966c14d79..be92e72bb 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config @@ -9,5 +9,4 @@ process { ].join(' ').trim()} ext.suffix = { "cram" } } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 45729f3b5..5586ab469 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -27,14 +27,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.bai[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.bam[0][1]).name, + file(process.out.bai[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("homo_sapiens - cram") { @@ -58,19 +56,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.cram[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.cram[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("sarscov2 - bam - stub") { config "./bam.config" options "-stub" - when { process { """ @@ -84,10 +79,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index d2a99ee27..7ec99fbb5 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -12,36 +12,15 @@ ] } ], + "timestamp": "2026-02-02T09:36:16.966842212", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:16.966842212" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - - }, - "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - "PICARD_ADDORREPLACEREADGROUPS", - "picard", - "3.4.0" - ] - ], "bai": [ ], @@ -65,11 +44,11 @@ ] } ], + "timestamp": "2026-02-19T17:34:40.3572859", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:29.861163004" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam": { "content": [ @@ -85,10 +64,10 @@ ] } ], + "timestamp": "2026-02-02T09:36:00.935196996", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:00.935196996" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index b13871f8c..96045b5dd 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -1,22 +1,22 @@ process PICARD_COLLECTHSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') tuple val(meta2), path(ref) tuple val(meta3), path(ref_fai) tuple val(meta4), path(ref_dict) - tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped + tuple val(meta5), path(ref_gzi) output: - tuple val(meta), path("*_metrics") , emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*_metrics"), emit: metrics + tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -28,41 +28,38 @@ process PICARD_COLLECTHSMETRICS { def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } def bait_interval_list = bait_intervals def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/){ + if (bait_intervals =~ /.(bed|bed.gz)$/) { bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } def target_interval_list = target_intervals def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/){ + if (target_intervals =~ /.(bed|bed.gz)$/) { target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } - - """ - - $bait_intervallist_cmd - $target_intervallist_cmd + ${bait_intervallist_cmd} + ${target_intervallist_cmd} picard \\ -Xmx${avail_mem}M \\ CollectHsMetrics \\ - $args \\ - $reference \\ - --BAIT_INTERVALS $bait_interval_list \\ - --TARGET_INTERVALS $target_interval_list \\ - --INPUT $bam \\ + ${args} \\ + ${reference} \\ + --BAIT_INTERVALS ${bait_interval_list} \\ + --TARGET_INTERVALS ${target_interval_list} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics - """ stub: diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index a21aa6ecd..89bc502c9 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -106,7 +106,7 @@ output: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -118,7 +118,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 07a9ccf42..d73661111 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -40,11 +40,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - gzippedfa") { @@ -78,17 +76,13 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - stub") { - options "-stub" - when { process { """ @@ -110,10 +104,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2 - bam - nofasta") { @@ -147,11 +140,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - bed") { @@ -186,11 +177,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - samebed") { @@ -225,10 +214,8 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } } diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 74d9441fa..43385314a 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -115,31 +115,15 @@ ] } ], + "timestamp": "2026-01-05T17:03:29.566021877", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:29.566021877" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ], "metrics": [ [ { @@ -158,11 +142,11 @@ ] } ], + "timestamp": "2026-02-19T17:36:03.822502867", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:13.333276975" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam - gzippedfa": { "content": [ @@ -280,11 +264,11 @@ ] } ], + "timestamp": "2026-01-05T17:03:04.382110367", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:04.382110367" + } }, "sarscov2 - bam - samebed": { "content": [ @@ -402,11 +386,11 @@ ] } ], + "timestamp": "2026-01-05T17:13:22.872920293", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:22.872920293" + } }, "sarscov2 - bam": { "content": [ @@ -524,11 +508,11 @@ ] } ], + "timestamp": "2026-01-05T17:02:47.615784738", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:02:47.615784738" + } }, "sarscov2 - bam - bed": { "content": [ @@ -646,10 +630,10 @@ ] } ], + "timestamp": "2026-01-05T17:13:02.812282052", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:02.812282052" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 3c6152e5f..9de927e69 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -1,21 +1,21 @@ process PICARD_COLLECTMULTIPLEMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: - tuple val(meta) , path(bam), path(bai) + tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val(meta), path("*.pdf") , emit: pdf, optional: true - tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*.pdf"), emit: pdf, optional: true + tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,19 +26,19 @@ process PICARD_COLLECTMULTIPLEMETRICS { def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectMultipleMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectMultipleMetrics \\ - $reference - + ${reference} """ stub: @@ -54,6 +54,5 @@ process PICARD_COLLECTMULTIPLEMETRICS { touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - """ } diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 1ea47244c..213d600be 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -81,7 +81,7 @@ output: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -93,7 +93,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test index 08456941b..0037acab6 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -16,16 +16,15 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] """ } } @@ -37,8 +36,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -49,13 +47,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] input[2] = [[id:'genome'],[]] - """ } } @@ -67,8 +64,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -79,19 +75,18 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] """ } } @@ -103,10 +98,89 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} + ) + } + } + + test("test-picard-collectmultiplemetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectmultiplemetrics-nofasta - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } + test("test-picard-collectmultiplemetrics-cram - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index 1acf37765..393ed1003 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -25,11 +25,107 @@ ] } ], + "timestamp": "2026-02-02T10:22:21.230301646", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:22:21.230301646" + } + }, + "test-picard-collectmultiplemetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:38.701455244", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectmultiplemetrics-nofasta - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:48.923918624", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -57,11 +153,11 @@ ] } ], + "timestamp": "2026-02-02T10:23:52.23446844", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:52.23446844" + } }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -89,10 +185,58 @@ ] } ], + "timestamp": "2026-02-02T10:23:27.387621193", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:27.387621193" + } + }, + "test-picard-collectmultiplemetrics-cram - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:57.11686549", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index aa77100c7..a5db512c0 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -1,51 +1,50 @@ process PICARD_COLLECTWGSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) - path intervallist + path intervallist output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 - def interval = intervallist ? "--INTERVALS ${intervallist}" : '' + def interval = intervallist ? "--INTERVALS ${intervallist}" : '' if (!task.memory) { - log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectWgsMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --REFERENCE_SEQUENCE ${fasta} \\ - $interval - + ${interval} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.CollectWgsMetrics.coverage_metrics - """ } diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index c59811d58..c5afe2e7c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -76,10 +76,9 @@ output: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -88,7 +87,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test index d6a60e6bf..1bda5980a 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test @@ -16,19 +16,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] """ } } @@ -37,10 +36,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -51,19 +49,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) """ } } @@ -72,12 +69,70 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-collectwgsmetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectwgsmetrics-with-interval - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index 375c2ef9d..79f1145ff 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -1,7 +1,34 @@ { + "test-picard-collectwgsmetrics-with-interval - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:35:04.636691319", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-collectwgsmetrics-with-interval": { "content": [ - true, + false, { "versions_picard": [ [ @@ -12,15 +39,42 @@ ] } ], + "timestamp": "2026-02-20T10:34:45.059411647", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectwgsmetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:34:54.347278951", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:55.091876466" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectwgsmetrics": { "content": [ - true, + false, { "versions_picard": [ [ @@ -31,10 +85,10 @@ ] } ], + "timestamp": "2026-02-20T10:34:25.744978033", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:11.334274481" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 186afc50f..da025c9b6 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -1,11 +1,11 @@ process PICARD_LIFTOVERVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(input_vcf) @@ -14,9 +14,9 @@ process PICARD_LIFTOVERVCF { tuple val(meta4), path(chain) output: - tuple val(meta), path("*.lifted.vcf.gz") , emit: vcf_lifted + tuple val(meta), path("*.lifted.vcf.gz"), emit: vcf_lifted tuple val(meta), path("*.unlifted.vcf.gz"), emit: vcf_unlifted - tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,21 +26,21 @@ process PICARD_LIFTOVERVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ LiftoverVcf \\ - $args \\ - --INPUT $input_vcf \\ + ${args} \\ + --INPUT ${input_vcf} \\ --OUTPUT ${prefix}.lifted.vcf.gz \\ - --CHAIN $chain \\ + --CHAIN ${chain} \\ --REJECT ${prefix}.unlifted.vcf.gz \\ - --REFERENCE_SEQUENCE $fasta - + --REFERENCE_SEQUENCE ${fasta} """ stub: @@ -48,6 +48,5 @@ process PICARD_LIFTOVERVCF { """ echo | gzip > ${prefix}.lifted.vcf.gz echo | gzip > ${prefix}.unlifted.vcf.gz - """ } diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index bc4baf2da..24253b41f 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -79,10 +79,9 @@ output: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -91,10 +90,9 @@ topics: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test index d0e35b45d..8317403ca 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -17,18 +17,17 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -37,33 +36,31 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf_lifted[0][1]).vcf.summary, - path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, + path(process.out.vcf_lifted[0][1]).vcf.summary, + path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } - test("test-picard-liftovervcf-stubs") { - options '-stub' + test("test-picard-liftovervcf - stub") { + options "-stub" when { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -71,14 +68,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.vcf_lifted[0][1]).name, - file(process.out.vcf_unlifted[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } - } diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index 9bb324bbe..c17b69349 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -1,9 +1,23 @@ { - "test-picard-liftovervcf-stubs": { + "test-picard-liftovervcf - stub": { "content": [ - "test.lifted.vcf.gz", - "test.unlifted.vcf.gz", { + "vcf_lifted": [ + [ + { + "id": "test" + }, + "test.lifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_unlifted": [ + [ + { + "id": "test" + }, + "test.unlifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], "versions_picard": [ [ "PICARD_LIFTOVERVCF", @@ -13,11 +27,11 @@ ] } ], + "timestamp": "2026-02-20T10:38:09.430447871", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:41:30.546426132" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-liftovervcf": { "content": [ @@ -33,10 +47,10 @@ ] } ], + "timestamp": "2026-02-02T11:40:19.064084452", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:40:19.064084452" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 10621e019..17bcf27ba 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -1,11 +1,11 @@ process PICARD_MARKDUPLICATES { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(reads) @@ -13,11 +13,11 @@ process PICARD_MARKDUPLICATES { tuple val(meta3), path(fai) output: - tuple val(meta), path("*.bam") , emit: bam, optional: true - tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.metrics.txt"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -25,37 +25,39 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ picard \\ -Xmx${avail_mem}M \\ MarkDuplicates \\ - $args \\ - --INPUT $reads \\ + ${args} \\ + --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} \\ - $reference \\ - --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - + ${reference} \\ + --METRICS_FILE ${prefix}.metrics.txt """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ touch ${prefix}.${suffix} touch ${prefix}.${suffix}.bai - touch ${prefix}.MarkDuplicates.metrics.txt - + touch ${prefix}.metrics.txt """ } diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 0ec99c7f1..aa0ddbdba 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -100,10 +100,9 @@ output: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -112,10 +111,9 @@ topics: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index e18723be0..4d0064531 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -114,7 +114,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -137,7 +137,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 848013849..4ea479a32 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -2,50 +2,13 @@ "sarscov2 [sorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -54,7 +17,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -66,7 +29,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -78,59 +41,22 @@ ] } ], + "timestamp": "2026-02-19T17:43:13.544887277", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:02.077382134" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -139,7 +65,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -151,7 +77,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -163,18 +89,18 @@ ] } ], + "timestamp": "2026-02-19T17:43:06.193033248", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:49.985589186" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -187,18 +113,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:40.574463587", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:42:49.704752548" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [sorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -211,18 +137,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:49.374645492", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:44:17.407572621" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram]": { "content": [ - "test.marked.cram", + "test.md.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.md.cram --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -235,59 +161,22 @@ ] } ], + "timestamp": "2026-02-19T17:42:59.07843756", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:33.412603893" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram] - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -299,7 +188,7 @@ "id": "test", "single_end": false }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metrics": [ @@ -308,7 +197,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -320,10 +209,10 @@ ] } ], + "timestamp": "2026-02-19T17:43:20.676018462", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:18.599127485" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config index 02818dd6e..f8dd0f1ca 100644 --- a/modules/nf-core/picard/markduplicates/tests/nextflow.config +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -1,6 +1,6 @@ process { withName: PICARD_MARKDUPLICATES { - ext.prefix = { "${meta.id}.marked" } + ext.prefix = { "${meta.id}.md" } ext.args = '--ASSUME_SORT_ORDER queryname' } } diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 6b02886bf..801ed9f26 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -1,19 +1,18 @@ - process PICARD_RENAMESAMPLEINVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -24,19 +23,18 @@ process PICARD_RENAMESAMPLEINVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - RenameSampleInVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ + RenameSampleInVcf \\ + --INPUT ${vcf} \\ --OUTPUT ${prefix}_renam.vcf.gz \\ - $extended_args - + ${extended_args} """ stub: diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 762780bd0..2b757b19d 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -44,10 +44,9 @@ output: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -56,10 +55,9 @@ topics: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test index 42e127a01..3e59c23bc 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -16,9 +16,8 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] """ } } @@ -27,12 +26,30 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.vcf[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-renamesampleinvcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index 86626ce81..2b6367ae7 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -12,10 +12,36 @@ ] } ], + "timestamp": "2026-02-02T15:51:56.010473", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T15:51:56.010473" + } + }, + "test-picard-renamesampleinvcf - stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_renam.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_RENAMESAMPLEINVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:39:17.132250662", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 782deba2b..92286e8a7 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -1,11 +1,11 @@ process PICARD_SORTVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process PICARD_SORTVCF { output: tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -22,23 +22,23 @@ process PICARD_SORTVCF { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def seq_dict = dict ? "--SEQUENCE_DICTIONARY $dict" : "" - def reference = fasta ? "--REFERENCE_SEQUENCE $fasta" : "" + def seq_dict = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - SortVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ - $args \\ - $seq_dict \\ - $reference \\ + SortVcf \\ + --INPUT ${vcf} \\ + ${args} \\ + ${seq_dict} \\ + ${reference} \\ --OUTPUT ${prefix}_sorted.vcf.gz """ diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index f6e327ff9..6cbe6b724 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -62,10 +62,9 @@ output: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -74,7 +73,7 @@ topics: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test index e8ef67501..a594b011b 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -16,15 +16,14 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] """ } } @@ -33,12 +32,36 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).linesGzip[3..7], + path(process.out.vcf[0][1]).linesGzip[3..7], process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-sortvcf stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index 9db773653..25dcb7ef6 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -1,4 +1,30 @@ { + "test-picard-sortvcf stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_SORTVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:40:26.218029661", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-sortvcf": { "content": [ [ @@ -18,10 +44,10 @@ ] } ], + "timestamp": "2026-02-02T11:47:50.61817621", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:47:50.61817621" + } } } \ No newline at end of file From 7f24cf3eb5fe758f96e73633801d0d6f5a90abe0 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:36:58 +0100 Subject: [PATCH 337/872] add haplocheck back --- modules.json | 5 + modules/nf-core/haplocheck/environment.yml | 7 ++ modules/nf-core/haplocheck/main.nf | 43 ++++++++ modules/nf-core/haplocheck/meta.yml | 65 ++++++++++++ modules/nf-core/haplocheck/tests/main.nf.test | 56 ++++++++++ .../haplocheck/tests/main.nf.test.snap | 100 ++++++++++++++++++ 6 files changed, 276 insertions(+) create mode 100644 modules/nf-core/haplocheck/environment.yml create mode 100644 modules/nf-core/haplocheck/main.nf create mode 100644 modules/nf-core/haplocheck/meta.yml create mode 100644 modules/nf-core/haplocheck/tests/main.nf.test create mode 100644 modules/nf-core/haplocheck/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index dcf570b57..3417c5ac5 100644 --- a/modules.json +++ b/modules.json @@ -286,6 +286,11 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, + "haplocheck": { + "branch": "master", + "git_sha": "dbc43f924a7410a2b828f2a022305f1d6e71ed84", + "installed_by": ["modules"] + }, "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml new file mode 100644 index 000000000..d74b4d7ed --- /dev/null +++ b/modules/nf-core/haplocheck/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf new file mode 100644 index 000000000..443156309 --- /dev/null +++ b/modules/nf-core/haplocheck/main.nf @@ -0,0 +1,43 @@ +process HAPLOCHECK { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': + 'biocontainers/haplocheck:1.3.3--h4a94de4_0' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.txt") , emit: txt + tuple val(meta), path("*.html"), emit: html + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + haplocheck --raw --out $prefix $vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.raw.txt + touch ${prefix}.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml new file mode 100644 index 000000000..692f7c5d7 --- /dev/null +++ b/modules/nf-core/haplocheck/meta.yml @@ -0,0 +1,65 @@ +name: "haplocheck" +description: | + Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing + the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides + users a graphical report to investigate the contamination further. Internally, it uses the + Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. +keywords: + - mitochondrial + - mtDNA + - contamination +tools: + - "haplocheck": + description: "Detects in-sample contamination in mtDNA or WGS sequencing studies + by analyzing the mitochondrial content." + homepage: "https://github.com/genepi/haplocheck" + documentation: "https://github.com/genepi/haplocheck" + tool_dev_url: "https://github.com/genepi/haplocheck" + doi: 10.1101/gr.256545.119 + licence: ["MIT"] + identifier: biotools:haplocheck +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + ontologies: [] +output: + txt: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Raw report in txt format + pattern: "*.{txt}" + ontologies: [] + html: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Haplocheck HTML report + pattern: "*.{html}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@lmtani" +maintainers: + - "@lmtani" diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test new file mode 100644 index 000000000..8957d02e2 --- /dev/null +++ b/modules/nf-core/haplocheck/tests/main.nf.test @@ -0,0 +1,56 @@ + +nextflow_process { + + name "Test Process HAPLOCHECK" + script "../main.nf" + process "HAPLOCHECK" + + tag "modules" + tag "modules_nfcore" + tag "haplocheck" + + test("test-haplocheck") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-haplocheck-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/haplocheck/tests/main.nf.test.snap b/modules/nf-core/haplocheck/tests/main.nf.test.snap new file mode 100644 index 000000000..abe1eab56 --- /dev/null +++ b/modules/nf-core/haplocheck/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "test-haplocheck-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ], + "html": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:41:40.703528" + }, + "test-haplocheck": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.html:md5,59d69052c86edff0301816956eaf4d5f" + ] + ], + "2": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ], + "html": [ + [ + { + "id": "test" + }, + "test.html:md5,59d69052c86edff0301816956eaf4d5f" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" + ] + ], + "versions": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:43:05.761086" + } +} \ No newline at end of file From 3194ef6ade77186755004479972ee4fe122f849b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 25 Feb 2026 15:36:15 +0100 Subject: [PATCH 338/872] saltshaker tweaks --- conf/test.config | 1 + modules/local/saltshaker/classify/main.nf | 1 + nextflow.config | 13 +++++- subworkflows/local/call_sv_MT/main.nf | 57 ++++++++++++----------- 4 files changed, 45 insertions(+), 27 deletions(-) diff --git a/conf/test.config b/conf/test.config index dc6dd262e..81140af1b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -29,6 +29,7 @@ env { } singularity.pullTimeout='2h' +singularity.cacheDir='/home/proj/stage/singularity_cache' params { config_profile_name = 'Test profile - default' diff --git a/modules/local/saltshaker/classify/main.nf b/modules/local/saltshaker/classify/main.nf index d5dbc81de..5ce9eb4c0 100644 --- a/modules/local/saltshaker/classify/main.nf +++ b/modules/local/saltshaker/classify/main.nf @@ -17,6 +17,7 @@ process SALTSHAKER_CLASSIFY { output: tuple val(meta), path("*_classify_metadata.tsv"), emit: classify + tuple val(meta), path("*_classify.txt") , emit: txt tuple val(meta), path("*saltshaker.vcf") , emit: vcf path "versions.yml" , emit: versions diff --git a/nextflow.config b/nextflow.config index bd520863d..33b461bae 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,6 +19,12 @@ params { local_genomes = null save_reference = false mito_name = 'chrM' + mito_length = 16569 + ori_h_start = 16081 + ori_h_end = 407 + ori_l_start = 5730 + ori_l_end = 5763 + // Main options analysis_type = 'wgs' @@ -125,14 +131,19 @@ params { // Mitosalt/saltshaker options breakspan = 15 breakthreshold = 2 - cluster_threshold = 2 + cluster_threshold = 5 deletion_threshold_max = 30000 deletion_threshold_min = 30 + dom_frac = 0.5 evalue_threshold = 0.00001 exclude = 5 flank = 15 + group_radius = 600 + high_het = 10 hplimit = 0.01 mitosalt_depth = 10000000 + mult_thresh = 5 + noise_thresh = 0.3 paired_distance = 1000 score_threshold = 80 sizelimit = 10000 diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6c35974a4..a481457b1 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -90,41 +90,46 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) + MITOSALT.out.cluster + .filter{ meta, out -> out.countLines() > 0 } + .set{ch_saltshaker_in} - SALTSHAKER_CALL( - MITOSALT.out.breakpoint, - MITOSALT.out.cluster, - ch_mt_fasta, - val_flank, - val_hplimit, - val_mito_length, - val_ori_h_start, - val_ori_h_end, - val_ori_l_start, - val_ori_l_end - ) + if (ch_saltshaker_in) { + SALTSHAKER_CALL( + MITOSALT.out.breakpoint, + ch_saltshaker_in, + ch_mt_fasta, + val_flank, + val_hplimit, + val_mito_length, + val_ori_h_start, + val_ori_h_end, + val_ori_l_start, + val_ori_l_end + ) - SALTSHAKER_CLASSIFY( - SALTSHAKER_CALL.out.call, - val_dom_frac, - val_group_radius, - val_high_het, - val_mult_thresh, - val_noise_thresh - ) - ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify + SALTSHAKER_CLASSIFY( + SALTSHAKER_CALL.out.call, + val_dom_frac, + val_group_radius, + val_high_het, + val_mult_thresh, + val_noise_thresh + ) + ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify - SALTSHAKER_PLOT( - SALTSHAKER_CLASSIFY.out.classify - ) - ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot - + SALTSHAKER_PLOT( + SALTSHAKER_CLASSIFY.out.classify + ) + ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot + } ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) emit: + mitosalt_classify = SALTSHAKER_CLASSIFY.out.txt // channel: [ val(meta), path(txt) ] mitosalt_vcf = ch_mitosalt_vcf // channel: [ val(meta), path(vcf) ] mitosalt_plot = ch_mitosalt_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] From f6d090a85a062e43748166373c9f86fcc06611ac Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 26 Feb 2026 10:53:40 +0100 Subject: [PATCH 339/872] change mitosalt container and update schema/snaps --- modules/local/mitosalt/main.nf | 4 +- nextflow_schema.json | 54 +++- tests/default.nf.test.snap | 4 +- tests/test_bam.nf.test.snap | 78 +++++- tests/test_singleton.nf.test.snap | 412 +++++++++++++++++++++++++++++- 5 files changed, 529 insertions(+), 23 deletions(-) diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index c2e03464b..fd498f0fe 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -4,8 +4,8 @@ process MITOSALT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0311c283e73736be01c2cbd1ca93ae826c209d9733ffa6d2d4d2caa31e7464cc/data': - 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:11434f3b6a01596d' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/13/130779a0dd5a8d86441f262a16a5fb1dfe562125edf93646b53c893d982b5519/data': + 'community.wave.seqera.io/library/bbmap_bedtools_bioconductor-biostrings_bioconductor-pwalign_pruned:856c05081cbd8239' }" input: tuple val(meta), path(reads) diff --git a/nextflow_schema.json b/nextflow_schema.json index c4113ff6c..37cb7a55a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -768,7 +768,7 @@ }, "cluster_threshold": { "type": "integer", - "default": 2, + "default": 5, "description": "minimum number of reads supporting a cluster" }, "deletion_threshold_max": { @@ -781,9 +781,14 @@ "default": 30, "description": "the minimum size of the gap between fragemtns of a split read for the split read to be considered as potentially spanning a deletion" }, + "dom_frac": { + "type": "number", + "default": 0.5, + "description": "fraction for dominant fraction for saltshaker classification" + }, "evalue_threshold": { "type": "number", - "default": 1e-5, + "default": 1e-05, "description": "alignment e-value cutoff" }, "exclude": { @@ -796,6 +801,16 @@ "default": 15, "description": "basepairs flanking a deletion" }, + "group_radius": { + "type": "integer", + "default": 600, + "description": "spatial clustering radius for saltshaker grouping" + }, + "high_het": { + "type": "integer", + "default": 10, + "description": "high heteroplasmy threshold for saltshaker classification" + }, "hplimit": { "type": "number", "default": 0.01, @@ -806,6 +821,41 @@ "default": 10000000, "description": "depth to subsample fastq files to before running mitosalt" }, + "mito_length": { + "type": "integer", + "default": 16569, + "description": "length of mitochondrial genome" + }, + "mult_thresh": { + "type": "integer", + "default": 5, + "description": "threshold for multiple saltshaker classification" + }, + "noise_thresh": { + "type": "number", + "default": 0.3, + "description": "heteroplasmy threshold for background noise" + }, + "ori_h_start": { + "type": "integer", + "default": 16081, + "description": "start of heavy strand origin" + }, + "ori_h_end": { + "type": "integer", + "default": 407, + "description": "end of heavy strand origin" + }, + "ori_l_start": { + "type": "integer", + "default": 5730, + "description": "start of light strand origin" + }, + "ori_l_end": { + "type": "integer", + "default": 5763, + "description": "end of light strand origin" + }, "paired_distance": { "type": "integer", "default": 1000, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bf8774f4c..8e3627e8b 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1109,8 +1109,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-11T05:27:37.311350676" + "timestamp": "2026-02-26T10:44:57.130309344" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 70af846c2..1b715c906 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 795, + 823, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -67,6 +67,10 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.19.2" + }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -144,6 +148,12 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, + "FASTP": { + "fastp": "1.0.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -236,9 +246,15 @@ "MANTA": { "manta": "1.6.0" }, + "MARKDUPLICATES": { + "picard": "3.4.0" + }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, "MOSDEPTH": { "mosdepth": "0.3.11" }, @@ -319,18 +335,30 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_INDEX_ALIGN": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX_MARKDUP": { + "samtools": 1.21 + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" + }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -346,6 +374,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -477,10 +508,19 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -652,9 +692,25 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "fastqc", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -1030,6 +1086,22 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -1038,8 +1110,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-16T22:08:02.449482922" + "timestamp": "2026-02-26T10:48:15.225678805" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index da510cdc4..9bf253968 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 365, + 823, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,6 +16,9 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.22 + }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -84,6 +87,12 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -365,6 +374,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -457,6 +469,12 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, + "UPD_REGIONS": { + "upd": 0.1 + }, + "UPD_SITES": { + "upd": 0.1 + }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -488,11 +506,21 @@ }, [ "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -500,6 +528,35 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", + "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -529,8 +586,87 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + 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"annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -556,22 +692,38 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", + "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/hugelymodelbat_LNUMBER1", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -584,6 +736,113 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman", + "qc_bam/earlycasualcaiman/css", + "qc_bam/earlycasualcaiman/css/agogo.css", + "qc_bam/earlycasualcaiman/css/ajax-loader.gif", + "qc_bam/earlycasualcaiman/css/basic.css", + "qc_bam/earlycasualcaiman/css/bgfooter.png", + "qc_bam/earlycasualcaiman/css/bgtop.png", + "qc_bam/earlycasualcaiman/css/comment-bright.png", + "qc_bam/earlycasualcaiman/css/comment-close.png", + "qc_bam/earlycasualcaiman/css/comment.png", + "qc_bam/earlycasualcaiman/css/doctools.js", + "qc_bam/earlycasualcaiman/css/down-pressed.png", + "qc_bam/earlycasualcaiman/css/down.png", + "qc_bam/earlycasualcaiman/css/file.png", + "qc_bam/earlycasualcaiman/css/jquery.js", + "qc_bam/earlycasualcaiman/css/minus.png", + "qc_bam/earlycasualcaiman/css/plus.png", + "qc_bam/earlycasualcaiman/css/pygments.css", + "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", + "qc_bam/earlycasualcaiman/css/report.css", + 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"qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/earlycasualcaiman/qualimapReport.html", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", + 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"qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/earlycasualcaiman_tidditcov.bed", + "qc_bam/earlycasualcaiman_tidditcov.bw", + "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + 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"qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.summary.txt", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/slowlycivilbuck_tidditcov.bed", + "qc_bam/slowlycivilbuck_tidditcov.bw", + "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -705,29 +1071,47 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "vcf2cytosure/earlycasualcaiman.cgh", + "vcf2cytosure/hugelymodelbat.cgh", + "vcf2cytosure/slowlycivilbuck.cgh" ] ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-11T19:08:15.435078959" + "timestamp": "2026-02-26T10:52:33.255838659" } } \ No newline at end of file From f8fb561f479ce38d46e304c285e1d54e387ac87f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 26 Feb 2026 10:51:07 +0000 Subject: [PATCH 340/872] [automated] Fix code linting --- .../resources/usr/bin/MitoSAlt1.1.1.pl | 110 +++++++++--------- nextflow_schema.json | 2 +- 2 files changed, 55 insertions(+), 57 deletions(-) diff --git a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl index c0a0be0e6..bbaf37d9b 100755 --- a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl +++ b/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl @@ -4,7 +4,7 @@ use List::Util qw(first min max sum); use Data::Dumper; -#INPUT +#INPUT my $config_file = $ARGV[0]; my $p1 = $ARGV[1]; my $p2 = $ARGV[2]; @@ -36,7 +36,7 @@ $User_Preferences->{$var} = $value; my $line = $_; print $line."\n"; -} +} #PROGRAMS my $hisat2 = $User_Preferences->{hisat2}; @@ -116,7 +116,7 @@ #EXTRACT READS print scalar(localtime).": Extract reads\n"; - system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); + system("$samtools view -@ $threads -bt $faindex tmp_$tag.sam|$samtools sort -@ $threads -o tmp_$tag.bam -"); system("$samtools index tmp_$tag.bam"); system("$samtools idxstats tmp_$tag.bam > indel/$tag.count.txt"); system("$samtools view -u -@ $threads -f 12 tmp_$tag.bam > tmp1_$tag.bam"); #flag to extract unmapped reads with mate also unmapped @@ -179,7 +179,7 @@ my $bedfile = "indel/$tag.bed"; my $breakpointfile = "indel/$tag.breakpoint"; my $clusterfile = "indel/$tag.cluster"; - + my $check_paired = &check_paired($infile); print scalar(localtime).": Build split read hash\n"; $hash = &build_hash($infile,$check_paired); @@ -256,7 +256,7 @@ sub build_hash{ } elsif($check_paired == 1){ my @name = split(/\//,$elements[6]); $id = $name[0]; - $mate = $name[1]; + $mate = $name[1]; } my $strand = $elements[9]; @@ -265,12 +265,12 @@ sub build_hash{ next if exists $check_hash->{$id}->{$start.$length}; $check_hash->{$id}->{$start.$length}++; $mate = 2 if $mate > 1; - #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; + #print "$id\t$mate\t$start\t$end\t$strand\t$len\t$score\t$eval\n"; #FILTER BY SCORE AND MAP EVALUE next if $score < $score_threshold; next if $evalue > $evalue_threshold; - + push(@{$hash->{$id}->{$mate}->{starts}},$start); push(@{$hash->{$id}->{$mate}->{ends}},$end); push(@{$hash->{$id}->{$mate}->{rstarts}},$read_start); @@ -316,7 +316,7 @@ sub remove_duplicates{ my @signatures = ($signature1,$signature2); @signatures = sort @signatures; - my $signature = join("",@signatures); + my $signature = join("",@signatures); if(exists $check_duplicates->{$signature} && $count1>0 && $count2>0){ @@ -337,17 +337,17 @@ sub print_bed{ open(ABED,">$filename"); for my $id (keys %{$hash}){ #print $id."\n"; - + for my $read(keys %{$hash->{$id}}){ my $name = $id."_".$read; #CHECK IF READ IS SPLIT ALIGNED my $count = @{$hash->{$id}->{$read}->{starts}}; next if $count > 1; - my $start = @{$hash->{$id}->{$read}->{starts}}[0]; + my $start = @{$hash->{$id}->{$read}->{starts}}[0]; my $end = @{$hash->{$id}->{$read}->{ends}}[0]; - print ABED "$refchr\t$start\t$end\t$name\n"; - } + print ABED "$refchr\t$start\t$end\t$name\n"; + } } system("sort -k2,2n $filename -o $filename"); close(ABED); @@ -377,7 +377,7 @@ sub process_hash{ next unless $min_len >= $split_length; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -389,11 +389,11 @@ sub process_hash{ elsif($read_starts[0]>$read_starts[1] && $read_local_starts[0]<$read_local_starts[1]){$read_check = 'yes';} elsif($read_starts[0]<=$read_starts[1] && $read_local_starts[0]<$read_local_starts[1] && $read_starts[1]<$read_ends[0] ){$read_check = 'yes';} elsif($read_starts[0]>=$read_starts[1] && $read_local_starts[0]>$read_local_starts[1] && $read_ends[1]>$read_starts[0] ){$read_check = 'yes';} - + #CHECK IF THE SPLIT READ FRAGMENTS SPAN THE DLOOP - my $min_start = min @{$hash->{$id}->{$read}->{starts}}; + my $min_start = min @{$hash->{$id}->{$read}->{starts}}; my $max_end = max @{$hash->{$id}->{$read}->{ends}}; - next if $min_start <= $dloop1 && $max_end >= $dloop2; + next if $min_start <= $dloop1 && $max_end >= $dloop2; my ($size,$start,$end) = &get_frag_distance(\@read_starts,\@read_ends,$read_check,$msize); next if $size < $deletion_threshold_min; @@ -402,7 +402,7 @@ sub process_hash{ #print "$name\t$start\t$end\t$size\n"; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #CHECK IF PAIRED READ EXISTS AND ITS ALIGNMENT POSITION SUPPORTS THE SPLIT READ my $pair = 1 if $read == 2; @@ -427,7 +427,7 @@ sub process_hash{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + $start = $len[2]; $end = $len[3]; $size = $len[4]; @@ -455,7 +455,7 @@ sub process_hash1{ my $bpe = shift; my $delhash; - + open(BP,">$breakpointfile"); open(BED,">$bedfile"); open(BPS,">$bps"); @@ -470,7 +470,7 @@ sub process_hash1{ next unless $count == 3; #GET DISTANCE BETWEEN THE FRAGMENTS AND THE BREAKPOINTS - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; my @read_strands = @{$hash->{$id}->{$read}->{strands}}; my @read_lengths = @{$hash->{$id}->{$read}->{lengths}}; @@ -540,7 +540,7 @@ sub process_hash1{ #CHECK IF THE SPLIT READ FRAGMENTS ARE ABOVE LENGTH THRESHOLD my $min_len = min @read_lengthsN; next unless $min_len >= $split_length; - + #LOOK FOR SPLIT READS WHICH MAP INVERSELY SPANNING THE D'LOOP my $read_check = 'no'; @@ -558,7 +558,7 @@ sub process_hash1{ $paired_support = 'yes' if $distance_paired_support <= $paired_distance; $start = 1 if $start == 0; - $end = 1 if $end == 0; + $end = 1 if $end == 0; #LOOK FOR SPLIT READS WITH LARGE UNMAPPED AREA my ($split_distance) = &get_split_distance(\@read_local_startsN,\@read_lengthsN); @@ -574,7 +574,7 @@ sub process_hash1{ $delhash->{$readid}->{readcheck}=$read_check; $delhash->{$readid}->{lenstart}=$len[0]; $delhash->{$readid}->{lenend}=$len[1]; - + #$start = $len[2]; #$end = $len[3]; #$size = $len[4]; @@ -603,10 +603,10 @@ sub paired_support{ my $distance1 = 0; my $distance2=0; - my @read_starts = @{$hash->{$id}->{$read}->{starts}}; + my @read_starts = @{$hash->{$id}->{$read}->{starts}}; my @read_ends = @{$hash->{$id}->{$read}->{ends}}; - - my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; + + my $pair_start = @{$hash->{$id}->{$pair}->{starts}}[0]; my $pair_end = @{$hash->{$id}->{$pair}->{ends}}[0]; $distance1 = $read_starts[0] - $pair_end if $read_starts[0] > $pair_end; @@ -632,10 +632,10 @@ sub get_frag_distance{ my $frag1_end = @{$ends}[0]; my $frag2_end = @{$ends}[1]; - + if($read_check eq 'no'){ if($frag1_start > $frag2_end){ - my $size = $frag1_start - $frag2_end; + my $size = $frag1_start - $frag2_end; @res = ($size,$frag2_end,$frag1_start); } elsif($frag2_start > $frag1_end){ @@ -662,7 +662,7 @@ sub get_frag_distance{ if($read_check eq 'yes'){ if($frag1_start > $frag2_end){ - my $size = ($msize -$frag1_end) + $frag2_start; + my $size = ($msize -$frag1_end) + $frag2_start; @res = ($size,$frag2_start,$frag1_end); } elsif($frag2_start > $frag1_end){ @@ -700,7 +700,7 @@ sub get_split_distance{ my $local1_length = @{$lengths}[0]; my $local2_length = @{$lengths}[1]; - + if($local1_start>$local2_start){ my $distance = $local1_start - $local2_start - $local2_length; @res = ($distance); @@ -708,7 +708,7 @@ sub get_split_distance{ if($local2_start>$local1_start){ my $distance = $local2_start - $local1_start - $local1_length; @res = ($distance); - } + } return @res; } @@ -721,7 +721,7 @@ sub generate_bed{ my $lengths = shift; my $scores = shift; my $strand = shift; - + my $size = shift; my $bstart = shift; my $bend = shift; @@ -751,7 +751,7 @@ sub generate_bed{ $size = $frag1_start - $frag2_end; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag1_start > $frag2_end && $strand eq '+'){ @@ -762,53 +762,53 @@ sub generate_bed{ $size = 1 + $msize- $frag1_end + $frag2_start; my $block_start=$frag1_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_end; $bend = $frag2_start; $size = $frag2_start - $frag1_end; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length,$bstart,$bend,$size); } elsif($frag2_start > $frag1_end && $strand eq '-'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag1_start; $bend = $frag2_end; $size = 1 + $msize - $frag2_end + $frag1_start; my $block_start=$frag2_start-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); } elsif($frag2_start < $frag1_end && $strand eq '+'){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; $bstart = $frag2_start; - $bend = $frag1_end; + $bend = $frag1_end; $size = $msize - $frag1_end + $frag2_start; my $block_start=$frag1_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } elsif($frag1_start < $frag2_end && $strand eq '-'){ $start = $frag2_start; - $end = $frag1_end; + $end = $frag1_end; $bstart = $frag1_start; - $bend = $frag2_end; + $bend = $frag2_end; $size = $msize - $frag2_end + $frag1_start; my $block_start=$frag2_end-$start; $start = 1 if $start == 0;$end = 1 if $end == 0;$bstart = 1 if $bstart == 0;$bend = 1 if $bend == 0; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length,$bstart,$bend,$size); - } + } return @len; } @@ -844,14 +844,14 @@ sub generate_bed1{ $start = $frag2_start; $end = $frag1_end; my $block_start=$frag1_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag2_length\,$frag1_length\t0\,$block_start\n"; @len = ($frag2_length,$frag1_length); } elsif($frag2_start > $frag1_end){ $start = $frag1_start; - $end = $frag2_end; + $end = $frag2_end; my $block_start=$frag2_start-$start; - print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; + print BED "$refchr\t$start\t$end\t$id\_$read\t$score\t$strand\t$start\t$end\t0\t2\t$frag1_length\,$frag2_length\t0\,$block_start\n"; @len = ($frag1_length,$frag2_length); } return @len; @@ -893,7 +893,7 @@ sub get_cluster{ $bpe_hash->{$readid} = $clusterid; } close(BPE); - + for my $readid(keys %{$delhash}){ next unless exists $bps_hash->{$readid}; next unless exists $bpe_hash->{$readid}; @@ -912,17 +912,17 @@ sub build_results{ my $refchr = shift; my $cluster_read_count_threshold = shift; my $tag = shift; - my $clustercount; + my $clustercount; my $nosplitbed_file = "tmp_".$tag."_nosplit.bed";; for my $clusterid (keys %{$clusterhash}){ - my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; - next if $cluster_read_count < $cluster_read_count_threshold; + my $cluster_read_count = scalar keys %{$clusterhash->{$clusterid}}; + next if $cluster_read_count < $cluster_read_count_threshold; print "Check $clusterid\n"; my $clustercheck; $clustercount->{$clusterid}->{wt} = 0; - $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; + $clustercount->{$clusterid}->{mt} = scalar keys %{$clusterhash->{$clusterid}}; my $splitbed_fileS = "tmp_".$tag.".split.start.bed"; my $splitbed_fileE = "tmp_".$tag.".split.end.bed"; @@ -1033,5 +1033,3 @@ sub print_result{ } close(CF); } - - diff --git a/nextflow_schema.json b/nextflow_schema.json index 37cb7a55a..5fb2f5035 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -788,7 +788,7 @@ }, "evalue_threshold": { "type": "number", - "default": 1e-05, + "default": 1e-5, "description": "alignment e-value cutoff" }, "exclude": { From 2d378e187b9958dc107f6233b8c7a883be7aef01 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Feb 2026 10:28:31 +0100 Subject: [PATCH 341/872] updated snaps --- tests/test_bam.nf.test.snap | 76 +----- tests/test_singleton.nf.test.snap | 410 +----------------------------- 2 files changed, 15 insertions(+), 471 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 1b715c906..a0e9f2131 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 823, + 795, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -67,10 +67,6 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" - }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.19.2" @@ -148,12 +144,6 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, - "FASTP": { - "fastp": "1.0.1" - }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -246,15 +236,9 @@ "MANTA": { "manta": "1.6.0" }, - "MARKDUPLICATES": { - "picard": "3.4.0" - }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, - "MITOSALT": { - "mitosalt": "1.1.1" - }, "MOSDEPTH": { "mosdepth": "0.3.11" }, @@ -335,30 +319,18 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 - }, - "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 - }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, - "SEQTK_SAMPLE": { - "seqtk": "1.4-r122" - }, "SMNCOPYNUMBERCALLER": { "SMNCopyNumberCaller": "1.1.2" }, @@ -374,9 +346,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -508,19 +477,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -692,25 +652,9 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "haplocheck", "haplocheck/earlycasualcaiman.raw.txt", "haplocheck/hugelymodelbat.raw.txt", @@ -1086,22 +1030,6 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -1112,6 +1040,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-26T10:48:15.225678805" + "timestamp": "2026-02-27T09:07:42.308738867" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 9bf253968..a3ba978fb 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 823, + 365, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,9 +16,6 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.22 - }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -87,12 +84,6 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -374,9 +365,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -469,12 +457,6 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.1" }, @@ -506,21 +488,11 @@ }, [ "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -528,35 +500,6 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -586,87 +529,8 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", @@ -692,38 +556,22 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - 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"haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.html", @@ -736,113 +584,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - 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"qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat", "qc_bam/hugelymodelbat/css", "qc_bam/hugelymodelbat/css/agogo.css", @@ -950,113 +691,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck", - "qc_bam/slowlycivilbuck/css", - "qc_bam/slowlycivilbuck/css/agogo.css", - 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"rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/earlycasualcaiman.cgh", - "vcf2cytosure/hugelymodelbat.cgh", - "vcf2cytosure/slowlycivilbuck.cgh" + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-26T10:52:33.255838659" + "timestamp": "2026-02-27T10:14:31.323250611" } } \ No newline at end of file From 4bc53094dcda9220ccd52c524e26a287d7b7339f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Feb 2026 13:23:52 +0100 Subject: [PATCH 342/872] update_snapshots --- tests/default.nf.test.snap | 17 ++++++++++++----- tests/test_bam.nf.test.snap | 11 +++++++++-- tests/test_singleton.nf.test.snap | 11 ++++++++--- 3 files changed, 29 insertions(+), 10 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0b1d006a7..11951c3da 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -228,6 +228,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -516,19 +519,19 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", "alignment/earlycasualcaiman_sorted_md.bam", "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", "alignment/slowlycivilbuck_sorted_md.bam", "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -717,6 +720,10 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", + "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", + "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1114,10 +1121,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-24T17:18:24.169571113", + "timestamp": "2026-02-27T12:45:44.180676148", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 7f9221f2d..8f422db16 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -219,6 +219,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -662,6 +665,10 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", + "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1043,10 +1050,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-24T23:58:33.320173721", + "timestamp": "2026-02-27T12:52:01.429826076", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 75dbcd61f..879db1de9 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -220,6 +220,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -499,9 +502,9 @@ "alignment", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -570,6 +573,8 @@ "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "haplocheck", + "haplocheck/hugelymodelbat.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -733,10 +738,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-02-25T02:33:23.251038469", + "timestamp": "2026-02-27T12:55:52.928711503", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file From ebb864f5bf4c5587bd94ad17a5e6073b6b62db04 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Feb 2026 15:52:45 +0100 Subject: [PATCH 343/872] update subworkflow snapshots --- .../local/align_MT/tests/main.nf.test.snap | 52 +++++++++---------- .../tests/main.nf.test.snap | 8 +-- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 978d90592..53cd47acd 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,aa29752265d70e5c2ed10de503fa8b33" ], [ { @@ -33,7 +33,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,011888be5d5c6e77b48d8b8fd81155a4" ], [ { @@ -49,7 +49,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,9934e5e180a1760490bc36aaf23ec10c" ] ], "1": [ @@ -67,7 +67,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d4ea71dac6170a728c27457e4d042a17" ], [ { @@ -83,7 +83,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,eba491066ead408a1cdfd13fd353fc1d" ], [ { @@ -99,7 +99,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,3263f88b4f8987f16b81a5980bf26aad" ] ], "marked_bai": [ @@ -117,7 +117,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,aa29752265d70e5c2ed10de503fa8b33" ], [ { @@ -133,7 +133,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,011888be5d5c6e77b48d8b8fd81155a4" ], [ { @@ -149,7 +149,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,9934e5e180a1760490bc36aaf23ec10c" ] ], "marked_bam": [ @@ -167,7 +167,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d4ea71dac6170a728c27457e4d042a17" ], [ { @@ -183,7 +183,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,eba491066ead408a1cdfd13fd353fc1d" ], [ { @@ -199,12 +199,12 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,3263f88b4f8987f16b81a5980bf26aad" ] ] } ], - "timestamp": "2026-02-20T00:15:07.330482228", + "timestamp": "2026-02-27T15:43:54.097536585", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -228,7 +228,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,bc1e2296080bc0d6d9878d3784892ee0" ], [ { @@ -244,7 +244,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,8df5c65448c3c2f20cd8f574182f5593" ], [ { @@ -260,7 +260,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,de7d63cfa5735162d2274d877bf0b85b" ] ], "1": [ @@ -278,7 +278,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,7ee847d7f586a961a446566f8d473c30" ], [ { @@ -294,7 +294,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d294ef713b4f83c621be387294d7937e" ], [ { @@ -310,7 +310,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,ffe465201f5119c2699a49cd110628d3" ] ], "marked_bai": [ @@ -328,7 +328,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,bc1e2296080bc0d6d9878d3784892ee0" ], [ { @@ -344,7 +344,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,8df5c65448c3c2f20cd8f574182f5593" ], [ { @@ -360,7 +360,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,de7d63cfa5735162d2274d877bf0b85b" ] ], "marked_bam": [ @@ -378,7 +378,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,7ee847d7f586a961a446566f8d473c30" ], [ { @@ -394,7 +394,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d294ef713b4f83c621be387294d7937e" ], [ { @@ -410,12 +410,12 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,ffe465201f5119c2699a49cd110628d3" ] ] } ], - "timestamp": "2026-02-20T00:32:17.118099572", + "timestamp": "2026-02-27T15:45:57.190438488", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index d73f1f5fe..09b3ed99d 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "24b5799be5403926a272596963f9683f" + "72b312c47e502b8272741a40e435b96" ] ], [ @@ -32,7 +32,7 @@ ] ] ], - "timestamp": "2026-02-17T15:13:51.33678644", + "timestamp": "2026-02-27T15:46:37.232286266", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -52,7 +52,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "b9b01b7ac356afa64bc411d6f10e741" + "40408ed51d46ab3f1524be98d6b31441" ] ], [ @@ -71,7 +71,7 @@ ] ] ], - "timestamp": "2026-02-17T15:14:44.637382457", + "timestamp": "2026-02-27T15:47:22.733461874", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From e8ef8ed16bc17818d1249af909bf68bedaa9b5d1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 16:16:41 +0100 Subject: [PATCH 344/872] move subwf to folders --- .../main.nf} | 6 ++-- .../main.nf} | 36 +++++++++---------- .../main.nf} | 8 ++--- .../main.nf} | 20 +++++------ .../main.nf} | 12 +++---- .../main.nf} | 18 +++++----- .../local/{call_snv.nf => call_snv/main.nf} | 14 ++++---- .../main.nf} | 12 +++---- .../main.nf} | 8 ++--- subworkflows/local/{gens.nf => gens/main.nf} | 12 +++---- .../main.nf} | 12 +++---- .../main.nf} | 6 ++-- workflows/raredisease.nf | 2 +- 13 files changed, 83 insertions(+), 83 deletions(-) rename subworkflows/local/{annotate_consequence_pli.nf => annotate_consequence_pli/main.nf} (69%) rename subworkflows/local/{annotate_genome_snvs.nf => annotate_genome_snvs/main.nf} (79%) rename subworkflows/local/{annotate_mobile_elements.nf => annotate_mobile_elements/main.nf} (84%) rename subworkflows/local/{annotate_mt_snvs.nf => annotate_mt_snvs/main.nf} (92%) rename subworkflows/local/{annotate_structural_variants.nf => annotate_structural_variants/main.nf} (85%) rename subworkflows/local/{call_mobile_elements.nf => call_mobile_elements/main.nf} (92%) rename subworkflows/local/{call_snv.nf => call_snv/main.nf} (92%) rename subworkflows/local/{call_structural_variants.nf => call_structural_variants/main.nf} (90%) rename subworkflows/local/{generate_cytosure_files.nf => generate_cytosure_files/main.nf} (94%) rename subworkflows/local/{gens.nf => gens/main.nf} (88%) rename subworkflows/local/{rank_variants.nf => rank_variants/main.nf} (70%) rename subworkflows/local/{variant_evaluation.nf => variant_evaluation/main.nf} (82%) diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli/main.nf similarity index 69% rename from subworkflows/local/annotate_consequence_pli.nf rename to subworkflows/local/annotate_consequence_pli/main.nf index 72b88487d..d1659cf21 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli/main.nf @@ -2,9 +2,9 @@ // A subworkflow to add most severe consequence and pli to a vep annotated vcf // -include { CUSTOM_ADDMOSTSEVERECONSEQUENCE } from '../../modules/nf-core/custom/addmostsevereconsequence' -include { CUSTOM_ADDMOSTSEVEREPLI } from '../../modules/nf-core/custom/addmostseverepli' -include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix/main' +include { CUSTOM_ADDMOSTSEVERECONSEQUENCE } from '../../../modules/nf-core/custom/addmostsevereconsequence' +include { CUSTOM_ADDMOSTSEVEREPLI } from '../../../modules/nf-core/custom/addmostseverepli' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CSQ_PLI { take: diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs/main.nf similarity index 79% rename from subworkflows/local/annotate_genome_snvs.nf rename to subworkflows/local/annotate_genome_snvs/main.nf index f5a1ef3e9..5f9088521 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -2,24 +2,24 @@ // A subworkflow to annotate snvs in the genome // -include { VCFANNO } from '../../modules/nf-core/vcfanno/main' -include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_ROH } from '../../modules/nf-core/bcftools/roh/main' -include { BCFTOOLS_VIEW } from '../../modules/nf-core/bcftools/view/main' -include { RHOCALL_ANNOTATE } from '../../modules/nf-core/rhocall/annotate/main' -include { UPD as UPD_SITES } from '../../modules/nf-core/upd/main' -include { UPD as UPD_REGIONS } from '../../modules/nf-core/upd/main' -include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../modules/nf-core/chromograph/main' -include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../modules/nf-core/chromograph/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_TABIX as TABIX_VEP } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_BCFTOOLS_CONCAT } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_BCFTOOLS_VIEW } from '../../modules/nf-core/tabix/tabix/main' -include { GATK4_SELECTVARIANTS } from '../../modules/nf-core/gatk4/selectvariants/main' -include { ANNOTATE_CADD } from './annotate_cadd' -include { ANNOTATE_RHOCALLVIZ } from './annotate_rhocallviz' +include { VCFANNO } from '../../../modules/nf-core/vcfanno/main' +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_ROH } from '../../../modules/nf-core/bcftools/roh/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { RHOCALL_ANNOTATE } from '../../../modules/nf-core/rhocall/annotate/main' +include { UPD as UPD_SITES } from '../../../modules/nf-core/upd/main' +include { UPD as UPD_REGIONS } from '../../../modules/nf-core/upd/main' +include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../../modules/nf-core/chromograph/main' +include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../../modules/nf-core/chromograph/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_BCFTOOLS_CONCAT } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_BCFTOOLS_VIEW } from '../../../modules/nf-core/tabix/tabix/main' +include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' +include { ANNOTATE_CADD } from '../annotate_cadd' +include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' workflow ANNOTATE_GENOME_SNVS { diff --git a/subworkflows/local/annotate_mobile_elements.nf b/subworkflows/local/annotate_mobile_elements/main.nf similarity index 84% rename from subworkflows/local/annotate_mobile_elements.nf rename to subworkflows/local/annotate_mobile_elements/main.nf index 4de40d209..f237a07bb 100644 --- a/subworkflows/local/annotate_mobile_elements.nf +++ b/subworkflows/local/annotate_mobile_elements/main.nf @@ -2,10 +2,10 @@ // A subworkflow to annotate structural variants. // -include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_FILTER } from '../../modules/nf-core/bcftools/view/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_ME } from '../../modules/nf-core/ensemblvep/vep/main' -include { PICARD_SORTVCF } from '../../modules/nf-core/picard/sortvcf/main' -include { SVDB_QUERY as SVDB_QUERY_DB } from '../../modules/nf-core/svdb/query/main' +include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_FILTER } from '../../../modules/nf-core/bcftools/view/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_ME } from '../../../modules/nf-core/ensemblvep/vep/main' +include { PICARD_SORTVCF } from '../../../modules/nf-core/picard/sortvcf/main' +include { SVDB_QUERY as SVDB_QUERY_DB } from '../../../modules/nf-core/svdb/query/main' workflow ANNOTATE_MOBILE_ELEMENTS { diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs/main.nf similarity index 92% rename from subworkflows/local/annotate_mt_snvs.nf rename to subworkflows/local/annotate_mt_snvs/main.nf index c174d5911..fd6218c87 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -2,16 +2,16 @@ // Annotate MT // -include { REPLACE_SPACES_IN_VCFINFO } from '../../modules/local/replace_spaces_in_vcfinfo' -include { BCFTOOLS_PLUGINSETGT } from '../../modules/nf-core/bcftools/pluginsetgt' -include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../modules/nf-core/tabix/bgziptabix/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../modules/nf-core/ensemblvep/vep/main' -include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../modules/nf-core/haplogrep3/classify/main' -include { VCFANNO as VCFANNO_MT } from '../../modules/nf-core/vcfanno/main' -include { ANNOTATE_CADD } from './annotate_cadd' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../modules/nf-core/tabix/bgziptabix/main' -include { HMTNOTE_ANNOTATE } from '../../modules/nf-core/hmtnote/annotate/main' +include { REPLACE_SPACES_IN_VCFINFO } from '../../../modules/local/replace_spaces_in_vcfinfo' +include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt' +include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../modules/nf-core/ensemblvep/vep/main' +include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../../modules/nf-core/haplogrep3/classify/main' +include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' +include { ANNOTATE_CADD } from '../annotate_cadd' +include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { HMTNOTE_ANNOTATE } from '../../../modules/nf-core/hmtnote/annotate/main' workflow ANNOTATE_MT_SNVS { take: diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants/main.nf similarity index 85% rename from subworkflows/local/annotate_structural_variants.nf rename to subworkflows/local/annotate_structural_variants/main.nf index aa29499df..d38a6c860 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -2,12 +2,12 @@ // A subworkflow to annotate structural variants. // -include { SVDB_QUERY as SVDB_QUERY_DB } from '../../modules/nf-core/svdb/query/main' -include { SVDB_QUERY as SVDB_QUERY_BEDPE } from '../../modules/nf-core/svdb/query/main' -include { PICARD_SORTVCF } from '../../modules/nf-core/picard/sortvcf/main' -include { BCFTOOLS_VIEW } from '../../modules/nf-core/bcftools/view/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_TABIX as TABIX_VEP } from '../../modules/nf-core/tabix/tabix/main' +include { SVDB_QUERY as SVDB_QUERY_DB } from '../../../modules/nf-core/svdb/query/main' +include { SVDB_QUERY as SVDB_QUERY_BEDPE } from '../../../modules/nf-core/svdb/query/main' +include { PICARD_SORTVCF } from '../../../modules/nf-core/picard/sortvcf/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_STRUCTURAL_VARIANTS { diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements/main.nf similarity index 92% rename from subworkflows/local/call_mobile_elements.nf rename to subworkflows/local/call_mobile_elements/main.nf index 8719eca4e..06cd34a5c 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -2,15 +2,15 @@ // A subworkflow to call mobile elements in the genome // -include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_ME } from '../../modules/nf-core/bcftools/reheader/main' -include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_ME } from '../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_ME } from '../../modules/nf-core/bcftools/sort/main' -include { RETROSEQ_CALL as RETROSEQ_CALL } from '../../modules/local/retroseq/call/main' -include { RETROSEQ_DISCOVER as RETROSEQ_DISCOVER } from '../../modules/local/retroseq/discover/main' -include { SAMTOOLS_VIEW as ME_SPLIT_ALIGNMENT } from '../../modules/nf-core/samtools/view/main' -include { TABIX_TABIX as TABIX_ME } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_ME_SPLIT } from '../../modules/nf-core/tabix/tabix/main' -include { SVDB_MERGE as SVDB_MERGE_ME } from '../../modules/nf-core/svdb/merge/main' +include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_ME } from '../../../modules/nf-core/bcftools/reheader/main' +include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_ME } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_SORT as BCFTOOLS_SORT_ME } from '../../../modules/nf-core/bcftools/sort/main' +include { RETROSEQ_CALL as RETROSEQ_CALL } from '../../../modules/local/retroseq/call/main' +include { RETROSEQ_DISCOVER as RETROSEQ_DISCOVER } from '../../../modules/local/retroseq/discover/main' +include { SAMTOOLS_VIEW as ME_SPLIT_ALIGNMENT } from '../../../modules/nf-core/samtools/view/main' +include { TABIX_TABIX as TABIX_ME } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_ME_SPLIT } from '../../../modules/nf-core/tabix/tabix/main' +include { SVDB_MERGE as SVDB_MERGE_ME } from '../../../modules/nf-core/svdb/merge/main' workflow CALL_MOBILE_ELEMENTS { diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv/main.nf similarity index 92% rename from subworkflows/local/call_snv.nf rename to subworkflows/local/call_snv/main.nf index 126d4f6e8..44b958dac 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv/main.nf @@ -2,13 +2,13 @@ // call Single-nucleotide Varinats // -include { CALL_SNV_DEEPVARIANT } from './call_snv_deepvariant' -include { CALL_SNV_SENTIEON } from './call_snv_sentieon' -include { CALL_SNV_MT } from './call_snv_MT' -include { CALL_SNV_MT as CALL_SNV_MT_SHIFT } from './call_snv_MT' -include { POSTPROCESS_MT_CALLS } from './postprocess_MT_calls' -include { GATK4_SELECTVARIANTS } from '../../modules/nf-core/gatk4/selectvariants/main' -include { BCFTOOLS_CONCAT } from '../../modules/nf-core/bcftools/concat' +include { CALL_SNV_DEEPVARIANT } from '../call_snv_deepvariant' +include { CALL_SNV_SENTIEON } from '../call_snv_sentieon' +include { CALL_SNV_MT } from '../call_snv_MT' +include { CALL_SNV_MT as CALL_SNV_MT_SHIFT } from '../call_snv_MT' +include { POSTPROCESS_MT_CALLS } from '../postprocess_MT_calls' +include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat' workflow CALL_SNV { take: diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants/main.nf similarity index 90% rename from subworkflows/local/call_structural_variants.nf rename to subworkflows/local/call_structural_variants/main.nf index f7ff6b90a..536d11a0c 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -2,12 +2,12 @@ // A nested subworkflow to call structural variants. // -include { CALL_SV_MANTA } from './call_sv_manta' -include { CALL_SV_TIDDIT } from './call_sv_tiddit' -include { SVDB_MERGE } from '../../modules/nf-core/svdb/merge/main' -include { CALL_SV_GERMLINECNVCALLER } from './call_sv_germlinecnvcaller' -include { CALL_SV_CNVNATOR } from './call_sv_cnvnator' -include { TABIX_TABIX } from '../../modules/nf-core/tabix/tabix/main' +include { CALL_SV_MANTA } from '../call_sv_manta' +include { CALL_SV_TIDDIT } from '../call_sv_tiddit' +include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' +include { CALL_SV_GERMLINECNVCALLER } from '../call_sv_germlinecnvcaller' +include { CALL_SV_CNVNATOR } from '../call_sv_cnvnator' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow CALL_STRUCTURAL_VARIANTS { diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files/main.nf similarity index 94% rename from subworkflows/local/generate_cytosure_files.nf rename to subworkflows/local/generate_cytosure_files/main.nf index 18f6ed80a..3c2444b9c 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files/main.nf @@ -2,10 +2,10 @@ // Convert VCF with structural variations to the “.CGH” format used by the CytoSure Interpret Software // -include { BCFTOOLS_VIEW as SPLIT_AND_FILTER_SV_VCF } from '../../modules/nf-core/bcftools/view/main' -include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_SV_VCF } from '../../modules/nf-core/bcftools/reheader/main' -include { TIDDIT_COV as TIDDIT_COV_VCF2CYTOSURE } from '../../modules/nf-core/tiddit/cov/main' -include { VCF2CYTOSURE } from '../../modules/nf-core/vcf2cytosure/main' +include { BCFTOOLS_VIEW as SPLIT_AND_FILTER_SV_VCF } from '../../../modules/nf-core/bcftools/view/main' +include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_SV_VCF } from '../../../modules/nf-core/bcftools/reheader/main' +include { TIDDIT_COV as TIDDIT_COV_VCF2CYTOSURE } from '../../../modules/nf-core/tiddit/cov/main' +include { VCF2CYTOSURE } from '../../../modules/nf-core/vcf2cytosure/main' workflow GENERATE_CYTOSURE_FILES { take: diff --git a/subworkflows/local/gens.nf b/subworkflows/local/gens/main.nf similarity index 88% rename from subworkflows/local/gens.nf rename to subworkflows/local/gens/main.nf index a75b2cbe5..207d0f6d8 100644 --- a/subworkflows/local/gens.nf +++ b/subworkflows/local/gens/main.nf @@ -2,12 +2,12 @@ // A preprocessing workflow for Gens // -include { GATK4_COLLECTREADCOUNTS as COLLECTREADCOUNTS } from '../../modules/nf-core/gatk4/collectreadcounts/main' -include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_FEMALE } from '../../modules/nf-core/gatk4/denoisereadcounts/main' -include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_MALE } from '../../modules/nf-core/gatk4/denoisereadcounts/main' -include { GENS as GENS_GENERATE } from '../../modules/local/gens/main' -include { TABIX_BGZIPTABIX as GENS_GENERATE_BAF_INDEX } from '../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as GENS_GENERATE_COV_INDEX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { GATK4_COLLECTREADCOUNTS as COLLECTREADCOUNTS } from '../../../modules/nf-core/gatk4/collectreadcounts/main' +include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_FEMALE } from '../../../modules/nf-core/gatk4/denoisereadcounts/main' +include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_MALE } from '../../../modules/nf-core/gatk4/denoisereadcounts/main' +include { GENS as GENS_GENERATE } from '../../../modules/local/gens/main' +include { TABIX_BGZIPTABIX as GENS_GENERATE_BAF_INDEX } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as GENS_GENERATE_COV_INDEX } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow GENS { take: diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants/main.nf similarity index 70% rename from subworkflows/local/rank_variants.nf rename to subworkflows/local/rank_variants/main.nf index 92fc42819..820fdd01e 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants/main.nf @@ -2,12 +2,12 @@ // A subworkflow to score and rank variants. // -include { GENMOD_ANNOTATE } from '../../modules/nf-core/genmod/annotate/main' -include { GENMOD_MODELS } from '../../modules/nf-core/genmod/models/main' -include { GENMOD_SCORE } from '../../modules/nf-core/genmod/score/main' -include { GENMOD_COMPOUND } from '../../modules/nf-core/genmod/compound/main' -include { BCFTOOLS_SORT } from '../../modules/nf-core/bcftools/sort/main' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { GENMOD_ANNOTATE } from '../../../modules/nf-core/genmod/annotate/main' +include { GENMOD_MODELS } from '../../../modules/nf-core/genmod/models/main' +include { GENMOD_SCORE } from '../../../modules/nf-core/genmod/score/main' +include { GENMOD_COMPOUND } from '../../../modules/nf-core/genmod/compound/main' +include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow RANK_VARIANTS { diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation/main.nf similarity index 82% rename from subworkflows/local/variant_evaluation.nf rename to subworkflows/local/variant_evaluation/main.nf index 5aa8f526b..73881b50d 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -2,9 +2,9 @@ // A subworkflow to evaluate variants using truth vcfs. // -include { RTGTOOLS_VCFEVAL } from '../../modules/nf-core/rtgtools/vcfeval/main' -include { BCFTOOLS_REHEADER } from '../../modules/nf-core/bcftools/reheader/main' -include { TABIX_TABIX as TABIX_TRUTHVCF } from '../../modules/nf-core/tabix/tabix/main' +include { RTGTOOLS_VCFEVAL } from '../../../modules/nf-core/rtgtools/vcfeval/main' +include { BCFTOOLS_REHEADER } from '../../../modules/nf-core/bcftools/reheader/main' +include { TABIX_TABIX as TABIX_TRUTHVCF } from '../../../modules/nf-core/tabix/tabix/main' workflow VARIANT_EVALUATION { diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d4c2b0503..ae3aee84e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -40,7 +40,7 @@ include { RENAME_ALIGN_FILES as RENAME_BAI } from '../modules/local/rename_align // include { ALIGN } from '../subworkflows/local/align' -include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli.nf' +include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_ME } from '../subworkflows/local/annotate_consequence_pli' include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_MT } from '../subworkflows/local/annotate_consequence_pli' include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SNV } from '../subworkflows/local/annotate_consequence_pli' include { ANNOTATE_CSQ_PLI as ANN_CSQ_PLI_SV } from '../subworkflows/local/annotate_consequence_pli' From 78b19187ac5cbde164d718c8a8b7d613e5ad2fd7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 17:09:06 +0100 Subject: [PATCH 345/872] commit annotate_consequence_pli tests --- .../tests/main.nf.test | 68 +++++++++++++++++++ .../tests/main.nf.test.snap | 24 +++++++ .../tests/nextflow.config | 8 +++ 3 files changed, 100 insertions(+) create mode 100644 subworkflows/local/annotate_consequence_pli/tests/main.nf.test create mode 100644 subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_consequence_pli/tests/nextflow.config diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test new file mode 100644 index 000000000..eefd009b8 --- /dev/null +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -0,0 +1,68 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_CSQ_PLI" + script "subworkflows/local/annotate_consequence_pli/main.nf" + workflow "ANNOTATE_CSQ_PLI" + tag "subworkflows" + tag "annotate_consequence_pli" + + config './nextflow.config' + + test("ANNOTATE_CSQ_PLI - no index") { + + when { + workflow { + """ + input[0] = channel.of([ + [id:'var_csq'], + file(params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt', checkIfExists: true) + ]).collect() + input[1] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ]) + input[2] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.vcf_ann[0][1].toString()).vcf.variantsMD5, + path(workflow.out.vcf_ann[0][1].toString()).vcf.summary + ).match() } + ) + } + } + + test("ANNOTATE_CSQ_PLI - with index") { + + when { + workflow { + """ + input[0] = channel.of([ + [id:'var_csq'], + file(params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt', checkIfExists: true) + ]).collect() + input[1] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ]) + input[2] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.vcf_ann[0][1].toString()).vcf.variantsMD5, + path(workflow.out.vcf_ann[0][1].toString()).vcf.summary + ).match() } + ) + } + } +} diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap new file mode 100644 index 000000000..f1765956b --- /dev/null +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap @@ -0,0 +1,24 @@ +{ + "ANNOTATE_CSQ_PLI - with index": { + "content": [ + "58d9c7a329ee86094acc0826b671652c", + "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]" + ], + "timestamp": "2026-03-01T17:08:30.607457875", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "ANNOTATE_CSQ_PLI - no index": { + "content": [ + "58d9c7a329ee86094acc0826b671652c", + "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]" + ], + "timestamp": "2026-03-01T17:08:08.450262918", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_consequence_pli/tests/nextflow.config b/subworkflows/local/annotate_consequence_pli/tests/nextflow.config new file mode 100644 index 000000000..5fcc87840 --- /dev/null +++ b/subworkflows/local/annotate_consequence_pli/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: "CUSTOM_ADDMOSTSEVEREPLI" { + ext.prefix = 'severepli' + } + withName: "CUSTOM_ADDMOSTSEVERECONSEQUENCE" { + ext.prefix = 'severecsq' + } +} From 9a212c88d0aff321f5be80bc7c6b06fddbaaaa8a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 17:17:22 +0100 Subject: [PATCH 346/872] add test for call_mobile_elements --- .../call_mobile_elements/tests/main.nf.test | 39 +++++++++++++++++++ .../tests/main.nf.test.snap | 17 ++++++++ 2 files changed, 56 insertions(+) create mode 100644 subworkflows/local/call_mobile_elements/tests/main.nf.test create mode 100644 subworkflows/local/call_mobile_elements/tests/main.nf.test.snap diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test b/subworkflows/local/call_mobile_elements/tests/main.nf.test new file mode 100644 index 000000000..58704f076 --- /dev/null +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test @@ -0,0 +1,39 @@ +nextflow_workflow { + + name "Test Workflow CALL_MOBILE_ELEMENTS" + script "subworkflows/local/call_mobile_elements/main.nf" + workflow "CALL_MOBILE_ELEMENTS" + tag "subworkflows" + tag "call_mobile_elements" + + test("CALL_MOBILE_ELEMENTS - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([id:'justhusky']) + input[1] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[4] = channel.of(['LINE', file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap new file mode 100644 index 000000000..ac97b2c1e --- /dev/null +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap @@ -0,0 +1,17 @@ +{ + "CALL_MOBILE_ELEMENTS - stub": { + "content": [ + [ + "justhusky_mobile_elements.vcf.gz" + ], + [ + "justhusky_mobile_elements.vcf.gz.tbi" + ] + ], + "timestamp": "2026-03-01T17:14:06.948018519", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 1a84807df284b7abf54667846e32179f503b111a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 17:28:31 +0100 Subject: [PATCH 347/872] add call_snv test --- .../local/call_snv/tests/main.nf.test | 71 +++++++++++++++++++ .../local/call_snv/tests/main.nf.test.snap | 20 ++++++ 2 files changed, 91 insertions(+) create mode 100644 subworkflows/local/call_snv/tests/main.nf.test create mode 100644 subworkflows/local/call_snv/tests/main.nf.test.snap diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test new file mode 100644 index 000000000..9329a562e --- /dev/null +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -0,0 +1,71 @@ +nextflow_workflow { + + name "Test Workflow CALL_SNV" + script "subworkflows/local/call_snv/main.nf" + workflow "CALL_SNV" + tag "subworkflows" + tag "call_snv" + + test("CALL_SNV - deepvariant wgs, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([[id:'interval'], []]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz', checkIfExists: true)]) + input[3] = channel.of([[id:'genome'], []]) + input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() + input[5] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[9] = channel.of([[id:'model'], []]) + input[10] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[11] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]).collect() + input[12] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[13] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[14] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt.intervals', checkIfExists: true)).collect() + input[15] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[16] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]).collect() + input[17] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[18] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[19] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt_shift8000.intervals', checkIfExists: true)).collect() + input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[21] = channel.of([[id:'par'], []]) + input[22] = channel.of([[id:'model'], []]) + input[23] = channel.of([[id:'target'], [], []]) + input[24] = 'wgs' + input[25] = false + input[26] = false + input[27] = 'deepvariant' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.genome_vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, + workflow.out.mt_vcf.collect { meta, vcf -> file(vcf).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap new file mode 100644 index 000000000..bf4b59fd2 --- /dev/null +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -0,0 +1,20 @@ +{ + "CALL_SNV - deepvariant wgs, stub": { + "content": [ + [ + "justhusky_snv.vcf.gz" + ], + [ + "justhusky_snv.vcf.gz.tbi" + ], + [ + "justhusky_mitochondria.vcf.gz" + ] + ], + "timestamp": "2026-03-01T17:27:18.706368747", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From bd57e137a94e744a3eea879572bd4e2d90545fa0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 17:37:14 +0100 Subject: [PATCH 348/872] add call_snv_MT tests --- .../local/call_snv_MT/tests/main.nf.test | 37 +++++++++++++++++++ .../local/call_snv_MT/tests/main.nf.test.snap | 17 +++++++++ 2 files changed, 54 insertions(+) create mode 100644 subworkflows/local/call_snv_MT/tests/main.nf.test create mode 100644 subworkflows/local/call_snv_MT/tests/main.nf.test.snap diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test b/subworkflows/local/call_snv_MT/tests/main.nf.test new file mode 100644 index 000000000..3dc9a5bf8 --- /dev/null +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test @@ -0,0 +1,37 @@ +nextflow_workflow { + + name "Test Workflow CALL_SNV_MT" + script "subworkflows/local/call_snv_MT/main.nf" + workflow "CALL_SNV_MT" + tag "subworkflows" + tag "call_snv_MT" + + test("CALL_SNV_MT - stub") { + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[2] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt.intervals', checkIfExists: true)).collect() + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test.snap b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap new file mode 100644 index 000000000..9814de4b8 --- /dev/null +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap @@ -0,0 +1,17 @@ +{ + "CALL_SNV_MT - stub": { + "content": [ + [ + "earlycasualcaiman_filtered.vcf.gz" + ], + [ + "earlycasualcaiman_filtered.vcf.gz.tbi" + ] + ], + "timestamp": "2026-03-01T17:35:07.245240789", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 41c50133b11ef0e78037b4acbe83e67ff95e4b38 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 18:14:43 +0100 Subject: [PATCH 349/872] add test for call_snv_deepvariant --- .../call_snv_deepvariant/tests/main.nf.test | 42 +++++++++++++++++++ .../tests/main.nf.test.snap | 18 ++++++++ 2 files changed, 60 insertions(+) create mode 100644 subworkflows/local/call_snv_deepvariant/tests/main.nf.test create mode 100644 subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test new file mode 100644 index 000000000..0d2b6af03 --- /dev/null +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -0,0 +1,42 @@ +nextflow_workflow { + + name "Test Workflow CALL_SNV_DEEPVARIANT" + script "subworkflows/local/call_snv_deepvariant/main.nf" + workflow "CALL_SNV_DEEPVARIANT" + tag "subworkflows" + tag "call_snv_deepvariant" + + test("CALL_SNV_DEEPVARIANT - wgs") { + + when { + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of([[id:'par'], []]) + input[7] = channel.of([[id:'target'], [], []]) + input[8] = 'wgs' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.vcf[0][1]).vcf.variantsMD5, + workflow.out.tabix.collect { meta, tbi -> file(tbi).name }, + workflow.out.gvcf.collect { meta, gvcf -> file(gvcf).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap new file mode 100644 index 000000000..96112588c --- /dev/null +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -0,0 +1,18 @@ +{ + "CALL_SNV_DEEPVARIANT - wgs": { + "content": [ + "e4e9e39859d7df52fd955fb32796fdb2", + [ + "justhusky_split_rmdup_info.vcf.gz.tbi" + ], + [ + "earlycasualcaiman_deepvar.g.vcf.gz" + ] + ], + "timestamp": "2026-03-01T18:14:03.103819136", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From c7c133c42d09b7c1ecec295eef2db83147b8a499 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 18:20:29 +0100 Subject: [PATCH 350/872] add test for call_structural_variants --- .../tests/main.nf.test | 61 +++++++++++++++++++ .../tests/main.nf.test.snap | 17 ++++++ 2 files changed, 78 insertions(+) create mode 100644 subworkflows/local/call_structural_variants/tests/main.nf.test create mode 100644 subworkflows/local/call_structural_variants/tests/main.nf.test.snap diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test new file mode 100644 index 000000000..dac34c84e --- /dev/null +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_workflow { + + name "Test Workflow CALL_STRUCTURAL_VARIANTS" + script "subworkflows/local/call_structural_variants/main.nf" + workflow "CALL_STRUCTURAL_VARIANTS" + tag "subworkflows" + tag "call_structural_variants" + + test("CALL_STRUCTURAL_VARIANTS - wgs, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true) + ]) + input[1] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[2] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[3] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[4] = channel.of([[id:'bwa'], []]) + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[6] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[7] = channel.of([id:'justhusky']) + input[8] = channel.of([[id:'target'], [], []]) + input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[10] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[11] = channel.of([[]]) + input[12] = channel.of([[id:'ploidy'], []]) + input[13] = channel.of([[id:'gcnvcaller'], []]) + input[14] = 'wgs' + input[15] = false + input[16] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap new file mode 100644 index 000000000..2577e99f7 --- /dev/null +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -0,0 +1,17 @@ +{ + "CALL_STRUCTURAL_VARIANTS - wgs, stub": { + "content": [ + [ + "justhusky_sv.vcf.gz" + ], + [ + "justhusky_sv.vcf.gz.tbi" + ] + ], + "timestamp": "2026-03-01T18:18:21.549692378", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From ef6db59e547572abe1c9f8eaabca37e13f761429 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 20:40:36 +0100 Subject: [PATCH 351/872] add test for call_sv_cnvnator --- .../local/call_sv_cnvnator/tests/main.nf.test | 40 +++++++++++++++++++ .../call_sv_cnvnator/tests/main.nf.test.snap | 26 ++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 subworkflows/local/call_sv_cnvnator/tests/main.nf.test create mode 100644 subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test new file mode 100644 index 000000000..fc2883e5f --- /dev/null +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test @@ -0,0 +1,40 @@ +nextflow_workflow { + + name "Test Workflow CALL_SV_CNVNATOR" + script "subworkflows/local/call_sv_cnvnator/main.nf" + workflow "CALL_SV_CNVNATOR" + tag "subworkflows" + tag "call_sv_cnvnator" + + config "./nextflow.config" + + test("CALL_SV_CNVNATOR") { + + when { + params { + cnvnator_binsize = "10000" + } + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'justhusky']) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap new file mode 100644 index 000000000..3d3df5679 --- /dev/null +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "CALL_SV_CNVNATOR": { + "content": [ + [ + "justhusky_cnvnator.vcf.gz" + ] + ], + "timestamp": "2026-03-01T20:36:50.087101237", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "CALL_SV_CNVNATOR - stub": { + "content": [ + [ + "justhusky_cnvnator.vcf.gz" + ] + ], + "timestamp": "2026-03-01T20:22:17.821272901", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 71a37ffd862fbae0811603d838926d8f54d2d701 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 20:40:47 +0100 Subject: [PATCH 352/872] add cnvnator test config --- .../call_sv_cnvnator/tests/nextflow.config | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 subworkflows/local/call_sv_cnvnator/tests/nextflow.config diff --git a/subworkflows/local/call_sv_cnvnator/tests/nextflow.config b/subworkflows/local/call_sv_cnvnator/tests/nextflow.config new file mode 100644 index 000000000..e919f3438 --- /dev/null +++ b/subworkflows/local/call_sv_cnvnator/tests/nextflow.config @@ -0,0 +1,37 @@ +process { + + withName: "CNVNATOR_HIST" { + tag = { "$meta2.id" } + ext.args = { "-his ${params.cnvnator_binsize}" } + } + + withName: "CNVNATOR_STAT" { + tag = { "$meta2.id" } + ext.args = { "-stat ${params.cnvnator_binsize}" } + } + + withName: "CNVNATOR_PARTITION" { + tag = { "$meta2.id" } + ext.args = { "-partition ${params.cnvnator_binsize}" } + } + + withName: "CNVNATOR_CALL" { + tag = { "$meta2.id" } + ext.args = { "-call ${params.cnvnator_binsize}" } + } + + withName: "CNVNATOR_CONVERT2VCF" { + ext.prefix = { "${meta.id}_cnvnator" } + ext.args = { "-call ${params.cnvnator_binsize}" } + } + + withName: "BCFTOOLS_VIEW_CNVNATOR" { + ext.prefix = { "${meta.id}_cnvnator_filter" } + ext.args = { '--apply-filters .,PASS --output-type z' } + } + + withName: 'SVDB_MERGE_CNVNATOR' { + ext.args = '--notag --pass_only' + ext.prefix = { "${meta.id}_cnvnator" } + } +} From 2900a4fe93152cbdaab3767a13e465475e845230 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 20:56:21 +0100 Subject: [PATCH 353/872] add test for call_sv_manta --- .../local/call_sv_manta/tests/main.nf.test | 53 +++++++++++++++++++ .../call_sv_manta/tests/main.nf.test.snap | 13 +++++ .../local/call_sv_manta/tests/nextflow.config | 7 +++ 3 files changed, 73 insertions(+) create mode 100644 subworkflows/local/call_sv_manta/tests/main.nf.test create mode 100644 subworkflows/local/call_sv_manta/tests/main.nf.test.snap create mode 100644 subworkflows/local/call_sv_manta/tests/nextflow.config diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test new file mode 100644 index 000000000..9559081e7 --- /dev/null +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -0,0 +1,53 @@ +nextflow_workflow { + + name "Test Workflow CALL_SV_MANTA" + script "subworkflows/local/call_sv_manta/main.nf" + workflow "CALL_SV_MANTA" + tag "subworkflows" + tag "call_sv_manta" + config "./nextflow.config" + + test("CALL_SV_MANTA - wgs") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true)] + ) + input[1] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)], + [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] + ) + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'justhusky']) + input[5] = channel.of([[id:'target'], [], []]) + input[6] = 'wgs' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.diploid_sv_vcf[0][1]).vcf.variantsMD5, + path(workflow.out.filtered_diploid_sv_vcf[0][1]).vcf.variantsMD5 + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test.snap b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap new file mode 100644 index 000000000..e7bd2d64a --- /dev/null +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap @@ -0,0 +1,13 @@ +{ + "CALL_SV_MANTA - wgs": { + "content": [ + "9f37331609347a1685ba4862d8583b2f", + "2111e88e54fdd01f0492901606bcea6f" + ], + "timestamp": "2026-03-01T20:55:33.556714847", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/call_sv_manta/tests/nextflow.config b/subworkflows/local/call_sv_manta/tests/nextflow.config new file mode 100644 index 000000000..34fd1a2e9 --- /dev/null +++ b/subworkflows/local/call_sv_manta/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: '.*CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA' { + ext.args = '--min-ac 1' + ext.prefix = { "${meta.id}_manta_filtered" } + } +} From 2019514eaf91e8a54ba11c2bf49a28587d110396 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 21:44:01 +0100 Subject: [PATCH 354/872] add test for call_sv_tiddit --- .../local/call_sv_tiddit/tests/main.nf.test | 59 +++++++++++++++++++ .../call_sv_tiddit/tests/main.nf.test.snap | 12 ++++ .../call_sv_tiddit/tests/nextflow.config | 15 +++++ 3 files changed, 86 insertions(+) create mode 100644 subworkflows/local/call_sv_tiddit/tests/main.nf.test create mode 100644 subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap create mode 100644 subworkflows/local/call_sv_tiddit/tests/nextflow.config diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test new file mode 100644 index 000000000..ad251659c --- /dev/null +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -0,0 +1,59 @@ +nextflow_workflow { + + name "Test Workflow CALL_SV_TIDDIT" + script "subworkflows/local/call_sv_tiddit/main.nf" + workflow "CALL_SV_TIDDIT" + tag "subworkflows" + tag "call_sv_tiddit" + config "./nextflow.config" + + test("CALL_SV_TIDDIT") { + + setup { + run("BWA_INDEX") { + script "modules/nf-core/bwa/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'genome'], + file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)], + [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = BWA_INDEX.out.index.collect() + input[3] = channel.of([id:'justhusky']) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.vcf[0][1]).vcf.variantsMD5 + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap new file mode 100644 index 000000000..a6f1f03f8 --- /dev/null +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap @@ -0,0 +1,12 @@ +{ + "CALL_SV_TIDDIT": { + "content": [ + "140ce993561670b54ecb907561e3a417" + ], + "timestamp": "2026-03-01T21:41:21.445553341", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/call_sv_tiddit/tests/nextflow.config b/subworkflows/local/call_sv_tiddit/tests/nextflow.config new file mode 100644 index 000000000..a4f70c367 --- /dev/null +++ b/subworkflows/local/call_sv_tiddit/tests/nextflow.config @@ -0,0 +1,15 @@ +process { + + withName: 'BCFTOOLS_VIEW_TIDDIT' { + ext.args = '--min-ac 1' + ext.prefix = { "${meta.id}_tiddit_filtered" } + } + + withName: 'INDEX_TIDDIT' { + ext.prefix = { "${meta.id}_tiddit" } + } + + withName: 'SVDB_MERGE_TIDDIT' { + ext.prefix = { "${meta.id}_svdb_tiddit" } + } +} From 2b84ad449ae26e4ec330580af855cce25f7548a9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 22:20:21 +0100 Subject: [PATCH 355/872] add test for call_sv_germlinecnvcaller --- .../tests/main.nf.test | 43 +++++++++++++++++++ .../tests/main.nf.test.snap | 14 ++++++ .../tests/nextflow.config | 23 ++++++++++ 3 files changed, 80 insertions(+) create mode 100644 subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test create mode 100644 subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test.snap create mode 100644 subworkflows/local/call_sv_germlinecnvcaller/tests/nextflow.config diff --git a/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test new file mode 100644 index 000000000..eb8ca9888 --- /dev/null +++ b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_workflow { + + name "Test Workflow CALL_SV_GERMLINECNVCALLER" + script "subworkflows/local/call_sv_germlinecnvcaller/main.nf" + workflow "CALL_SV_GERMLINECNVCALLER" + tag "subworkflows" + tag "call_sv_germlinecnvcaller" + + config "./nextflow.config" + + test("CALL_SV_GERMLINECNVCALLER - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[3] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/target.interval_list', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([[id:'ploidy'], []]) + input[6] = channel.of([[id:'gcnvcaller'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)])//Just a placeholder + input[7] = channel.of([id:'justhusky']) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.genotyped_filtered_segments_vcf.collect { meta, vcf -> file(vcf).name } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test.snap b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test.snap new file mode 100644 index 000000000..9ff12a7d4 --- /dev/null +++ b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test.snap @@ -0,0 +1,14 @@ +{ + "CALL_SV_GERMLINECNVCALLER - stub": { + "content": [ + [ + "justhusky_gcnvcaller.vcf.gz" + ] + ], + "timestamp": "2026-03-01T22:17:21.509267479", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/call_sv_germlinecnvcaller/tests/nextflow.config b/subworkflows/local/call_sv_germlinecnvcaller/tests/nextflow.config new file mode 100644 index 000000000..d09f408c3 --- /dev/null +++ b/subworkflows/local/call_sv_germlinecnvcaller/tests/nextflow.config @@ -0,0 +1,23 @@ + +process { + + withName: "GATK4_COLLECTREADCOUNTS" { + ext.args = "--format TSV" + } + + withName: "GATK4_DETERMINEGERMLINECONTIGPLOIDY" { + ext.prefix = { "${meta.id}_ploidy" } + } + + withName: "GATK4_GERMLINECNVCALLER" { + ext.args = "--run-mode CASE" + } + + withName: 'BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_gatkcnv_segments_refiltered" } + } + + withName: 'SVDB_MERGE_GCNVCALLER' { + ext.prefix = { "${meta.id}_gcnvcaller" } + } +} From 757f5004cfc71a0d9fc808c3ec812a94b0bd55de Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 22:30:39 +0100 Subject: [PATCH 356/872] add test for convert_mt_bam_to_fastq --- .../tests/main.nf.test | 35 +++++ .../tests/main.nf.test.snap | 129 ++++++++++++++++++ 2 files changed, 164 insertions(+) create mode 100644 subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test create mode 100644 subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap diff --git a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test new file mode 100644 index 000000000..57b7c62ad --- /dev/null +++ b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_workflow { + + name "Test Workflow CONVERT_MT_BAM_TO_FASTQ" + script "subworkflows/local/convert_mt_bam_to_fastq/main.nf" + workflow "CONVERT_MT_BAM_TO_FASTQ" + tag "subworkflows" + tag "convert_mt_bam_to_fastq" + + test("CONVERT_MT_BAM_TO_FASTQ") { + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out + ).match() } + ) + } + } +} diff --git a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap new file mode 100644 index 000000000..5851f631c --- /dev/null +++ b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap @@ -0,0 +1,129 @@ +{ + "CONVERT_MT_BAM_TO_FASTQ": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.bam:md5,424fcb1e097f4a0423e83e5af2c16ccf", + "earlycasualcaiman.bam.bai:md5,0c6f0728a82e2c893f2106b92e280648" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_1.fastq.gz:md5,e22db895fb1dd8bc4673f2a70fc87260", + "earlycasualcaiman_2.fastq.gz:md5,a4f49dbd116ebaec797c7beea82696db" + ] + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.reverted.bam:md5,11a20cf34d72d3b8b4abf753099bbb90" + ] + ], + "bam_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.bam:md5,424fcb1e097f4a0423e83e5af2c16ccf", + "earlycasualcaiman.bam.bai:md5,0c6f0728a82e2c893f2106b92e280648" + ] + ], + "fastq": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_1.fastq.gz:md5,e22db895fb1dd8bc4673f2a70fc87260", + "earlycasualcaiman_2.fastq.gz:md5,a4f49dbd116ebaec797c7beea82696db" + ] + ] + ], + "ubam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.reverted.bam:md5,11a20cf34d72d3b8b4abf753099bbb90" + ] + ] + } + ], + "timestamp": "2026-03-01T22:25:34.791929735", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 9f818eb8b095abcea9ec17655d18534f8ee19b1b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 23:24:35 +0100 Subject: [PATCH 357/872] add tests for subsample mt --- .../subsample_mt_frac/tests/main.nf.test | 33 +++++++++++++++++++ .../subsample_mt_frac/tests/nextflow.config | 12 +++++++ .../subsample_mt_reads/tests/main.nf.test | 32 ++++++++++++++++++ .../subsample_mt_reads/tests/nextflow.config | 27 +++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 subworkflows/local/subsample_mt_frac/tests/main.nf.test create mode 100644 subworkflows/local/subsample_mt_frac/tests/nextflow.config create mode 100644 subworkflows/local/subsample_mt_reads/tests/main.nf.test create mode 100644 subworkflows/local/subsample_mt_reads/tests/nextflow.config diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test b/subworkflows/local/subsample_mt_frac/tests/main.nf.test new file mode 100644 index 000000000..296f122c0 --- /dev/null +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test @@ -0,0 +1,33 @@ +nextflow_workflow { + + name "Test Workflow SUBSAMPLE_MT_FRAC" + script "subworkflows/local/subsample_mt_frac/main.nf" + workflow "SUBSAMPLE_MT_FRAC" + tag "subworkflows" + tag "subsample_mt_frac" + config "./nextflow.config" + + test("SUBSAMPLE_MT_FRAC") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = 150 + input[2] = 30 + """ + } + } + + then { + assert workflow.success + } + } +} diff --git a/subworkflows/local/subsample_mt_frac/tests/nextflow.config b/subworkflows/local/subsample_mt_frac/tests/nextflow.config new file mode 100644 index 000000000..1f4c04be9 --- /dev/null +++ b/subworkflows/local/subsample_mt_frac/tests/nextflow.config @@ -0,0 +1,12 @@ +process { + + withName: '.*SUBSAMPLE_MT_FRAC:BEDTOOLS_GENOMECOV' { + ext.args = { "-dz" } + ext.prefix = { "${meta.id}" } + } + + withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_VIEW' { + ext.args = { "--output-fmt BAM -h -F 4 -s ${meta.seedfrac}" } + ext.prefix = { "${meta.id}_mt_subsample" } + } +} diff --git a/subworkflows/local/subsample_mt_reads/tests/main.nf.test b/subworkflows/local/subsample_mt_reads/tests/main.nf.test new file mode 100644 index 000000000..3a83af0f1 --- /dev/null +++ b/subworkflows/local/subsample_mt_reads/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_workflow { + + name "Test Workflow SUBSAMPLE_MT_READS" + script "subworkflows/local/subsample_mt_reads/main.nf" + workflow "SUBSAMPLE_MT_READS" + tag "subworkflows" + tag "subsample_mt_reads" + config "./nextflow.config" + + test("SUBSAMPLE_MT_READS") { + + when { + params { + mt_subsample_reads = 18000 + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assert workflow.success + } + } +} diff --git a/subworkflows/local/subsample_mt_reads/tests/nextflow.config b/subworkflows/local/subsample_mt_reads/tests/nextflow.config new file mode 100644 index 000000000..7a3393855 --- /dev/null +++ b/subworkflows/local/subsample_mt_reads/tests/nextflow.config @@ -0,0 +1,27 @@ +process { + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_VIEW' { + ext.args = { "--output-fmt bam -F 0x400" } + ext.prefix = { "${meta.id}_mt_nodups" } + } + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE' { + ext.args = { "--output-fmt sam" } + ext.prefix = { "${meta.id}_mt_nodups_collate" } + } + + withName: '.*SUBSAMPLE_MT_READS:GAWK' { + ext.args2 = { "'/^@/ { print; next } count < ${params.mt_subsample_reads} || last == \$1 { print; last = \$1; count++ }'" } + ext.prefix = { "${meta.id}_mt_nodups_collate_awk" } + ext.suffix = "sam" + } + + withName: '.*SUBSAMPLE_MT_READS:SAM_TO_BAM' { + ext.args = { "--output-fmt bam" } + ext.prefix = { "${meta.id}_mt_nodups_collate_awk" } + } + + withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}_mt_subsample" } + } +} From 41cb73652b4d34ccf894de52a6179e09915e90e1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 1 Mar 2026 23:25:14 +0100 Subject: [PATCH 358/872] fix call_sv_germlinecnvcaller --- subworkflows/local/call_sv_germlinecnvcaller/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index e388fd4b4..aea59f5f3 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -59,7 +59,7 @@ workflow CALL_SV_GERMLINECNVCALLER { TABIX_TABIX(GATK4_POSTPROCESSGERMLINECNVCALLS.out.segments) GATK4_POSTPROCESSGERMLINECNVCALLS.out.segments - .join(TABIX_TABIX.out.tbi, failOnMismatch:true) + .join(TABIX_TABIX.out.index, failOnMismatch:true) .set {ch_segments_in} // Filter out reference only (0/0) segments BCFTOOLS_VIEW (ch_segments_in , [], [], [] ) From 6cfb856ab55898777f69ea9eb700d2b209119d33 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 09:37:42 +0100 Subject: [PATCH 359/872] restore hmtnote/annotate --- .../nf-core/hmtnote/annotate/environment.yml | 6 +++++- .../hmtnote/annotate/hmtnote-annotate.diff | 5 ++++- modules/nf-core/hmtnote/annotate/meta.yml | 18 +++++++++++------- 3 files changed, 20 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/hmtnote/annotate/environment.yml b/modules/nf-core/hmtnote/annotate/environment.yml index 1d9d20e3f..d5e7d3bbc 100644 --- a/modules/nf-core/hmtnote/annotate/environment.yml +++ b/modules/nf-core/hmtnote/annotate/environment.yml @@ -1,5 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::hmtnote=0.7.2 + - conda-forge::pip=21.3.1 + - conda-forge::python=3.6 + - pip: + - hmtnote==0.7.2 diff --git a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff b/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff index 745e98637..21993e931 100644 --- a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff +++ b/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff @@ -1,5 +1,4 @@ Changes in component 'nf-core/hmtnote/annotate' -'modules/nf-core/hmtnote/annotate/environment.yml' is unchanged 'modules/nf-core/hmtnote/annotate/meta.yml' is unchanged Changes in 'hmtnote/annotate/main.nf': --- modules/nf-core/hmtnote/annotate/main.nf @@ -48,4 +47,8 @@ Changes in 'hmtnote/annotate/main.nf': """ } +'modules/nf-core/hmtnote/annotate/environment.yml' is unchanged +'modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/hmtnote/annotate/tests/nextflow.config' is unchanged +'modules/nf-core/hmtnote/annotate/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/hmtnote/annotate/meta.yml b/modules/nf-core/hmtnote/annotate/meta.yml index 661d5cde0..92348f434 100644 --- a/modules/nf-core/hmtnote/annotate/meta.yml +++ b/modules/nf-core/hmtnote/annotate/meta.yml @@ -22,9 +22,10 @@ input: type: file description: vcf file pattern: "*.vcf" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -32,11 +33,14 @@ output: type: file description: annotated vcf pattern: "*_annotated.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@sysbiocoder" maintainers: From a60e8ef42b24ec119c9b21f86d0aadaccd8c45b3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:08:36 +0100 Subject: [PATCH 360/872] Update CHANGELOG.md --- CHANGELOG.md | 53 ++++++++++++++++++++++++++-------------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 35f2d8ba0..2c60fb1d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -50,32 +50,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| --------------------- | ----------- | ----------- | -| bcftools | 1.20 | 1.21 | -| bwa | 0.7.18 | 0.7.19 | -| deepvariant | 1.8.0 | 1.9.0 | -| eKLIPse | 1.8 | | -| ensemblverp/filtervep | 113 | 115.2 | -| fastp | 0.23.4 | 1.0.1 | -| gatk4 | 4.5.0.0 | 4.6.2.0 | -| genmod | 3.9 | 3.10.2 | -| gens-preproc | 1.0.11 | 1.1.2 | -| htslib | 1.20 | 1.21 | -| MitoSalt | | 1.1.1 | -| mosdepth | 0.3.8 | 0.3.11 | -| multiqc | 1.32 | 1.33 | -| ngsbits | 202411 | 202512 | -| picard | 3.3.0 | 3.4.0 | -| pigz | 2.3.4 | 2.8 | -| sambamba | | 1.0.1 | -| samtools | 1.21 | 1.22.1 | -| sentieon | 202503 | 202503.02 | -| stranger | 0.9.4 | 0.10.0 | -| tiddit | 3.6.1 | 3.9.4 | -| ucsc | 447 | 482 | -| vcfanno | 0.3.5 | 0.3.7 | -| vcf2cytosure | 0.9.1 | 0.9.3 | +| Tool | Old version | New version | +| -------------------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| bwa | 0.7.18 | 0.7.19 | +| deepvariant | 1.8.0 | 1.9.0 | +| eKLIPse | 1.8 | | +| ensemblvep/vep | 110 | 110.1 | +| ensemblvep/filtervep | 113 | 115.2 | +| fastp | 0.23.4 | 1.0.1 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | +| genmod | 3.9 | 3.10.2 | +| gens-preproc | 1.0.11 | 1.1.2 | +| htslib | 1.20 | 1.21 | +| MitoSalt | | 1.1.1 | +| mosdepth | 0.3.8 | 0.3.11 | +| multiqc | 1.32 | 1.33 | +| ngsbits | 202411 | 202512 | +| picard | 3.3.0 | 3.4.0 | +| pigz | 2.3.4 | 2.8 | +| sambamba | | 1.0.1 | +| samtools | 1.21 | 1.22.1 | +| sentieon | 202503 | 202503.02 | +| stranger | 0.9.4 | 0.10.0 | +| tiddit | 3.6.1 | 3.9.4 | +| ucsc | 447 | 482 | +| vcfanno | 0.3.5 | 0.3.7 | +| vcf2cytosure | 0.9.1 | 0.9.3 | ## 2.6.0 - Cacofonix [2025-06-25] From de3925a154653739989d5ec24501faa2c57bb984 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:11:30 +0100 Subject: [PATCH 361/872] run_mt_for_wes to val_run_mt_for_wes --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d4c2b0503..d3c94500c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -628,7 +628,7 @@ workflow RAREDISEASE { CALL MITOCHONDRIAL SVs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CALL_SV_MT( ch_mapped.genome_marked_bam_bai, ch_genome_chrsizes, From 1bd35d466cd373094ba4bdaa8fd428f4bc80b182 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:22:23 +0100 Subject: [PATCH 362/872] review suggestions and nextflow lint --- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 2 +- subworkflows/local/annotate_cadd/main.nf | 2 +- subworkflows/local/call_structural_variants.nf | 2 -- workflows/raredisease.nf | 2 -- 4 files changed, 2 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 65e7b1256..fb7a850e3 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -62,7 +62,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return[meta,fasta,fai,[]]}) + SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 0d571e48b..33557bea1 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -55,7 +55,7 @@ workflow ANNOTATE_CADD { TABIX_VIEW(BCFTOOLS_VIEW.out.vcf) - CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources) + CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, [[:], []]) TABIX_CADD(CADD.out.tsv) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index f7ff6b90a..8d4cbcf6c 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -15,7 +15,6 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] @@ -27,7 +26,6 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] val_analysis_type // string: "wes", "wgs", or "mito" - run_mt_for_wes // boolean skip_germlinecnvcaller // boolean main: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d3c94500c..0c28a798d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -543,7 +543,6 @@ workflow RAREDISEASE { ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, ch_mapped.genome_marked_bam_bai, - ch_mapped.mt_bam_bai, ch_genome_bwaindex, ch_genome_fasta, ch_genome_fai, @@ -555,7 +554,6 @@ workflow RAREDISEASE { ch_ploidy_model, ch_gcnvcaller_model, val_analysis_type, - val_run_mt_for_wes, skip_germlinecnvcaller, ) ch_versions = ch_versions.mix(CALL_STRUCTURAL_VARIANTS.out.versions) From ce2e982a6ca2fc6759c6224025bc6c42dccbe061 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 3 Mar 2026 09:42:54 +0100 Subject: [PATCH 363/872] long args, single process, and conda yamls --- modules/local/saltshaker/call/environment.yaml | 7 +++++++ modules/local/saltshaker/call/main.nf | 14 +++++++------- modules/local/saltshaker/classify/environment.yaml | 7 +++++++ modules/local/saltshaker/classify/main.nf | 2 +- modules/local/saltshaker/plot/environment.yaml | 7 +++++++ modules/local/saltshaker/plot/main.nf | 2 +- 6 files changed, 30 insertions(+), 9 deletions(-) create mode 100644 modules/local/saltshaker/call/environment.yaml create mode 100644 modules/local/saltshaker/classify/environment.yaml create mode 100644 modules/local/saltshaker/plot/environment.yaml diff --git a/modules/local/saltshaker/call/environment.yaml b/modules/local/saltshaker/call/environment.yaml new file mode 100644 index 000000000..e2f67c93f --- /dev/null +++ b/modules/local/saltshaker/call/environment.yaml @@ -0,0 +1,7 @@ +channels: +- conda-forge +- bioconda +dependencies: +- pip +- pip: + - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf index 072ae75c6..66a941418 100644 --- a/modules/local/saltshaker/call/main.nf +++ b/modules/local/saltshaker/call/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_CALL { tag "$meta.id" - label "process_low" + label "process_single" conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -30,12 +30,12 @@ process SALTSHAKER_CALL { saltshaker call \\ --prefix $prefix \\ --output-dir . \\ - -r $mtfasta \\ - -c $cluster \\ - -p $breakpoint \\ - -f $flank \\ - -H $hplimit \\ - -g $mito_length \\ + --reference $mtfasta \\ + --cluster $cluster \\ + --breakpoint $breakpoint \\ + --flank-size $flank \\ + --het-limit $hplimit \\ + --genome-length $mito_length \\ --ori-h-start $ori_h_start \\ --ori-h-end $ori_h_end \\ --ori-l-start $ori_l_start \\ diff --git a/modules/local/saltshaker/classify/environment.yaml b/modules/local/saltshaker/classify/environment.yaml new file mode 100644 index 000000000..e2f67c93f --- /dev/null +++ b/modules/local/saltshaker/classify/environment.yaml @@ -0,0 +1,7 @@ +channels: +- conda-forge +- bioconda +dependencies: +- pip +- pip: + - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/classify/main.nf b/modules/local/saltshaker/classify/main.nf index 5ce9eb4c0..ee33ce9ac 100644 --- a/modules/local/saltshaker/classify/main.nf +++ b/modules/local/saltshaker/classify/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_CLASSIFY { tag "$meta.id" - label "process_low" + label "process_single" conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/local/saltshaker/plot/environment.yaml b/modules/local/saltshaker/plot/environment.yaml new file mode 100644 index 000000000..e2f67c93f --- /dev/null +++ b/modules/local/saltshaker/plot/environment.yaml @@ -0,0 +1,7 @@ +channels: +- conda-forge +- bioconda +dependencies: +- pip +- pip: + - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/plot/main.nf b/modules/local/saltshaker/plot/main.nf index 98e80ab38..aa54ab023 100644 --- a/modules/local/saltshaker/plot/main.nf +++ b/modules/local/saltshaker/plot/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_PLOT { tag "$meta.id" - label "process_low" + label "process_single" conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From 88abcc714f0df9a3d8759b2c145ee0b83913954b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:33:58 +0100 Subject: [PATCH 364/872] Update snapshots --- tests/default.nf.test.snap | 15 ++++----------- tests/test_bam.nf.test.snap | 17 +++++------------ tests/test_singleton.nf.test.snap | 15 +++++---------- 3 files changed, 14 insertions(+), 33 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bf8774f4c..fad7ba357 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -219,9 +219,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -710,10 +707,6 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1107,10 +1100,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-03-03T10:21:06.035670185", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T05:27:37.311350676" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 70af846c2..19b43e8d0 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 795, + 792, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -210,9 +210,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -655,10 +652,6 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1036,10 +1029,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-03-03T10:27:29.654590007", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-16T22:08:02.449482922" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index da510cdc4..a4e348cc6 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 365, + 364, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -211,9 +211,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -563,8 +560,6 @@ "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", - "haplocheck", - "haplocheck/hugelymodelbat.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -724,10 +719,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], + "timestamp": "2026-03-03T10:31:17.265377549", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T19:08:15.435078959" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 9f65cc3fb202b83e1348cd77b6d9fe505bdd0c81 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:38:10 +0100 Subject: [PATCH 365/872] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3309acd15..9f074e9ce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763) - Sambamba depth now filters on not duplicates and not failed_quality_control [#768](https://github.com/nf-core/raredisease/pull/768) - Removed eKLIPse [#743](https://github.com/nf-core/raredisease/pull/743) +- Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) ### `Fixed` @@ -53,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | --------------------- | ----------- | ----------- | | bcftools | 1.20 | 1.21 | +| haplocheck | 1.3.3 | | | htslib | 1.20 | 1.21 | | mosdepth | 0.3.8 | 0.3.11 | | ngs-bits | 2023_02 | 2024_11 | From f30bbe4a140987816f214682995e0c0894a08e9b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 3 Mar 2026 09:42:38 +0000 Subject: [PATCH 366/872] [automated] Fix code linting --- conf/modules/call_snv_MT.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config index f6a49bf50..72442a992 100644 --- a/conf/modules/call_snv_MT.config +++ b/conf/modules/call_snv_MT.config @@ -43,4 +43,4 @@ process { ext.prefix = { "${meta.id}_filtered_shifted" } } -} \ No newline at end of file +} From 1adf8f8c4acf625d67675bc534f4f8f3f75f1f63 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 11:51:08 +0100 Subject: [PATCH 367/872] update output.md --- docs/output.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/docs/output.md b/docs/output.md index 5c5d0401a..f8fbf02b5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -77,6 +77,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Annotating mobile elements](#annotating-mobile-elements) - [Variant evaluation](#variant-evaluation) - [Gens](#gens) + - [Peddy](#peddy) - [Pipeline information](#pipeline-information) ### Alignment @@ -454,6 +455,7 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e - `annotate_sv/` - `_svdbquery_vep.vcf.gz`: file containing svdb query, and vep annotations. - `_svdbquery_vep.vcf.gz.tbi`: index of the file containing bcftools roh, vcfanno, and vep annotations. + - `_svdbquery_vep_summary.html`: vep summary. @@ -641,6 +643,26 @@ The sequencing data can be prepared for visualization of CNVs in [Gens](https:// +### Peddy + +[Peddy](https://github.com/brentp/peddy) compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF. + +
    +Output files + +- `peddy/` + - `*.het_check.csv` + - `*.het_check.png` + - `*.html` + - `*.pca_check.png` + - `*.ped_check.csv` + - `*.ped_check.png` + - `*.ped_check.rel-difference.csv` + - `*.peddy.ped` + - `*.sex_check.csv` + - `*.sex_check.png` + - `*.vs.html` + ### Pipeline information [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. From 4a552dd457908468fca306e7ed3b548a220d290c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 3 Mar 2026 15:10:40 +0100 Subject: [PATCH 368/872] better param and val names, fix versions, fix stubs, citations --- CITATIONS.md | 10 +- conf/modules/call_sv_MT.config | 12 +-- modules/local/saltshaker/call/main.nf | 38 +++---- modules/local/saltshaker/classify/main.nf | 15 +-- modules/local/saltshaker/plot/main.nf | 12 +-- nextflow.config | 51 +++++---- subworkflows/local/call_sv_MT/main.nf | 124 +++++++++++----------- workflows/raredisease.nf | 47 ++++---- 8 files changed, 142 insertions(+), 167 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index bd5c97d4f..3b7a118cb 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -42,10 +42,6 @@ > Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235 -- [eKLIPse](https://www.nature.com/articles/s41436-018-0350-8) - - > Goudenège D, Bris C, Hoffmann V, et al. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 21, 1407–1416 (2019). doi:10.1038/s41436-018-0350-8 - - [Ensembl VEP](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4) > McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4 @@ -92,6 +88,10 @@ > Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220-1222. doi:10.1093/bioinformatics/btv710 +- [Mitosalt](https://sourceforge.net/projects/mitosalt/) + + > Basu S, Xie X, Uhler JP, et al. Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing. PLoS Genet. 2020;16(12):e1009242. doi: 10.1371/journal.pgen.1009242 + - [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630?login=true) > Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Hancock J, ed. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699 @@ -122,6 +122,8 @@ > John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, and Francisco M. De La Vega. "Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines." bioRxiv, 2015. doi:10.1101/023754. +- [saltshaker](https://pypi.org/project/saltshaker/) + - [Sentieon DNAscope](https://www.biorxiv.org/content/10.1101/2022.05.20.492556v1.abstract) > Freed D, Pan R, Chen H, Li Z, Hu J, Aldana R. DNAscope: High Accuracy Small Variant Calling Using Machine Learning. Bioinformatics; 2022. doi:10.1101/2022.05.20.492556 diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 35cda22dd..4c9610c60 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -22,16 +22,14 @@ process { ext.prefix = { "${meta.id}_mitochondria_deletions" } publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } withName: '.*CALL_SV_MT:MITOSALT' { publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } @@ -43,8 +41,7 @@ process { ext.args = '--blacklist' publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } @@ -52,8 +49,7 @@ process { ext.args = '--blacklist --genes' publishDir = [ path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf index 66a941418..983b172ce 100644 --- a/modules/local/saltshaker/call/main.nf +++ b/modules/local/saltshaker/call/main.nf @@ -9,19 +9,19 @@ process SALTSHAKER_CALL { input: tuple val(meta), path(breakpoint) - tuple val(meta), path(cluster) - tuple val(meta2), path(mtfasta) + tuple val(meta2), path(cluster) + tuple val(meta3), path(mtfasta) val flank - val hplimit + val heteroplasmy_limit val mito_length - val ori_h_start - val ori_h_end - val ori_l_start - val ori_l_end + val heavy_strand_origin_start + val heavy_strand_origin_end + val light_strand_origin_start + val light_strand_origin_end output: tuple val(meta), path("*_call_metadata.tsv"), emit: call - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker script: def args = task.ext.args ?: '' @@ -34,30 +34,22 @@ process SALTSHAKER_CALL { --cluster $cluster \\ --breakpoint $breakpoint \\ --flank-size $flank \\ - --het-limit $hplimit \\ + --het-limit $heteroplasmy_limit \\ --genome-length $mito_length \\ - --ori-h-start $ori_h_start \\ - --ori-h-end $ori_h_end \\ - --ori-l-start $ori_l_start \\ - --ori-l-end $ori_l_end \\ + --ori-h-start $heavy_strand_origin_start \\ + --ori-h-end $heavy_strand_origin_end \\ + --ori-l-start $light_strand_origin_start \\ + --ori-l-end $light_strand_origin_end \\ $args - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_call: \$(echo \$(saltshaker call 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_call_metadata.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_call: \$(echo \$(saltshaker call 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS + touch ${prefix}.saltshaker_call_metadata.tsv + """ } diff --git a/modules/local/saltshaker/classify/main.nf b/modules/local/saltshaker/classify/main.nf index ee33ce9ac..a473b5979 100644 --- a/modules/local/saltshaker/classify/main.nf +++ b/modules/local/saltshaker/classify/main.nf @@ -19,7 +19,7 @@ process SALTSHAKER_CLASSIFY { tuple val(meta), path("*_classify_metadata.tsv"), emit: classify tuple val(meta), path("*_classify.txt") , emit: txt tuple val(meta), path("*saltshaker.vcf") , emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker script: def args = task.ext.args ?: '' @@ -36,23 +36,16 @@ process SALTSHAKER_CLASSIFY { --noise $noise_thresh \\ $args - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_classify: \$(echo \$(saltshaker classify 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf - touch ${prefix}_call_metadata.tsv + touch ${prefix}.saltshaker.vcf + touch ${prefix}.saltshaker_classify.txt + touch ${prefix}.saltshaker_classify_metadata.tsv - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_classify: \$(echo \$(saltshaker classify 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/local/saltshaker/plot/main.nf b/modules/local/saltshaker/plot/main.nf index aa54ab023..fcfd9455f 100644 --- a/modules/local/saltshaker/plot/main.nf +++ b/modules/local/saltshaker/plot/main.nf @@ -12,7 +12,7 @@ process SALTSHAKER_PLOT { output: tuple val(meta), path("*saltshaker.png"), emit: plot - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker script: def args = task.ext.args ?: '' @@ -23,22 +23,14 @@ process SALTSHAKER_PLOT { --input-dir . \\ $args - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_plot: \$(echo \$(saltshaker plot 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.png + touch ${prefix}.saltshaker.png - cat <<-END_VERSIONS > versions.yml - "${task.process}": - saltshaker_plot: \$(echo \$(saltshaker plot 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/nextflow.config b/nextflow.config index 33b461bae..477d58e02 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,17 +14,16 @@ params { // References genome = 'GRCh38' + heavy_strand_origin_start = 16081 + heavy_strand_origin_end = 407 igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + light_strand_origin_start = 5730 + light_strand_origin_end = 5763 local_genomes = null save_reference = false mito_name = 'chrM' mito_length = 16569 - ori_h_start = 16081 - ori_h_end = 407 - ori_l_start = 5730 - ori_l_end = 5763 - // Main options analysis_type = 'wgs' @@ -128,27 +127,27 @@ params { sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE' variant_type = 'snp,indel' - // Mitosalt/saltshaker options - breakspan = 15 - breakthreshold = 2 - cluster_threshold = 5 - deletion_threshold_max = 30000 - deletion_threshold_min = 30 - dom_frac = 0.5 - evalue_threshold = 0.00001 - exclude = 5 - flank = 15 - group_radius = 600 - high_het = 10 - hplimit = 0.01 - mitosalt_depth = 10000000 - mult_thresh = 5 - noise_thresh = 0.3 - paired_distance = 1000 - score_threshold = 80 - sizelimit = 10000 - split_distance_threshold = 5 - split_length = 15 + // Mitosalt and saltshaker options + mitosalt_breakspan = 15 + mitosalt_breakthreshold = 2 + mitosalt_cluster_threshold = 5 + mitosalt_deletion_threshold_max = 30000 + mitosalt_deletion_threshold_min = 30 + mitosalt_evalue_threshold = 0.00001 + mitosalt_exclude = 5 + mitosalt_flank = 15 + mitosalt_heteroplasmy_limit = 0.01 + mitosalt_depth = 10000000 + mitosalt_paired_distance = 1000 + mitosalt_score_threshold = 80 + mitosalt_sizelimit = 10000 + mitosalt_split_distance_threshold = 5 + mitosalt_split_length = 15 + saltshaker_dominant_fraction = 0.5 + saltshaker_group_radius = 600 + saltshaker_high_heteroplasmy = 10 + saltshaker_multiple_threshold = 5 + saltshaker_noise_threshold = 0.3 // MultiQC options multiqc_config = null diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index a481457b1..e77bead34 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -12,44 +12,44 @@ include { SALTSHAKER_PLOT } from '../../../modules/local/saltshaker/plot/mai workflow CALL_SV_MT { take: - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] - ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] - ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - val_breakspan // string: [mandatory] mitosalt_break_span - val_breakthreshold // string: [mandatory] mitosalt_break_threshold - val_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold - val_deletion_threshold_max // string: [mandatory] mitosalt_del_threshold_max - val_deletion_threshold_min // string: [mandatory] mitosalt_del_threshold_min - val_dom_frac // string: [mandatory] saltshaker_dominant_fraction - val_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold - val_exclude // string: [mandatory] mitosalt_exclude - val_flank // string: [mandatory] mitosalt_flank - val_group_radius // string: [mandatory] saltshaker_group_radius - val_high_het // string: [mandatory] saltshaker_high_heteroplasmy - val_hplimit // string: [mandatory] mitosalt_hp_limit - val_mito_length // string: [mandatory] mito_length - val_mito_name // string: [mandatory] mito_name - val_mult_thresh // string: [mandatory] saltshaker_multi_threshold - val_noise_thresh // string: [mandatory] saltshaker_noise_threshold - val_ori_h_start // string: [mandatory] mito_ori_h_start - val_ori_h_end // string: [mandatory] mito_ori_h_end - val_ori_l_start // string: [mandatory] mito_ori_l_start - val_ori_l_end // string: [mandatory] mito_ori_l_end - val_paired_distance // string: [mandatory] mitosalt_paired_distance - val_score_threshold // string: [mandatory] mitosalt_score_threshold - val_sizelimit // string: [mandatory] mitosalt_size_limit - val_split_distance_threshold // string: [mandatory] mitosalt_split_dist_threshold - val_split_length // string: [mandatory] mitosalt_split_length + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start + val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end + val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start + val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end + val_mito_length // string: [mandatory] mito_length + val_mito_name // string: [mandatory] mito_name + val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan + val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold + val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold + val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max + val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min + val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold + val_mitosalt_exclude // string: [mandatory] mitosalt_exclude + val_mitosalt_flank // string: [mandatory] mitosalt_flank + val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit + val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance + val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold + val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit + val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold + val_mitosalt_split_length // string: [mandatory] mitosalt_split_length + val_saltshaker_dominant_fraction // string: [mandatory] saltshaker_dominant_fraction + val_saltshaker_group_radius // string: [mandatory] saltshaker_group_radius + val_saltshaker_high_heteroplasmy // string: [mandatory] saltshaker_high_heteroplasmy + val_saltshaker_multiple_threshold // string: [mandatory] saltshaker_multiple_threshold + val_saltshaker_noise_threshold // string: [mandatory] saltshaker_noise_threshold main: - ch_versions = Channel.empty() + ch_versions = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -63,21 +63,21 @@ workflow CALL_SV_MT { ch_mt_fai, ch_mt_fasta, ch_mt_lastdb, - val_breakspan, - val_breakthreshold, - val_cluster_threshold, - val_deletion_threshold_max, - val_deletion_threshold_min, - val_evalue_threshold, - val_exclude, - val_flank, - val_hplimit, + val_mitosalt_breakspan, + val_mitosalt_breakthreshold, + val_mitosalt_cluster_threshold, + val_mitosalt_deletion_threshold_max, + val_mitosalt_deletion_threshold_min, + val_mitosalt_evalue_threshold, + val_mitosalt_exclude, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, val_mito_name, - val_paired_distance, - val_score_threshold, - val_sizelimit, - val_split_distance_threshold, - val_split_length + val_mitosalt_paired_distance, + val_mitosalt_score_threshold, + val_mitosalt_sizelimit, + val_mitosalt_split_distance_threshold, + val_mitosalt_split_length ) MITOSALT( @@ -99,27 +99,27 @@ workflow CALL_SV_MT { MITOSALT.out.breakpoint, ch_saltshaker_in, ch_mt_fasta, - val_flank, - val_hplimit, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, val_mito_length, - val_ori_h_start, - val_ori_h_end, - val_ori_l_start, - val_ori_l_end + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end ) SALTSHAKER_CLASSIFY( SALTSHAKER_CALL.out.call, - val_dom_frac, - val_group_radius, - val_high_het, - val_mult_thresh, - val_noise_thresh + val_saltshaker_dominant_fraction, + val_saltshaker_group_radius, + val_saltshaker_high_heteroplasmy, + val_saltshaker_multiple_threshold, + val_saltshaker_noise_threshold ) ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify SALTSHAKER_PLOT( - SALTSHAKER_CLASSIFY.out.classify + ch_mitosalt_vcf ) ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 21c256e2f..391d4bd06 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -654,31 +654,32 @@ workflow RAREDISEASE { ch_mt_lastdb, ch_input_fastqs, ch_subdepth, - params.breakspan, - params.breakthreshold, - params.cluster_threshold, - params.deletion_threshold_max, - params.deletion_threshold_min, - params.dom_frac, - params.evalue_threshold, - params.exclude, - params.flank, - params.group_radius, - params.high_het, - params.hplimit, + params.heavy_strand_origin_start, + params.heavy_strand_origin_end, + params.light_strand_origin_start, + params.light_strand_origin_end, params.mito_length, params.mito_name, - params.mult_thresh, - params.noise_thresh, - params.ori_h_start, - params.ori_h_end, - params.ori_l_start, - params.ori_l_end, - params.paired_distance, - params.score_threshold, - params.sizelimit, - params.split_distance_threshold, - params.split_length + params.mitosalt_breakspan, + params.mitosalt_breakthreshold, + params.mitosalt_cluster_threshold, + params.mitosalt_deletion_threshold_max, + params.mitosalt_deletion_threshold_min, + params.mitosalt_evalue_threshold, + params.mitosalt_exclude, + params.mitosalt_flank, + params.mitosalt_heteroplasmy_limit, + params.mitosalt_paired_distance, + params.mitosalt_score_threshold, + params.mitosalt_sizelimit, + params.mitosalt_split_distance_threshold, + params.mitosalt_split_length, + params.saltshaker_dominant_fraction, + params.saltshaker_group_radius, + params.saltshaker_high_heteroplasmy, + params.saltshaker_multiple_threshold, + params.saltshaker_noise_threshold + ) ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } From bae928138d754e4a8f24734e04df5829576942ba Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Tue, 3 Mar 2026 15:25:42 +0100 Subject: [PATCH 369/872] remove_hmtnote_annotate --- subworkflows/local/annotate_mt_snvs.nf | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index ee2c04fe8..8de4e3c06 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -2,16 +2,17 @@ // Annotate MT // -include { REPLACE_SPACES_IN_VCFINFO } from '../../modules/local/replace_spaces_in_vcfinfo' +//include { REPLACE_SPACES_IN_VCFINFO } from '../../modules/local/replace_spaces_in_vcfinfo' include { BCFTOOLS_PLUGINSETGT } from '../../modules/nf-core/bcftools/pluginsetgt' +include { TABIX_TABIX as TABIX_TABIX_MT } from '../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../modules/nf-core/tabix/bgziptabix/main' +//include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../modules/nf-core/tabix/bgziptabix/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../modules/nf-core/ensemblvep/vep/main' include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../modules/nf-core/haplogrep3/classify/main' include { VCFANNO as VCFANNO_MT } from '../../modules/nf-core/vcfanno/main' include { ANNOTATE_CADD } from './annotate_cadd' include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../modules/nf-core/tabix/bgziptabix/main' -include { HMTNOTE_ANNOTATE } from '../../modules/nf-core/hmtnote/annotate/main' +//include { HMTNOTE_ANNOTATE } from '../../modules/nf-core/hmtnote/annotate/main' workflow ANNOTATE_MT_SNVS { take: @@ -36,7 +37,7 @@ workflow ANNOTATE_MT_SNVS { ch_versions = channel.empty() ch_haplog = channel.empty() - // add prefix to meta +/* // add prefix to meta ch_mt_vcf .map { meta, vcf -> return [meta+ [prefix: vcf.simpleName + "_hmtnote"], vcf] @@ -46,10 +47,15 @@ workflow ANNOTATE_MT_SNVS { // HMTNOTE ANNOTATE HMTNOTE_ANNOTATE(ch_hmtnote_in) REPLACE_SPACES_IN_VCFINFO(HMTNOTE_ANNOTATE.out.vcf) - ZIP_TABIX_HMTNOTE_MT(REPLACE_SPACES_IN_VCFINFO.out.vcf) + ZIP_TABIX_HMTNOTE_MT(REPLACE_SPACES_IN_VCFINFO.out.vcf) */ + TABIX_TABIX_MT(ch_mt_vcf) // meta, tbi + // => TABIX_TABIX_MT(ch_mt_vcf) a associer avec ch_mt_vcf [meta, vcf] pour avoir [meta, vcf, tbi] + + ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) // Vcfanno - ZIP_TABIX_HMTNOTE_MT.out.gz_index + //ZIP_TABIX_HMTNOTE_MT.out.gz_index // = meta, vcf, tbi + ch_mt_vcf_index .combine(ch_vcfanno_extra) .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } @@ -124,7 +130,7 @@ workflow ANNOTATE_MT_SNVS { } ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) - ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) + //ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) emit: haplog = ch_haplog // channel: [ val(meta), path(txt) ] From 61b35bbac495eff59aef28a17a0cadb3b3a95364 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Tue, 3 Mar 2026 15:42:11 +0100 Subject: [PATCH 370/872] fixed bug in output name --- subworkflows/local/annotate_mt_snvs.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 8de4e3c06..52aba9ad9 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -57,7 +57,7 @@ workflow ANNOTATE_MT_SNVS { //ZIP_TABIX_HMTNOTE_MT.out.gz_index // = meta, vcf, tbi ch_mt_vcf_index .combine(ch_vcfanno_extra) - .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]} + .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) From 3f6527b0599f9f0abf2028094a8661f3c9f227eb Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 16:02:31 +0100 Subject: [PATCH 371/872] Update snapshots --- tests/default.nf.test.snap | 25 +++++++------------------ tests/test_bam.nf.test.snap | 27 ++++++++------------------- tests/test_singleton.nf.test.snap | 27 ++++++++------------------- 3 files changed, 23 insertions(+), 56 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index bf8774f4c..dbfa8140e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -228,9 +228,6 @@ "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, - "HMTNOTE_ANNOTATE": { - "hmtnote": "0.7.2" - }, "INDEX_CNVNATOR": { "bgzip": 1.21, "tabix": 1.21 @@ -309,10 +306,6 @@ "RENAME_BAM": { "coreutils": 9.5 }, - "REPLACE_SPACES_IN_VCFINFO": { - "python": "3.14.3", - "replace_spaces_in_vcfinfo": 1.0 - }, "RETROSEQ_CALL": { "retroseq": 1.5 }, @@ -486,10 +479,6 @@ "Workflow": { "nf-core/raredisease": "v2.7.0dev" }, - "ZIP_TABIX_HMTNOTE_MT": { - "bgzip": 1.21, - "tabix": 1.21 - }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 @@ -667,9 +656,9 @@ "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.json.gz", "annotate_sv/justhusky_svdbquery_vep.summary.html", @@ -1107,10 +1096,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-03-03T15:50:11.194748118", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T05:27:37.311350676" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 70af846c2..dfa3781b1 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 795, + 793, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -219,9 +219,6 @@ "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, - "HMTNOTE_ANNOTATE": { - "hmtnote": "0.7.2" - }, "INDEX_CNVNATOR": { "bgzip": 1.21, "tabix": 1.21 @@ -294,10 +291,6 @@ "RENAME_BAM": { "coreutils": 9.5 }, - "REPLACE_SPACES_IN_VCFINFO": { - "python": "3.14.3", - "replace_spaces_in_vcfinfo": 1.0 - }, "RETROSEQ_CALL": { "retroseq": 1.5 }, @@ -456,10 +449,6 @@ "Workflow": { "nf-core/raredisease": "v2.7.0dev" }, - "ZIP_TABIX_HMTNOTE_MT": { - "bgzip": 1.21, - "tabix": 1.21 - }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 @@ -628,9 +617,9 @@ "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.json.gz", "annotate_sv/justhusky_svdbquery_vep.summary.html", @@ -1036,10 +1025,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-03-03T15:56:22.149796815", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-16T22:08:02.449482922" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index da510cdc4..a00486cc5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 365, + 363, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -220,9 +220,6 @@ "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, - "HMTNOTE_ANNOTATE": { - "hmtnote": "0.7.2" - }, "INDEX_CNVNATOR": { "bgzip": 1.21, "tabix": 1.21 @@ -301,10 +298,6 @@ "RENAME_BAM": { "coreutils": 9.5 }, - "REPLACE_SPACES_IN_VCFINFO": { - "python": "3.14.3", - "replace_spaces_in_vcfinfo": 1.0 - }, "RETROSEQ_CALL": { "retroseq": 1.5 }, @@ -469,10 +462,6 @@ "Workflow": { "nf-core/raredisease": "v2.7.0dev" }, - "ZIP_TABIX_HMTNOTE_MT": { - "bgzip": 1.21, - "tabix": 1.21 - }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 @@ -532,9 +521,9 @@ "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", "annotate_snv/mitochondria", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_hmtnote_vcfanno_vep_haplogrep.txt", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.json.gz", "annotate_sv/justhusky_svdbquery_vep.summary.html", @@ -724,10 +713,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], + "timestamp": "2026-03-03T16:00:11.328624107", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T19:08:15.435078959" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 21b34d23c2ad01e381038c206e69bda6f2681a5f Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 3 Mar 2026 16:17:25 +0100 Subject: [PATCH 372/872] updated test stuff --- conf/test.config | 3 --- modules/local/mitosalt/main.nf | 2 +- tests/default.nf.test.snap | 23 ++++++++++++++++++++++- tests/test_singleton.nf.test.snap | 17 +++++++++++++++-- 4 files changed, 38 insertions(+), 7 deletions(-) diff --git a/conf/test.config b/conf/test.config index 81140af1b..ae58fad6f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,9 +28,6 @@ env { MPLCONFIGDIR="." } -singularity.pullTimeout='2h' -singularity.cacheDir='/home/proj/stage/singularity_cache' - params { config_profile_name = 'Test profile - default' config_profile_description = 'Minimal test dataset to check pipeline function' diff --git a/modules/local/mitosalt/main.nf b/modules/local/mitosalt/main.nf index fd498f0fe..3eee65aa3 100644 --- a/modules/local/mitosalt/main.nf +++ b/modules/local/mitosalt/main.nf @@ -37,7 +37,7 @@ process MITOSALT { """ cat $msconfig | sed "s/threads = 1/threads = ${task.cpus}/" > new-${msconfig} touch ${prefix}.breakpoint - touch ${prefix}.cluster + echo 'cluster' > ${prefix}.cluster """ } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8e3627e8b..e19360563 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -325,6 +325,15 @@ "RHOCALL_VIZ": { "rhocall": "0.5.1" }, + "SALTSHAKER_CALL": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_CLASSIFY": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_PLOT": { + "saltshaker": "1.0.0" + }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" }, @@ -693,12 +702,24 @@ "call_sv/mitochondria", "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker.png", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker.vcf", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker_classify.txt", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker_classify_metadata.tsv", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker.png", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker.vcf", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker_classify.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker_classify_metadata.tsv", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker.png", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker.vcf", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker_classify.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker_classify_metadata.tsv", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -1111,6 +1132,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-26T10:44:57.130309344" + "timestamp": "2026-03-03T15:58:44.610805525" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a3ba978fb..edb7bb7fe 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 365, + 368, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -317,6 +317,15 @@ "RHOCALL_VIZ": { "rhocall": "0.5.1" }, + "SALTSHAKER_CALL": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_CLASSIFY": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_PLOT": { + "saltshaker": "1.0.0" + }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" }, @@ -558,6 +567,10 @@ "call_sv/mitochondria", "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker.png", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker.vcf", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker_classify.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker_classify_metadata.tsv", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", @@ -728,6 +741,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-02-27T10:14:31.323250611" + "timestamp": "2026-03-03T16:11:07.735178695" } } \ No newline at end of file From aacad8eafcc5605aa7166b5bc37b5ec16df29b39 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 20:43:37 +0100 Subject: [PATCH 373/872] Update tests --- .../local/call_snv/tests/main.nf.test | 22 +++++++++---------- .../local/call_snv/tests/main.nf.test.snap | 18 +++++++++++++++ .../local/call_snv_MT/tests/main.nf.test | 2 +- .../local/call_snv_MT/tests/main.nf.test.snap | 15 +++++++++++++ 4 files changed, 44 insertions(+), 13 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 9329a562e..cef6bdfb6 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -6,9 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "call_snv" - test("CALL_SNV - deepvariant wgs, stub") { - - options "-stub" + test("CALL_SNV - deepvariant wgs") { when { workflow { @@ -17,7 +15,7 @@ nextflow_workflow { input[1] = channel.of([id:'justhusky']) input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz', checkIfExists: true)]) input[3] = channel.of([[id:'genome'], []]) - input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() + input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() input[5] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), @@ -32,20 +30,20 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[11] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]).collect() - input[12] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[13] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[11] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[12] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[13] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[14] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt.intervals', checkIfExists: true)).collect() input[15] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[16] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]).collect() - input[17] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[18] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[19] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt_shift8000.intervals', checkIfExists: true)).collect() - input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[16] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.dict', checkIfExists: true)]).collect() + input[17] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.fasta.fai', checkIfExists: true)]).collect() + input[18] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.fasta', checkIfExists: true)]).collect() + input[19] = channel.of(file(params.pipelines_testdata_base_path + 'reference/mt_shift8000.intervals', checkIfExists: true)).collect() + input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/mt_shift8000.back_chain', checkIfExists: true)]).collect() input[21] = channel.of([[id:'par'], []]) input[22] = channel.of([[id:'model'], []]) input[23] = channel.of([[id:'target'], [], []]) diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index bf4b59fd2..5d3984055 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -1,4 +1,22 @@ { + "CALL_SNV - deepvariant wgs": { + "content": [ + [ + "justhusky_snv.vcf.gz" + ], + [ + "justhusky_snv.vcf.gz.tbi" + ], + [ + "justhusky_mitochondria.vcf.gz" + ] + ], + "timestamp": "2026-03-03T19:48:35.971369089", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CALL_SNV - deepvariant wgs, stub": { "content": [ [ diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test b/subworkflows/local/call_snv_MT/tests/main.nf.test index 3dc9a5bf8..7aada2df4 100644 --- a/subworkflows/local/call_snv_MT/tests/main.nf.test +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "call_snv_MT" - test("CALL_SNV_MT - stub") { + test("CALL_SNV_MT") { when { workflow { diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test.snap b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap index 9814de4b8..9de7d0544 100644 --- a/subworkflows/local/call_snv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap @@ -13,5 +13,20 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "CALL_SNV_MT": { + "content": [ + [ + "earlycasualcaiman_filtered.vcf.gz" + ], + [ + "earlycasualcaiman_filtered.vcf.gz.tbi" + ] + ], + "timestamp": "2026-03-03T20:17:50.085712628", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 9f76155fab447d1b35de16b982b22096f198ba74 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 21:12:24 +0100 Subject: [PATCH 374/872] Update main.nf.test --- .../tests/main.nf.test | 30 ++++++++----------- 1 file changed, 12 insertions(+), 18 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index dac34c84e..139d26d58 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -26,24 +26,18 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[3] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ]) - input[4] = channel.of([[id:'bwa'], []]) - input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[6] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[7] = channel.of([id:'justhusky']) - input[8] = channel.of([[id:'target'], [], []]) - input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() - input[10] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[11] = channel.of([[]]) - input[12] = channel.of([[id:'ploidy'], []]) - input[13] = channel.of([[id:'gcnvcaller'], []]) - input[14] = 'wgs' - input[15] = false - input[16] = true + input[3] = channel.of([[id:'bwa'], []]) + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[6] = channel.of([id:'justhusky']) + input[7] = channel.of([[id:'target'], [], []]) + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[9] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[10] = channel.of([[]]) + input[11] = channel.of([[id:'ploidy'], []]) + input[12] = channel.of([[id:'gcnvcaller'], []]) + input[13] = 'wgs' + input[14] = true """ } } From 12ed04396a565c5ffb6ed25707f5d6f3b1700501 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 22:40:37 +0100 Subject: [PATCH 375/872] Update tiddit snapshots --- subworkflows/local/call_sv_tiddit/tests/main.nf.test | 2 +- subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index ad251659c..e7b28fcf1 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -51,7 +51,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - path(workflow.out.vcf[0][1]).vcf.variantsMD5 + path(workflow.out.vcf[0][1]).vcf.summary ).match() } ) } diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap index a6f1f03f8..4327bc183 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap @@ -1,9 +1,9 @@ { "CALL_SV_TIDDIT": { "content": [ - "140ce993561670b54ecb907561e3a417" + "VcfFile [chromosomes=[MT, 21], sampleCount=3, variantCount=178, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-01T21:41:21.445553341", + "timestamp": "2026-03-03T22:37:56.960203544", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 3795ca2169a1a40891ff1f44a3bb4751a9b22bcc Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 20 Feb 2026 13:51:03 +0100 Subject: [PATCH 376/872] removed haplocheck --- CITATIONS.md | 4 - assets/multiqc_config.yml | 3 - conf/modules/call_snv_MT.config | 14 +-- docs/output.md | 13 --- modules.json | 5 - modules/nf-core/haplocheck/environment.yml | 5 - modules/nf-core/haplocheck/main.nf | 44 -------- modules/nf-core/haplocheck/meta.yml | 60 ----------- modules/nf-core/haplocheck/tests/main.nf.test | 56 ---------- .../haplocheck/tests/main.nf.test.snap | 100 ------------------ subworkflows/local/call_snv_MT/main.nf | 6 -- 11 files changed, 1 insertion(+), 309 deletions(-) delete mode 100644 modules/nf-core/haplocheck/environment.yml delete mode 100644 modules/nf-core/haplocheck/main.nf delete mode 100644 modules/nf-core/haplocheck/meta.yml delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test delete mode 100644 modules/nf-core/haplocheck/tests/main.nf.test.snap diff --git a/CITATIONS.md b/CITATIONS.md index bd5c97d4f..7c25c42cf 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -76,10 +76,6 @@ > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081 -- [Haplocheck](https://genome.cshlp.org/content/31/2/309.long) - - > Weissensteiner H, Forer L, Fendt L, et al. Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Res. 2021;31(2):309-316. doi:10.1101/gr.256545.119 - - [HaploGrep 2](https://academic.oup.com/nar/article/44/W1/W58/2499296) > Weissensteiner H, Pacher D, Kloss-Brandstätter A, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58-W63. doi:10.1093/nar/gkw233 diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 0fa4b51ef..2e69f6a3d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -20,7 +20,6 @@ export_plots: true run_modules: - fastqc - fastp - - haplocheck - qualimap - picard - mosdepth @@ -42,8 +41,6 @@ module_order: name: "fastp" - mosdepth: name: "Mosdepth" - - haplocheck: - name: "haplocheck" - ngsbits: name: "ngsbits" - peddy: diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config index f77d2f6b1..f6a49bf50 100644 --- a/conf/modules/call_snv_MT.config +++ b/conf/modules/call_snv_MT.config @@ -26,14 +26,6 @@ process { ext.prefix = { "${meta.id}_filtered" } } - withName: '.*CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT' { - publishDir = [ - path: { "${params.outdir}/haplocheck" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.endsWith(".txt") ? filename : null } - ] - } - } // @@ -51,8 +43,4 @@ process { ext.prefix = { "${meta.id}_filtered_shifted" } } - withName: '.*CALL_SNV_MT_SHIFT:HAPLOCHECK_MT' { - ext.when = false - } - -} +} \ No newline at end of file diff --git a/docs/output.md b/docs/output.md index 5c5d0401a..1a9ff5a9e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -59,7 +59,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [SVDB query](#svdb-query) - [VEP](#vep-1) - [Mitochondrial analysis](#mitochondrial-analysis) - - [Haplocheck](#haplocheck) - [Alignment and variant calling](#alignment-and-variant-calling) - [MT deletion script](#mt-deletion-script) - [eKLIPse](#eklipse) @@ -461,18 +460,6 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e Mitochondrial analysis is run by default. If you want to turn off annotations set `--skip_subworkflows mt_annotation`. -#### Haplocheck - -[Haplocheck](https://github.com/genepi/haplocheck/) analyses the mitochondrial content to detect contamination in samples. The results are displayed in MultiQC. - -
    -Output files - -- `{outputdir}/haplocheck/` - - `.raw.txt`: haplocheck raw output. Read more about the file content [here](https://mitoverse.readthedocs.io/haplocheck/haplocheck/#textual-report-file-raw). - -
    - #### Alignment and variant calling [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-) The mitochondrial genome poses several challenges to the identification and understanding of somatic variants. The circularity of the mitochondrial genome means that the breakpoint in the reference genome is at an arbitrary position in the non-coding control region, creating a challenge in analyzing variation. Additionally, insertions of mitochondrial DNA into the nuclear genome (NuMTs) complicate the mapping of the mitochondrial genome and the distinction between NuMTs and the mitochondrial contig of interest. Lastly, mitochondrial variants often have very low heteroplasmy. Such low allele fraction (AF) variants can thus be mistaken for inherent sequencer noise. diff --git a/modules.json b/modules.json index 12ce80fb0..1849a5759 100644 --- a/modules.json +++ b/modules.json @@ -286,11 +286,6 @@ "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8", "installed_by": ["modules"] }, - "haplocheck": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "haplogrep3/classify": { "branch": "master", "git_sha": "c95c60597ce23da23ac21f4e6c5d7c0cdb711b8f", diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml deleted file mode 100644 index 4fb40238b..000000000 --- a/modules/nf-core/haplocheck/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf deleted file mode 100644 index 0d26c449e..000000000 --- a/modules/nf-core/haplocheck/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process HAPLOCHECK { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': - 'biocontainers/haplocheck:1.3.3--h4a94de4_0' }" - - input: - tuple val(meta), path(vcf) - - output: - tuple val(meta), path("*.txt") , emit: txt - tuple val(meta), path("*.html"), emit: html - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - haplocheck --raw --out $prefix $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.raw.txt - touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml deleted file mode 100644 index 25e6127a7..000000000 --- a/modules/nf-core/haplocheck/meta.yml +++ /dev/null @@ -1,60 +0,0 @@ -name: "haplocheck" -description: | - Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing - the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides - users a graphical report to investigate the contamination further. Internally, it uses the - Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. -keywords: - - mitochondrial - - mtDNA - - contamination -tools: - - "haplocheck": - description: "Detects in-sample contamination in mtDNA or WGS sequencing studies - by analyzing the mitochondrial content." - homepage: "https://github.com/genepi/haplocheck" - documentation: "https://github.com/genepi/haplocheck" - tool_dev_url: "https://github.com/genepi/haplocheck" - doi: 10.1101/gr.256545.119 - licence: ["MIT"] - identifier: biotools:haplocheck -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" -output: - - txt: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.txt": - type: file - description: Raw report in txt format - pattern: "*.{txt}" - - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: Haplocheck HTML report - pattern: "*.{html}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@lmtani" -maintainers: - - "@lmtani" diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test deleted file mode 100644 index 8957d02e2..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test +++ /dev/null @@ -1,56 +0,0 @@ - -nextflow_process { - - name "Test Process HAPLOCHECK" - script "../main.nf" - process "HAPLOCHECK" - - tag "modules" - tag "modules_nfcore" - tag "haplocheck" - - test("test-haplocheck") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test-haplocheck-stub") { - options '-stub' - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} diff --git a/modules/nf-core/haplocheck/tests/main.nf.test.snap b/modules/nf-core/haplocheck/tests/main.nf.test.snap deleted file mode 100644 index abe1eab56..000000000 --- a/modules/nf-core/haplocheck/tests/main.nf.test.snap +++ /dev/null @@ -1,100 +0,0 @@ -{ - "test-haplocheck-stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:41:40.703528" - }, - "test-haplocheck": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "2": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ], - "html": [ - [ - { - "id": "test" - }, - "test.html:md5,59d69052c86edff0301816956eaf4d5f" - ] - ], - "txt": [ - [ - { - "id": "test" - }, - "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" - ] - ], - "versions": [ - "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-02T13:43:05.761086" - } -} \ No newline at end of file diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 353e96e0e..14c4c4701 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -2,7 +2,6 @@ // Call SNV MT // -include { HAPLOCHECK as HAPLOCHECK_MT } from '../../../modules/nf-core/haplocheck/main' include { GATK4_MUTECT2 as GATK4_MUTECT2_MT } from '../../../modules/nf-core/gatk4/mutect2/main' include { GATK4_FILTERMUTECTCALLS as GATK4_FILTERMUTECTCALLS_MT } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' @@ -21,9 +20,6 @@ workflow CALL_SNV_MT { GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) - HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf) - ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions) - // Filter Mutect2 calls ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) ch_mutect_out = ch_mutect_vcf.join(GATK4_MUTECT2_MT.out.stats, failOnMismatch:true, failOnDuplicate:true) @@ -36,10 +32,8 @@ workflow CALL_SNV_MT { emit: filt_stats = GATK4_FILTERMUTECTCALLS_MT.out.stats // channel: [ val(meta), path(tsv) ] - html = HAPLOCHECK_MT.out.html // channel: [ val(meta), path(html) ] stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] - txt = HAPLOCHECK_MT.out.txt // channel: [ val(meta), path(txt) ] vcf = GATK4_FILTERMUTECTCALLS_MT.out.vcf // channel: [ val(meta), path(vcf) ] versions = ch_versions // channel: [ path(versions.yml) ] } From 5eb9a7ad0a8797a211f169901deb2cd0afc87409 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 20 Feb 2026 15:02:03 +0100 Subject: [PATCH 377/872] remove references to haplocheck txt --- subworkflows/local/call_snv.nf | 3 --- workflows/raredisease.nf | 3 --- 2 files changed, 6 deletions(-) diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 4f6acd6c1..1e0fc8047 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -50,7 +50,6 @@ workflow CALL_SNV { ch_mt_vcf = channel.empty() ch_mt_tabix = channel.empty() ch_mt_vcf_tabix = channel.empty() - ch_mt_txt = channel.empty() ch_sentieon_vcf = channel.empty() ch_sentieon_tbi = channel.empty() ch_sentieon_gvcf = channel.empty() @@ -139,7 +138,6 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_mt_txt = CALL_SNV_MT.out.txt ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions) ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions) } @@ -159,6 +157,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - mt_txt = ch_mt_txt // channel: [ val(meta), path(txt) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3dd3ace7c..dcfe3487c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -206,7 +206,6 @@ workflow RAREDISEASE { main: ch_multiqc_files = channel.empty() - ch_mt_txt = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -394,7 +393,6 @@ workflow RAREDISEASE { val_variant_caller ) ch_versions = ch_versions.mix(CALL_SNV.out.versions) - ch_mt_txt = CALL_SNV.out.mt_txt // // ANNOTATE GENOME SNVs @@ -894,7 +892,6 @@ workflow RAREDISEASE { if (!skip_fastqc) { ch_multiqc_files = ch_multiqc_files.mix(fastqc_report.collect{_meta, reports -> reports}.ifEmpty([])) } - ch_multiqc_files = ch_multiqc_files.mix(ch_mt_txt.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) From bc71d8406f9381eab9b8178efc2e2fec26df5a93 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:33:58 +0100 Subject: [PATCH 378/872] Update snapshots --- tests/default.nf.test.snap | 9 +-------- tests/test_bam.nf.test.snap | 11 ++--------- tests/test_singleton.nf.test.snap | 9 ++------- 3 files changed, 5 insertions(+), 24 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dbfa8140e..4cb1b4477 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -219,9 +219,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -699,10 +696,6 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1096,7 +1089,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T15:50:11.194748118", + "timestamp": "2026-03-03T10:21:06.035670185", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index dfa3781b1..3adea4c33 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 793, + 792, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -210,9 +210,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -644,10 +641,6 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", - "haplocheck", - "haplocheck/earlycasualcaiman.raw.txt", - "haplocheck/hugelymodelbat.raw.txt", - "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1025,7 +1018,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T15:56:22.149796815", + "timestamp": "2026-03-03T10:27:29.654590007", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a00486cc5..f54271b71 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 363, + 364, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -211,9 +211,6 @@ "GLNEXUS": { "glnexus": "1.4.1-0-g68e25e5" }, - "HAPLOCHECK_MT": { - "haplocheck": "1.3.3" - }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -552,8 +549,6 @@ "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", - "haplocheck", - "haplocheck/hugelymodelbat.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -713,7 +708,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-03T16:00:11.328624107", + "timestamp": "2026-03-03T10:31:17.265377549", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 092328cfefd65cf03b521bcab0184a1818761aca Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 10:38:10 +0100 Subject: [PATCH 379/872] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3309acd15..9f074e9ce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed parameter `bwa_as_fallback` [#763](https://github.com/nf-core/raredisease/pull/763) - Sambamba depth now filters on not duplicates and not failed_quality_control [#768](https://github.com/nf-core/raredisease/pull/768) - Removed eKLIPse [#743](https://github.com/nf-core/raredisease/pull/743) +- Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) ### `Fixed` @@ -53,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | --------------------- | ----------- | ----------- | | bcftools | 1.20 | 1.21 | +| haplocheck | 1.3.3 | | | htslib | 1.20 | 1.21 | | mosdepth | 0.3.8 | 0.3.11 | | ngs-bits | 2023_02 | 2024_11 | From d02b2427e51a66aecbce08c57e81bc853332e677 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Feb 2026 16:41:19 +0100 Subject: [PATCH 380/872] update modules --- modules.json | 70 ++-- modules/nf-core/bwa/index/environment.yml | 10 +- modules/nf-core/bwa/index/main.nf | 23 +- modules/nf-core/bwa/index/meta.yml | 44 ++- modules/nf-core/bwa/index/tests/main.nf.test | 26 +- .../nf-core/bwa/index/tests/main.nf.test.snap | 73 +++- modules/nf-core/bwa/index/tests/tags.yml | 2 - modules/nf-core/bwamem2/index/environment.yml | 10 +- modules/nf-core/bwamem2/index/main.nf | 23 +- modules/nf-core/bwamem2/index/meta.yml | 48 ++- .../nf-core/bwamem2/index/tests/main.nf.test | 25 +- .../bwamem2/index/tests/main.nf.test.snap | 75 ++++- modules/nf-core/bwamem2/index/tests/tags.yml | 2 - modules/nf-core/bwamem2/mem/environment.yml | 11 +- modules/nf-core/bwamem2/mem/main.nf | 21 +- modules/nf-core/bwamem2/mem/meta.yml | 75 +++-- .../nf-core/bwamem2/mem/tests/main.nf.test | 8 +- .../bwamem2/mem/tests/main.nf.test.snap | 100 ++++-- modules/nf-core/bwamem2/mem/tests/tags.yml | 2 - .../cnvnator/convert2vcf/tests/main.nf.test | 9 +- .../convert2vcf/tests/main.nf.test.snap | 4 +- .../convert2vcf/tests/nextflow.config | 13 +- .../nf-core/gatk4/collectreadcounts/main.nf | 4 +- .../nf-core/gatk4/collectreadcounts/meta.yml | 17 +- .../collectreadcounts/tests/main.nf.test | 32 +- .../collectreadcounts/tests/main.nf.test.snap | 25 +- .../gatk4/createsequencedictionary/meta.yml | 3 +- .../tests/main.nf.test | 11 +- .../tests/main.nf.test.snap | 8 +- .../nf-core/gatk4/denoisereadcounts/main.nf | 2 +- .../nf-core/gatk4/denoisereadcounts/meta.yml | 1 - .../denoisereadcounts/tests/main.nf.test | 17 +- .../denoisereadcounts/tests/main.nf.test.snap | 2 +- .../determinegermlinecontigploidy/main.nf | 6 +- .../tests/main.nf.test | 9 +- .../tests/main.nf.test.snap | 28 +- .../nf-core/gatk4/filtermutectcalls/main.nf | 12 +- .../filtermutectcalls/tests/main.nf.test | 10 +- .../filtermutectcalls/tests/main.nf.test.snap | 44 +-- .../nf-core/gatk4/germlinecnvcaller/main.nf | 6 +- .../germlinecnvcaller/tests/main.nf.test | 27 +- .../germlinecnvcaller/tests/main.nf.test.snap | 42 +-- .../nf-core/gatk4/intervallisttools/main.nf | 3 - .../intervallisttools/tests/main.nf.test | 7 +- .../intervallisttools/tests/main.nf.test.snap | 8 +- .../nf-core/gatk4/mergebamalignment/main.nf | 2 - .../mergebamalignment/tests/main.nf.test | 26 +- .../mergebamalignment/tests/main.nf.test.snap | 8 +- modules/nf-core/gatk4/mergevcfs/main.nf | 8 +- .../gatk4/mergevcfs/tests/main.nf.test | 46 +-- .../gatk4/mergevcfs/tests/main.nf.test.snap | 30 +- modules/nf-core/gatk4/mutect2/main.nf | 8 +- .../nf-core/gatk4/mutect2/tests/main.nf.test | 166 ++++----- .../gatk4/mutect2/tests/main.nf.test.snap | 40 +-- .../gatk4/postprocessgermlinecnvcalls/main.nf | 18 +- .../tests/main.nf.test | 76 ++--- .../tests/main.nf.test.snap | 24 +- modules/nf-core/gatk4/printreads/main.nf | 4 +- .../gatk4/printreads/tests/main.nf.test | 39 +-- .../gatk4/printreads/tests/main.nf.test.snap | 4 +- .../gatk4/revertsam/tests/main.nf.test | 14 +- .../gatk4/revertsam/tests/main.nf.test.snap | 4 +- .../gatk4/samtofastq/tests/main.nf.test | 16 +- .../gatk4/samtofastq/tests/main.nf.test.snap | 6 +- modules/nf-core/gatk4/selectvariants/main.nf | 12 +- .../gatk4/selectvariants/tests/main.nf.test | 24 +- modules/nf-core/gatk4/shiftfasta/main.nf | 23 +- .../gatk4/shiftfasta/tests/main.nf.test | 9 +- .../gatk4/shiftfasta/tests/main.nf.test.snap | 2 +- .../gatk4/splitintervals/tests/main.nf.test | 36 +- .../splitintervals/tests/main.nf.test.snap | 6 +- .../nf-core/gatk4/variantfiltration/main.nf | 2 +- .../variantfiltration/tests/main.nf.test | 34 +- .../variantfiltration/tests/main.nf.test.snap | 24 +- modules/nf-core/gawk/main.nf | 12 +- modules/nf-core/gawk/meta.yml | 52 ++- modules/nf-core/gawk/tests/main.nf.test | 56 ++-- modules/nf-core/gawk/tests/main.nf.test.snap | 138 +++----- modules/nf-core/haplogrep3/classify/meta.yml | 14 +- modules/nf-core/multiqc/meta.yml | 2 +- modules/nf-core/sambamba/depth/main.nf | 2 +- .../nf-core/sambamba/depth/tests/main.nf.test | 10 +- .../sambamba/depth/tests/main.nf.test.snap | 40 ++- modules/nf-core/samtools/collate/main.nf | 12 +- modules/nf-core/samtools/collate/meta.yml | 26 +- .../samtools/collate/tests/main.nf.test | 47 +-- .../samtools/collate/tests/main.nf.test.snap | 203 ++++++----- .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 16 +- modules/nf-core/samtools/index/meta.yml | 29 +- .../nf-core/samtools/index/tests/main.nf.test | 27 +- .../samtools/index/tests/main.nf.test.snap | 278 +++++---------- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/samtools/view/meta.yml | 4 +- .../nf-core/samtools/view/tests/bam.config | 3 - .../samtools/view/tests/bam_index.config | 3 - .../samtools/view/tests/cram_index.config | 3 - .../nf-core/samtools/view/tests/main.nf.test | 182 +++++----- .../samtools/view/tests/main.nf.test.snap | 225 +++++-------- .../samtools/view/tests/nextflow.config | 5 + modules/nf-core/untar/environment.yml | 5 + modules/nf-core/untar/main.nf | 45 +-- modules/nf-core/untar/meta.yml | 52 ++- modules/nf-core/untar/tests/main.nf.test | 20 +- modules/nf-core/untar/tests/main.nf.test.snap | 176 ++++------ modules/nf-core/untar/tests/tags.yml | 2 - modules/nf-core/upd/environment.yml | 2 + modules/nf-core/upd/main.nf | 18 +- modules/nf-core/upd/meta.yml | 32 +- modules/nf-core/upd/tests/main.nf.test.snap | 40 ++- modules/nf-core/vcf2cytosure/environment.yml | 4 +- modules/nf-core/vcf2cytosure/main.nf | 22 +- modules/nf-core/vcf2cytosure/meta.yml | 44 ++- .../nf-core/vcf2cytosure/tests/main.nf.test | 10 +- .../vcf2cytosure/tests/main.nf.test.snap | 56 ++-- modules/nf-core/vcf2cytosure/tests/tags.yml | 2 - modules/nf-core/vcfanno/environment.yml | 6 +- modules/nf-core/vcfanno/main.nf | 30 +- modules/nf-core/vcfanno/meta.yml | 92 +++-- modules/nf-core/vcfanno/tests/main.nf.test | 6 +- .../nf-core/vcfanno/tests/main.nf.test.snap | 96 +++++- modules/nf-core/vcfanno/tests/nextflow.config | 6 +- modules/nf-core/vcfanno/tests/tags.yml | 2 - .../nf-core/verifybamid/verifybamid2/main.nf | 25 +- .../nf-core/verifybamid/verifybamid2/meta.yml | 50 ++- .../verifybamid2/tests/main.nf.test | 75 ++++- .../verifybamid2/tests/main.nf.test.snap | 317 +++++++++--------- subworkflows/local/align_MT/main.nf | 1 - .../local/align_bwa_bwamem2_bwameme/main.nf | 5 - subworkflows/local/annotate_cadd/main.nf | 2 - subworkflows/local/annotate_genome_snvs.nf | 3 - subworkflows/local/generate_cytosure_files.nf | 1 - subworkflows/local/prepare_references/main.nf | 5 - subworkflows/local/qc_bam/main.nf | 2 - subworkflows/local/subsample_mt_reads/main.nf | 7 - workflows/raredisease.nf | 1 - 136 files changed, 2266 insertions(+), 2102 deletions(-) delete mode 100644 modules/nf-core/bwa/index/tests/tags.yml delete mode 100644 modules/nf-core/bwamem2/index/tests/tags.yml delete mode 100644 modules/nf-core/bwamem2/mem/tests/tags.yml delete mode 100644 modules/nf-core/samtools/view/tests/bam.config delete mode 100644 modules/nf-core/samtools/view/tests/bam_index.config delete mode 100644 modules/nf-core/samtools/view/tests/cram_index.config create mode 100644 modules/nf-core/samtools/view/tests/nextflow.config delete mode 100644 modules/nf-core/untar/tests/tags.yml delete mode 100644 modules/nf-core/vcf2cytosure/tests/tags.yml delete mode 100644 modules/nf-core/vcfanno/tests/tags.yml diff --git a/modules.json b/modules.json index 1849a5759..cf86afdf4 100644 --- a/modules.json +++ b/modules.json @@ -67,7 +67,7 @@ }, "bwa/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", "installed_by": ["modules"] }, "bwa/mem": { @@ -77,12 +77,12 @@ }, "bwamem2/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", "installed_by": ["modules"] }, "bwamem2/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", "installed_by": ["modules"] }, "bwameme/index": { @@ -117,7 +117,7 @@ }, "cnvnator/convert2vcf": { "branch": "master", - "git_sha": "9d43cc3f4b065a99d62dcd58f10d5f4e9feb4bd8", + "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", "installed_by": ["modules"] }, "custom/addmostsevereconsequence": { @@ -168,97 +168,97 @@ }, "gatk4/collectreadcounts": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/denoisereadcounts": { "branch": "master", - "git_sha": "8fd24bb3fd2c54b8837813c9e7c0d2e8aa3f2fde", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/filtermutectcalls": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "86308d628760125908c5c77540517effe0f8880f", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "c0f2c49d596cb63ab16b88e0dbc85fbc8c425456", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/mergebamalignment": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "6881702b1f6671b9471e69f4a75ea4e49a0d0349", "installed_by": ["modules"] }, "gatk4/mutect2": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/postprocessgermlinecnvcalls": { "branch": "master", - "git_sha": "a3f854ee60b2d8b129f03a0848362ea7aaa1aeb5", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/printreads": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/revertsam": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/samtofastq": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/selectvariants": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/shiftfasta": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/splitintervals": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "abc869e0c3d8aaa9c73f6f28726062a7f91fb505", + "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", + "git_sha": "76b1f53edcf72798d8515c82f4728ad44b3dd902", "installed_by": ["modules"] }, "genmod/annotate": { @@ -283,12 +283,12 @@ }, "glnexus": { "branch": "master", - "git_sha": "bcf36bc95e3e5605e9859b8e9a49648841e04fe8", + "git_sha": "9b696bde5b422831751df1a4f2ba728567ec51fd", "installed_by": ["modules"] }, "haplogrep3/classify": { "branch": "master", - "git_sha": "c95c60597ce23da23ac21f4e6c5d7c0cdb711b8f", + "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", "installed_by": ["modules"] }, "hisat2/build": { @@ -319,7 +319,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "80cba9452fb1e9bb79884976fa1ca0e671949aa2", + "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b", "installed_by": ["modules"] }, "ngsbits/samplegender": { @@ -399,12 +399,12 @@ }, "sambamba/depth": { "branch": "master", - "git_sha": "b093f74ddc3ada57a84a209f0e4fb3871bacf2ad", + "git_sha": "ca6da11b05740de461b1e2714037345c0f856201", "installed_by": ["modules"] }, "samtools/collate": { "branch": "master", - "git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1", + "git_sha": "a77125b43fb8973f37c36e2ff137626657de3b21", "installed_by": ["modules"] }, "samtools/faidx": { @@ -414,7 +414,7 @@ }, "samtools/index": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9", "installed_by": ["modules"] }, "samtools/merge": { @@ -434,7 +434,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", + "git_sha": "d2ceed2ec5fccf922638f116a15e02f6458288fb", "installed_by": ["modules"] }, "sentieon/bwaindex": { @@ -539,27 +539,27 @@ }, "untar": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", "installed_by": ["modules"] }, "upd": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index d8789a209..54e679492 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -1,5 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::bwa=0.7.18 + # renovate: datasource=conda depName=bioconda/bwa + - bioconda::bwa=0.7.19 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 2e48b6caa..6be2c43b7 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -1,18 +1,20 @@ process BWA_INDEX { tag "$fasta" - label 'process_single' + // NOTE requires 5.37N memory where N is the size of the database + // source: https://bio-bwa.sourceforge.net/bwa.shtml#8 + memory { 6.B * fasta.size() } conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa:0.7.18--he4a0461_0' : - 'biocontainers/bwa:0.7.18--he4a0461_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data' : + 'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0' }" input: tuple val(meta), path(fasta) output: - tuple val(meta), path(bwa) , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("bwa"), emit: index + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa when: task.ext.when == null || task.ext.when @@ -27,27 +29,16 @@ process BWA_INDEX { $args \\ -p bwa/${prefix} \\ $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${fasta.baseName}" """ mkdir bwa - touch bwa/${prefix}.amb touch bwa/${prefix}.ann touch bwa/${prefix}.bwt touch bwa/${prefix}.pac touch bwa/${prefix}.sa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 4884bca2a..f5bf7f52a 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] - identifier: "" + identifier: "biotools:bwa" input: - - meta: type: map @@ -24,26 +24,48 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: + - edam: "http://edamontology.org/data_2044" # Sequence + - edam: "http://edamontology.org/format_1929" # FASTA output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing reference information. e.g. [ id:'test', single_end:false ] - bwa: - type: file - description: BWA genome index files + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] pattern: "*.{amb,ann,bwt,pac,sa}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/data_3210" # Genome index + versions_bwa: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - bwa: + type: string + description: The tool name + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: string + description: The command used to generate the version of the tool authors: - "@drpatelh" - "@maxulysse" maintainers: - - "@drpatelh" - "@maxulysse" - "@gallvp" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index af33e73ca..f0fba82a1 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -22,8 +22,32 @@ nextflow_process { } then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } + + test("BWA index - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap index 7c8f04657..21a6f73c3 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -1,4 +1,57 @@ { + "BWA index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-23T16:58:59.966558606" + }, "BWA index": { "content": [ { @@ -17,7 +70,11 @@ ] ], "1": [ - "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] ], "index": [ [ @@ -33,15 +90,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" + "versions_bwa": [ + [ + "BWA_INDEX", + "bwa", + "0.7.19-r1273" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-16T11:40:09.925307" + "timestamp": "2026-01-23T16:58:53.330725134" } } \ No newline at end of file diff --git a/modules/nf-core/bwa/index/tests/tags.yml b/modules/nf-core/bwa/index/tests/tags.yml deleted file mode 100644 index 28bb483c4..000000000 --- a/modules/nf-core/bwa/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwa/index: - - modules/nf-core/bwa/index/** diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml index 15cee2387..f3637444a 100644 --- a/modules/nf-core/bwamem2/index/environment.yml +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -1,5 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::bwa-mem2=2.2.1 + # renovate: datasource=conda depName=bioconda/bwa-mem2 + - bwa-mem2=2.3 + # renovate: datasource=conda depName=bioconda/htslib + - htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.22.1 diff --git a/modules/nf-core/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf index b7688285d..cb2c4bb2f 100644 --- a/modules/nf-core/bwamem2/index/main.nf +++ b/modules/nf-core/bwamem2/index/main.nf @@ -1,18 +1,20 @@ process BWAMEM2_INDEX { tag "$fasta" - label 'process_single' + // NOTE Requires 28N GB memory where N is the size of the reference sequence, floor of 280M + // source: https://github.com/bwa-mem2/bwa-mem2/issues/9 + memory { 280.MB * Math.ceil(fasta.size() / 10000000) * task.attempt } conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa-mem2:2.2.1--he513fc3_0' : - 'biocontainers/bwa-mem2:2.2.1--he513fc3_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : + 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("bwamem2"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions when: task.ext.when == null || task.ext.when @@ -25,12 +27,8 @@ process BWAMEM2_INDEX { bwa-mem2 \\ index \\ $args \\ - $fasta -p bwamem2/${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS + -p bwamem2/${prefix} \\ + $fasta """ stub: @@ -43,10 +41,5 @@ process BWAMEM2_INDEX { touch bwamem2/${prefix}.pac touch bwamem2/${prefix}.amb touch bwamem2/${prefix}.bwt.2bit.64 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index 74f54ef0d..120748601 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -12,8 +12,9 @@ tools: a large reference genome, such as the human genome. homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage - licence: ["MIT"] - identifier: "" + licence: + - "MIT" + identifier: "biotools:bwa-mem2" input: - - meta: type: map @@ -23,22 +24,49 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bwamem2: - type: file + type: string description: BWA genome index files pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/data_3210" + versions_bwamem2: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test b/modules/nf-core/bwamem2/index/tests/main.nf.test index dbf11132c..3ee91048a 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test @@ -8,7 +8,30 @@ nextflow_process { script "../main.nf" process "BWAMEM2_INDEX" - test("BWAMEM2 index") { + test("fasta") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("fasta - stub") { + + options "-stub" when { process { diff --git a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap index 69b268ee4..776e87be1 100644 --- a/modules/nf-core/bwamem2/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/index/tests/main.nf.test.snap @@ -1,5 +1,58 @@ { - "BWAMEM2 index": { + "fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwamem2": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-09T16:19:38.013344" + }, + "fasta": { "content": [ { "0": [ @@ -17,7 +70,11 @@ ] ], "1": [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] ], "index": [ [ @@ -33,15 +90,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,9ffd13d12e7108ed15c58566bc4717d6" + "versions_bwamem2": [ + [ + "BWAMEM2_INDEX", + "bwamem2", + "2.2.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-18T12:59:39.132616" + "timestamp": "2026-02-09T16:19:32.542622" } } \ No newline at end of file diff --git a/modules/nf-core/bwamem2/index/tests/tags.yml b/modules/nf-core/bwamem2/index/tests/tags.yml deleted file mode 100644 index 3953018ee..000000000 --- a/modules/nf-core/bwamem2/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwamem2/index: - - modules/nf-core/bwamem2/index/** diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 7e0b5a347..f3637444a 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,8 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bwa-mem2=2.2.1 - - htslib=1.19.1 - - samtools=1.19.2 + # renovate: datasource=conda depName=bioconda/bwa-mem2 + - bwa-mem2=2.3 + # renovate: datasource=conda depName=bioconda/htslib + - htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - samtools=1.22.1 diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index 729428c4e..d1c0ac8f6 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -4,8 +4,8 @@ process BWAMEM2_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' : - 'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : + 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" input: tuple val(meta), path(reads) @@ -19,7 +19,7 @@ process BWAMEM2_MEM { tuple val(meta), path("*.cram") , emit: cram, optional:true tuple val(meta), path("*.crai") , emit: crai, optional:true tuple val(meta), path("*.csi") , emit: csi , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions when: task.ext.when == null || task.ext.when @@ -46,24 +46,15 @@ process BWAMEM2_MEM { \$INDEX \\ $reads \\ | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" def create_index = "" @@ -76,11 +67,5 @@ process BWAMEM2_MEM { """ touch ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index c6333ca17..bcfd006df 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -16,8 +16,9 @@ tools: homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 - licence: ["MIT"] - identifier: "" + licence: + - "MIT" + identifier: "biotools:bwa-mem2" input: - - meta: type: map @@ -29,6 +30,9 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1930" - - meta2: type: map description: | @@ -38,6 +42,8 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + ontologies: + - edam: "http://edamontology.org/data_3210" - - meta3: type: map description: | @@ -47,13 +53,16 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fa,fasta,fna}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - sam: - - meta: + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -62,8 +71,10 @@ output: type: file description: Output SAM file containing read alignments pattern: "*.{sam}" - - bam: - - meta: + ontologies: + - edam: "http://edamontology.org/format_2573" + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -72,8 +83,10 @@ output: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: + ontologies: + - edam: "http://edamontology.org/format_2572" + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -82,8 +95,10 @@ output: type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - crai: - - meta: + ontologies: + - edam: "http://edamontology.org/format_3462" + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -92,8 +107,9 @@ output: type: file description: Index file for CRAM file pattern: "*.{crai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -102,11 +118,28 @@ output: type: file description: Index file for BAM file pattern: "*.{csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwamem2: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: The name of the tool + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwamem2: + type: string + description: The name of the tool + - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 9e0ab14ae..20e372545 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -46,7 +46,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -75,7 +75,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -107,7 +107,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } @@ -139,7 +139,7 @@ nextflow_process { { assert snapshot( bam(process.out.bam[0][1]).getHeaderMD5(), bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index 69bc3612b..74763935c 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -1,17 +1,23 @@ { "sarscov2 - [fastq1, fastq2], index, fasta, false": { "content": [ - "eefa0f44493fd0504e734efd2f1f4a9e", + "e414c2d48e2e44c2c52c20ecd88e8bd8", "57aeef88ed701a8ebc8e2f0a381b2a6", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:37.929675" + "timestamp": "2026-02-09T16:25:00.500092" }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ @@ -44,7 +50,11 @@ ] ], "5": [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] ], "bam": [ [ @@ -73,57 +83,79 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:12:06.693567" + "timestamp": "2026-02-09T16:25:22.004027" }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ - "7aba324f82d5b4e926a5dd7b46029cb4", + "716ed1ef39deaad346ca7cf86e08f959", "af8628d9df18b2d3d4f6fd47ef2bb872", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:53.488374" + "timestamp": "2026-02-09T16:25:14.131056" }, "sarscov2 - fastq, index, fasta, false": { "content": [ - "bc02b41697b3a8f1021b02becec24052", + "283a83f604f3f5338acedfee349dccf4", "798439cbd7fd81cbcc5078022dc5479d", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:05.644682" + "timestamp": "2026-02-09T16:24:34.624533" }, "sarscov2 - fastq, index, fasta, true": { "content": [ - "e41d67320815d29ba5f6e9d1ae21902a", + "ed99048bb552cac58e39923b550b6d5b", "94fcf617f5b994584c4e8d4044e16b4f", - [ - "versions.yml:md5,1c1a9566f189ec077b5179bbf453c51a" - ] + { + "versions_bwamem2": [ + [ + "BWAMEM2_MEM", + "bwamem2", + "2.2.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:21.837763" + "timestamp": "2026-02-09T16:24:47.191245" } } \ No newline at end of file diff --git a/modules/nf-core/bwamem2/mem/tests/tags.yml b/modules/nf-core/bwamem2/mem/tests/tags.yml deleted file mode 100644 index 134efb2b3..000000000 --- a/modules/nf-core/bwamem2/mem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwamem2/mem: - - "modules/nf-core/bwamem2/mem/**" diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test index 723a32226..c1d239682 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { input[1] = [[:],[]] input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "rd" """ } } @@ -38,6 +39,7 @@ nextflow_process { input[1] = CNVNATOR_RD.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "his" """ } } @@ -51,6 +53,7 @@ nextflow_process { input[1] = CNVNATOR_HIST.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "stat" """ } } @@ -64,6 +67,7 @@ nextflow_process { input[1] = CNVNATOR_STAT.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "partition" """ } } @@ -77,6 +81,7 @@ nextflow_process { input[1] = CNVNATOR_PARTITION.out.root input[2] = [[:],[]] input[3] = [[:],[]] + input[4] = "call" """ } } @@ -90,7 +95,7 @@ nextflow_process { cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' - cnvnator_call_args = '-call 1000' + cnvnator_args = '-call 1000' } process { """ @@ -118,7 +123,7 @@ nextflow_process { cnvnator_hist_args = '-his 1000' cnvnator_stat_args = '-stat 1000' cnvnator_partition_args = '-partition 1000' - cnvnator_call_args = '-call 1000' + cnvnator_args = '-call 1000' } process { """ diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap index c8e740009..d51b4befb 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap +++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:02:17.740405" + "timestamp": "2026-02-05T13:53:33.545892" }, "test_cnvnator_convert2vcf -- stub": { "content": [ @@ -59,6 +59,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-02T15:02:31.268041" + "timestamp": "2026-02-06T13:38:10.965597" } } \ No newline at end of file diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config index f056ed315..9a9f9a920 100644 --- a/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config +++ b/modules/nf-core/cnvnator/convert2vcf/tests/nextflow.config @@ -1,20 +1,21 @@ process { withName: "CNVNATOR_RD" { - ext.args = params.cnvnator_rd_args + ext.args = {params.cnvnator_rd_args} } + withName: "CNVNATOR_HIST" { - ext.args = params.cnvnator_hist_args + ext.args = {params.cnvnator_hist_args} } withName: "CNVNATOR_STAT" { - ext.args = params.cnvnator_stat_args + ext.args = {params.cnvnator_stat_args} } withName: "CNVNATOR_PARTITION" { - ext.args = params.cnvnator_partition_args + ext.args = {params.cnvnator_partition_args} } - withName: "CNVNATOR_CALL" { - ext.args = params.cnvnator_call_args + withName: "CNVNATOR_CNVNATOR" { + ext.args = {params.cnvnator_args} } } diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index 750923375..4dbb80169 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -15,7 +15,7 @@ process GATK4_COLLECTREADCOUNTS { output: tuple val(meta), path("*.hdf5"), emit: hdf5, optional: true - tuple val(meta), path("*.tsv"), emit: tsv, optional: true + tuple val(meta), path("*.tsv"), emit: tsv, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -48,7 +48,6 @@ process GATK4_COLLECTREADCOUNTS { ${reference} \\ --tmp-dir . \\ ${args} - """ stub: @@ -61,6 +60,5 @@ process GATK4_COLLECTREADCOUNTS { : "hdf5" """ touch ${prefix}.${extension} - """ } diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index a65f7f065..abd202997 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,7 +1,6 @@ name: "gatk4_collectreadcounts" -description: Collects read counts at specified intervals. The count for each - interval is calculated by counting the number of read starts that lie in the - interval. +description: Collects read counts at specified intervals. The count for each interval + is calculated by counting the number of read starts that lie in the interval. keywords: - collectreadcounts - bam @@ -9,11 +8,11 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences - Platform at the Broad Institute, the toolkit offers a wide variety of - tools with a primary focus on variant discovery and genotyping. Its - powerful processing engine and high-performance computing features make it - capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk @@ -94,7 +93,7 @@ output: description: The read counts in TSV format pattern: "*.tsv" ontologies: - - edam: http://edamontology.org/format_3475 + - edam: http://edamontology.org/format_3475 # TSV versions_gatk4: - - ${task.process}: type: string diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test index 0832cf85a..963103ed6 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test @@ -19,26 +19,25 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[],[]] input[2] = [[],[]] input[3] = [[],[]] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( file(process.out.hdf5[0][1]).name, process.out.tsv, - ).match() - } + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -52,21 +51,20 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[],[]] input[2] = [[],[]] input[3] = [[],[]] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -81,24 +79,22 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), ] input[1] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)] input[2] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)] input[3] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap index ca6304c51..d7d3357ba 100644 --- a/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectreadcounts/tests/main.nf.test.snap @@ -44,22 +44,31 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:04:47.877494" + "timestamp": "2026-01-21T15:57:24.675555145" }, "test-gatk4-collectreadcounts-hdf5": { "content": [ "test.hdf5", [ - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_COLLECTREADCOUNTS", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-08-26T13:02:48.607644" + "timestamp": "2026-01-21T15:56:53.979162756" }, "test-gatk4-collectreadcounts-tsv": { "content": [ @@ -106,8 +115,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:04:25.535499" + "timestamp": "2026-01-21T15:57:08.386074318" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 9a5c9f235..5fdfcc20a 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -14,8 +14,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: - - "Apache-2.0" + licence: ["Apache-2.0"] identifier: "" input: - - meta: diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test index a8a9c6d2e..076eb0d84 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test @@ -16,18 +16,17 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("sarscov2 - fasta - stub") { @@ -39,18 +38,16 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] + ] """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 497c8cf09..357cd58ee 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -36,9 +36,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:24:16.167358" + "timestamp": "2026-01-21T16:01:50.146061464" }, "sarscov2 - fasta": { "content": [ @@ -77,8 +77,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.2" }, - "timestamp": "2026-02-03T11:24:00.222321" + "timestamp": "2026-01-21T16:01:38.694508582" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/denoisereadcounts/main.nf b/modules/nf-core/gatk4/denoisereadcounts/main.nf index 73790c636..c86a6f45a 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/main.nf +++ b/modules/nf-core/gatk4/denoisereadcounts/main.nf @@ -13,7 +13,7 @@ process GATK4_DENOISEREADCOUNTS { output: tuple val(meta), path("*_standardizedCR.tsv"), emit: standardized - tuple val(meta), path("*_denoisedCR.tsv"), emit: denoised + tuple val(meta), path("*_denoisedCR.tsv"), emit: denoised tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/denoisereadcounts/meta.yml b/modules/nf-core/gatk4/denoisereadcounts/meta.yml index 0c7835a7e..cac8142e0 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/meta.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/meta.yml @@ -84,7 +84,6 @@ topics: - gatk --version | sed -n '/GATK.*v/s/.*v//p': type: eval description: The expression to obtain the version of the tool - authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test index 34268f630..9eba43aeb 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test @@ -19,9 +19,9 @@ nextflow_process { script "../../preprocessintervals/main.nf" process { """ - input[0] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[0] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) input[3] = [[],[]] input[4] = [[],[]] """ @@ -32,13 +32,13 @@ nextflow_process { process { """ intervals = GATK4_PREPROCESSINTERVALS.out.interval_list.map {meta, list -> list} - input[0] = Channel.of( + input[0] = channel.of( [[ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)], ) .combine( intervals) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) """ } } @@ -62,8 +62,8 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.standardized, process.out.denoised, @@ -71,6 +71,5 @@ nextflow_process { ).match() } ) } - } } diff --git a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap index 26892e208..abdeb59b8 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/denoisereadcounts/tests/main.nf.test.snap @@ -33,6 +33,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T11:36:00.92882" + "timestamp": "2026-02-05T15:25:28.341041619" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index f23d3ee9d..da9480b60 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -24,10 +24,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def intervals = bed ? "--intervals ${bed}" : "" - def exclude = exclude_beds ? exclude_beds.collect { "--exclude-intervals ${it}" }.join(" ") : "" + def exclude = exclude_beds ? exclude_beds.collect { bed_ -> "--exclude-intervals ${bed_}" }.join(" ") : "" def contig_ploidy = contig_ploidy_table ? "--contig-ploidy-priors ${contig_ploidy_table}" : "" def model = ploidy_model ? "--model ${ploidy_model}" : "" - def input_list = counts.collect { "--input ${it}" }.join(" ") + def input_list = counts.collect { count -> "--input ${count}" }.join(" ") def avail_mem = 3072 if (!task.memory) { @@ -53,7 +53,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { ${model} \\ --tmp-dir . \\ ${args} - """ stub: @@ -61,6 +60,5 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { """ touch ${prefix}-calls touch ${prefix}-model - """ } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test index e7187b03c..d89b1f22c 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test @@ -60,16 +60,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.calls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.model[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - bam - stub") { @@ -94,12 +93,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap index 213238f85..8c56e743a 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/tests/main.nf.test.snap @@ -1,15 +1,6 @@ { "homo sapiens - bam": { "content": [ - { - "versions_gatk4": [ - [ - "GATK4_DETERMINEGERMLINECONTIGPLOIDY", - "gatk4", - "4.6.2.0" - ] - ] - }, [ "SAMPLE_0", "SAMPLE_1" @@ -23,13 +14,22 @@ "ploidy_config.json", "std_mean_bias_j_interval__.tsv", "std_psi_j_log__.tsv" - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_DETERMINEGERMLINECONTIGPLOIDY", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:46:07.36352943" + "timestamp": "2026-02-05T15:27:49.742708767" }, "homo sapiens - bam - stub": { "content": [ @@ -84,8 +84,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:47:11.516191863" + "timestamp": "2026-02-05T15:27:58.764956454" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf index b3fb9116d..cd463b1b4 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/main.nf +++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf @@ -14,8 +14,8 @@ process GATK4_FILTERMUTECTCALLS { tuple val(meta4), path(dict) output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val(meta), path("*.filteringStats.tsv"), emit: stats tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -26,10 +26,10 @@ process GATK4_FILTERMUTECTCALLS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def orientationbias_command = orientationbias ? orientationbias.collect { "--orientation-bias-artifact-priors ${it}" }.join(' ') : '' - def segmentation_command = segmentation ? segmentation.collect { "--tumor-segmentation ${it}" }.join(' ') : '' + def orientationbias_command = orientationbias ? orientationbias.collect { orientationbias_ -> "--orientation-bias-artifact-priors ${orientationbias_}" }.join(' ') : '' + def segmentation_command = segmentation ? segmentation.collect { segmentation_ -> "--tumor-segmentation ${segmentation_}" }.join(' ') : '' def estimate_command = estimate ? " --contamination-estimate ${estimate} " : '' - def table_command = table ? table.collect { "--contamination-table ${it}" }.join(' ') : '' + def table_command = table ? table.collect { table_ -> "--contamination-table ${table_}" }.join(' ') : '' def avail_mem = 3072 if (!task.memory) { @@ -50,7 +50,6 @@ process GATK4_FILTERMUTECTCALLS { ${table_command} \\ --tmp-dir . \\ ${args} - """ stub: @@ -59,6 +58,5 @@ process GATK4_FILTERMUTECTCALLS { echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi touch ${prefix}.vcf.gz.filteringStats.tsv - """ } diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test index f775f3ed2..64007fc1a 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test @@ -47,7 +47,7 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0] - ).match() } + ).match() } ) } @@ -90,10 +90,9 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0..5] - ).match() } + ).match() } ) } - } test("human - vcf - use-val") { @@ -133,10 +132,9 @@ nextflow_process { path(process.out.vcf[0][1]).vcf.variantsMD5, path(process.out.tbi[0][1]).linesGzip.toString().contains("TBI"), file(process.out.stats[0][1]).readLines()[0] - ).match() } + ).match() } ) } - } test("human - vcf - stub") { @@ -176,7 +174,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap index 6856af7e7..dee66a039 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/filtermutectcalls/tests/main.nf.test.snap @@ -18,19 +18,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:33.782781" - }, - "versions_with-files": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:22:04.77036932" + "timestamp": "2026-02-05T14:24:16.387135961" }, "human - vcf - stub": { "content": [ @@ -103,31 +91,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:52.944908" - }, - "versions_use-val": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:22:18.790658915" - }, - "versions_base": { - "content": [ - [ - "versions.yml:md5,c2ea194472224d673edc89a3bb125fbd" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T14:21:49.569533374" + "timestamp": "2026-02-05T12:44:42.986778135" }, "human - vcf - with-files": { "content": [ @@ -155,7 +119,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:24:11.396747" + "timestamp": "2026-02-05T14:24:03.785317232" }, "human - vcf - base": { "content": [ @@ -176,6 +140,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T13:23:48.108444" + "timestamp": "2026-02-05T14:22:02.165177275" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index c3e6b114e..c7b68ab55 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -13,7 +13,7 @@ process GATK4_GERMLINECNVCALLER { output: tuple val(meta), path("*-cnv-model/*-calls"), emit: cohortcalls, optional: true tuple val(meta), path("*-cnv-model/*-model"), emit: cohortmodel, optional: true - tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true + tuple val(meta), path("*-cnv-calls/*-calls"), emit: casecalls, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -25,7 +25,7 @@ process GATK4_GERMLINECNVCALLER { def intervals_command = intervals ? "--intervals ${intervals}" : "" def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" def model_command = model ? "--model ${model}" : "" - def input_list = tsv.collect { "--input ${it}" }.join(' ') + def input_list = tsv.collect { tsv_ -> "--input ${tsv_}" }.join(' ') def output_command = model ? "--output ${prefix}-cnv-calls" : "--output ${prefix}-cnv-model" def avail_mem = 3072 @@ -50,7 +50,6 @@ process GATK4_GERMLINECNVCALLER { ${args} \\ ${intervals_command} \\ ${model_command} - """ stub: @@ -59,6 +58,5 @@ process GATK4_GERMLINECNVCALLER { mkdir -p ${prefix}-cnv-calls/${prefix}-calls mkdir -p ${prefix}-cnv-model/${prefix}-model mkdir -p ${prefix}-cnv-model/${prefix}-calls - """ } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test index a3bb985ea..640a17d49 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { script "../../collectreadcounts/main.nf" process { """ - input[0] = Channel.of( + input[0] = channel.of( [ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), @@ -31,18 +31,19 @@ nextflow_process { file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) - input[2] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) - input[3] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]) + input[2] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists:true)]) + input[3] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } + run("GATK4_DETERMINEGERMLINECONTIGPLOIDY") { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + bed = channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) contig_ploidy_table = file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv", checkIfExists:true) input[0] = GATK4_COLLECTREADCOUNTS.out.tsv @@ -55,12 +56,13 @@ nextflow_process { """ } } + run("GATK4_BEDTOINTERVALLIST") { script "../../bedtointervallist/main.nf" process { """ - input[0] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) - input[1] = Channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) + input[0] = channel.of([[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)]) + input[1] = channel.value([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]) """ } } @@ -81,16 +83,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - bam - stub") { @@ -111,16 +112,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.cohortcalls[0][1]).list().sort().collect { path -> file(path).name }, file(process.out.cohortmodel[0][1]).list().sort().collect { path -> file(path).name }, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap index 311076984..aa736b8ed 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/germlinecnvcaller/tests/main.nf.test.snap @@ -1,15 +1,6 @@ { "homo sapiens - bam": { "content": [ - { - "versions_gatk4": [ - [ - "GATK4_GERMLINECNVCALLER", - "gatk4", - "4.6.2.0" - ] - ] - }, [ "SAMPLE_0", "SAMPLE_1", @@ -32,16 +23,31 @@ "std_ard_u_interval__.tsv", "std_log_mean_bias_t.tsv", "std_psi_t_log__.tsv" - ] + ], + { + "versions_gatk4": [ + [ + "GATK4_GERMLINECNVCALLER", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:09:50.216500599" + "timestamp": "2026-02-05T15:54:16.716891653" }, "homo sapiens - bam - stub": { "content": [ + [ + + ], + [ + + ], { "versions_gatk4": [ [ @@ -50,18 +56,12 @@ "4.6.2.0" ] ] - }, - [ - - ], - [ - - ] + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:12:05.192665905" + "timestamp": "2026-02-05T15:54:30.034729289" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 2d69d3819..257399cdf 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -29,7 +29,6 @@ process GATK4_INTERVALLISTTOOLS { avail_mem = (task.memory.mega * 0.8).intValue() } """ - mkdir ${prefix}_split gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ @@ -48,7 +47,6 @@ process GATK4_INTERVALLISTTOOLS { newName = os.path.join(directory, str(i + 1) + filename) os.rename(interval, newName) CODE - """ stub: @@ -62,6 +60,5 @@ process GATK4_INTERVALLISTTOOLS { touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list - """ } diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test index 2891bf9e4..19089f485 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test @@ -40,12 +40,11 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() }, ) } - } test("test_gatk4_intervallisttools -stub") { @@ -61,12 +60,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() }, ) } - } - } diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 143136148..100aec5fc 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -46,9 +46,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:44:06.410817008" + "timestamp": "2026-02-05T16:30:27.100653045" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -97,8 +97,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T15:45:07.987268525" + "timestamp": "2026-02-05T16:30:35.391255689" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergebamalignment/main.nf b/modules/nf-core/gatk4/mergebamalignment/main.nf index 016b275f3..912f585a6 100644 --- a/modules/nf-core/gatk4/mergebamalignment/main.nf +++ b/modules/nf-core/gatk4/mergebamalignment/main.nf @@ -39,13 +39,11 @@ process GATK4_MERGEBAMALIGNMENT { --REFERENCE_SEQUENCE ${fasta} \\ --TMP_DIR . \\ ${args} - """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam - """ } diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test index d5878f4de..f12d8dc1f 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test @@ -16,28 +16,26 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -48,26 +46,24 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap index 2ebca8687..15212afd4 100644 --- a/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergebamalignment/tests/main.nf.test.snap @@ -36,9 +36,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T19:42:44.250559934" + "timestamp": "2026-02-05T16:39:42.649628142" }, "test-gatk4-mergebamalignment": { "content": [ @@ -55,8 +55,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T19:42:06.516476761" + "timestamp": "2026-02-05T16:39:36.797699941" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 95f1eccc9..93112900a 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -13,7 +13,7 @@ process GATK4_MERGEVCFS { output: tuple val(meta), path('*.vcf.gz'), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -22,7 +22,7 @@ process GATK4_MERGEVCFS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input_list = vcf.collect { "--INPUT ${it}" }.join(' ') + def input_list = vcf.collect { vcf_ -> "--INPUT ${vcf_}" }.join(' ') def reference_command = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" def avail_mem = 3072 @@ -40,14 +40,12 @@ process GATK4_MERGEVCFS { ${reference_command} \\ --TMP_DIR . \\ ${args} - """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - """ } diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index f9765aab5..fd9972b0a 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -20,18 +20,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } test("test_gatk4_mergevcfs_no_dict") { @@ -45,18 +42,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs_no_dict") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } test("test_gatk4_mergevcfs_no_dict_stub") { @@ -73,18 +67,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, - file(process.out.vcf.get(0).get(1)).name, - file(process.out.tbi.get(0).get(1)).name - ).match("test_gatk4_mergevcfs_no_dict_stub") - }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() }, ) } - } - } diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 14170940e..38e555502 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,6 +1,8 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -9,18 +11,18 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:51:23.679671657" + "timestamp": "2026-02-05T16:40:17.349813218" }, "test_gatk4_mergevcfs": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -29,18 +31,18 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:49:37.159554677" + "timestamp": "2026-02-05T16:40:03.274024419" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -49,14 +51,12 @@ "4.6.2.0" ] ] - }, - "test.vcf.gz", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T20:50:41.376990748" + "timestamp": "2026-02-05T16:40:10.948156303" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf index 269c605f5..828206403 100644 --- a/modules/nf-core/gatk4/mutect2/main.nf +++ b/modules/nf-core/gatk4/mutect2/main.nf @@ -20,9 +20,9 @@ process GATK4_MUTECT2 { path panel_of_normals_tbi output: - tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi - tuple val(meta), path("*.stats"), emit: stats + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.stats"), emit: stats tuple val(meta), path("*.f1r2.tar.gz"), emit: f1r2, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -36,7 +36,7 @@ process GATK4_MUTECT2 { def interval_command = intervals ? "--intervals ${intervals}" : "" def pon_command = panel_of_normals ? "--panel-of-normals ${panel_of_normals}" : "" def gr_command = germline_resource ? "--germline-resource ${germline_resource}" : "" - def a_command = alleles ? "--alleles ${alleles}": "" + def a_command = alleles ? "--alleles ${alleles}" : "" def avail_mem = 3072 if (!task.memory) { diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test b/modules/nf-core/gatk4/mutect2/tests/main.nf.test index 8917fd212..3f7afea60 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test @@ -57,17 +57,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -119,17 +117,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2.collect { file(it[1]).getName() }, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2.collect { file(it[1]).getName() }, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -170,17 +166,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -221,17 +215,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -272,17 +264,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -323,17 +313,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -374,17 +362,15 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -438,12 +424,11 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("human - bam - tumor_normal_pair - force_call") { @@ -493,17 +478,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } @@ -544,19 +527,16 @@ nextflow_process { } } then { + assert process.success assertAll( - { assert process.success }, - { - assert snapshot( - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - process.out.tbi.collect { file(it[1]).getName() }, - process.out.stats, - process.out.f1r2, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.tbi.collect { file(it[1]).getName() }, + process.out.stats, + process.out.f1r2, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } } - } diff --git a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap index 76db52e05..73ffa9fc3 100644 --- a/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap @@ -28,9 +28,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:26:03.059145991" + "timestamp": "2026-02-05T16:54:59.699672374" }, "human - bam - tumor_only - force_call": { "content": [ @@ -61,9 +61,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:37:31.740160738" + "timestamp": "2026-02-05T17:02:15.006936591" }, "human - bam - tumor_normal_pair": { "content": [ @@ -96,9 +96,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:10:46.039204223" + "timestamp": "2026-02-05T16:44:25.776848294" }, "human - cram": { "content": [ @@ -129,9 +129,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:22:38.825106184" + "timestamp": "2026-02-05T16:52:48.795368727" }, "mitochondria - bam": { "content": [ @@ -162,9 +162,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:26:44.448416009" + "timestamp": "2026-02-05T16:55:10.945977864" }, "human - bam - tumor_only": { "content": [ @@ -195,9 +195,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:19:10.024181048" + "timestamp": "2026-02-05T16:50:29.074224171" }, "mitochondria - bam - gz_ref": { "content": [ @@ -228,9 +228,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:27:29.464429837" + "timestamp": "2026-02-05T16:55:22.160325012" }, "human - bam - tumor_normal_pair - force_call": { "content": [ @@ -263,9 +263,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:33:21.41092687" + "timestamp": "2026-02-05T16:59:14.299303803" }, "human - bam - tumor_normal_pair_f1r2 - stub": { "content": [ @@ -368,9 +368,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:28:08.170677731" + "timestamp": "2026-02-05T16:55:48.221310078" }, "human - bam - tumor_normal_pair_f1r2": { "content": [ @@ -403,8 +403,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T21:15:39.798158102" + "timestamp": "2026-02-05T16:47:43.194989668" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf index f87511d5f..2c29c87cc 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf @@ -12,8 +12,8 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { output: tuple val(meta), path("*_genotyped_intervals.vcf.gz"), emit: intervals, optional: true - tuple val(meta), path("*_genotyped_segments.vcf.gz"), emit: segments, optional: true - tuple val(meta), path("*_denoised.vcf.gz"), emit: denoised, optional: true + tuple val(meta), path("*_genotyped_segments.vcf.gz"), emit: segments, optional: true + tuple val(meta), path("*_denoised.vcf.gz"), emit: denoised, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: @@ -22,8 +22,8 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def calls_command = calls ? calls.collect { "--calls-shard-path ${it}" }.join(' ') : "" - def model_command = model ? model.collect { "--model-shard-path ${it}" }.join(' ') : "" + def calls_command = calls ? calls.collect { call -> "--calls-shard-path ${call}" }.join(' ') : "" + def model_command = model ? model.collect { mode -> "--model-shard-path ${mode}" }.join(' ') : "" def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" def avail_mem = 3072 @@ -46,11 +46,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\ --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\ --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -59,10 +54,5 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { echo "" | gzip > ${prefix}_genotyped_intervals.vcf.gz echo "" | gzip > ${prefix}_genotyped_segments.vcf.gz echo "" | gzip > ${prefix}_denoised.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test index 00415fd0a..f18e2fb0c 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test @@ -21,32 +21,29 @@ nextflow_process { """ intervals = [[ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)] dict = [ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)] - input = [intervals, dict] """ } } + run("GATK4_COLLECTREADCOUNTS"){ script "../../collectreadcounts/main.nf" process { """ - input_bam = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), - ], - [ - [ id:'test2', single_end:false ], // meta map - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) + input_bam = channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true), + ], + [ [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true) ]) - - fasta = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() - fai = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() - dict = Channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() - + fasta = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)]).collect() + fai = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)]).collect() + dict = channel.of([ [ id:'test' ], file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.dict", checkIfExists: true)]).collect() input = [input_bam, fasta, fai, dict] """ } @@ -55,7 +52,7 @@ nextflow_process { script "../../determinegermlinecontigploidy/main.nf" process { """ - bed = Channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) + bed = channel.value(file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.multi_intervals.bed", checkIfExists: true)) input = [ GATK4_COLLECTREADCOUNTS.out.tsv .map({ meta, tsv -> [[id:'test'], tsv ] }) @@ -68,28 +65,30 @@ nextflow_process { """ } } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_COHORT") { script "../../germlinecnvcaller/main.nf" process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .map({ meta, tsv -> [[id:'test'], tsv ] }) - .groupTuple() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) - .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) + .map({ meta, tsv -> [[id:'test'], tsv ] }) + .groupTuple() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_BEDTOINTERVALLIST.out.interval_list) + .map({ meta, counts, meta2, calls, meta3, bed -> [ meta, counts, bed, calls, [] ]}) """ } } + run("GATK4_GERMLINECNVCALLER", alias: "GATK4_GERMLINECNVCALLER_CASE") { script "../../germlinecnvcaller/main.nf" process { """ input[0] = GATK4_COLLECTREADCOUNTS.out.tsv - .first() - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) + .first() + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .map({ meta, counts, meta2, calls, meta3, model -> [ [id:'test'], counts, [], calls, model ]}) """ } } @@ -101,25 +100,24 @@ nextflow_process { process { """ input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.intervals[0][1]).name, file(process.out.segments[0][1]).name, file(process.out.denoised[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } test("homo sapiens - counts - stub") { @@ -130,25 +128,23 @@ nextflow_process { process { """ input[0] = GATK4_GERMLINECNVCALLER_COHORT.out.cohortcalls - .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) - .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) - .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) + .combine(GATK4_GERMLINECNVCALLER_COHORT.out.cohortmodel) + .combine(GATK4_DETERMINEGERMLINECONTIGPLOIDY_COHORT.out.calls) + .map({ meta, calls, meta2, model, meta3, ploidy -> [[id:'test'], calls, model, ploidy ]}) """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( - process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.intervals[0][1]).name, file(process.out.segments[0][1]).name, file(process.out.denoised[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap index 15ae1944a..71182fe84 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/tests/main.nf.test.snap @@ -1,6 +1,9 @@ { "homo sapiens - counts - stub": { "content": [ + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz", { "versions_gatk4": [ [ @@ -9,19 +12,19 @@ "4.6.2.0" ] ] - }, - "test_genotyped_intervals.vcf.gz", - "test_genotyped_segments.vcf.gz", - "test_denoised.vcf.gz" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T22:29:17.166798377" + "timestamp": "2026-02-05T17:13:11.168329663" }, "homo sapiens - counts": { "content": [ + "test_genotyped_intervals.vcf.gz", + "test_genotyped_segments.vcf.gz", + "test_denoised.vcf.gz", { "versions_gatk4": [ [ @@ -30,15 +33,12 @@ "4.6.2.0" ] ] - }, - "test_genotyped_intervals.vcf.gz", - "test_genotyped_segments.vcf.gz", - "test_denoised.vcf.gz" + } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-02-03T22:26:44.628515186" + "timestamp": "2026-02-05T17:12:53.53221471" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf index 62b771650..66e7f2a6e 100644 --- a/modules/nf-core/gatk4/printreads/main.nf +++ b/modules/nf-core/gatk4/printreads/main.nf @@ -14,9 +14,9 @@ process GATK4_PRINTREADS { tuple val(meta4), path(dict) output: - tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true - tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test b/modules/nf-core/gatk4/printreads/tests/main.nf.test index f86f08a1d..126c780c3 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test @@ -17,36 +17,31 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ] - input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.cram, process.out.sam, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -58,38 +53,32 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) ] - input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.bam, bam(process.out.cram[0][1]).getHeaderMD5(), process.out.sam, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } - } diff --git a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap index e47cdcae4..26aa18f4e 100644 --- a/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/printreads/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:04:26.642559" + "timestamp": "2026-02-05T17:13:29.864614856" }, "test-gatk4-printreads-cram": { "content": [ @@ -47,6 +47,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:04:46.522705" + "timestamp": "2026-02-05T17:13:38.337993548" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test b/modules/nf-core/gatk4/revertsam/tests/main.nf.test index e06c041f4..a051a9abd 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test @@ -16,21 +16,19 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( bam(process.out.bam[0][1]).getReadsMD5(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match() } ) } } @@ -41,19 +39,17 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap index 3858e13bf..e782cdcb2 100644 --- a/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/revertsam/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:08:17.497786" + "timestamp": "2026-02-05T17:58:02.45058488" }, "test-gatk4-revertsam-stubs": { "content": [ @@ -57,6 +57,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:08:32.702485" + "timestamp": "2026-02-05T17:49:32.744361592" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test index b9af8b189..df9393461 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test @@ -16,16 +16,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( path(process.out.fastq[0][1]).linesGzip[3..7], process.out.findAll { key, val -> key.startsWith("versions") } @@ -41,16 +40,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { path(it).linesGzip[3..7] }, process.out.findAll { key, val -> key.startsWith("versions") } @@ -66,16 +64,15 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end: true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) ] ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot( process.out.fastq[0][1].collect { file(it).name }, process.out.findAll { key, val -> key.startsWith("versions") } @@ -84,5 +81,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap index abeb9291f..84f2cc5f7 100644 --- a/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/samtofastq/tests/main.nf.test.snap @@ -22,7 +22,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:22.128687" + "timestamp": "2026-02-05T17:59:04.980254114" }, "test-gatk4-samtofastq-paired-end-stubs": { "content": [ @@ -45,7 +45,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:53.540133" + "timestamp": "2026-02-05T17:59:18.479857005" }, "test-gatk4-samtofastq-paired-end": { "content": [ @@ -79,6 +79,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:11:38.875774" + "timestamp": "2026-02-05T17:59:12.509833732" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf index 9e1d021c2..11ec406b8 100644 --- a/modules/nf-core/gatk4/selectvariants/main.nf +++ b/modules/nf-core/gatk4/selectvariants/main.nf @@ -11,7 +11,7 @@ process GATK4_SELECTVARIANTS { tuple val(meta), path(vcf), path(vcf_idx), path(intervals) output: - tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz"), emit: vcf tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -38,11 +38,6 @@ process GATK4_SELECTVARIANTS { ${interval} \\ --tmp-dir . \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -50,10 +45,5 @@ process GATK4_SELECTVARIANTS { """ echo "" | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test index 3fea99ec1..c9dfee2bb 100644 --- a/modules/nf-core/gatk4/selectvariants/tests/main.nf.test +++ b/modules/nf-core/gatk4/selectvariants/tests/main.nf.test @@ -11,10 +11,6 @@ nextflow_process { test("selectvariants - vcf input") { when { - params { - // define parameters here. Example: - // outdir = "tests/results" - } process { """ input[0] = [ @@ -28,14 +24,14 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - - } test("selectvariants - gz input") { @@ -54,13 +50,13 @@ nextflow_process { } then { + assert process.success assertAll( - {assert process.success}, - {assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - {assert path(process.out.vcf[0][1]).linesGzip.contains("##fileformat=VCFv4.2")} + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") }, + { assert snapshot( + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf index 5ccc867ea..797167913 100644 --- a/modules/nf-core/gatk4/shiftfasta/main.nf +++ b/modules/nf-core/gatk4/shiftfasta/main.nf @@ -13,11 +13,11 @@ process GATK4_SHIFTFASTA { tuple val(meta3), path(dict) output: - tuple val(meta), path("*_shift.fasta"), emit: shift_fa - tuple val(meta), path("*_shift.fasta.fai"), emit: shift_fai - tuple val(meta), path("*_shift.back_chain"), emit: shift_back_chain - tuple val(meta), path("*_shift.dict"), emit: dict, optional: true - tuple val(meta), path("*.intervals"), emit: intervals, optional: true + tuple val(meta), path("*_shift.fasta"), emit: shift_fa + tuple val(meta), path("*_shift.fasta.fai"), emit: shift_fai + tuple val(meta), path("*_shift.back_chain"), emit: shift_back_chain + tuple val(meta), path("*_shift.dict"), emit: dict, optional: true + tuple val(meta), path("*.intervals"), emit: intervals, optional: true tuple val(meta), path("*.shifted.intervals"), emit: shift_intervals, optional: true tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 @@ -48,12 +48,13 @@ process GATK4_SHIFTFASTA { """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" """ - touch test.intervals - touch test_shift.back_chain - touch test_shift.dict - touch test.shifted.intervals - touch test_shift.fasta - touch test_shift.fasta.fai + touch ${prefix}.intervals + touch ${prefix}_shift.back_chain + touch ${prefix}_shift.dict + touch ${prefix}.shifted.intervals + touch ${prefix}_shift.fasta + touch ${prefix}_shift.fasta.fai """ } diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test index d11d144ea..843354e9a 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test @@ -18,15 +18,15 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ @@ -34,11 +34,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap index a465dc485..a4fe7d3af 100644 --- a/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/shiftfasta/tests/main.nf.test.snap @@ -136,6 +136,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:25:05.997054" + "timestamp": "2026-02-05T17:51:13.969347846" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test index 26c20f88f..41d5c8f4b 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test @@ -17,26 +17,25 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true) + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -49,25 +48,24 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } @@ -82,28 +80,26 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] - """ } } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } } - } diff --git a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap index 092b26007..77cc7afe8 100644 --- a/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitintervals/tests/main.nf.test.snap @@ -44,7 +44,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:38.084533" + "timestamp": "2026-02-05T17:52:08.822076018" }, "test-gatk4-splitintervals-bed": { "content": [ @@ -91,7 +91,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:18.658962" + "timestamp": "2026-02-05T17:52:01.205689288" }, "test-gatk4-splitintervals-intervals-stub": { "content": [ @@ -138,6 +138,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:27:55.618457" + "timestamp": "2026-02-05T17:52:15.297589219" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index b3c0e340f..6256351b1 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -16,7 +16,7 @@ process GATK4_VARIANTFILTRATION { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi + tuple val(meta), path("*.tbi"), emit: tbi tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test index 65ba4124c..cbb647c47 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test @@ -40,14 +40,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("gatk4_variantfiltration - human - vcf - fasta.gz") { @@ -81,14 +82,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("gatk4_variantfiltration - human - vcf.gz - fasta") { @@ -122,14 +124,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }, - path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, - file(process.out.tbi.get(0).get(1)).name).match() }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap index 3a621b227..e1a3c785a 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -1,6 +1,8 @@ { "gatk4_variantfiltration - human - vcf - fasta.gz": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -9,18 +11,18 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:33.543304" + "timestamp": "2026-02-05T18:03:01.467326216" }, "gatk4_variantfiltration - human - vcf.gz - fasta": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -29,18 +31,18 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:51.020309" + "timestamp": "2026-02-05T18:03:09.049097033" }, "gatk4_variantfiltration - human - vcf - fasta": { "content": [ + "cf0477cc14953b16caacbf5be507b88", + "test.vcf.gz.tbi", { "versions_gatk4": [ [ @@ -49,14 +51,12 @@ "4.6.2.0" ] ] - }, - "cf0477cc14953b16caacbf5be507b88", - "test.vcf.gz.tbi" + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:38:15.367356" + "timestamp": "2026-02-05T18:02:52.913618285" } } \ No newline at end of file diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index da79a0ed3..a76851dff 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -14,7 +14,7 @@ process GAWK { output: tuple val(meta), path("*.${suffix}"), emit: output - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('gawk'), eval("awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//'"), topic: versions, emit: versions_gawk when: task.ext.when == null || task.ext.when @@ -47,11 +47,6 @@ process GAWK { ${output} ${cleanup} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS """ stub: @@ -61,10 +56,5 @@ process GAWK { """ ${create_cmd} ${prefix}.${suffix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') - END_VERSIONS """ } diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 732e18a97..96cd0c72b 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -15,7 +15,8 @@ tools: homepage: "https://www.gnu.org/software/gawk/" documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -25,22 +26,22 @@ input: e.g. [ id:'test', single_end:false ] - input: type: file - description: The input file - Specify the logic that needs to be executed on - this file on the `ext.args2` or in the program file. If the files have a `.gz` - extension, they will be unzipped using `zcat`. + description: The input file - Specify the logic that needs to be executed + on this file on the `ext.args2` or in the program file. If the files + have a `.gz` extension, they will be unzipped using `zcat`. pattern: "*" ontologies: [] - program_file: type: file - description: Optional file containing logic for awk to execute. If you don't wish - to use a file, you can use `ext.args2` to specify the logic. + description: Optional file containing logic for awk to execute. If you don't + wish to use a file, you can use `ext.args2` to specify the logic. pattern: "*" ontologies: [] - disable_redirect_output: type: boolean - description: Disable the redirection of awk output to a given file. This is useful - if you want to use awk's built-in redirect to write files instead of the shell's - redirect. + description: Disable the redirection of awk output to a given file. This is + useful if you want to use awk's built-in redirect to write files instead + of the shell's redirect. output: output: - - meta: @@ -50,18 +51,33 @@ output: e.g. [ id:'test', single_end:false ] - "*.${suffix}": type: file - description: The output file - if using shell redirection, specify the name - of this file using `ext.prefix` and the extension using `ext.suffix`. Otherwise, - ensure the awk program produces files with the extension in `ext.suffix`. + description: The output file - if using shell redirection, specify the + name of this file using `ext.prefix` and the extension using + `ext.suffix`. Otherwise, ensure the awk program produces files with + the extension in `ext.suffix`. pattern: "*" ontologies: [] + versions_gawk: + - - ${task.process}: + type: string + description: The name of the process + - gawk: + type: string + description: The name of the tool + - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gawk: + type: string + description: The name of the tool + - awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index fc6e240fd..5fa9daf16 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -29,10 +29,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -45,7 +43,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = Channel.of('BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }').collectFile(name:"program.awk") @@ -55,10 +53,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -71,7 +67,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -81,10 +77,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -97,7 +91,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] ] @@ -108,10 +102,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -124,7 +116,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] ] @@ -135,10 +127,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -151,7 +141,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[1] = [] @@ -161,10 +151,8 @@ nextflow_process { } then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) + assert process.success + assert snapshot(sanitizeOutput(process.out)).match() } } @@ -178,7 +166,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'hello' ], // meta map + [ id:'hello' ], [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] ] @@ -189,10 +177,8 @@ nextflow_process { } then { - assertAll( - { assert process.failed }, - { assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } - ) + assert process.failed + assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") } } } diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index d8e8ac755..1444c4688 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "Compress after processing": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -10,32 +10,25 @@ "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-27T17:11:20.054143406" + "timestamp": "2026-02-05T16:42:17.741168488" }, "Convert fasta to bed": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -43,32 +36,25 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T13:14:02.347809811" + "timestamp": "2026-02-05T16:41:46.810784678" }, "Convert fasta to bed with program file": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -76,32 +62,25 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T13:14:11.894616209" + "timestamp": "2026-02-05T16:41:52.884002736" }, "Extract first column from multiple files": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -109,32 +88,25 @@ "test.bed:md5,566c51674bd643227bb2d83e0963376d" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,566c51674bd643227bb2d83e0963376d" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T22:04:47.729300129" + "timestamp": "2026-02-05T16:42:05.455428454" }, "Unzip files before processing": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -142,32 +114,25 @@ "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-19T22:08:19.533527657" + "timestamp": "2026-02-05T16:42:11.976164295" }, "Convert fasta to bed using awk redirect instead of shell redirect": { "content": [ { - "0": [ + "output": [ [ { "id": "test" @@ -175,26 +140,19 @@ "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" ] ], - "1": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" - ], - "output": [ + "versions_gawk": [ [ - { - "id": "test" - }, - "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + "GAWK", + "gawk", + "5.3.0" ] - ], - "versions": [ - "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-03-05T08:31:09.88842854" + "timestamp": "2026-02-05T16:41:58.777371598" } } \ No newline at end of file diff --git a/modules/nf-core/haplogrep3/classify/meta.yml b/modules/nf-core/haplogrep3/classify/meta.yml index 53e40aa64..54b7efdf7 100644 --- a/modules/nf-core/haplogrep3/classify/meta.yml +++ b/modules/nf-core/haplogrep3/classify/meta.yml @@ -42,9 +42,10 @@ output: - haplogrep3: type: string description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': - type: string - description: The command used to generate the version of the tool + - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + topics: versions: - - ${task.process}: @@ -53,9 +54,10 @@ topics: - haplogrep3: type: string description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\': - type: string - description: The command used to generate the version of the tool + - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool + authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 861cd7f76..9fd34f37c 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -71,7 +71,7 @@ output: - "*_plots": type: file description: Plots created by MultiQC - pattern: "*_data" + pattern: "*_plots" ontologies: [] versions: - - ${task.process}: diff --git a/modules/nf-core/sambamba/depth/main.nf b/modules/nf-core/sambamba/depth/main.nf index e1404c7b0..42a1a80a3 100644 --- a/modules/nf-core/sambamba/depth/main.nf +++ b/modules/nf-core/sambamba/depth/main.nf @@ -50,7 +50,7 @@ process SAMBAMBA_DEPTH { cat <<-END_VERSIONS > versions.yml "${task.process}": - sambamba: \$(sambamba --version) + sambamba: \$(echo \$(sambamba --version 2>&1) | awk '{print \$2}' ) END_VERSIONS """ } diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test b/modules/nf-core/sambamba/depth/tests/main.nf.test index 3f5105986..3f6fce50b 100644 --- a/modules/nf-core/sambamba/depth/tests/main.nf.test +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test @@ -30,7 +30,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } ) } } @@ -85,7 +88,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } ) } } diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap index 7f4951e62..d1eb47aaa 100644 --- a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap +++ b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap @@ -29,10 +29,10 @@ } ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:57:58.097957" + "timestamp": "2025-12-05T12:03:11.190921915" }, "test-sambamba-depth": { "content": [ @@ -61,13 +61,20 @@ "versions": [ "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ] - } + }, + [ + { + "SAMBAMBA_DEPTH": { + "sambamba": "1.0.1" + } + } + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:57:42.031913" + "timestamp": "2025-12-05T12:03:07.689091449" }, "test-sambamba-depth-stub": { "content": [ @@ -82,7 +89,7 @@ ] ], "1": [ - "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ], "bed": [ [ @@ -94,14 +101,21 @@ ] ], "versions": [ - "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce" + "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57" ] - } + }, + [ + { + "SAMBAMBA_DEPTH": { + "sambamba": "1.0.1" + } + } + ] ], "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2025-12-03T15:58:13.647811" + "timestamp": "2025-12-05T12:03:14.737096819" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index c07cd8a98..b92410cd6 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -15,7 +15,7 @@ process SAMTOOLS_COLLATE { tuple val(meta), path("*.bam"), emit: bam, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.sam"), emit: sam, optional: true - path "versions.yml", emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -37,11 +37,6 @@ process SAMTOOLS_COLLATE { -@ $task.cpus \\ -o ${prefix}.${extension} \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -53,10 +48,5 @@ process SAMTOOLS_COLLATE { "bam" """ touch ${prefix}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index 96fdc2fc9..f6069abc4 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -71,13 +71,27 @@ output: description: Sorted SAM pattern: "*.{sam}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test index 2e547c7e8..2918f9e3d 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -14,23 +14,18 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) - ]) + ] input[1] = [ [id:'fasta'], [] ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, - { assert snapshot(process.out.cram).match("bam_cram") }, - { assert snapshot(process.out.sam).match("bam_sam") }, - { assert snapshot(process.out.versions).match("bam_versions") } - ) + assert process.success + assert snapshot(process.out).match() } } @@ -40,26 +35,21 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) - ]) - input[1] = Channel.of([ + ] + input[1] = [ [ id:'fasta'], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("cram_fasta_bam") }, - { assert snapshot(process.out.cram).match("cram_fasta_cram") }, - { assert snapshot(process.out.sam).match("cram_fasta_sam") }, - { assert snapshot(process.out.versions).match("cram_fasta_versions") } - ) + assert process.success + assert snapshot(process.out).match() } } @@ -69,23 +59,18 @@ nextflow_process { when { process { """ - input[0] = Channel.of([ + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) - ]) + ] input[1] = [ [id:'fasta'], [] ] """ } } then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out, - path(process.out.versions[0]).yaml - ).match() }, - ) + assert process.success + assert snapshot(process.out).match() } } diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test.snap b/modules/nf-core/samtools/collate/tests/main.nf.test.snap index b0c8f4dce..49c054f96 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collate/tests/main.nf.test.snap @@ -1,52 +1,4 @@ { - "cram_fasta_versions": { - "content": [ - [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-09-10T13:02:45.779649" - }, - "bam_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:01.611698" - }, - "cram_fasta_cram": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.325375" - }, - "cram_fasta_sam": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.328907" - }, "sarscov2 - bam -- stub": { "content": [ { @@ -65,7 +17,11 @@ ], "3": [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -81,64 +37,125 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] ] - }, - { - "SAMTOOLS_COLLATE": { - "samtools": "1.22.1" - } } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-10T13:02:50.413313" + "timestamp": "2026-02-04T14:56:50.33210565" }, - "cram_fasta_bam": { + "sarscov2 - bam": { "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:48.322144" - }, - "bam_bam": { - "content": [ - "test.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-02T16:56:01.608677" - }, - "bam_sam": { - "content": [ - [ - - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,06aa42b8b8dff9eb8c693dc1a9767e23" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,06aa42b8b8dff9eb8c693dc1a9767e23" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-02-02T16:56:01.613225" + "timestamp": "2026-02-04T14:56:36.179835312" }, - "bam_versions": { + "homo_sapiens - cram + fasta": { "content": [ - [ - "versions.yml:md5,dc74fe3bb06955a6b01e69c20f57b3e1" - ] + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,aefab9d7e786892bef3fca019494abda" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,aefab9d7e786892bef3fca019494abda" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions_samtools": [ + [ + "SAMTOOLS_COLLATE", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-10T13:02:39.72811" + "timestamp": "2026-02-04T14:56:44.148216078" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 62054fc97..89e12a645 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 7019a72e4..e2a0e56da 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : - 'biocontainers/samtools:1.21--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' : + 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: tuple val(meta), path(input) @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX { tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.crai"), optional:true, emit: crai - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -27,11 +27,6 @@ process SAMTOOLS_INDEX { -@ ${task.cpus} \\ $args \\ $input - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: @@ -40,10 +35,5 @@ process SAMTOOLS_INDEX { "crai" : args.contains("-c") ? "csi" : "bai" """ touch ${input}.${extension} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 1bed6bca6..c6d4ce259 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -14,7 +14,8 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:samtools input: - - meta: @@ -60,13 +61,27 @@ output: description: BAM/CRAM/SAM index file pattern: "*.{bai,crai,sai}" ontologies: [] + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5cd..c96cec860 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -23,7 +23,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -43,7 +46,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -67,7 +73,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.csi[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) } @@ -89,7 +95,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -110,7 +119,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.crai, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -133,7 +145,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.csi, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 72d65e81a..afc8a1ff6 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,250 +1,156 @@ { "csi - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - - ], - "csi": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:25.261127166" + "timestamp": "2026-01-28T17:52:10.030187" }, "crai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:12.653194876" + "timestamp": "2026-01-28T17:51:59.125484" }, "bai - stub": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], { - "0": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:21:01.854932651" + "timestamp": "2026-01-28T17:51:47.277042" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", - [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ] + { + "versions_samtools": [ + [ + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:51.485364222" + "timestamp": "2026-01-28T17:51:35.758735" }, "crai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], { - "0": [ - - ], - "1": [ - - ], - "2": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:40.518873972" + "timestamp": "2026-01-28T17:51:26.561965" }, "bai": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" - ], - "bai": [ + "versions_samtools": [ [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + "SAMTOOLS_INDEX", + "samtools", + "1.22.1" ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-09-16T08:20:21.184050361" + "timestamp": "2026-01-28T17:51:15.299035" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index aab585ac4..87b3333f6 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -22,7 +22,7 @@ process SAMTOOLS_VIEW { tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"), emit: unselected_index, optional: true - tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 167206773..215222661 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -147,7 +147,7 @@ output: - samtools: type: string description: Name of the tool - - samtools --version | head -1 | sed -e "s/samtools //": + - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool @@ -159,7 +159,7 @@ topics: - samtools: type: string description: Name of the tool - - samtools --version | head -1 | sed -e "s/samtools //": + - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config deleted file mode 100644 index 83ad29f02..000000000 --- a/modules/nf-core/samtools/view/tests/bam.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt bam" -} diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config deleted file mode 100644 index 60b96d426..000000000 --- a/modules/nf-core/samtools/view/tests/bam_index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt bam --write-index" -} diff --git a/modules/nf-core/samtools/view/tests/cram_index.config b/modules/nf-core/samtools/view/tests/cram_index.config deleted file mode 100644 index ed87c3349..000000000 --- a/modules/nf-core/samtools/view/tests/cram_index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-fmt cram --write-index" -} diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index de57b8e36..74e1c49fd 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process SAMTOOLS_VIEW" script "../main.nf" + config "./nextflow.config" process "SAMTOOLS_VIEW" tag "modules" @@ -10,15 +11,17 @@ nextflow_process { tag "samtools/view" test("bam") { - when { + params { + samtools_args = "" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = [] @@ -35,17 +38,17 @@ nextflow_process { } test("bam_csi_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'csi' @@ -62,17 +65,17 @@ nextflow_process { } test("bam_bai_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'bai' @@ -89,17 +92,17 @@ nextflow_process { } test("bam_bai_index_unselected") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -117,17 +120,17 @@ nextflow_process { } test("cram_crai_index_unselected") { - - config "./cram_index.config" - when { + params { + samtools_args = "--output-fmt cram --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -145,19 +148,21 @@ nextflow_process { } test("cram") { - when { + params { + samtools_args = "" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -173,21 +178,21 @@ nextflow_process { } test("cram_to_bam") { - - config "./bam.config" - when { + params { + samtools_args = "--output-fmt bam" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -203,21 +208,21 @@ nextflow_process { } test("cram_to_bam_index") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) + ] input[2] = [] input[3] = [] """ @@ -233,22 +238,23 @@ nextflow_process { } test("cram_to_bam_index_qname") { - - config "./bam_index.config" - when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map + ] + input[1] = [ + [ id:'genome' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) - input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) + ] + input[2] = Channel.of("testN:2817", "testN:2814") + .collectFile(name: "readnames.list", newLine: true) input[3] = [] """ } @@ -265,16 +271,18 @@ nextflow_process { test("bam_stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = [] @@ -293,16 +301,18 @@ nextflow_process { test("bam_csi_index - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'csi' @@ -321,16 +331,18 @@ nextflow_process { test("bam_bai_index - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = [] input[3] = 'bai' @@ -349,16 +361,18 @@ nextflow_process { test("bam_bai_index_uselected - stub") { options "-stub" - config "./bam_index.config" when { + params { + samtools_args = "--output-fmt bam --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') @@ -378,16 +392,18 @@ nextflow_process { test("cram_crai_index_unselected - stub") { options "-stub" - config "./cram_index.config" when { + params { + samtools_args = "--output-fmt cram --write-index" + } process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map + input[0] = [ + [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] - ]) + ] input[1] = [[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6ee160cd4..95205e56f 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -8,8 +8,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -23,8 +22,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -48,10 +46,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:48.952660444" + "timestamp": "2026-02-03T16:49:14.82588493" }, "bam_csi_index - stub": { "content": [ @@ -59,8 +57,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -77,8 +74,7 @@ "4": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -105,8 +101,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -120,8 +115,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -145,10 +139,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:14.881335093" + "timestamp": "2026-02-03T16:49:31.409368544" }, "bam_csi_index": { "content": [ @@ -159,8 +153,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -174,8 +167,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -199,10 +191,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:40:50.701779393" + "timestamp": "2026-02-03T16:48:46.36824035" }, "cram_to_bam_index_qname": { "content": [ @@ -213,8 +205,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -228,8 +219,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi:md5,15d725bced7ececd45b4312b2af99a6b" ] @@ -240,8 +230,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam" ] @@ -249,8 +238,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi" ] @@ -265,10 +253,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:58.085628072" + "timestamp": "2026-02-03T16:49:20.747636525" }, "bam_bai_index_unselected": { "content": [ @@ -276,8 +264,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai" ] @@ -285,8 +272,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -306,8 +292,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam" ] @@ -315,8 +300,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi" ] @@ -331,10 +315,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:10.249194373" + "timestamp": "2026-02-03T16:48:57.713608154" }, "cram_crai_index_unselected - stub": { "content": [ @@ -345,8 +329,7 @@ "1": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -363,8 +346,7 @@ "5": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -372,8 +354,7 @@ "6": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -381,8 +362,7 @@ "7": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -403,8 +383,7 @@ "crai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -412,8 +391,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -427,8 +405,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -436,8 +413,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -452,10 +428,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:39.3240134" + "timestamp": "2026-02-03T16:49:48.092654899" }, "bam": { "content": [ @@ -466,8 +442,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -500,10 +475,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:40:42.829284764" + "timestamp": "2026-02-03T16:48:27.608944526" }, "bam_bai_index": { "content": [ @@ -511,8 +486,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai" ] @@ -520,8 +494,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -554,10 +527,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:00.734899949" + "timestamp": "2026-02-03T16:48:52.047178732" }, "cram_to_bam": { "content": [ @@ -568,8 +541,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -602,10 +574,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:40.148480065" + "timestamp": "2026-02-03T16:50:41.727031999" }, "bam_bai_index - stub": { "content": [ @@ -613,8 +585,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -628,8 +599,7 @@ "3": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -656,8 +626,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -665,8 +634,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -699,10 +667,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:22.748940869" + "timestamp": "2026-02-03T16:49:36.783381688" }, "cram": { "content": [ @@ -719,8 +687,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram" ] @@ -747,10 +714,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:41:30.602610389" + "timestamp": "2026-02-03T16:49:09.393102901" }, "bam_bai_index_uselected - stub": { "content": [ @@ -758,8 +725,7 @@ "0": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -773,8 +739,7 @@ "3": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -788,8 +753,7 @@ "6": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -797,8 +761,7 @@ "7": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -813,8 +776,7 @@ "bai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -822,8 +784,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -843,8 +804,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -852,8 +812,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -868,10 +827,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:31.1133801" + "timestamp": "2026-02-03T16:49:42.344755528" }, "cram_crai_index_unselected": { "content": [ @@ -885,8 +844,7 @@ "crai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram.crai" ] @@ -894,8 +852,7 @@ "cram": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.cram:md5,9b6eeca8f6b4b744297ae7cc87c031a4" ] @@ -909,8 +866,7 @@ "unselected": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram" ] @@ -918,8 +874,7 @@ "unselected_index": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.unselected.cram.crai" ] @@ -934,10 +889,10 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:49:09.738258028" + "timestamp": "2026-02-03T16:49:03.431621547" }, "bam_stub": { "content": [ @@ -948,8 +903,7 @@ "bam": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam" ] @@ -963,8 +917,7 @@ "csi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "test.bam.csi" ] @@ -988,9 +941,9 @@ } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-10-29T15:42:06.108061867" + "timestamp": "2026-02-03T16:49:26.152824543" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/nextflow.config b/modules/nf-core/samtools/view/tests/nextflow.config new file mode 100644 index 000000000..37c564396 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SAMTOOLS_VIEW { + ext.args = params.samtools_args + } +} diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index c7794856d..9b926b1ff 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,7 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 9bd8f5546..b9c324dac 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -1,56 +1,52 @@ process UNTAR { - tag "$archive" + tag "${archive}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : - 'nf-core/ubuntu:22.04' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(archive) output: - tuple val(meta), path("$prefix"), emit: untar - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}"), emit: untar + tuple val("${task.process}"), val('untar'), eval('tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//"'), emit: versions_untar, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) """ - mkdir $prefix + mkdir ${prefix} ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ - -C $prefix --strip-components 1 \\ + -C ${prefix} --strip-components 1 \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} else tar \\ - -C $prefix \\ + -C ${prefix} \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} fi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ stub: - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ mkdir ${prefix} ## Dry-run untaring the archive to get the files and place all in prefix @@ -75,10 +71,5 @@ process UNTAR { fi done fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index 290346b3f..571d8078a 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -1,5 +1,5 @@ name: untar -description: Extract files. +description: Extract files from tar, tar.gz, tar.bz2, tar.xz archives keywords: - untar - uncompress @@ -7,7 +7,7 @@ keywords: tools: - untar: description: | - Extract tar.gz files. + Extract tar, tar.gz, tar.bz2, tar.xz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] identifier: "" @@ -19,24 +19,48 @@ input: e.g. [ id:'test', single_end:false ] - archive: type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + description: File to be untarred + pattern: "*.{tar,tar.gz,tar.bz2,tar.xz}" + ontologies: + - edam: http://edamontology.org/format_3981 # TAR format + - edam: http://edamontology.org/format_3989 # GZIP format output: - - untar: - - meta: + untar: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*/" + - ${prefix}: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - $prefix: - type: directory - description: Directory containing contents of archive pattern: "*/" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_untar: + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - untar: + type: string + description: The name of the tool + - tar --version 2>&1 | head -1 | sed "s/tar (GNU tar) //; s/ Copyright.*//": + type: eval + description: The expression to obtain the version of the tool + authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index c957517aa..fde8db16a 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -20,7 +20,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -38,7 +41,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -58,7 +64,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } @@ -78,7 +87,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot( + process.out.untar, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() }, ) } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index ceb91b792..51a414dd4 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,158 +1,118 @@ { "test_untar_onlyfiles": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:28.231047" + "timestamp": "2026-01-28T17:49:32.000491" }, "test_untar_onlyfiles - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:45.773103" + "timestamp": "2026-01-28T17:49:58.812479" }, "test_untar - stub": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", - "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:36.777441" + "timestamp": "2026-01-28T17:49:48.119456" }, "test_untar": { "content": [ - { - "0": [ + [ + [ + [ + + ], [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" ] - ], - "1": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" - ], - "untar": [ + ] + ], + { + "versions_untar": [ [ - [ - - ], - [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" - ] + "UNTAR", + "untar", + "1.34" ] - ], - "versions": [ - "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-07-10T12:04:19.377674" + "timestamp": "2026-01-28T17:49:17.252494" } } \ No newline at end of file diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml deleted file mode 100644 index feb6f15c0..000000000 --- a/modules/nf-core/untar/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -untar: - - modules/nf-core/untar/** diff --git a/modules/nf-core/upd/environment.yml b/modules/nf-core/upd/environment.yml index 307f13b37..a45a25cd9 100644 --- a/modules/nf-core/upd/environment.yml +++ b/modules/nf-core/upd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/upd/main.nf b/modules/nf-core/upd/main.nf index c4bcaf175..1196a03c8 100644 --- a/modules/nf-core/upd/main.nf +++ b/modules/nf-core/upd/main.nf @@ -9,14 +9,14 @@ process UPD { 'biocontainers/upd:0.1.1--pyhdfd78af_0' }" input: - tuple val(meta), path(vcf) + tuple val(meta), path(vcf) output: - tuple val(meta), path("*.bed"), emit: bed - path "versions.yml" , emit: versions + tuple val(meta), path("*.bed"), emit: bed + tuple val("${task.process}"), val('upd'), eval("upd --version 2>&1 | sed 's/upd, version //'"), topic: versions, emit: versions_upd when: - task.ext.when == null || task.ext.when + task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' @@ -26,22 +26,12 @@ process UPD { --vcf $vcf \\ $args \\ | sort -k 1,1 -k 2,2n >${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - upd: \$( upd --version 2>&1 | sed 's/upd, version //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - upd: \$( upd --version 2>&1 | sed 's/upd, version //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/upd/meta.yml b/modules/nf-core/upd/meta.yml index a0e900632..650cf217d 100644 --- a/modules/nf-core/upd/meta.yml +++ b/modules/nf-core/upd/meta.yml @@ -24,9 +24,10 @@ input: type: file description: VCF file pattern: "*.{vcf,vcf.gz}" + ontologies: [] output: - - bed: - - meta: + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -35,11 +36,28 @@ output: type: file description: BED file pattern: "*.{bed}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_upd: + - - ${task.process}: + type: string + description: The name of the process + - upd: + type: string + description: The name of the tool + - upd --version 2>&1 | sed 's/upd, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - upd: + type: string + description: The name of the tool + - upd --version 2>&1 | sed 's/upd, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@hrydbeck" maintainers: diff --git a/modules/nf-core/upd/tests/main.nf.test.snap b/modules/nf-core/upd/tests/main.nf.test.snap index 866792f11..d6af9ef77 100644 --- a/modules/nf-core/upd/tests/main.nf.test.snap +++ b/modules/nf-core/upd/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + [ + "UPD", + "upd", + "0.1" + ] ], "bed": [ [ @@ -23,16 +27,20 @@ "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + "versions_upd": [ + [ + "UPD", + "upd", + "0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T11:51:33.816939" + "timestamp": "2026-02-04T15:38:45.859374" }, "test-upd": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + [ + "UPD", + "upd", + "0.1" + ] ], "bed": [ [ @@ -58,15 +70,19 @@ "test.bed:md5,beea3890636075d5c99db1b0d74f9ff5" ] ], - "versions": [ - "versions.yml:md5,3fef0b4c41b8cbf95be59f62771e38ea" + "versions_upd": [ + [ + "UPD", + "upd", + "0.1" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T11:51:29.35452" + "timestamp": "2026-02-04T15:38:42.052606" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml index d078bfaed..32517278a 100644 --- a/modules/nf-core/vcf2cytosure/environment.yml +++ b/modules/nf-core/vcf2cytosure/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::vcf2cytosure=0.9.1 + - bioconda::vcf2cytosure=0.9.3 diff --git a/modules/nf-core/vcf2cytosure/main.nf b/modules/nf-core/vcf2cytosure/main.nf index 92351337a..f356456b3 100644 --- a/modules/nf-core/vcf2cytosure/main.nf +++ b/modules/nf-core/vcf2cytosure/main.nf @@ -4,8 +4,8 @@ process VCF2CYTOSURE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vcf2cytosure:0.9.1--pyh7cba7a3_1': - 'biocontainers/vcf2cytosure:0.9.1--pyh7cba7a3_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/58/584cf1de62ed0d65a064456ec0d052d6b657b3245c8f10c626bca7131884c0fc/data': + 'community.wave.seqera.io/library/pip_vcf2cytosure:6852c55eb4c9d406' }" input: tuple val(meta), path(sv_vcf) @@ -16,7 +16,7 @@ process VCF2CYTOSURE { output: tuple val(meta), path("*.cgh"), emit: cgh - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('vcf2cytosure'), eval("vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p'"), topic: versions, emit: versions_vcf2cytosure when: task.ext.when == null || task.ext.when @@ -40,27 +40,11 @@ process VCF2CYTOSURE { $snv \\ $blacklist \\ $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2cytosure: \$(echo \$(vcf2cytosure --version 2>&1) | sed 's/^.* cytosure //' ) - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def coverage = coverage_bed ? "--coverage ${coverage_bed}" : '' - def cnvkit = cns ? ( coverage_bed ? '' : "--cn ${cns}" ) : '' - def snv = snv_vcf ? ( coverage_bed ? '' : "--snv ${snv_vcf}" ) : '' - def blacklist = blacklist_bed ? "--blacklist ${blacklist_bed}" : '' def prefix = task.ext.prefix ?: "${meta.id}" - """ touch ${prefix}.cgh - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2cytosure: \$(echo \$(vcf2cytosure --version 2>&1) | sed 's/^.* cytosure //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml index 0c38d9c8d..517f80fdd 100644 --- a/modules/nf-core/vcf2cytosure/meta.yml +++ b/modules/nf-core/vcf2cytosure/meta.yml @@ -25,6 +25,7 @@ input: type: file description: VCF file with structural variants pattern: "*.{vcf,vcf.gz}" + ontologies: [] - - meta2: type: map description: | @@ -34,6 +35,7 @@ input: type: file description: Bed file with coverage data pattern: "*.bed" + ontologies: [] - - meta3: type: map description: | @@ -42,6 +44,7 @@ input: - cns: type: file description: CN file from CNVkit, not compatible with coverage_bed file + ontologies: [] - - meta4: type: map description: | @@ -53,13 +56,15 @@ input: VCF file with SNVs to calculate probe coverage, not compatible with coverage_bed pattern: "*.{vcf,vcf.gz}" - - - blacklist_bed: - type: file - description: Bed file with regions to exclude - pattern: "*.bed" + ontologies: [] + - blacklist_bed: + type: file + description: Bed file with regions to exclude + pattern: "*.bed" + ontologies: [] output: - - cgh: - - meta: + cgh: + - - meta: type: map description: | Groovy Map containing sample information @@ -68,10 +73,27 @@ output: type: file description: SV:s in CytoSure format pattern: "*.cgh" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_vcf2cytosure: + - - ${task.process}: + type: string + description: The name of the process + - vcf2cytosure: + type: string + description: The name of the tool + - vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - vcf2cytosure: + type: string + description: The name of the tool + - vcf2cytosure --version 2>&1 | sed -n 's/.*cytosure //p': + type: eval + description: The expression to obtain the version of the tool authors: - "@jemten" diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test b/modules/nf-core/vcf2cytosure/tests/main.nf.test index edd3063d6..a6d4bcd34 100644 --- a/modules/nf-core/vcf2cytosure/tests/main.nf.test +++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test @@ -31,8 +31,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.cgh).match("cgh") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.cgh, + process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -63,8 +64,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.cgh).match("cgh - stub") }, - { assert snapshot(process.out.versions).match("versions - stub") } + { assert snapshot( + process.out.cgh, + process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } diff --git a/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap index 0a0fae292..d0e0b8135 100644 --- a/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap +++ b/modules/nf-core/vcf2cytosure/tests/main.nf.test.snap @@ -1,26 +1,31 @@ { - "cgh": { + "homo sapiens - vcf - bed": { "content": [ [ [ { "id": "test" }, - "test.cgh:md5,fc3f1ffac5b797881d992994d5d56550" + "test.cgh:md5,c9bcda3fafe67359e353bedf02d041e8" ] - ] - ], - "timestamp": "2023-12-21T18:33:25.202806" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb" - ] + ], + { + "versions_vcf2cytosure": [ + [ + "VCF2CYTOSURE", + "vcf2cytosure", + "0.9.3" + ] + ] + } ], - "timestamp": "2023-12-21T18:33:25.205826" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:29:44.501025" }, - "cgh - stub": { + "homo sapiens - vcf - bed - stub": { "content": [ [ [ @@ -29,16 +34,21 @@ }, "test.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ] - ], - "timestamp": "2023-12-21T18:38:06.660655" - }, - "versions - stub": { - "content": [ - [ - "versions.yml:md5,a1850e66d57cee0b98adb056c1dc3ebb" - ] + ], + { + "versions_vcf2cytosure": [ + [ + "VCF2CYTOSURE", + "vcf2cytosure", + "0.9.3" + ] + ] + } ], - "timestamp": "2023-12-21T18:38:06.663571" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:29:50.263249" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2cytosure/tests/tags.yml b/modules/nf-core/vcf2cytosure/tests/tags.yml deleted file mode 100644 index 88ff60385..000000000 --- a/modules/nf-core/vcf2cytosure/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -vcf2cytosure: - - "modules/nf-core/vcf2cytosure/**" diff --git a/modules/nf-core/vcfanno/environment.yml b/modules/nf-core/vcfanno/environment.yml index 32c48b15b..a625e831c 100644 --- a/modules/nf-core/vcfanno/environment.yml +++ b/modules/nf-core/vcfanno/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - bioconda::vcfanno=0.3.5 + - bioconda::htslib=1.23 + - bioconda::vcfanno=0.3.7 diff --git a/modules/nf-core/vcfanno/main.nf b/modules/nf-core/vcfanno/main.nf index 25c131b1d..8c5e466f4 100644 --- a/modules/nf-core/vcfanno/main.nf +++ b/modules/nf-core/vcfanno/main.nf @@ -4,8 +4,8 @@ process VCFANNO { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vcfanno:0.3.5--h9ee0642_0': - 'biocontainers/vcfanno:0.3.5--h9ee0642_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b23fffa38d9740616e3b414df24e44c22fbc0510264f79b5062b3eecd619393f/data': + 'community.wave.seqera.io/library/htslib_vcfanno:c88d6077509197fe' }" input: tuple val(meta), path(vcf), path(tbi), path(specific_resources) @@ -14,15 +14,18 @@ process VCFANNO { path resources output: - tuple val(meta), path("*.vcf") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz") , emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , emit: tbi + tuple val("${task.process}"), val('vcfanno'), eval("vcfanno 2>&1 | sed -n 's/.*version \\([0-9.]\\+\\).*/\\1/p'"), topic: versions, emit: versions_vcfanno when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def lua_cmd = lua ? "--lua ${lua}" : "" """ vcfanno \\ @@ -31,22 +34,17 @@ process VCFANNO { ${lua_cmd} \\ ${toml} \\ ${vcf} \\ - > ${prefix}.vcf + | bgzip ${args2} --threads ${task.cpus} \\ + > ${prefix}.vcf.gz \\ + && tabix ${args3} ${prefix}.vcf.gz - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) - END_VERSIONS """ } diff --git a/modules/nf-core/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml index 18d27127c..70d5e4f7e 100644 --- a/modules/nf-core/vcfanno/meta.yml +++ b/modules/nf-core/vcfanno/meta.yml @@ -1,6 +1,6 @@ name: vcfanno -description: quickly annotate your VCF with any number of INFO fields from any number - of VCFs or BED files +description: quickly annotate your VCF with any number of INFO fields from any + number of VCFs or BED files keywords: - vcf - bed @@ -26,45 +26,83 @@ input: type: file description: query VCF file pattern: "*.{vcf, vcf.gz}" + ontologies: [] - tbi: type: file description: tabix index file for the query VCF pattern: "*.tbi" + ontologies: [] - specific_resources: type: map - description: A list of sample specific reference files defined in toml config, - must also include indices if bgzipped. - - - toml: - type: file - description: configuration file with reference file basenames - pattern: "*.toml" - - - lua: - type: file - description: Lua file for custom annotations - pattern: "*.lua" - - - resources: - type: map - description: List of reference files defined in toml config, must also include - indices if bgzipped. + description: A list of sample specific reference files defined in toml + config, must also include indices if bgzipped. + - toml: + type: file + description: configuration file with reference file basenames + pattern: "*.toml" + ontologies: [] + - lua: + type: file + description: Lua file for custom annotations + pattern: "*.lua" + ontologies: [] + - resources: + type: map + description: List of reference files defined in toml config, must also + include indices if bgzipped. output: - - vcf: - - meta: + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.vcf.gz" + - "*.vcf.gz.tbi": type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.vcf": - type: file - description: Annotated VCF file - pattern: "*.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + pattern: "*.vcf.gz.tbi" + versions_vcfanno: + - - ${task.process}: + type: string + description: The name of the process + - vcfanno: + type: string + description: The name of the tool + - vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - vcfanno: + type: string + description: The name of the tool + - vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p': + type: eval + description: The expression to obtain the version of the tool authors: - "@projectoriented" - "@matthdsm" + - "@nvnieuwk" maintainers: - "@projectoriented" - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test index 8bbcfd894..ef6eb4b5d 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test +++ b/modules/nf-core/vcfanno/tests/main.nf.test @@ -24,7 +24,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } @@ -54,7 +54,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } @@ -86,7 +86,7 @@ nextflow_process { input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi",checkIfExists: true) - ] + ] """ } } diff --git a/modules/nf-core/vcfanno/tests/main.nf.test.snap b/modules/nf-core/vcfanno/tests/main.nf.test.snap index 7e5f737c5..731848b5d 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test.snap +++ b/modules/nf-core/vcfanno/tests/main.nf.test.snap @@ -1,12 +1,14 @@ { "sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi] - stub": { "content": [ - "test_compressed.vcf", - [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" - ] + "test_compressed.vcf.gz", + null ], - "timestamp": "2023-12-06T12:18:25.69588598" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T13:57:00.201785" }, "sarscov2 - [vcf(gz), tbi, vcf], [], toml, [vcf, tbi]": { "content": [ @@ -17,11 +19,33 @@ "id": "test_compressed", "single_end": false }, - "test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_compressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], "1": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + [ + { + "id": "test_compressed", + "single_end": false + }, + "test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] + ], + "2": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] + ], + "tbi": [ + [ + { + "id": "test_compressed", + "single_end": false + }, + "test_compressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] ], "vcf": [ [ @@ -29,15 +53,23 @@ "id": "test_compressed", "single_end": false }, - "test_compressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_compressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], - "versions": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + "versions_vcfanno": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] ] } ], - "timestamp": "2023-12-06T12:21:13.209704154" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:57:31.157631" }, "sarscov2 - [vcf, [], vcf], [], toml, [vcf, tbi]": { "content": [ @@ -48,11 +80,33 @@ "id": "test_uncompressed", "single_end": false }, - "test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_uncompressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], "1": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + [ + { + "id": "test_uncompressed", + "single_end": false + }, + "test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] + ], + "2": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] + ], + "tbi": [ + [ + { + "id": "test_uncompressed", + "single_end": false + }, + "test_uncompressed.vcf.gz.tbi:md5,67a4272d5897fea5cc395dc87afc3629" + ] ], "vcf": [ [ @@ -60,14 +114,22 @@ "id": "test_uncompressed", "single_end": false }, - "test_uncompressed.vcf:md5,d3cf5a6eaf6cca5b957833a313c5fbf4" + "test_uncompressed.vcf.gz:md5,f816458edc4df57f2617070fe1b939ea" ] ], - "versions": [ - "versions.yml:md5,5ff0991b612706ce15d82eb1564513b0" + "versions_vcfanno": [ + [ + "VCFANNO", + "vcfanno", + "0.3.7" + ] ] } ], - "timestamp": "2023-12-06T12:21:19.255212216" + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:57:35.91459" } } \ No newline at end of file diff --git a/modules/nf-core/vcfanno/tests/nextflow.config b/modules/nf-core/vcfanno/tests/nextflow.config index af28ad82e..b22599fc2 100644 --- a/modules/nf-core/vcfanno/tests/nextflow.config +++ b/modules/nf-core/vcfanno/tests/nextflow.config @@ -1,4 +1,4 @@ process { - - -} \ No newline at end of file + + +} diff --git a/modules/nf-core/vcfanno/tests/tags.yml b/modules/nf-core/vcfanno/tests/tags.yml deleted file mode 100644 index e861bd53e..000000000 --- a/modules/nf-core/vcfanno/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -vcfanno: - - "modules/nf-core/vcfanno/**" diff --git a/modules/nf-core/verifybamid/verifybamid2/main.nf b/modules/nf-core/verifybamid/verifybamid2/main.nf index 9568fee95..7bf68ce98 100644 --- a/modules/nf-core/verifybamid/verifybamid2/main.nf +++ b/modules/nf-core/verifybamid/verifybamid2/main.nf @@ -3,9 +3,9 @@ process VERIFYBAMID_VERIFYBAMID2 { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/verifybamid2:2.0.1--hbb20b25_6' : - 'biocontainers/verifybamid2:2.0.1--h19d48f6_8' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/97/9700eb810dc7a72011c9149b8ab6cc7fa9d273795632ddd00af019ab32816811/data' + : 'community.wave.seqera.io/library/verifybamid2:2.0.1--166cf392bec584ce'}" input: tuple val(meta), path(bam), path(bai) @@ -20,7 +20,7 @@ process VERIFYBAMID_VERIFYBAMID2 { tuple val(meta), path("*.mu") , optional:true, emit: mu tuple val(meta), path("*.selfSM") , optional:true, emit: self_sm tuple val(meta), path("*.Ancestry") , optional:true, emit: ancestry - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('verifybamid2'), eval("verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p'"), topic: versions, emit: versions_verifybamid2 when: task.ext.when == null || task.ext.when @@ -36,23 +36,19 @@ process VERIFYBAMID_VERIFYBAMID2 { "--SVDPrefix ${svd_ud.baseName}" : "--UDPath ${svd_ud} --MeanPath ${svd_mu} --BedPath ${svd_bed}" def refvcf_args = "${refvcf}".endsWith(".vcf") ? "--RefVCF ${refvcf}" : "" - def reference_args = ("$references".endsWith('.fasta')) ? - "--Reference ${references}" : '' + def reference_args = "${references}".matches(/.+((fasta)|(fa)|(fna))(\.gz)*$/) + ? "--Reference ${references}" + : '' """ verifybamid2 \\ - --NumThread $task.cpus \\ + --NumThread ${task.cpus} \\ ${svd_args} \\ ${bam_file} \\ ${refvcf_args} \\ ${reference_args} \\ ${args_list.join(' ')} \\ > ${prefix}.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - verifybamid: \$(echo \$(verifybamid2 --help 2>&1 | sed -e '3p;d' | sed -e 's/ Version://')) - END_VERSIONS """ stub: @@ -64,10 +60,5 @@ process VERIFYBAMID_VERIFYBAMID2 { touch ${prefix}.mu touch ${prefix}.selfSM touch ${prefix}.Ancestry - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - verifybamid: \$(echo \$(verifybamid2 --help 2>&1 | sed -e '3p;d' | sed -e 's/ Version://')) - END_VERSIONS """ } diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index 8b6f2bdf8..210e1e852 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -1,7 +1,7 @@ name: "VERIFYBAMID_VERIFYBAMID2" -description: Detecting and estimating inter-sample DNA contamination became a crucial - quality assessment step to ensure high quality sequence reads and reliable downstream - analysis. +description: Detecting and estimating inter-sample DNA contamination became a + crucial quality assessment step to ensure high quality sequence reads and + reliable downstream analysis. keywords: - contamination - bam @@ -15,7 +15,8 @@ tools: documentation: "http://griffan.github.io/VerifyBamID" tool_dev_url: "https://github.com/Griffan/VerifyBamID" doi: "10.1101/gr.246934.118" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:verifybamid input: - - meta: @@ -45,13 +46,14 @@ input: ontologies: [] - svd_bed: type: file - description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] + description: .Bed file for markers used in this + analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] pattern: "*.bed" ontologies: [] - refvcf: type: file - description: Reference panel VCF with genotype information, for generation of - .UD .mu .bed files [Optional] + description: Reference panel VCF with genotype information, for generation + of .UD .mu .bed files [Optional] pattern: "*.vcf" ontologies: [] - references: @@ -101,8 +103,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.mu": type: file - description: .mu matrix file of genotype matrix from customized reference - vcf input + description: .mu matrix file of genotype matrix from customized + reference vcf input pattern: "*.mu" ontologies: [] self_sm: @@ -113,8 +115,8 @@ output: e.g. [ id:'test', single_end:false ] - "*.selfSM": type: file - description: Shares the same format as legacy VB1 and the key information - FREEMIX indicates the estimated contamination level. + description: Shares the same format as legacy VB1 and the key + information FREEMIX indicates the estimated contamination level. pattern: "*.selfSM" ontologies: [] ancestry: @@ -128,13 +130,27 @@ output: description: Ancestry information pattern: "*.Ancestry" ontologies: [] + versions_verifybamid2: + - - ${task.process}: + type: string + description: The name of the process + - verifybamid2: + type: string + description: The name of the tool + - verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - verifybamid2: + type: string + description: The name of the tool + - verifybamid2 --help 2>&1 | sed -n '3s/.*Version://p': + type: eval + description: The expression to obtain the version of the tool authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test index 99acd6844..e9f2e0101 100644 --- a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test +++ b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test @@ -60,13 +60,14 @@ nextflow_process { process.out.mu, process.out.self_sm, process.out.ancestry, - process.out.versions, + process.out.findAll { key, val -> key.startsWith("versions") }, file(process.out.ud[0][1]).name ).match() } ) } } + test("Should run with panel input") { config "./nextflow.config" @@ -90,7 +91,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.log[0][1]).name, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) } @@ -119,7 +120,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } @@ -145,7 +147,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } @@ -173,8 +176,68 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } + ) + } + } + + test("Should run with alternative .fa reference input -stub") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ] + input[1] = [ [], [], [] ] + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf') + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log[0][1]).name, + process.out.bed, + process.out.mu, + process.out.self_sm, + process.out.ancestry, + process.out.findAll { key, val -> key.startsWith("versions") }, + file(process.out.ud[0][1]).name + ).match() } + ) + } + } + + test("Should run with alternative .fa reference input") { + config "./nextflow.config" + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam'), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai') ] + input[1] = [ [], [], [] ] + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf') + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz') + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["log", "bed", "mu", "ud", "self_sm", "ancestry"]) + ).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap index 9bc0853a4..31316fe0a 100644 --- a/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap +++ b/modules/nf-core/verifybamid/verifybamid2/tests/main.nf.test.snap @@ -1,78 +1,77 @@ { - "Should run with panel input": { + "Should run with alternative .fa reference input -stub": { "content": [ "test.log", [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ] + [ + { + "id": "test", + "single_end": false + }, + "test.genome.vcf.bed:md5,47106c764019ee359b1936410e2efa1e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.genome.vcf.mu:md5,0810db02af2a176fa5ddc0f404911b66" + ] + ], + [ + + ], + [ + + ], + { + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + }, + "test.genome.vcf.UD" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-10-22T13:02:25.962766167" + "timestamp": "2026-02-04T15:06:31.079305" }, - "Should run with panel input - stub": { + "Should run with panel input": { "content": [ + "test.log", { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ + "versions_verifybamid2": [ [ - { - "id": "test", - "single_end": false - }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:06:11.925134" + }, + "Should run with panel input - stub": { + "content": [ + { "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -81,7 +80,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -90,7 +89,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -99,7 +98,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -108,84 +107,103 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:46:04.375799563" + "timestamp": "2026-02-04T15:12:24.048732" }, "Should run with RefVCF input - stub": { "content": [ { - "0": [ + "ancestry": [ [ { "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], - "1": [ - - ], - "2": [ + "bed": [ [ { "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], - "3": [ + "log": [ [ { "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], - "4": [ + "mu": [ [ { "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], - "5": [ + "self_sm": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "ud": [ + ], + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-04T15:12:19.940733" + }, + "Should run with alternative .fa reference input": { + "content": [ + { "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -194,7 +212,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -203,7 +221,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -212,7 +230,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -221,22 +239,26 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:45:57.687144464" + "timestamp": "2026-02-04T15:12:37.072815" }, "Should run with SVD input": { "content": [ @@ -278,7 +300,11 @@ ] ], "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ], "ancestry": [ [ @@ -316,16 +342,20 @@ "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-05T20:51:39.853534509" + "timestamp": "2026-02-04T15:00:42.110941" }, "Should run with RefVCF input": { "content": [ @@ -354,78 +384,33 @@ [ ], - [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], + { + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] + ] + }, "test.genome.vcf.UD" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-11-20T13:43:20.984216864" + "timestamp": "2026-02-04T15:06:07.266104" }, "Should run with SVD input - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" - ], "ancestry": [ [ { "id": "test", "single_end": false }, - "test.Ancestry:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Ancestry" ] ], "bed": [ @@ -434,7 +419,7 @@ "id": "test", "single_end": false }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bed" ] ], "log": [ @@ -443,7 +428,7 @@ "id": "test", "single_end": false }, - "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.log" ] ], "mu": [ @@ -452,7 +437,7 @@ "id": "test", "single_end": false }, - "test.mu:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.mu" ] ], "self_sm": [ @@ -461,21 +446,25 @@ "id": "test", "single_end": false }, - "test.selfSM:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.selfSM" ] ], "ud": [ ], - "versions": [ - "versions.yml:md5,199f2e02b570926d6a249055c917c6b1" + "versions_verifybamid2": [ + [ + "VERIFYBAMID_VERIFYBAMID2", + "verifybamid2", + "2.0.1" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.6" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-05-05T16:40:02.231564621" + "timestamp": "2026-02-04T15:12:16.230109" } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 5a1dbbf4f..da40874e9 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -27,7 +27,6 @@ workflow ALIGN_MT { if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) ch_align = BWAMEM2_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM_MT.out.versions) } else if (val_mt_aligner.equals("sentieon")) { SENTIEON_BWAMEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, ch_fai ) ch_align = SENTIEON_BWAMEM_MT.out.bam_and_bai.map{ meta, bam, _bai -> [meta, bam] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 0c95d6ef1..b0284b4b9 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -43,7 +43,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEM2_MEM.out.versions) } SAMTOOLS_INDEX_ALIGN ( ch_align ) @@ -76,16 +75,12 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_EXTRACT.out.versions) } // Marking duplicates MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGN.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_MARKDUP.out.versions) - emit: marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index fb7828b92..0d571e48b 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -28,10 +28,8 @@ workflow ANNOTATE_CADD { if (val_genome.equals('GRCh38')) { REFERENCE_TO_CADD_CHRNAMES ( ch_fai , [], false ) - ch_versions = ch_versions.mix(REFERENCE_TO_CADD_CHRNAMES.out.versions) CADD_TO_REFERENCE_CHRNAMES ( ch_fai , [], false ) - ch_versions = ch_versions.mix(CADD_TO_REFERENCE_CHRNAMES.out.versions) CADD_TO_REFERENCE_CHRNAMES.out.output.map { _meta, txt -> txt } .set { ch_rename_chrs } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index 1f2bd6953..e0f30eb91 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -195,9 +195,6 @@ workflow ANNOTATE_GENOME_SNVS { ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(VCFANNO.out.versions) - ch_versions = ch_versions.mix(UPD_SITES.out.versions) - ch_versions = ch_versions.mix(UPD_REGIONS.out.versions) ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) emit: diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index fd8600298..4a72744eb 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -89,7 +89,6 @@ workflow GENERATE_CYTOSURE_FILES { ) ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) - ch_versions = ch_versions.mix(VCF2CYTOSURE.out.versions) emit: versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a6817d5b4..ac06731a5 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -112,7 +112,6 @@ workflow PREPARE_REFERENCES { if (!val_bwa) { if (!val_aligner.equals("sentieon") || val_mtaligner.equals("bwa")) { ch_bwa = BWA_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWA_INDEX_GENOME.out.versions) } if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { ch_bwa = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() @@ -123,7 +122,6 @@ workflow PREPARE_REFERENCES { if (!val_bwamem2 && (val_aligner.equals("bwamem2") || val_mtaligner.equals("bwamem2"))) { ch_genome_bwamem2_index = BWAMEM2_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEM2_INDEX_GENOME.out.versions) } else if (val_bwamem2) { ch_genome_bwamem2_index = channel.fromPath(val_bwamem2).map {it -> [[id:it.simpleName], it]}.collect() } @@ -177,12 +175,10 @@ workflow PREPARE_REFERENCES { if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwamem2")) { ch_mt_bwamem2_index = BWAMEM2_INDEX_MT(ch_mt_fasta).index.collect() ch_mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEM2_INDEX_MT.out.versions, BWAMEM2_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("bwa")) { ch_mt_bwa_index = BWA_INDEX_MT(ch_mt_fasta).index.collect() ch_mtshift_bwa_index = BWA_INDEX_MT_SHIFT(ch_mtshift_fasta).index.collect() - ch_versions = ch_versions.mix(BWA_INDEX_MT.out.versions, BWA_INDEX_MT_SHIFT.out.versions) } if ((val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) && val_mtaligner.equals("sentieon")) { ch_mt_bwa_index = SENTIEON_BWAINDEX_MT(ch_mt_fasta).index.collect() @@ -261,7 +257,6 @@ workflow PREPARE_REFERENCES { if (val_vep_cache) { if (val_vep_cache.endsWith("tar.gz")) { ch_vep_resources = UNTAR_VEP_CACHE (channel.fromPath(val_vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()).untar.map{ _meta, files -> [files]}.collect() - ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions) } else { ch_vep_resources = channel.fromPath(val_vep_cache).collect() } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 8b755908b..89aceb143 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -101,8 +101,6 @@ workflow QC_BAM { ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) - ch_versions = ch_versions.mix(VERIFYBAMID_VERIFYBAMID2.out.versions) - ch_versions = ch_versions.mix(SAMBAMBA_DEPTH.out.versions) emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index e7663da39..52ae75a9a 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -14,8 +14,6 @@ workflow SUBSAMPLE_MT_READS { ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] main: - ch_versions = channel.empty() - SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) @@ -28,9 +26,4 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') - ch_versions = ch_versions.mix(SAMTOOLS_COLLATE.out.versions) - ch_versions = ch_versions.mix(GAWK.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index dcfe3487c..9b64191c5 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -290,7 +290,6 @@ workflow RAREDISEASE { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, ) - ch_versions = ch_versions.mix(SUBSAMPLE_MT_READS.out.versions) } } From 9efe8d4338c2f16677532af902ced4a9baa04a5e Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Feb 2026 10:43:03 +0100 Subject: [PATCH 381/872] update modules draft --- modules.json | 42 +-- modules/nf-core/bwameme/index/environment.yml | 6 +- modules/nf-core/bwameme/index/main.nf | 19 +- modules/nf-core/bwameme/index/meta.yml | 32 +- .../bwameme/index/tests/main.nf.test.snap | 40 ++- modules/nf-core/bwameme/index/tests/tags.yml | 2 - modules/nf-core/bwameme/mem/environment.yml | 6 +- modules/nf-core/bwameme/mem/main.nf | 24 +- modules/nf-core/bwameme/mem/meta.yml | 93 ++++-- .../nf-core/bwameme/mem/tests/main.nf.test | 2 +- .../bwameme/mem/tests/main.nf.test.snap | 90 ++--- modules/nf-core/bwameme/mem/tests/tags.yml | 2 - .../addmostsevereconsequence/environment.yml | 7 + .../custom/addmostsevereconsequence/main.nf | 20 +- .../custom/addmostsevereconsequence/meta.yml | 55 +++- .../usr/bin/add_most_severe_consequence.py | 2 +- .../tests/main.nf.test | 146 ++++++++ .../tests/main.nf.test.snap | 112 +++++++ .../tests/nextflow.config | 1 + .../custom/addmostseverepli/environment.yml | 7 + .../nf-core/custom/addmostseverepli/main.nf | 20 +- .../nf-core/custom/addmostseverepli/meta.yml | 55 +++- .../resources/usr/bin/add_most_severe_pli.py | 2 +- .../addmostseverepli/tests/main.nf.test | 60 ++++ .../addmostseverepli/tests/main.nf.test.snap | 112 +++++++ .../addmostseverepli/tests/nextflow.config | 1 + modules/nf-core/glnexus/environment.yml | 3 + modules/nf-core/glnexus/main.nf | 20 +- modules/nf-core/glnexus/meta.yml | 44 ++- modules/nf-core/glnexus/tests/main.nf.test | 126 +++++++ .../nf-core/glnexus/tests/main.nf.test.snap | 166 ++++++++++ modules/nf-core/hisat2/build/main.nf | 12 +- modules/nf-core/hisat2/build/meta.yml | 28 +- .../nf-core/hisat2/build/tests/main.nf.test | 10 +- .../hisat2/build/tests/main.nf.test.snap | 96 ++---- modules/nf-core/last/lastdb/main.nf | 12 +- modules/nf-core/last/lastdb/meta.yml | 28 +- .../last/lastdb/tests/main.nf.test.snap | 54 ++- .../ngsbits/samplegender/environment.yml | 3 +- modules/nf-core/ngsbits/samplegender/main.nf | 16 +- modules/nf-core/ngsbits/samplegender/meta.yml | 41 ++- .../samplegender/tests/main.nf.test.snap | 20 +- modules/nf-core/qualimap/bamqc/main.nf | 16 +- modules/nf-core/qualimap/bamqc/meta.yml | 26 +- .../nf-core/qualimap/bamqc/tests/main.nf.test | 4 +- .../qualimap/bamqc/tests/main.nf.test.snap | 38 ++- .../nf-core/rtgtools/format/environment.yml | 4 +- modules/nf-core/rtgtools/format/main.nf | 16 +- modules/nf-core/rtgtools/format/meta.yml | 56 +++- .../rtgtools/format/tests/fastq.config | 3 + .../rtgtools/format/tests/main.nf.test | 138 ++++++++ .../rtgtools/format/tests/main.nf.test.snap | 144 ++++++++ .../nf-core/rtgtools/format/tests/sam.config | 3 + .../nf-core/rtgtools/vcfeval/environment.yml | 4 +- modules/nf-core/rtgtools/vcfeval/main.nf | 17 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 136 +++++--- .../rtgtools/vcfeval/tests/main.nf.test.snap | 90 +++-- modules/nf-core/samtools/collate/main.nf | 2 +- modules/nf-core/samtools/collate/meta.yml | 13 +- .../samtools/collate/tests/main.nf.test | 7 +- modules/nf-core/samtools/faidx/main.nf | 3 +- modules/nf-core/samtools/faidx/meta.yml | 17 +- .../nf-core/samtools/faidx/tests/main.nf.test | 118 +++---- .../samtools/faidx/tests/main.nf.test.snap | 311 ++---------------- modules/nf-core/samtools/merge/main.nf | 4 +- modules/nf-core/samtools/merge/meta.yml | 10 - .../nf-core/samtools/merge/tests/main.nf.test | 35 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/samtools/view/meta.yml | 13 +- .../nf-core/samtools/view/tests/main.nf.test | 32 +- modules/nf-core/seqtk/sample/main.nf | 12 +- modules/nf-core/seqtk/sample/meta.yml | 30 +- .../seqtk/sample/tests/main.nf.test.snap | 80 ++++- .../seqtk/sample/tests/standard.config | 2 +- .../smncopynumbercaller/environment.yml | 2 + modules/nf-core/smncopynumbercaller/main.nf | 15 +- modules/nf-core/smncopynumbercaller/meta.yml | 40 ++- .../tests/main.nf.test.snap | 40 ++- modules/nf-core/spring/decompress/main.nf | 20 +- modules/nf-core/spring/decompress/meta.yml | 42 ++- .../spring/decompress/tests/main.nf.test | 2 +- .../spring/decompress/tests/main.nf.test.snap | 160 ++++----- .../spring/decompress/tests/nextflow.config | 4 +- modules/nf-core/tiddit/cov/environment.yml | 2 +- modules/nf-core/tiddit/cov/main.nf | 40 +-- modules/nf-core/tiddit/cov/meta.yml | 39 ++- modules/nf-core/tiddit/cov/tests/main.nf.test | 32 +- .../tiddit/cov/tests/main.nf.test.snap | 159 ++++++--- modules/nf-core/tiddit/sv/environment.yml | 4 +- modules/nf-core/tiddit/sv/main.nf | 38 +-- modules/nf-core/tiddit/sv/meta.yml | 47 ++- modules/nf-core/tiddit/sv/tests/main.nf.test | 24 +- .../nf-core/tiddit/sv/tests/main.nf.test.snap | 132 +++++--- modules/nf-core/tiddit/sv/tests/tags.yml | 2 - .../nf-core/ucsc/wigtobigwig/environment.yml | 2 +- modules/nf-core/ucsc/wigtobigwig/main.nf | 25 +- modules/nf-core/ucsc/wigtobigwig/meta.yml | 31 +- .../ucsc/wigtobigwig/tests/main.nf.test.snap | 44 ++- subworkflows/local/align/main.nf | 2 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 5 +- subworkflows/local/align_sentieon/main.nf | 2 +- .../local/annotate_consequence_pli.nf | 6 - .../local/annotate_rhocallviz/main.nf | 1 - subworkflows/local/call_mobile_elements.nf | 2 +- .../local/call_snv_deepvariant/main.nf | 2 - .../local/call_structural_variants.nf | 1 - subworkflows/local/call_sv_MT/main.nf | 1 - subworkflows/local/call_sv_tiddit/main.nf | 3 - subworkflows/local/generate_cytosure_files.nf | 6 - subworkflows/local/prepare_references/main.nf | 10 +- subworkflows/local/qc_bam/main.nf | 7 - subworkflows/local/subsample_mt_frac/main.nf | 2 +- subworkflows/local/subsample_mt_reads/main.nf | 6 +- subworkflows/local/variant_evaluation.nf | 7 - workflows/raredisease.nf | 12 - 115 files changed, 2574 insertions(+), 1470 deletions(-) delete mode 100644 modules/nf-core/bwameme/index/tests/tags.yml delete mode 100644 modules/nf-core/bwameme/mem/tests/tags.yml create mode 100644 modules/nf-core/custom/addmostsevereconsequence/environment.yml create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config create mode 100644 modules/nf-core/custom/addmostseverepli/environment.yml create mode 100644 modules/nf-core/custom/addmostseverepli/tests/main.nf.test create mode 100644 modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/addmostseverepli/tests/nextflow.config create mode 100644 modules/nf-core/glnexus/tests/main.nf.test create mode 100644 modules/nf-core/glnexus/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/format/tests/fastq.config create mode 100644 modules/nf-core/rtgtools/format/tests/main.nf.test create mode 100644 modules/nf-core/rtgtools/format/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/format/tests/sam.config delete mode 100644 modules/nf-core/tiddit/sv/tests/tags.yml diff --git a/modules.json b/modules.json index cf86afdf4..9bba47184 100644 --- a/modules.json +++ b/modules.json @@ -87,12 +87,12 @@ }, "bwameme/index": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", "installed_by": ["modules"] }, "bwameme/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", "installed_by": ["modules"] }, "cadd": { @@ -122,12 +122,12 @@ }, "custom/addmostsevereconsequence": { "branch": "master", - "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "custom/addmostseverepli": { "branch": "master", - "git_sha": "56f5268d044a61636f55c3935e2d5b23b65437e1", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "deepvariant/rundeepvariant": { @@ -283,7 +283,7 @@ }, "glnexus": { "branch": "master", - "git_sha": "9b696bde5b422831751df1a4f2ba728567ec51fd", + "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, "haplogrep3/classify": { @@ -293,7 +293,7 @@ }, "hisat2/build": { "branch": "master", - "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726", + "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c", "installed_by": ["modules"] }, "hmtnote/annotate": { @@ -304,7 +304,7 @@ }, "last/lastdb": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d92ad4055433d66d3e3eb4fd8d729d6ae9f75693", "installed_by": ["modules"] }, "manta/germline": { @@ -324,7 +324,7 @@ }, "ngsbits/samplegender": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "54c18191be1e99d78832cb62dc6fb9513ed97eae", "installed_by": ["modules"] }, "peddy": { @@ -374,7 +374,7 @@ }, "qualimap/bamqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "aa50b51492f79e0bf3ca9ca6e34640e3435b60ba", "installed_by": ["modules"] }, "rhocall/annotate": { @@ -389,12 +389,12 @@ }, "rtgtools/format": { "branch": "master", - "git_sha": "167a20a2e267261af397e9ea5bf58426e6345ce7", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", - "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", + "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, "sambamba/depth": { @@ -404,12 +404,12 @@ }, "samtools/collate": { "branch": "master", - "git_sha": "a77125b43fb8973f37c36e2ff137626657de3b21", + "git_sha": "18ef126d5c91f6f4ad94fe6b939647771d5bc7b0", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "samtools/index": { @@ -419,7 +419,7 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "9a48bce39a67e2cb34b8f125fc1d50f0ad98b616", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "samtools/sort": { @@ -434,7 +434,7 @@ }, "samtools/view": { "branch": "master", - "git_sha": "d2ceed2ec5fccf922638f116a15e02f6458288fb", + "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", "installed_by": ["modules"] }, "sentieon/bwaindex": { @@ -479,17 +479,17 @@ }, "seqtk/sample": { "branch": "master", - "git_sha": "af2861c63a6db77168f039ac265d84cfecd9efc2", + "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33", "installed_by": ["modules"] }, "smncopynumbercaller": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "spring/decompress": { "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "stranger": { @@ -524,17 +524,17 @@ }, "tiddit/cov": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/bwameme/index/environment.yml b/modules/nf-core/bwameme/index/environment.yml index f209d62e8..21fb9c42f 100644 --- a/modules/nf-core/bwameme/index/environment.yml +++ b/modules/nf-core/bwameme/index/environment.yml @@ -1,5 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" + - bioconda::bwa-meme=1.0.6 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwameme/index/main.nf b/modules/nf-core/bwameme/index/main.nf index 870f494cc..ca13f8971 100644 --- a/modules/nf-core/bwameme/index/main.nf +++ b/modules/nf-core/bwameme/index/main.nf @@ -4,15 +4,16 @@ process BWAMEME_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa-meme:1.0.6--hdcf5f25_2': - 'biocontainers/bwa-meme:1.0.6--hdcf5f25_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9ddd41b93c5e182db9d643ca266dd1677e59593a9cb49904b982ff45ad5aa8c3/data': + 'community.wave.seqera.io/library/bwa-meme_mbuffer_samtools:03f3f60b6c289776' }" input: tuple val(meta), path(fasta) output: tuple val(meta), path("bwameme"), emit: index - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwameme'), val('1.0.6'), topic: versions, emit: versions_bwameme + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -20,7 +21,6 @@ process BWAMEME_INDEX { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${fasta}" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ mkdir bwameme @@ -31,16 +31,10 @@ process BWAMEME_INDEX { $fasta build_rmis_dna.sh bwameme/$prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${fasta}" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ mkdir bwameme touch bwameme/${prefix}.0123 @@ -52,10 +46,5 @@ process BWAMEME_INDEX { touch bwameme/${prefix}.suffixarray_uint64_L0_PARAMETERS touch bwameme/${prefix}.suffixarray_uint64_L1_PARAMETERS touch bwameme/${prefix}.suffixarray_uint64_L2_PARAMETERS - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/bwameme/index/meta.yml b/modules/nf-core/bwameme/index/meta.yml index e0cb04a63..b89af8713 100644 --- a/modules/nf-core/bwameme/index/meta.yml +++ b/modules/nf-core/bwameme/index/meta.yml @@ -23,9 +23,10 @@ input: - fasta: type: file description: Input genome fasta file + ontologies: [] output: - - index: - - meta: + index: + - - meta: type: map description: | Groovy Map containing sample information @@ -34,11 +35,28 @@ output: type: file description: BWA-MEME genome index files pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwameme: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/index/tests/main.nf.test.snap b/modules/nf-core/bwameme/index/tests/main.nf.test.snap index e608af8b9..282e2e7f3 100644 --- a/modules/nf-core/bwameme/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwameme/index/tests/main.nf.test.snap @@ -21,7 +21,11 @@ ] ], "1": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ], "index": [ [ @@ -41,16 +45,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + "versions_bwameme": [ + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T13:44:38.551252246" + "timestamp": "2026-02-13T18:49:37.030181" }, "BWAMEME index": { "content": [ @@ -74,7 +82,11 @@ ] ], "1": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ], "index": [ [ @@ -94,15 +106,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,c80b8097b8a9c022e4c1e2617771ea3d" + "versions_bwameme": [ + [ + "BWAMEME_INDEX", + "bwameme", + "1.0.6" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-05-15T13:44:25.040725565" + "timestamp": "2026-02-13T18:49:29.151239" } } \ No newline at end of file diff --git a/modules/nf-core/bwameme/index/tests/tags.yml b/modules/nf-core/bwameme/index/tests/tags.yml deleted file mode 100644 index ddbcab044..000000000 --- a/modules/nf-core/bwameme/index/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwameme/index: - - "modules/nf-core/bwameme/index/**" diff --git a/modules/nf-core/bwameme/mem/environment.yml b/modules/nf-core/bwameme/mem/environment.yml index cad794404..21fb9c42f 100644 --- a/modules/nf-core/bwameme/mem/environment.yml +++ b/modules/nf-core/bwameme/mem/environment.yml @@ -4,6 +4,6 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::bwa-meme=1.0.6" - - "bioconda::mbuffer=20160228" - - "bioconda::samtools=1.20" + - bioconda::bwa-meme=1.0.6 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwameme/mem/main.nf b/modules/nf-core/bwameme/mem/main.nf index 2efc8c0fa..14421453b 100644 --- a/modules/nf-core/bwameme/mem/main.nf +++ b/modules/nf-core/bwameme/mem/main.nf @@ -4,8 +4,8 @@ process BWAMEME_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-ed29b84fa94419f5a7bf6a841ddbcb964768825b:139b5e403886ad278b9ad139174967441c1c6ff3-0': - 'biocontainers/mulled-v2-ed29b84fa94419f5a7bf6a841ddbcb964768825b:139b5e403886ad278b9ad139174967441c1c6ff3-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9ddd41b93c5e182db9d643ca266dd1677e59593a9cb49904b982ff45ad5aa8c3/data': + 'community.wave.seqera.io/library/bwa-meme_mbuffer_samtools:03f3f60b6c289776' }" input: tuple val(meta), path(reads) @@ -21,7 +21,8 @@ process BWAMEME_MEM { tuple val(meta), path("*.cram") , emit: cram, optional:true tuple val(meta), path("*.crai") , emit: crai, optional:true tuple val(meta), path("*.csi") , emit: csi , optional:true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwameme'), val('1.0.6'), topic: versions, emit: versions_bwameme + tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), topic: versions, emit: versions_samtools // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -50,7 +51,6 @@ process BWAMEME_MEM { def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` @@ -62,24 +62,15 @@ process BWAMEME_MEM { $reads \\ $mbuffer_command \\ | samtools $samtools_command $args2 $mem_per_thread -@ $threads ${reference} -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" def create_index = "" @@ -88,15 +79,8 @@ process BWAMEME_MEM { } else if (extension == "bam") { create_index = "touch ${prefix}.csi" } - def VERSION = '1.0.6' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions. """ touch ${prefix}.${extension} ${create_index} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwameme: $VERSION - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml index 070aefebf..324d96245 100644 --- a/modules/nf-core/bwameme/mem/meta.yml +++ b/modules/nf-core/bwameme/mem/meta.yml @@ -31,6 +31,7 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] - - meta2: type: map description: | @@ -40,6 +41,7 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + ontologies: [] - - meta3: type: map description: | @@ -49,19 +51,20 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fa,fasta,fna}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" - - - mbuffer: - type: integer - description: memory for mbuffer in megabytes (default 3072) - - - samtools_threads: - type: integer - description: number of threads for samtools (default 2) + ontologies: [] + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" + - mbuffer: + type: integer + description: memory for mbuffer in megabytes (default 3072) + - samtools_threads: + type: integer + description: number of threads for samtools (default 2) output: - - sam: - - meta: + sam: + - - meta: type: map description: | Groovy Map containing sample information @@ -70,8 +73,9 @@ output: type: file description: Output SAM file containing read alignments pattern: "*.{sam}" - - bam: - - meta: + ontologies: [] + bam: + - - meta: type: map description: | Groovy Map containing sample information @@ -80,8 +84,9 @@ output: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: + ontologies: [] + cram: + - - meta: type: map description: | Groovy Map containing sample information @@ -90,8 +95,9 @@ output: type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - crai: - - meta: + ontologies: [] + crai: + - - meta: type: map description: | Groovy Map containing sample information @@ -100,8 +106,9 @@ output: type: file description: Index file for CRAM file pattern: "*.{crai}" - - csi: - - meta: + ontologies: [] + csi: + - - meta: type: map description: | Groovy Map containing sample information @@ -110,11 +117,47 @@ output: type: file description: Index file for BAM file pattern: "*.{csi}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwameme: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwameme: + type: string + description: The name of the tool + - 1.0.6: + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: Name of the process + - samtools: + type: string + description: Name of the tool + - samtools version | sed "1!d;s/.* //": + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test b/modules/nf-core/bwameme/mem/tests/main.nf.test index 6d93fd6eb..fd378c0b3 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test @@ -187,4 +187,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap index bc845155c..5c6487e75 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap @@ -1,59 +1,51 @@ { "sarscov2 - [fastq1, fastq2], index, fasta, false, 0, 4": { "content": [ - "640e6a53bedb535837cc35cc1c145dcb", + "b537f2936bcb8c120127251ab44d917b", "57aeef88ed701a8ebc8e2f0a381b2a6", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:25:03.99184" + "timestamp": "2026-02-13T19:51:39.510097" }, - "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''": { + "sarscov2 - fastq, index, fasta, true, 2048, 4": { "content": [ - "7af5d6b93d3f8bd4f53d4f9ace7ee981", - "af8628d9df18b2d3d4f6fd47ef2bb872", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + "91c0b36a7aa238cca2acbce1997d94e8", + "94fcf617f5b994584c4e8d4044e16b4f", + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:26:17.237557" + "timestamp": "2026-02-13T19:51:19.196468" }, - "sarscov2 - fastq, index, fasta, true, 2048, 4": { + "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''": { "content": [ - "4ccda5ce5d3b09b697786589b3753825", - "94fcf617f5b994584c4e8d4044e16b4f", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + "ffc18373a0992612ccb5df41a245947b", + "af8628d9df18b2d3d4f6fd47ef2bb872", + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:24:07.289865" + "timestamp": "2026-02-13T19:52:00.628046" }, "sarscov2 - fastq, index, fasta, false, 0, 4": { "content": [ - "a58fa4a997be7d13a3dc62c9c9eb83d2", + "585cc3d6cdff0dce2e30b6e8c1542669", "798439cbd7fd81cbcc5078022dc5479d", - [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" - ] + null ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:23:17.201419" + "timestamp": "2026-02-13T19:50:58.198221" }, "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, 4 - stub": { "content": [ @@ -86,7 +78,18 @@ ] ], "5": [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "6": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] ], "bam": [ [ @@ -115,15 +118,26 @@ "sam": [ ], - "versions": [ - "versions.yml:md5,700d57071f430eb29b3c67d0a199eb95" + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-02T12:31:46.777111" + "timestamp": "2026-02-13T19:52:05.913267" } } \ No newline at end of file diff --git a/modules/nf-core/bwameme/mem/tests/tags.yml b/modules/nf-core/bwameme/mem/tests/tags.yml deleted file mode 100644 index 9e3a26cfe..000000000 --- a/modules/nf-core/bwameme/mem/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bwameme/mem: - - "modules/nf-core/bwameme/mem/**" diff --git a/modules/nf-core/custom/addmostsevereconsequence/environment.yml b/modules/nf-core/custom/addmostsevereconsequence/environment.yml new file mode 100644 index 000000000..315b7489e --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.21 + - conda-forge::python=3.13.2 diff --git a/modules/nf-core/custom/addmostsevereconsequence/main.nf b/modules/nf-core/custom/addmostsevereconsequence/main.nf index c4dacf3e9..5dfbd8798 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/main.nf +++ b/modules/nf-core/custom/addmostsevereconsequence/main.nf @@ -14,7 +14,8 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('addmostsevereconsequence'), val("1.1"), topic: versions, emit: versions_addmostsevereconsequence + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -23,8 +24,6 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. - """ add_most_severe_consequence.py \\ $args \\ @@ -36,26 +35,11 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { $args2 \\ --threads ${task.cpus} \\ ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. """ echo | gzip > ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_consequence: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ } diff --git a/modules/nf-core/custom/addmostsevereconsequence/meta.yml b/modules/nf-core/custom/addmostsevereconsequence/meta.yml index 07f69da7e..3f4e97af1 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/meta.yml +++ b/modules/nf-core/custom/addmostsevereconsequence/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_addmostsevereconsequence" description: Annotate a VEP annotated VCF with the most severe consequence field keywords: @@ -11,9 +10,9 @@ tools: description: "Custom module to annotate a VEP annotated VCF with the most severe consequence field" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostsevereconsequence/main.nf" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map @@ -34,7 +33,6 @@ input: type: file description: File with VEP variant consequences, one per line. pattern: "*" - ontologies: [] output: vcf: @@ -47,17 +45,48 @@ output: type: file description: Annotated VCF file pattern: "*.vcf.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 + versions_addmostsevereconsequence: + - - ${task.process}: + type: string + description: The name of the process + - addmostsevereconsequence: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - addmostsevereconsequence: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" - "@fellen31" diff --git a/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py index b3aa22a0c..a3902c062 100755 --- a/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py +++ b/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py @@ -7,7 +7,7 @@ import gzip import sys from pathlib import Path -from typing import Tuple, TextIO +from typing import TextIO, Tuple def parse_vep_csq_transcripts( diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test new file mode 100644 index 000000000..4664c198b --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test @@ -0,0 +1,146 @@ +// nf-core modules test custom/addmostsevereconsequence +nextflow_process { + + name "Test Process CUSTOM_ADDMOSTSEVERECONSEQUENCE" + script "../main.nf" + process "CUSTOM_ADDMOSTSEVERECONSEQUENCE" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/addmostsevereconsequence" + config "./nextflow.config" + + test("vcf") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + input[1] = Channel.of([ + "transcript_ablation", + "splice_acceptor_variant", + "splice_donor_variant", + "stop_gained", + "frameshift_variant", + "stop_lost", + "start_lost", + "transcript_amplification", + "feature_elongation", + "feature_truncation", + "inframe_insertion", + "inframe_deletion", + "missense_variant", + "protein_altering_variant", + "splice_donor_5th_base_variant", + "splice_region_variant", + "splice_donor_region_variant", + "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", + "start_retained_variant", + "stop_retained_variant", + "synonymous_variant", + "coding_sequence_variant", + "mature_miRNA_variant", + "5_prime_UTR_variant", + "3_prime_UTR_variant", + "non_coding_transcript_exon_variant", + "intron_variant", + "NMD_transcript_variant", + "non_coding_transcript_variant", + "coding_transcript_variant", + "upstream_gene_variant", + "downstream_gene_variant", + "TFBS_ablation", + "TFBS_amplification", + "TF_binding_site_variant", + "regulatory_region_ablation", + "regulatory_region_amplification", + "regulatory_region_variant", + "intergenic_variant", + "sequence_variant" + ]).collectFile(name: 'variant_consequences.txt', newLine:true).map { file -> [ [ id: file.simpleName ], file ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + input[1] = Channel.of([ + "transcript_ablation", + "splice_acceptor_variant", + "splice_donor_variant", + "stop_gained", + "frameshift_variant", + "stop_lost", + "start_lost", + "transcript_amplification", + "feature_elongation", + "feature_truncation", + "inframe_insertion", + "inframe_deletion", + "missense_variant", + "protein_altering_variant", + "splice_donor_5th_base_variant", + "splice_region_variant", + "splice_donor_region_variant", + "splice_polypyrimidine_tract_variant", + "incomplete_terminal_codon_variant", + "start_retained_variant", + "stop_retained_variant", + "synonymous_variant", + "coding_sequence_variant", + "mature_miRNA_variant", + "5_prime_UTR_variant", + "3_prime_UTR_variant", + "non_coding_transcript_exon_variant", + "intron_variant", + "NMD_transcript_variant", + "non_coding_transcript_variant", + "coding_transcript_variant", + "upstream_gene_variant", + "downstream_gene_variant", + "TFBS_ablation", + "TFBS_amplification", + "TF_binding_site_variant", + "regulatory_region_ablation", + "regulatory_region_amplification", + "regulatory_region_variant", + "intergenic_variant", + "sequence_variant" + ]).collectFile(name: 'variant_consequences.txt', newLine:true).map { file -> [ [ id: file.simpleName ], file ] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap new file mode 100644 index 000000000..5fad697fd --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap @@ -0,0 +1,112 @@ +{ + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d82db60282f5c594c105c010b3a76639" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d82db60282f5c594c105c010b3a76639" + ] + ], + "versions_addmostsevereconsequence": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:54:09.581706", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_addmostsevereconsequence": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "addmostsevereconsequence", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVERECONSEQUENCE", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:54:14.314711", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config b/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config new file mode 100644 index 000000000..651f0b86a --- /dev/null +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config @@ -0,0 +1 @@ +nextflow.enable.moduleBinaries = true diff --git a/modules/nf-core/custom/addmostseverepli/environment.yml b/modules/nf-core/custom/addmostseverepli/environment.yml new file mode 100644 index 000000000..315b7489e --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::htslib=1.21 + - conda-forge::python=3.13.2 diff --git a/modules/nf-core/custom/addmostseverepli/main.nf b/modules/nf-core/custom/addmostseverepli/main.nf index 0d252c046..f3fd3122c 100644 --- a/modules/nf-core/custom/addmostseverepli/main.nf +++ b/modules/nf-core/custom/addmostseverepli/main.nf @@ -12,7 +12,8 @@ process CUSTOM_ADDMOSTSEVEREPLI { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('addmostseverepli'), val("1.1"), topic: versions, emit: versions_addmostseverepli + tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: task.ext.when == null || task.ext.when @@ -21,8 +22,6 @@ process CUSTOM_ADDMOSTSEVEREPLI { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. - """ add_most_severe_pli.py \\ $args \\ @@ -33,26 +32,11 @@ process CUSTOM_ADDMOSTSEVEREPLI { $args2 \\ --threads ${task.cpus} \\ ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1' // WARN: Version information not provided by tool on CLI. """ echo | gzip > ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - add_most_severe_pli: $VERSION - bgzip: \$(bgzip --version |& sed '1!d ; s/bgzip (htslib) //') - END_VERSIONS """ } diff --git a/modules/nf-core/custom/addmostseverepli/meta.yml b/modules/nf-core/custom/addmostseverepli/meta.yml index f69423822..e17225229 100644 --- a/modules/nf-core/custom/addmostseverepli/meta.yml +++ b/modules/nf-core/custom/addmostseverepli/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_addmostseverepli" description: Annotate a VEP annotated VCF with the most severe pLi field keywords: @@ -11,9 +10,9 @@ tools: description: "Custom module to annotate a VEP annotated VCF with the most severe pLi field" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/addmostseverepli/main.nf" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map @@ -24,7 +23,6 @@ input: type: file description: VEP annotated VCF file pattern: "*.{vcf,vcf.gz}" - ontologies: [] output: vcf: @@ -37,17 +35,48 @@ output: type: file description: Annotated VCF file pattern: "*.vcf.gz" - ontologies: - - edam: http://edamontology.org/format_3989 # GZIP format + - edam: http://edamontology.org/format_3989 + versions_addmostseverepli: + - - ${task.process}: + type: string + description: The name of the process + - addmostseverepli: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + versions_bgzip: + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - addmostseverepli: + type: string + description: The name of the tool + - "1.1": + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - bgzip: + type: string + description: The name of the tool + - bgzip --version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" - "@fellen31" diff --git a/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py index 6ef40515a..8c0b3d00d 100755 --- a/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py +++ b/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py @@ -57,7 +57,7 @@ def construct_most_severe_pli_info(line: str, pli_ind: int) -> list: except ValueError: pli_max = "" if pli_max: - columns[7] += ";most_severe_pli={:.2f}".format(float(pli_max)) + columns[7] += f";most_severe_pli={float(pli_max):.2f}" return columns diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test new file mode 100644 index 000000000..5263f5c5c --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test @@ -0,0 +1,60 @@ +// nf-core modules test custom/addmostseverepli +nextflow_process { + + name "Test Process CUSTOM_ADDMOSTSEVEREPLI" + script "../main.nf" + process "CUSTOM_ADDMOSTSEVEREPLI" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/addmostseverepli" + config "./nextflow.config" + + test("vcf") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap new file mode 100644 index 000000000..d492bb3ce --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap @@ -0,0 +1,112 @@ +{ + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d29918951676cc028d980aaab161db21" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,d29918951676cc028d980aaab161db21" + ] + ], + "versions_addmostseverepli": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:53:27.215565", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "2": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_addmostseverepli": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "addmostseverepli", + "1.1" + ] + ], + "versions_bgzip": [ + [ + "CUSTOM_ADDMOSTSEVEREPLI", + "bgzip", + "1.21" + ] + ] + } + ], + "timestamp": "2026-02-16T10:53:31.072965", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/addmostseverepli/tests/nextflow.config b/modules/nf-core/custom/addmostseverepli/tests/nextflow.config new file mode 100644 index 000000000..651f0b86a --- /dev/null +++ b/modules/nf-core/custom/addmostseverepli/tests/nextflow.config @@ -0,0 +1 @@ +nextflow.enable.moduleBinaries = true diff --git a/modules/nf-core/glnexus/environment.yml b/modules/nf-core/glnexus/environment.yml index 9190508a9..c9e4703dc 100644 --- a/modules/nf-core/glnexus/environment.yml +++ b/modules/nf-core/glnexus/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: + - bioconda::bcftools=1.21 - bioconda::glnexus=1.4.1 diff --git a/modules/nf-core/glnexus/main.nf b/modules/nf-core/glnexus/main.nf index 191f04995..65180995e 100644 --- a/modules/nf-core/glnexus/main.nf +++ b/modules/nf-core/glnexus/main.nf @@ -4,16 +4,16 @@ process GLNEXUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' : - 'biocontainers/glnexus:1.4.1--h40d77a6_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6c/6cf504ad8e4ebda286609fa3c1a5f9af68dbca9ec06bb4428e219e84754bd140/data' : + 'community.wave.seqera.io/library/bcftools_glnexus:cf380f1a6410f606' }" input: - tuple val(meta), path(gvcfs) + tuple val(meta), path(gvcfs), path(custom_config) tuple val(meta2), path(bed) output: tuple val(meta), path("*.bcf"), emit: bcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('glnexus'), eval("glnexus_cli 2>&1 | grep -oE '[0-9]+\\.[0-9]+\\.[0-9]+'"), topic: versions, emit: versions_glnexus when: task.ext.when == null || task.ext.when @@ -24,7 +24,7 @@ process GLNEXUS { def regions = bed ? "--bed ${bed}" : "" // Make list of GVCFs to merge - def input = gvcfs.collect { it.toString() } + def input = gvcfs.collect {vcf -> vcf.toString() } def avail_mem = 3 if (!task.memory) { log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' @@ -39,21 +39,11 @@ process GLNEXUS { $args \\ ${input.join(' ')} \\ > ${prefix}.bcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index 8f18bf3f8..cacfa5c90 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -23,6 +23,12 @@ input: type: list description: Input genomic vcf files pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + - custom_config: + type: file + description: Custom YML config for additional profiles + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML - - meta2: type: map description: | @@ -33,20 +39,38 @@ input: description: Input BED file pattern: "*.bed" output: - - bcf: - - meta: - type: file - description: merged BCF file - pattern: "*.bcf" + bcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] - "*.bcf": type: file description: merged BCF file pattern: "*.bcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_glnexus: + - - ${task.process}: + type: string + description: The name of the process + - glnexus: + type: string + description: The name of the tool + - glnexus_cli 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - glnexus: + type: string + description: The name of the tool + - glnexus_cli 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/glnexus/tests/main.nf.test b/modules/nf-core/glnexus/tests/main.nf.test new file mode 100644 index 000000000..647373559 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test @@ -0,0 +1,126 @@ +nextflow_process { + + name "Test Process GLNEXUS" + script "../main.nf" + process "GLNEXUS" + + tag "modules" + tag "modules_nfcore" + tag "glnexus" + + test("vcfs, []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, [], custom_config") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + file(params.modules_testdata_base_path + '/delete_me/glnexus/gatk.yml', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("vcfs, bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), + ], + [] + ]) + input[1] = [ + [ id:'region' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/glnexus/tests/main.nf.test.snap b/modules/nf-core/glnexus/tests/main.nf.test.snap new file mode 100644 index 000000000..00426dd67 --- /dev/null +++ b/modules/nf-core/glnexus/tests/main.nf.test.snap @@ -0,0 +1,166 @@ +{ + "vcfs, bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:43:16.499731323" + }, + "vcfs, [], custom_config": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:39:47.593781473" + }, + "vcfs, bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:41:26.083883984" + }, + "vcfs, []": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "1": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ], + "bcf": [ + [ + { + "id": "test" + }, + "test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" + ] + ], + "versions_glnexus": [ + [ + "GLNEXUS", + "glnexus", + "1.4.1" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-14T22:36:50.552668413" + } +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 1d9370107..906d36fe5 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -15,7 +15,7 @@ process HISAT2_BUILD { output: tuple val(meta), path("hisat2"), emit: index - path "versions.yml", emit: versions + tuple val("${task.process}"), val('hisat2'), eval("hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'"), emit: versions_hisat2, topic: versions when: task.ext.when == null || task.ext.when @@ -55,20 +55,10 @@ process HISAT2_BUILD { ${args} \\ ${fasta} \\ hisat2/${fasta.baseName} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) - END_VERSIONS """ stub: """ mkdir hisat2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) - END_VERSIONS """ } diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index ede99d0cc..805804910 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -59,13 +59,29 @@ output: description: HISAT2 genome index file pattern: "*.ht2" ontologies: [] + versions_hisat2: + - - ${task.process}: + type: string + description: The name of the process + - hisat2: + type: string + description: The name of the tool + - "hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - hisat2: + type: string + description: The name of the tool + - "hisat2 --version | sed -n 's/.*version \\([^ ]*\\).*/\\1/p'": + type: eval + description: The expression to obtain the version of the tool + authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index 948f98eae..9bee5f676 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -46,7 +46,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } @@ -91,7 +94,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } ) } } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index 68fc7ffba..99b33cb2c 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,90 +1,54 @@ { "Should run without failures - stub": { "content": [ + [ + [ + { + "id": "genome" + }, + "hisat2" + ] + ], { - "0": [ - [ - { - "id": "genome" - }, - [ - - ] - ] - ], - "1": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ], - "index": [ + "versions_hisat2": [ [ - { - "id": "genome" - }, - [ - - ] + "HISAT2_BUILD", + "hisat2", + "2.2.1" ] - ], - "versions": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-06-20T18:18:08.896422" + "timestamp": "2026-02-02T15:53:37.611420605" }, "Should run without failures": { "content": [ + [ + [ + { + "id": "genome" + }, + "hisat2" + ] + ], { - "0": [ - [ - { - "id": "genome" - }, - [ - "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", - "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", - "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", - "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" - ] - ] - ], - "1": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ], - "index": [ + "versions_hisat2": [ [ - { - "id": "genome" - }, - [ - "genome.1.ht2:md5,057cfa8a22b97ee9cff4c8d342498803", - "genome.2.ht2:md5,47b153cd1319abc88dda532462651fcf", - "genome.3.ht2:md5,4ed93abba181d8dfab2e303e33114777", - "genome.4.ht2:md5,c25be5f8b0378abf7a58c8a880b87626", - "genome.5.ht2:md5,91198831aaba993acac1734138c5f173", - "genome.6.ht2:md5,265e1284ce85686516fae5d35540994a", - "genome.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "genome.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" - ] + "HISAT2_BUILD", + "hisat2", + "2.2.1" ] - ], - "versions": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2023-10-16T14:42:22.381609786" + "timestamp": "2026-02-02T15:53:31.34596606" } } \ No newline at end of file diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index ae1df8b42..43d84750b 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -12,7 +12,8 @@ process LAST_LASTDB { output: tuple val(meta), path("lastdb"), emit: index - path "versions.yml" , emit: versions + // last-dotplot has no --version option so let's use lastal from the same suite + tuple val("${task.process}"), val('last'), eval("lastal --version | sed 's/lastal //'"), emit: versions_last, topic: versions when: task.ext.when == null || task.ext.when @@ -27,11 +28,6 @@ process LAST_LASTDB { -P $task.cpus \\ lastdb/${prefix} \\ $fastx - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - last: \$(lastdb --version 2>&1 | sed 's/lastdb //') - END_VERSIONS """ stub: @@ -47,9 +43,5 @@ process LAST_LASTDB { touch lastdb/${prefix}.suf touch lastdb/${prefix}.tis - cat <<-END_VERSIONS > versions.yml - "${task.process}": - last: \$(lastdb --version 2>&1 | sed 's/lastdb //') - END_VERSIONS """ } diff --git a/modules/nf-core/last/lastdb/meta.yml b/modules/nf-core/last/lastdb/meta.yml index 9a5bcbb0a..4c041d211 100644 --- a/modules/nf-core/last/lastdb/meta.yml +++ b/modules/nf-core/last/lastdb/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +cd# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastdb" description: Prepare sequences for subsequent alignment with lastal. keywords: @@ -38,13 +38,27 @@ output: type: directory description: directory containing the files of the LAST index pattern: "lastdb/" + versions_last: + - - "${task.process}": + type: string + description: The name of the process + - last: + type: string + description: The name of the tool + - "lastal --version | sed 's/lastal //'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - "${task.process}": + type: string + description: The name of the process + - last: + type: string + description: The name of the tool + - "lastal --version | sed 's/lastal //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap index 382b364ba..e54777878 100644 --- a/modules/nf-core/last/lastdb/tests/main.nf.test.snap +++ b/modules/nf-core/last/lastdb/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -37,16 +41,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:34.761783" + "timestamp": "2026-01-13T10:40:55.31640271" }, "sarscov2 - fastq gzipped": { "content": [ @@ -68,7 +76,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -86,16 +98,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:20.038195" + "timestamp": "2026-01-13T10:40:49.204117613" }, "sarscov2 - fasta": { "content": [ @@ -117,7 +133,11 @@ ] ], "1": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + [ + "LAST_LASTDB", + "last", + "1611" + ] ], "index": [ [ @@ -135,15 +155,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,a0aad4eacbb831df9f84d73678be09a1" + "versions_last": [ + [ + "LAST_LASTDB", + "last", + "1611" + ] ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.10.2" }, - "timestamp": "2025-03-10T10:48:04.861781" + "timestamp": "2026-01-13T10:40:42.992657054" } } \ No newline at end of file diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml index 906277c5d..b8793f52a 100644 --- a/modules/nf-core/ngsbits/samplegender/environment.yml +++ b/modules/nf-core/ngsbits/samplegender/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ngs-bits=2024_11 + # renovate: datasource=conda depName=bioconda/ngs-bits + - bioconda::ngs-bits=2025_12 diff --git a/modules/nf-core/ngsbits/samplegender/main.nf b/modules/nf-core/ngsbits/samplegender/main.nf index 655149084..39ab69b4c 100644 --- a/modules/nf-core/ngsbits/samplegender/main.nf +++ b/modules/nf-core/ngsbits/samplegender/main.nf @@ -4,8 +4,8 @@ process NGSBITS_SAMPLEGENDER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ngs-bits:2024_11--py312hd80e9a6_0': - 'biocontainers/ngs-bits:2024_11--py312hd80e9a6_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data': + 'community.wave.seqera.io/library/ngs-bits:2025_12--958625b0e620100a' }" input: tuple val(meta), path(bam), path(bai) @@ -15,7 +15,7 @@ process NGSBITS_SAMPLEGENDER { output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('ngsbits'), eval("SampleGender --version 2>&1 | sed 's/SampleGender //'"), topic: versions, emit: versions_ngsbits when: task.ext.when == null || task.ext.when @@ -31,21 +31,11 @@ process NGSBITS_SAMPLEGENDER { -out ${prefix}.tsv \\ ${ref} \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ngs-bits: \$(echo \$(SampleGender --version 2>&1) | sed 's/SampleGender //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ngs-bits: \$(echo \$(SampleGender --version 2>&1) | sed 's/SampleGender //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml index 4b79dfca3..8d4773efe 100644 --- a/modules/nf-core/ngsbits/samplegender/meta.yml +++ b/modules/nf-core/ngsbits/samplegender/meta.yml @@ -11,7 +11,8 @@ tools: homepage: "https://github.com/imgag/ngs-bits" documentation: "https://github.com/imgag/ngs-bits" tool_dev_url: "https://github.com/imgag/ngs-bits" - licence: ["MIT"] + licence: + - "MIT" identifier: "" input: - - meta: @@ -36,7 +37,8 @@ input: e.g. [ id:'test' ] - fasta: type: file - description: The reference FASTA to use (mandatory when CRAM files are used) + description: The reference FASTA to use (mandatory when CRAM files are + used) pattern: "*.{fasta,fa,fna}" ontologies: [] - - meta3: @@ -51,8 +53,8 @@ input: ontologies: [] - method: type: string - description: The method to use to define the gender (possibilities are 'xy', 'hetx' - and 'sry') + description: The method to use to define the gender (possibilities are 'xy', + 'hetx' and 'sry') pattern: "(xy|hetx|sry)" output: tsv: @@ -63,17 +65,32 @@ output: e.g. [ id:'test', single_end:false ] - "*.tsv": type: file - description: An output TSV file containing the results of the gender prediction + description: An output TSV file containing the results of the gender + prediction pattern: "*.tsv" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 + versions_ngsbits: + - - ${task.process}: + type: string + description: The name of the process + - ngsbits: + type: string + description: The name of the tool + - SampleGender --version 2>&1 | sed 's/SampleGender //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - ngsbits: + type: string + description: The name of the tool + - SampleGender --version 2>&1 | sed 's/SampleGender //': + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap index cb493a2c2..f6343474d 100644 --- a/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap +++ b/modules/nf-core/ngsbits/samplegender/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" + [ + "NGSBITS_SAMPLEGENDER", + "ngsbits", + "2025_12" + ] ], "tsv": [ [ @@ -21,15 +25,19 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,9c2c2b8cf880d89b4eb1c06e3b7f7333" + "versions_ngsbits": [ + [ + "NGSBITS_SAMPLEGENDER", + "ngsbits", + "2025_12" + ] ] } ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.1" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-12-10T13:36:08.650020628" + "timestamp": "2026-02-16T09:21:42.78314623" } } \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index 8140e143e..5d7109bed 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -4,8 +4,8 @@ process QUALIMAP_BAMQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' : - 'biocontainers/qualimap:2.3--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b795495fdae4cb3319d19ed4a694302366aa574ba15a0613b85c602f0de4911/data' : + 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' }" input: tuple val(meta), path(bam) @@ -13,7 +13,7 @@ process QUALIMAP_BAMQC { output: tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap when: task.ext.when == null || task.ext.when @@ -46,11 +46,6 @@ process QUALIMAP_BAMQC { $collect_pairs \\ -outdir $prefix \\ -nt $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS """ stub: @@ -114,10 +109,5 @@ process QUALIMAP_BAMQC { touch genome_results.txt touch qualimapReport.html cd ../ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 6a563fa4c..e93a99137 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -43,13 +43,27 @@ output: type: directory description: Qualimap results dir pattern: "*/*" + versions_qualimap: + - - ${task.process}: + type: string + description: The name of the process + - qualimap: + type: string + description: The name of the tool + - qualimap -h | sed -n 's/^QualiMap v.//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - qualimap: + type: string + description: The name of the tool + - qualimap -h | sed -n 's/^QualiMap v.//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@phue" maintainers: diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test index eec1a41a1..7deb086dd 100644 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test @@ -29,7 +29,7 @@ nextflow_process { { assert snapshot( file("${process.out.results[0][1]}/qualimapReport.html").name, path("${process.out.results[0][1]}/genome_results.txt"), - process.out.versions) + process.out.findAll {key, value -> key.startsWith("versions")}) .match() } ) } @@ -58,4 +58,4 @@ nextflow_process { ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap index fb6e23e49..0f67dee18 100644 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap @@ -69,7 +69,11 @@ ] ], "1": [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] ], "results": [ [ @@ -137,29 +141,39 @@ ] ] ], - "versions": [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" + "versions_qualimap": [ + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-22T12:27:15.04081" + "timestamp": "2026-02-13T22:03:27.280522" }, "homo_sapiens [bam]": { "content": [ "qualimapReport.html", "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3", - [ - "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" - ] + { + "versions_qualimap": [ + [ + "QUALIMAP_BAMQC", + "qualimap", + "2.3" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-07-22T11:21:02.541915" + "timestamp": "2026-02-13T22:12:46.38879" } } \ No newline at end of file diff --git a/modules/nf-core/rtgtools/format/environment.yml b/modules/nf-core/rtgtools/format/environment.yml index 8aa83cdc4..27597a220 100644 --- a/modules/nf-core/rtgtools/format/environment.yml +++ b/modules/nf-core/rtgtools/format/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::rtg-tools=3.12.1 + - bioconda::rtg-tools=3.13 diff --git a/modules/nf-core/rtgtools/format/main.nf b/modules/nf-core/rtgtools/format/main.nf index 9cae7f99c..ffbbbdfb9 100644 --- a/modules/nf-core/rtgtools/format/main.nf +++ b/modules/nf-core/rtgtools/format/main.nf @@ -4,15 +4,15 @@ process RTGTOOLS_FORMAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dca5ba13b7ec38bf7cacf00a33517b9080067bea638745c05d50a4957c75fc2e/data': + 'community.wave.seqera.io/library/rtg-tools:3.13--3465421f1b0be0ce' }" input: tuple val(meta), path(input1), path(input2), path(sam_rg) output: tuple val(meta), path("*.sdf"), emit: sdf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('rtgtools'), eval("rtg version | head -n 1 | sed 's/Product: RTG Tools //'"), topic: versions, emit: versions_rtgtools when: task.ext.when == null || task.ext.when @@ -38,11 +38,6 @@ process RTGTOOLS_FORMAT { ${rg} \\ --output ${prefix}.sdf \\ ${input} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ stub: @@ -56,10 +51,5 @@ process RTGTOOLS_FORMAT { } """ touch ${prefix}.sdf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ } diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index e09aff3af..309a9ffb0 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -1,6 +1,6 @@ name: "rtgtools_format" -description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into - the RTG Sequence Data File (SDF) format. +description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) + into the RTG Sequence Data File (SDF) format. keywords: - rtg - fasta @@ -12,9 +12,10 @@ tools: description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" - documentation: "https://github.com/RealTimeGenomics/rtg-tools" + documentation: "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: ["BSD"] + licence: + - "BSD" identifier: "" input: - - meta: @@ -24,34 +25,57 @@ input: e.g. [ id:'test', single_end:false ] - input1: type: file - description: FASTA, FASTQ, BAM or SAM file. This should be the left input file - when using paired end FASTQ/FASTA data + description: FASTA, FASTQ, BAM or SAM file. This should be the left input + file when using paired end FASTQ/FASTA data pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ - input2: type: file description: The right input file when using paired end FASTQ/FASTA data pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ - sam_rg: type: file - description: A file containing a single readgroup header as a SAM header. This - can also be supplied as a string in `task.ext.args` as `--sam-rg `. + description: A file containing a single readgroup header as a SAM header. + This can also be supplied as a string in `task.ext.args` as `--sam-rg + `. pattern: "*.{txt,sam}" + ontologies: [] output: - - sdf: - - meta: + sdf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.sdf": type: directory - description: The sequence dictionary format folder created from the input file(s) + description: The sequence dictionary format folder created from the + input file(s) pattern: "*.sdf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions_rtgtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | head -n 1 | sed 's/Product: RTG Tools //'": + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/format/tests/fastq.config b/modules/nf-core/rtgtools/format/tests/fastq.config new file mode 100644 index 000000000..24540986e --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/fastq.config @@ -0,0 +1,3 @@ +process { + ext.args = "--format fastq" +} diff --git a/modules/nf-core/rtgtools/format/tests/main.nf.test b/modules/nf-core/rtgtools/format/tests/main.nf.test new file mode 100644 index 000000000..d768da7d8 --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/main.nf.test @@ -0,0 +1,138 @@ +nextflow_process { + + name "Test Process RTGTOOLS_FORMAT" + script "../main.nf" + process "RTGTOOLS_FORMAT" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/format" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - fastqs") { + + config "./fastq.config" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - bam, rg") { + + config "./sam.config" + + when { + process { + """ + def rg = Channel.of("@RG\tID:READGROUP1\tSM:SAMPLE\tPL:ILLUMINA") + .collectFile(name:'sam_rg.txt') + + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true), + [] + ]).combine(rg) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.sdf[0][1]).list().collect { file(it.toString()).name }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/rtgtools/format/tests/main.nf.test.snap b/modules/nf-core/rtgtools/format/tests/main.nf.test.snap new file mode 100644 index 000000000..437afa7af --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/main.nf.test.snap @@ -0,0 +1,144 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.sdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ], + "sdf": [ + [ + { + "id": "test" + }, + "test.sdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:42.538436462", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - fasta": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "suffixIndex0", + "suffixdata0", + "suffixpointer0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:07.354438336", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - fastqs": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "qualitydata0", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "suffixIndex0", + "suffixdata0", + "suffixpointer0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:19.613328433", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + }, + "sarscov2 - bam, rg": { + "content": [ + [ + "done", + "format.log", + "mainIndex", + "nameIndex0", + "namedata0", + "namepointer0", + "progress", + "qualitydata0", + "seqdata0", + "seqpointer0", + "sequenceIndex0", + "summary.txt" + ], + { + "versions_rtgtools": [ + [ + "RTGTOOLS_FORMAT", + "rtgtools", + "3.13" + ] + ] + } + ], + "timestamp": "2026-02-12T14:17:31.66811346", + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/format/tests/sam.config b/modules/nf-core/rtgtools/format/tests/sam.config new file mode 100644 index 000000000..5ccfdb27b --- /dev/null +++ b/modules/nf-core/rtgtools/format/tests/sam.config @@ -0,0 +1,3 @@ +process { + ext.args = "--format sam-se" +} diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index 8aa83cdc4..27597a220 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::rtg-tools=3.12.1 + - bioconda::rtg-tools=3.13 diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 330a1f3d9..82477eb11 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -4,8 +4,8 @@ process RTGTOOLS_VCFEVAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0': - 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dca5ba13b7ec38bf7cacf00a33517b9080067bea638745c05d50a4957c75fc2e/data': + 'community.wave.seqera.io/library/rtg-tools:3.13--3465421f1b0be0ce' }" input: tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(regions_bed) @@ -25,7 +25,8 @@ process RTGTOOLS_VCFEVAL { tuple val(meta), path("*.weighted_roc.tsv.gz") , emit: weighted_roc tuple val(meta), path("*.summary.txt") , emit: summary tuple val(meta), path("*.phasing.txt") , emit: phasing - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('rtgtools'), eval("rtg version | sed 's/Product: RTG Tools //; q'"), topic: versions, emit: versions_rtgtools + when: task.ext.when == null || task.ext.when @@ -57,11 +58,6 @@ process RTGTOOLS_VCFEVAL { mv done progress .. for f in * ; do mv "\$f" "../${prefix}.\$f" ; done cd .. - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ stub: @@ -81,10 +77,5 @@ process RTGTOOLS_VCFEVAL { echo | gzip > ${prefix}.weighted_roc.tsv.gz touch ${prefix}.summary.txt touch ${prefix}.phasing.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}')) - END_VERSIONS """ } diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 4c59bab52..bfe06aa94 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -1,6 +1,6 @@ name: "rtgtools_vcfeval" -description: The VCFeval tool of RTG tools. It is used to evaluate called variants - for agreement with a baseline variant set +description: The VCFeval tool of RTG tools. It is used to evaluate called + variants for agreement with a baseline variant set keywords: - benchmarking - vcf @@ -10,9 +10,10 @@ tools: description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" - documentation: "https://github.com/RealTimeGenomics/rtg-tools" + documentation: "https://cdn.jsdelivr.net/gh/RealTimeGenomics/rtg-tools@master/installer/resources/tools/RTGOperationsManual.pdf" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: ["BSD"] + licence: + - "BSD" identifier: "" input: - - meta: @@ -24,30 +25,37 @@ input: type: file description: A VCF with called variants to benchmark against the standard pattern: "*.{vcf,vcf.gz}" + ontologies: [] - query_vcf_tbi: type: file - description: The index of the VCF file with called variants to benchmark against the standard + description: The index of the VCF file with called variants to benchmark + against the standard pattern: "*.{vcf.gz.tbi, vcf.tbi}" + ontologies: [] - truth_vcf: type: file description: A standard VCF to compare against pattern: "*.{vcf,vcf.gz}" + ontologies: [] - truth_vcf_tbi: type: file description: The index of the standard VCF to compare against pattern: "*.{vcf.gz.tbi, vcf.tbi}" + ontologies: [] - truth_bed: type: file - description: A BED file containining the strict regions where VCFeval should - only evaluate the fully overlapping variants (optional) - This input should be used to provide the golden truth BED files. + description: A BED file containing the strict regions where VCFeval should + only evaluate the fully overlapping variants (optional) This input + should be used to provide the golden truth BED files. pattern: "*.bed" + ontologies: [] - regions_bed: type: file - description: A BED file containing the regions where VCFeval will evaluate every - fully and partially overlapping variant (optional) - This input should be used to provide the regions used by the analysis + description: A BED file containing the regions where VCFeval will evaluate + every fully and partially overlapping variant (optional) This input + should be used to provide the regions used by the analysis pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -55,10 +63,12 @@ input: e.g. [ id:'test', single_end:false ] - sdf: type: file - description: The SDF (RTG Sequence Data File) folder of the reference genome + description: The SDF (RTG Sequence Data File) folder of the reference + genome + ontologies: [] output: - - tp_vcf: - - meta: + tp_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -67,8 +77,10 @@ output: type: file description: A VCF file for the true positive variants pattern: "*.tp.vcf.gz" - - tp_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + tp_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -77,8 +89,9 @@ output: type: file description: The index of the VCF file for the true positive variants pattern: "*.tp.vcf.gz.tbi" - - fn_vcf: - - meta: + ontologies: [] + fn_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -87,8 +100,10 @@ output: type: file description: A VCF file for the false negative variants pattern: "*.fn.vcf.gz" - - fn_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + fn_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -97,8 +112,9 @@ output: type: file description: The index of the VCF file for the false negative variants pattern: "*.fn.vcf.gz.tbi" - - fp_vcf: - - meta: + ontologies: [] + fp_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -107,8 +123,10 @@ output: type: file description: A VCF file for the false positive variants pattern: "*.fp.vcf.gz" - - fp_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + fp_tbi: + - - meta: type: map description: | Groovy Map containing sample information @@ -117,8 +135,9 @@ output: type: file description: The index of the VCF file for the false positive variants pattern: "*.fp.vcf.gz.tbi" - - baseline_vcf: - - meta: + ontologies: [] + baseline_vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -127,19 +146,22 @@ output: type: file description: A VCF file for the true positive variants from the baseline pattern: "*.tp-baseline.vcf.gz" - - baseline_tbi: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + baseline_tbi: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*.tp-baseline.vcf.gz.tbi": type: file - description: The index of the VCF file for the true positive variants from the - baseline + description: The index of the VCF file for the true positive variants + from the baseline pattern: "*.tp-baseline.vcf.gz.tbi" - - snp_roc: - - meta: + ontologies: [] + snp_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -148,8 +170,10 @@ output: type: file description: TSV files containing ROC data for the SNPs pattern: "*.snp_roc.tsv.gz" - - non_snp_roc: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + non_snp_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -158,8 +182,10 @@ output: type: file description: TSV files containing ROC data for all variants except SNPs pattern: "*.non_snp_roc.tsv.gz" - - weighted_roc: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + weighted_roc: + - - meta: type: map description: | Groovy Map containing sample information @@ -168,8 +194,10 @@ output: type: file description: TSV files containing weighted ROC data for all variants pattern: "*.weighted_snp_roc.tsv.gz" - - summary: - - meta: + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + summary: + - - meta: type: map description: | Groovy Map containing sample information @@ -178,8 +206,9 @@ output: type: file description: A TXT file containing the summary of the evaluation pattern: "*.summary.txt" - - phasing: - - meta: + ontologies: [] + phasing: + - - meta: type: map description: | Groovy Map containing sample information @@ -188,11 +217,28 @@ output: type: file description: A TXT file containing the data on the phasing pattern: "*.phasing.txt" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rtgtools: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | sed 's/Product: RTG Tools //; q'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - rtgtools: + type: string + description: The name of the tool + - "rtg version | sed 's/Product: RTG Tools //; q'": + type: eval + description: The expression to obtain the version of the tool authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap index 4f39e2d46..f85d503e5 100644 --- a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap @@ -23,7 +23,7 @@ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + "test.weighted_roc.tsv.gz:md5,c0155caab6b8a314c303ca1b481ba1af" ] ], "11": [ @@ -43,7 +43,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -98,7 +102,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + "test.snp_roc.tsv.gz:md5,6c8977c744a08c90123a21f22c0f4e54" ] ], "9": [ @@ -106,7 +110,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + "test.non_snp_roc.tsv.gz:md5,574afefc756c4102bb3aefb0cde19dff" ] ], "baseline_tbi": [ @@ -162,7 +166,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + "test.non_snp_roc.tsv.gz:md5,574afefc756c4102bb3aefb0cde19dff" ] ], "phasing": [ @@ -178,7 +182,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + "test.snp_roc.tsv.gz:md5,6c8977c744a08c90123a21f22c0f4e54" ] ], "summary": [ @@ -205,24 +209,28 @@ "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + "test.weighted_roc.tsv.gz:md5,c0155caab6b8a314c303ca1b481ba1af" ] ] } ], + "timestamp": "2026-02-12T13:43:20.930061214", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:17:31.564974666" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } }, "homo_sapiens - [vcf, [], truth, [], [], []], sdf": { "content": [ @@ -248,7 +256,7 @@ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + "test.weighted_roc.tsv.gz:md5,599331bcba15312abc402bdffc8d2e30" ] ], "11": [ @@ -268,7 +276,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -323,7 +335,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + "test.snp_roc.tsv.gz:md5,7906ac0bdf54d34ac9b52bfd101cddfd" ] ], "9": [ @@ -331,7 +343,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + "test.non_snp_roc.tsv.gz:md5,0917d6986ae90818f431c316b1cbea27" ] ], "baseline_tbi": [ @@ -387,7 +399,7 @@ { "id": "test" }, - "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + "test.non_snp_roc.tsv.gz:md5,0917d6986ae90818f431c316b1cbea27" ] ], "phasing": [ @@ -403,7 +415,7 @@ { "id": "test" }, - "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + "test.snp_roc.tsv.gz:md5,7906ac0bdf54d34ac9b52bfd101cddfd" ] ], "summary": [ @@ -430,24 +442,28 @@ "test.tp.vcf.gz:md5,5125ee41457c9d93f46b19e32788edb4" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ { "id": "test" }, - "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + "test.weighted_roc.tsv.gz:md5,599331bcba15312abc402bdffc8d2e30" ] ] } ], + "timestamp": "2026-02-12T13:43:44.651308348", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:18:04.344989466" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } }, "homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub": { "content": [ @@ -493,7 +509,11 @@ ] ], "13": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "2": [ [ @@ -655,8 +675,12 @@ "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + "versions_rtgtools": [ + [ + "RTGTOOLS_VCFEVAL", + "rtgtools", + "3.13" + ] ], "weighted_roc": [ [ @@ -668,10 +692,10 @@ ] } ], + "timestamp": "2026-02-12T13:44:03.078796934", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-30T15:23:21.165461388" + "nf-test": "0.9.3", + "nextflow": "25.04.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index b92410cd6..a81622ba2 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_COLLATE { input: tuple val(meta), path(input) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) output: tuple val(meta), path("*.bam"), emit: bam, optional: true diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index f6069abc4..5e4c71548 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -29,12 +29,17 @@ input: - - meta2: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file - description: FASTA ref file - pattern: "*.fasta" + description: Reference genome file + pattern: "*.{fa,fasta}" + ontologies: [] + - fai: + type: file + description: Reference genome index file + pattern: "*.fai" ontologies: [] output: #Only when we have meta diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test b/modules/nf-core/samtools/collate/tests/main.nf.test index 2918f9e3d..b2dedc717 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test +++ b/modules/nf-core/samtools/collate/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - input[1] = [ [id:'fasta'], [] ] + input[1] = [ [id:'fasta'], [], [] ] """ } } @@ -41,7 +41,8 @@ nextflow_process { ] input[1] = [ [ id:'fasta'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + [] ] """ } @@ -63,7 +64,7 @@ nextflow_process { [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ] - input[1] = [ [id:'fasta'], [] ] + input[1] = [ [id:'fasta'], [], [] ] """ } } diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 57a03497f..97bfb578f 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -8,8 +8,7 @@ process SAMTOOLS_FAIDX { 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: - tuple val(meta), path(fasta) - tuple val(meta2), path(fai) + tuple val(meta), path(fasta), path(fai) val get_sizes output: diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 163c30151..80aae1dae 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -1,5 +1,6 @@ name: samtools_faidx -description: Index FASTA file, and optionally generate a file of chromosome sizes +description: Index FASTA file, and optionally generate a file of chromosome + sizes keywords: - index - fasta @@ -14,7 +15,8 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:samtools input: - - meta: @@ -27,11 +29,6 @@ input: description: FASTA file pattern: "*.{fa,fasta}" ontologies: [] - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - fai: type: file description: FASTA index file @@ -40,7 +37,6 @@ input: - get_sizes: type: boolean description: use cut to get the sizes of the index (true) or not (false) - output: fa: - - meta: @@ -94,9 +90,8 @@ output: type: string description: The tool name - "samtools version | sed '1!d;s/.* //'": - type: string + type: eval description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -106,7 +101,7 @@ topics: type: string description: The tool name - "samtools version | sed '1!d;s/.* //'": - type: string + type: eval description: The command used to generate the version of the tool authors: - "@drpatelh" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test index 02ba5040c..9a86db862 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -18,10 +18,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -29,7 +31,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -42,10 +44,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -53,7 +57,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -66,11 +70,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = false """ } } @@ -78,7 +83,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -92,11 +97,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = false """ } } @@ -104,7 +110,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -118,10 +124,12 @@ nextflow_process { } process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - input[1] = [[],[]] - input[2] = false + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = false """ } } @@ -129,7 +137,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -142,12 +150,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -155,7 +163,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -168,12 +176,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -181,7 +189,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -196,12 +204,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -209,7 +217,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } @@ -224,12 +232,12 @@ nextflow_process { } process { """ - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) - ]) - input[1] = [[],[]] - input[2] = true + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + [] + ] + input[1] = true """ } } @@ -237,7 +245,7 @@ nextflow_process { then { assert process.success assertAll( - { assert snapshot(process.out).match()} + { assert snapshot(sanitizeOutput(process.out)).match()} ) } } diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 565d20e71..416974442 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -2,39 +2,13 @@ "test_samtools_faidx": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] @@ -56,47 +30,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:02:40.159309157" + "timestamp": "2026-02-10T15:39:12.541649151" }, "test_samtools_faidx_get_sizes_bgzip - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -135,42 +75,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:39.550619177" + "timestamp": "2026-02-10T15:41:44.040426987" }, "test_samtools_faidx_get_sizes": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -204,52 +115,20 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:16.844965756" + "timestamp": "2026-02-10T15:47:03.653912015" }, "test_samtools_faidx_bgzip": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" ] @@ -257,8 +136,7 @@ "gzi": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" ] @@ -277,43 +155,17 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:02:47.301476131" + "timestamp": "2026-02-10T15:50:04.023566795" }, "test_samtools_faidx_fasta": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" ] @@ -338,42 +190,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T09:44:40.559583279" + "timestamp": "2026-02-10T15:39:23.529404162" }, "test_samtools_faidx_get_sizes - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -407,43 +230,17 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:31.989929281" + "timestamp": "2026-02-10T15:41:39.039834304" }, "test_samtools_faidx_stub_fasta": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "extract.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -468,46 +265,20 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T09:44:48.295693103" + "timestamp": "2026-02-10T15:39:28.961701609" }, "test_samtools_faidx_stub_fai": { "content": [ { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], "fai": [ [ { - "id": "test", - "single_end": false + "id": "test" }, "genome.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" ] @@ -529,47 +300,13 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:09.784289542" + "timestamp": "2026-02-10T15:39:34.471028474" }, "test_samtools_faidx_get_sizes_bgzip": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.sizes:md5,a57c401f27ae5133823fb09fb21c8a3c" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" - ] - ], - "4": [ - [ - "SAMTOOLS_FAIDX", - "samtools", - "1.22.1" - ] - ], "fa": [ ], @@ -608,8 +345,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2025-12-23T14:03:24.814967939" + "timestamp": "2026-02-10T15:39:45.439016495" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 6785f22e8..87ebc5014 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -9,9 +9,7 @@ process SAMTOOLS_MERGE { input: tuple val(meta), path(input_files, stageAs: "?/*") - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(gzi) + tuple val(meta2), path(fasta), path(fai), path(gzi) output: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 4237ce74e..31cc576bc 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -37,21 +37,11 @@ input: description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - fai: type: file description: Index of the reference file the CRAM was created with (optional) pattern: "*.fai" ontologies: [] - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - gzi: type: file description: Index of the compressed reference file the CRAM was created with diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index 08ef26945..a784c8367 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -24,9 +24,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -61,13 +59,10 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true), + [] ] - input[2] = [ - [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [[],[]] """ } } @@ -103,14 +98,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) - ] - input[2] = [ - [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) - ] - input[3] = [ - [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) ] """ @@ -145,9 +134,7 @@ nextflow_process { [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -183,9 +170,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } @@ -214,9 +199,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[],[]] """ } } diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 87b3333f6..b189b5ba4 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -9,7 +9,7 @@ process SAMTOOLS_VIEW { input: tuple val(meta), path(input), path(index) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) path qname val index_format diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 215222661..23a1af338 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -36,12 +36,19 @@ input: type: map description: | Groovy Map containing reference information - e.g. [ id:'test' ] + e.g. [ id:'genome' ] - fasta: type: file - description: Reference file the CRAM was created with (optional) + description: Fasta reference file pattern: "*.{fasta,fa}" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_1929 # FASTA + - fai: + type: file + description: Fasta reference file index + pattern: "*.{fai}" + ontologies: + - edam: http://edamontology.org/format_3326 # Index - qname: type: file description: Optional file with read names to output only select alignments diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 74e1c49fd..8d8f292fb 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = [] """ @@ -49,7 +49,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'csi' """ @@ -76,7 +76,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'bai' """ @@ -103,7 +103,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'bai' @@ -131,7 +131,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'crai' @@ -161,7 +161,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -191,7 +192,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -221,7 +223,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = [] input[3] = [] @@ -251,7 +254,8 @@ nextflow_process { ] input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] input[2] = Channel.of("testN:2817", "testN:2814") .collectFile(name: "readnames.list", newLine: true) @@ -283,7 +287,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = [] """ @@ -313,7 +317,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'csi' """ @@ -343,7 +347,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = [] input[3] = 'bai' """ @@ -373,7 +377,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'bai' @@ -404,7 +408,7 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), [] ] - input[1] = [[],[]] + input[1] = [[],[],[]] input[2] = Channel.of('testN:1') .collectFile(name: 'selected_reads.txt') input[3] = 'crai' diff --git a/modules/nf-core/seqtk/sample/main.nf b/modules/nf-core/seqtk/sample/main.nf index 0c2aaeda2..1a5d8cd72 100644 --- a/modules/nf-core/seqtk/sample/main.nf +++ b/modules/nf-core/seqtk/sample/main.nf @@ -12,7 +12,7 @@ process SEQTK_SAMPLE { output: tuple val(meta), path("*.fastq.gz"), emit: reads - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('seqtk'), eval("seqtk 2>&1 | sed -n 's/^Version: //p'"), emit: versions_seqtk, topic: versions when: task.ext.when == null || task.ext.when @@ -36,11 +36,6 @@ process SEQTK_SAMPLE { $sample_size \\ | gzip --no-name > ${prefix}_\$(basename \$f) done - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ stub: @@ -48,11 +43,6 @@ process SEQTK_SAMPLE { """ echo "" | gzip > ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml index ed1f3325c..9574c705c 100644 --- a/modules/nf-core/seqtk/sample/meta.yml +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -6,8 +6,8 @@ keywords: - reads tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in - the FASTA or FASTQ format. Seqtk sample command subsamples sequences. + description: Seqtk is a fast and lightweight tool for processing sequences + in the FASTA or FASTQ format. Seqtk sample command subsamples sequences. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk @@ -39,13 +39,27 @@ output: description: Subsampled FastQ files pattern: "*.{fastq.gz}" ontologies: [] + versions_seqtk: + - - ${task.process}: + type: string + description: The name of the process + - seqtk: + type: string + description: The name of the tool + - "seqtk 2>&1 | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - seqtk: + type: string + description: The name of the tool + - "seqtk 2>&1 | sed -n 's/^Version: //p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@kaurravneet4123" - "@sidorov-si" diff --git a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap index aa6991e6c..c770b22e1 100644 --- a/modules/nf-core/seqtk/sample/tests/main.nf.test.snap +++ b/modules/nf-core/seqtk/sample/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -23,12 +27,20 @@ "test.sampled.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:45.902956" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:11.92830069" }, "sarscov2_sample_pairedend_fqgz": { "content": [ @@ -43,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -54,12 +70,20 @@ "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:37.679954" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:00.582612488" }, "sarscov2_sample_singleend_fqgz": { "content": [ @@ -74,7 +98,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -85,12 +113,20 @@ "test.sampled_test_1.fastq.gz:md5,e5f44fafd7351c5abb9925a075132941" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2024-02-22T15:58:29.474491" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:28:47.676166475" }, "sarscov2_sample_singleend_frac": { "content": [ @@ -105,7 +141,11 @@ ] ], "1": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ], "reads": [ [ @@ -116,11 +156,19 @@ "test.sampled_test_1.fastq.gz:md5,7552511dcd914f5183d80fae459bf917" ] ], - "versions": [ - "versions.yml:md5,0529f2d163df9e2cd2ae8254dfb63806" + "versions_seqtk": [ + [ + "SEQTK_SAMPLE", + "seqtk", + "1.4-r122" + ] ] } ], - "timestamp": "2025-07-15T09:48:30.275951" + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.10.2" + }, + "timestamp": "2026-01-14T12:29:23.3474291" } } \ No newline at end of file diff --git a/modules/nf-core/seqtk/sample/tests/standard.config b/modules/nf-core/seqtk/sample/tests/standard.config index b2dd4b9f9..8d1db62fd 100644 --- a/modules/nf-core/seqtk/sample/tests/standard.config +++ b/modules/nf-core/seqtk/sample/tests/standard.config @@ -3,4 +3,4 @@ process { ext.args = '-s100' ext.prefix = { "${meta.id}.sampled" } } -} \ No newline at end of file +} diff --git a/modules/nf-core/smncopynumbercaller/environment.yml b/modules/nf-core/smncopynumbercaller/environment.yml index afbc40076..6102e6333 100644 --- a/modules/nf-core/smncopynumbercaller/environment.yml +++ b/modules/nf-core/smncopynumbercaller/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/smncopynumbercaller/main.nf b/modules/nf-core/smncopynumbercaller/main.nf index efe0a639e..6fa8811f0 100644 --- a/modules/nf-core/smncopynumbercaller/main.nf +++ b/modules/nf-core/smncopynumbercaller/main.nf @@ -13,7 +13,8 @@ process SMNCOPYNUMBERCALLER { output: tuple val(meta), path("out/*.tsv"), emit: smncopynumber tuple val(meta), path("out/*.json"), emit: run_metrics - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('smncopynumbercaller'), val('1.1.2'), topic: versions, emit: versions_smncopynumbercaller + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when @@ -21,7 +22,6 @@ process SMNCOPYNUMBERCALLER { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.1.2" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. """ echo $bam | tr ' ' ' ' > manifest.txt @@ -31,24 +31,13 @@ process SMNCOPYNUMBERCALLER { --prefix $prefix \\ --outDir "out" \\ --threads $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - SMNCopyNumberCaller: $VERSION - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.1.2" """ mkdir out touch out/${prefix}.tsv touch out/${prefix}.json - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - SMNCopyNumberCaller: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/smncopynumbercaller/meta.yml b/modules/nf-core/smncopynumbercaller/meta.yml index 9d91fc096..c0f4078bf 100644 --- a/modules/nf-core/smncopynumbercaller/meta.yml +++ b/modules/nf-core/smncopynumbercaller/meta.yml @@ -27,13 +27,15 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - bai: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" + ontologies: [] output: - - smncopynumber: - - meta: + smncopynumber: + - - meta: type: map description: | Groovy Map containing sample information @@ -42,8 +44,10 @@ output: type: file description: File containing the output of SMNCopyNumberCaller pattern: "*.{tsv}" - - run_metrics: - - meta: + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + run_metrics: + - - meta: type: map description: | Groovy Map containing sample information @@ -52,11 +56,29 @@ output: type: file description: File containing run parameters of SMNCopyNumberCaller pattern: "*.{json}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3464 # JSON + versions_smncopynumbercaller: + - - ${task.process}: + type: string + description: The name of the process + - smncopynumbercaller: + type: string + description: The name of the tool + - 1.1.2: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - smncopynumbercaller: + type: string + description: The name of the tool + - 1.1.2: + type: string + description: The expression to obtain the version of the tool authors: - "@peterpru" maintainers: diff --git a/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap b/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap index 834fe67b9..22c1f1fc8 100644 --- a/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap +++ b/modules/nf-core/smncopynumbercaller/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "2": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ], "run_metrics": [ [ @@ -37,16 +41,20 @@ "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + "versions_smncopynumbercaller": [ + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T12:54:27.295453" + "timestamp": "2026-02-11T21:26:46.783248" }, "test-smncopynumbercaller": { "content": [ @@ -68,7 +76,11 @@ ] ], "2": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ], "run_metrics": [ [ @@ -86,15 +98,19 @@ "test.tsv:md5,0de62f196972c17e1701aa8cea0849f9" ] ], - "versions": [ - "versions.yml:md5,084e44557eacbb00c1a24dc71ed022cf" + "versions_smncopynumbercaller": [ + [ + "SMNCOPYNUMBERCALLER", + "smncopynumbercaller", + "1.1.2" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-08-27T12:54:21.71312" + "timestamp": "2026-02-11T21:26:43.145754" } } \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/main.nf b/modules/nf-core/spring/decompress/main.nf index 86ced2690..316080482 100644 --- a/modules/nf-core/spring/decompress/main.nf +++ b/modules/nf-core/spring/decompress/main.nf @@ -4,8 +4,8 @@ process SPRING_DECOMPRESS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/spring:1.1.1--h4ac6f70_2' : - 'biocontainers/spring:1.1.1--h4ac6f70_2' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f6/f67f27c8cb2d1a149564f1a10f5f2b7a6acfa87ef3d3d27d2d8752dbe95e6acf/data' : + 'community.wave.seqera.io/library/spring:1.1.1--911a17b4ccfb85ee' }" input: tuple val(meta), path(spring) @@ -13,7 +13,8 @@ process SPRING_DECOMPRESS { output: tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('spring'), val('1.1.1'), topic: versions, emit: versions_spring + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when @@ -21,9 +22,7 @@ process SPRING_DECOMPRESS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def output = write_one_fastq_gz ? "-o ${prefix}.fastq.gz" : "-o ${prefix}_R1.fastq.gz ${prefix}_R2.fastq.gz" - """ spring \\ -d \\ @@ -32,23 +31,12 @@ process SPRING_DECOMPRESS { $args \\ -i ${spring} \\ ${output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - spring: ${VERSION} - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def output = write_one_fastq_gz ? "echo '' | gzip > ${prefix}.fastq.gz" : "echo '' | gzip > ${prefix}_R1.fastq.gz; echo '' | gzip > ${prefix}_R2.fastq.gz" """ ${output} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - spring: ${VERSION} - END_VERSIONS """ } diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml index 72b72b75d..e41c4bf90 100644 --- a/modules/nf-core/spring/decompress/meta.yml +++ b/modules/nf-core/spring/decompress/meta.yml @@ -24,14 +24,15 @@ input: type: file description: Spring file to decompress. pattern: "*.{spring}" - - - write_one_fastq_gz: - type: boolean - description: | - Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions - pattern: "true or false" + ontologies: [] + - write_one_fastq_gz: + type: boolean + description: | + Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions + pattern: "true or false" output: - - fastq: - - meta: + fastq: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,11 +41,28 @@ output: type: file description: Decompressed FASTQ file(s). pattern: "*.{fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_spring: + - - ${task.process}: + type: string + description: The name of the process + - spring: + type: string + description: The name of the tool + - 1.1.1: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - spring: + type: string + description: The name of the tool + - 1.1.1: + type: string + description: The expression to obtain the version of the tool authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/spring/decompress/tests/main.nf.test b/modules/nf-core/spring/decompress/tests/main.nf.test index c7ac2b1f3..f960b0d5b 100644 --- a/modules/nf-core/spring/decompress/tests/main.nf.test +++ b/modules/nf-core/spring/decompress/tests/main.nf.test @@ -151,4 +151,4 @@ nextflow_process { } } -} \ No newline at end of file +} diff --git a/modules/nf-core/spring/decompress/tests/main.nf.test.snap b/modules/nf-core/spring/decompress/tests/main.nf.test.snap index 7dcadbab6..dd6cc252d 100644 --- a/modules/nf-core/spring/decompress/tests/main.nf.test.snap +++ b/modules/nf-core/spring/decompress/tests/main.nf.test.snap @@ -1,76 +1,4 @@ { - "Write-One-File stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" - ] - ], - "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ], - "fastq": [ - [ - { - "id": "test" - }, - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" - ] - ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T10:03:50.626223289" - }, - "Write-Two-Files stub": { - "content": [ - { - "0": [ - [ - { - "id": "test2" - }, - [ - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" - ] - ] - ], - "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ], - "fastq": [ - [ - { - "id": "test2" - }, - [ - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", - "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" - ] - ] - ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T10:03:57.417015606" - }, "Write-Two-Files": { "content": [ { @@ -86,7 +14,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -99,16 +31,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:00.074323", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T13:41:46.090761471" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-One-File": { "content": [ @@ -122,7 +58,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -132,16 +72,20 @@ "test.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:15:54.633046", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T13:02:07.466039653" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-One-File-stub": { "content": [ @@ -155,7 +99,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -165,16 +113,20 @@ "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:04.953817", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T13:55:53.594615215" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "Write-Two-Files-stub": { "content": [ @@ -191,7 +143,11 @@ ] ], "1": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ], "fastq": [ [ @@ -204,15 +160,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + "versions_spring": [ + [ + "SPRING_DECOMPRESS", + "spring", + "1.1.1" + ] ] } ], + "timestamp": "2026-02-11T11:16:09.98067", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-08T13:56:01.212228909" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/tests/nextflow.config b/modules/nf-core/spring/decompress/tests/nextflow.config index 50f50a7a3..8730f1c4b 100644 --- a/modules/nf-core/spring/decompress/tests/nextflow.config +++ b/modules/nf-core/spring/decompress/tests/nextflow.config @@ -1,5 +1,5 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file + +} diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index a33b14c85..df74ec81e 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.6.1 + - bioconda::tiddit=3.9.4 diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 20d4720e7..690a8b62b 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -4,48 +4,38 @@ process TIDDIT_COV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' : - 'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" input: - tuple val(meta), path(input) + tuple val(meta), path(input), path(index) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bed"), optional: true, emit: cov - tuple val(meta), path("*.wig"), optional: true, emit: wig - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bed"), optional: true, emit: cov + tuple val(meta), path("${prefix}.wig"), optional: true, emit: wig + tuple val("${task.process}"), val('tiddit'), eval("tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'"), topic: versions, emit: versions_tiddit when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reference = fasta ? "--ref $fasta" : "" + prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--ref ${fasta}" : "" """ tiddit \\ --cov \\ - -o $prefix \\ - $args \\ - --bam $input \\ - $reference - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + -o ${prefix} \\ + ${args} \\ + --bam ${input} \\ + ${reference} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.wig - touch ${prefix}.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + echo "" > ${prefix}.wig + echo "" > ${prefix}.bed """ } diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml index 71bbf7864..0f28625d9 100644 --- a/modules/nf-core/tiddit/cov/meta.yml +++ b/modules/nf-core/tiddit/cov/meta.yml @@ -11,7 +11,8 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: "10.12688/f1000research.11168.1" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:tiddit input: - - meta: @@ -24,6 +25,12 @@ input: description: BAM/CRAM file pattern: "*.{bam,cram}" ontologies: [] + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai,csi}" + ontologies: + - edam: http://edamontology.org/format_3327 - - meta2: type: map description: | @@ -43,7 +50,7 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.bed": + - ${prefix}.bed: type: file description: The coverage of different regions in bed format. Optional. pattern: "*.bed" @@ -54,18 +61,32 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.wig": + - ${prefix}.wig: type: file description: The coverage of different regions in WIG format. Optional. pattern: "*.wig" ontologies: [] + versions_tiddit: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test b/modules/nf-core/tiddit/cov/tests/main.nf.test index 24c273d86..97d386460 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test @@ -16,7 +16,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -33,7 +34,7 @@ nextflow_process { { assert process.out.cov[0][1] ==~ ".*/test.bed" }, { assert snapshot( process.out.cov, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -48,7 +49,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] ] input[1] = [ [:], [] ] """ @@ -61,7 +63,7 @@ nextflow_process { { assert process.out.cov[0][1] ==~ ".*/test.bed" }, { assert snapshot( process.out.cov, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -78,7 +80,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -95,7 +98,7 @@ nextflow_process { { assert process.out.wig[0][1] ==~ ".*/test.wig" }, { assert snapshot( process.out.wig, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -112,7 +115,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] ] input[1] = [ [:], [] ] @@ -126,7 +130,7 @@ nextflow_process { { assert process.out.wig[0][1] ==~ ".*/test.wig" }, { assert snapshot( process.out.wig, - process.out.versions + process.out.findAll { key, val -> key.startsWith("versions") } ).match() } ) @@ -145,7 +149,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] ] input[1] = [ @@ -159,14 +164,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.cov[0][1] ==~ ".*/test.bed" }, - { assert process.out.wig[0][1] ==~ ".*/test.wig" }, - { assert snapshot( - process.out.cov, - process.out.wig, - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap index 5067886d6..977b8c768 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap @@ -10,15 +10,21 @@ "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:36:08.358493", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:07.66262" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - cram - wig": { "content": [ @@ -31,45 +37,82 @@ "test.wig:md5,7c46b6ef30574acdce0ad854f40126ae" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:36:03.766699", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:01.397993" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wig:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "2": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ], + "cov": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ], + "wig": [ + [ + { + "id": "test", + "single_end": false + }, + "test.wig:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] - ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + } ], + "timestamp": "2026-02-16T11:40:15.064301", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:44:12.873466" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens - bam - bed": { "content": [ @@ -82,15 +125,21 @@ "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:35:59.061703", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:43:54.542951" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } }, "homo_sapiens - cram - bed": { "content": [ @@ -103,14 +152,20 @@ "test.bed:md5,caf0742f2d4a6f713ceb85268dd48c14" ] ], - [ - "versions.yml:md5,49dfdb5a33d1c11db488fb02d1c95c5a" - ] + { + "versions_tiddit": [ + [ + "TIDDIT_COV", + "tiddit", + "3.9.4" + ] + ] + } ], + "timestamp": "2026-02-11T20:35:54.066148", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-30T09:43:47.441318" + "nf-test": "0.9.3", + "nextflow": "25.10.3" + } } } \ No newline at end of file diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index 2fd01cfd4..df74ec81e 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.6.1 + - bioconda::tiddit=3.9.4 diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index f350e3144..c3808ed3d 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -4,8 +4,8 @@ process TIDDIT_SV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tiddit:3.6.1--py38h24c8ff8_0' : - 'biocontainers/tiddit:3.6.1--py38h24c8ff8_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" input: tuple val(meta), path(input), path(input_index) @@ -13,44 +13,34 @@ process TIDDIT_SV { tuple val(meta3), path(bwa_index) output: - tuple val(meta), path("*.vcf") , emit: vcf - tuple val(meta), path("*.ploidies.tab"), emit: ploidy - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf") , emit: vcf + tuple val(meta), path("${prefix}.ploidies.tab"), emit: ploidy + tuple val("${task.process}"), val('tiddit'), eval("tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'"), topic: versions, emit: versions_tiddit when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def bwa_command = bwa_index ? "[[ -d $bwa_index ]] && for i in $bwa_index/*; do [[ -f $fasta && ! \"\$i\" =~ .*\"$fasta.\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : "" + prefix = task.ext.prefix ?: "${meta.id}" + def bwa_command = bwa_index ? "[[ -d ${bwa_index} ]] && for i in ${bwa_index}/*; do [[ -f ${fasta} && ! \"\$i\" =~ .*\"${fasta}.\".* ]] && ln -s \$i ${fasta}.\${i##*.} || ln -s \$i .; done" : "" """ $bwa_command tiddit \\ --sv \\ - $args \\ + ${args} \\ --threads $task.cpus \\ - --bam $input \\ - --ref $fasta \\ - -o $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + --bam ${input} \\ + --ref ${fasta} \\ + -o ${prefix} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf - touch ${prefix}.ploidies.tab - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//') - END_VERSIONS + echo "" > ${prefix}.vcf + echo "" > ${prefix}.ploidies.tab """ } diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index 21527baf1..b27987926 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -10,7 +10,8 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:tiddit input: - - meta: @@ -22,10 +23,12 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram}" + ontologies: [] - input_index: type: file description: BAM/CRAM index file pattern: "*.{bai,crai}" + ontologies: [] - - meta2: type: map description: | @@ -35,6 +38,7 @@ input: type: file description: Input FASTA file pattern: "*.{fasta,fa}" + ontologies: [] - - meta3: type: map description: | @@ -44,32 +48,51 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.vcf": + - "${prefix}.vcf": type: file description: vcf pattern: "*.{vcf}" - - ploidy: - - meta: + ontologies: [] + ploidy: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.ploidies.tab": + - "${prefix}.ploidies.tab": type: file description: tab pattern: "*.{ploidies.tab}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_tiddit: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - tiddit: + type: string + description: The name of the tool + - "tiddit | sed -n 's/^usage: tiddit-//; s/ .*//p'": + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test b/modules/nf-core/tiddit/sv/tests/main.nf.test index 6e32b9e1c..090175ee4 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test @@ -46,9 +46,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("bam_bwa_version") } + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -78,9 +77,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("bam_version") } + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } ) } @@ -122,11 +120,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("cram_bwa_version") }) + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } + ) } - } test("human - cram - no_bwa") { @@ -153,11 +150,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).readLines().contains("##fileformat=VCFv4.1") }, - { assert path(process.out.ploidy.get(0).get(1)).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, - { assert snapshot(process.out.versions).match("cram_version") }) + { assert path(process.out.ploidy[0][1]).readLines().contains("Chromosome Ploidy Ploidy_rounded Mean_coverage") }, + { assert snapshot(path(process.out.vcf[0][1]).vcf.header.getColumnCount(), process.out.findAll { key, val -> key.startsWith("versions") }).match() } + ) } - } test("sarscov2 - bam - stub") { diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap index 541c48bbd..6927d6916 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap @@ -1,28 +1,4 @@ { - "cram_bwa_version": { - "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-22T10:33:01.300519" - }, - "cram_version": { - "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-03-22T10:27:12.52902" - }, "sarscov2 - bam - stub": { "content": [ { @@ -31,7 +7,7 @@ { "id": "test" }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.vcf:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -39,18 +15,22 @@ { "id": "test" }, - "test.ploidies.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ploidies.tab:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "2": [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] ], "ploidy": [ [ { "id": "test" }, - "test.ploidies.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ploidies.tab:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "vcf": [ @@ -58,42 +38,98 @@ { "id": "test" }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.vcf:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-11T13:40:16.597914" + }, + "sarscov2 - bam - bwa": { + "content": [ + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-11T21:38:47.040361" + }, + "human - cram - bwa": { + "content": [ + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:21:51.950503" + "timestamp": "2026-02-11T21:37:13.220785" }, - "bam_bwa_version": { + "sarscov2 - bam - no_bwa": { "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:31:40.918479" + "timestamp": "2026-02-11T21:38:54.658816" }, - "bam_version": { + "human - cram - no_bwa": { "content": [ - [ - "versions.yml:md5,0ffcce416e40bcc98da2243f1d7e348a" - ] + 10, + { + "versions_tiddit": [ + [ + "TIDDIT_SV", + "tiddit", + "3.9.4" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2024-03-22T10:21:38.449053" + "timestamp": "2026-02-11T21:39:11.028105" } } \ No newline at end of file diff --git a/modules/nf-core/tiddit/sv/tests/tags.yml b/modules/nf-core/tiddit/sv/tests/tags.yml deleted file mode 100644 index aac5351ec..000000000 --- a/modules/nf-core/tiddit/sv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -tiddit/sv: - - "modules/nf-core/tiddit/sv/**" diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml index e80eb6d09..6bd9f2509 100644 --- a/modules/nf-core/ucsc/wigtobigwig/environment.yml +++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-wigtobigwig=447 + - bioconda::ucsc-wigtobigwig=482 diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf index 4b7adb62f..e7c4c6cb8 100644 --- a/modules/nf-core/ucsc/wigtobigwig/main.nf +++ b/modules/nf-core/ucsc/wigtobigwig/main.nf @@ -5,46 +5,35 @@ process UCSC_WIGTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:447--h2a80c09_1' : - 'biocontainers/ucsc-wigtobigwig:447--h2a80c09_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/03/0394161be68e8dd5b30a47f0b19ffa00cb3226bb2e6c9fe3ec89e571a50b871d/data' : + 'community.wave.seqera.io/library/ucsc-wigtobigwig:482--7b910cc21c32327e' }" input: tuple val(meta), path(wig) path sizes output: - tuple val(meta), path("*.bw"), emit: bw - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.bw"), emit: bw + tuple val("${task.process}"), val('ucsc'), val('482'), topic: versions, emit: versions_ucsc + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ wigToBigWig \\ $args \\ $wig \\ $sizes \\ ${prefix}.bw - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ucsc: $VERSION - END_VERSIONS """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bw - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ucsc: $VERSION - END_VERSIONS """ } diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml index bc82734da..3bbd3e312 100644 --- a/modules/nf-core/ucsc/wigtobigwig/meta.yml +++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml @@ -10,7 +10,8 @@ tools: Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) to binary big wig format homepage: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html - licence: ["varies; see http://genome.ucsc.edu/license"] + licence: + - "varies; see http://genome.ucsc.edu/license" identifier: "" input: - - meta: @@ -34,18 +35,32 @@ output: description: bigwig file pattern: "*.{bw}" ontologies: [] - - "*.bw": + - ${prefix}.bw: type: file description: bigwig file pattern: "*.{bw}" ontologies: [] + versions_ucsc: + - - ${task.process}: + type: string + description: The name of the process + - ucsc: + type: string + description: The name of the tool + - "482": + type: string + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - ucsc: + type: string + description: The name of the tool + - "482": + type: string + description: The expression to obtain the version of the tool authors: - "@jianhong" - "@projectoriented" diff --git a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap index acc59555c..ee8704437 100644 --- a/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/wigtobigwig/tests/main.nf.test.snap @@ -12,7 +12,11 @@ ] ], "1": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ], "bw": [ [ @@ -23,16 +27,20 @@ "test.bw:md5,b64af7003665dc51fae958216b06ed95" ] ], - "versions": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + "versions_ucsc": [ + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ] } ], + "timestamp": "2026-02-16T09:50:37.235738", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-27T11:54:03.735102" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-ucsc-wigtobigwig-stub": { "content": [ @@ -47,7 +55,11 @@ ] ], "1": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ], "bw": [ [ @@ -58,15 +70,19 @@ "test.bw:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e99b51033a14e1602fe195965a109feb" + "versions_ucsc": [ + [ + "UCSC_WIGTOBIGWIG", + "ucsc", + "482" + ] ] } ], + "timestamp": "2026-02-16T09:50:41.464164", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-27T11:54:07.924401" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 88895ccdb..c946c1d18 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -156,7 +156,7 @@ workflow ALIGN { } if (val_save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta, [], 'crai' ) + SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) } emit: diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index b0284b4b9..42a19c489 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -39,7 +39,6 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam - ch_versions = ch_versions.mix(BWAMEME_MEM.out.versions) } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam @@ -66,14 +65,14 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta, ch_genome_fai, [[:], []] ) + SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return[meta,fasta,fai,[]]}) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) - EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta, [], '') + EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta.join(ch_genome_fai), [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 498c1b64f..31d3541ad 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -40,7 +40,7 @@ workflow ALIGN_SENTIEON { // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { - EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta, [], 'bai') + EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai), [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) } diff --git a/subworkflows/local/annotate_consequence_pli.nf b/subworkflows/local/annotate_consequence_pli.nf index af57747d9..72b88487d 100644 --- a/subworkflows/local/annotate_consequence_pli.nf +++ b/subworkflows/local/annotate_consequence_pli.nf @@ -13,8 +13,6 @@ workflow ANNOTATE_CSQ_PLI { val_index // bool main: - ch_versions = channel.empty() - CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) CUSTOM_ADDMOSTSEVEREPLI (CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.vcf) @@ -23,10 +21,6 @@ workflow ANNOTATE_CSQ_PLI { TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) } - ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.versions) - ch_versions = ch_versions.mix(CUSTOM_ADDMOSTSEVEREPLI.out.versions) - emit: vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index ac5db5cc8..120f36013 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -55,7 +55,6 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) emit: versions = ch_versions // channel: [ path(versions.yml) ] diff --git a/subworkflows/local/call_mobile_elements.nf b/subworkflows/local/call_mobile_elements.nf index 45ad5ece7..8719eca4e 100644 --- a/subworkflows/local/call_mobile_elements.nf +++ b/subworkflows/local/call_mobile_elements.nf @@ -40,7 +40,7 @@ workflow CALL_MOBILE_ELEMENTS { .set { ch_genome_bam_bai_interval } // Split bam file on chromosome and index - ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], []], [], 'bai' ) + ME_SPLIT_ALIGNMENT ( ch_genome_bam_bai_interval, [[:], [], []], [], 'bai' ) ME_SPLIT_ALIGNMENT.out.bam .join( ME_SPLIT_ALIGNMENT.out.bai, failOnMismatch: true, failOnDuplicate: true ) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index dbec9449b..96c8ec4f7 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -82,8 +82,6 @@ workflow CALL_SNV_DEEPVARIANT { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_versions = ch_versions.mix(GLNEXUS.out.versions) - emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index e7c0bb5c2..f7ff6b90a 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -47,7 +47,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .vcf .collect{ _meta, vcf -> vcf } .set { tiddit_vcf } - ch_versions = ch_versions.mix(CALL_SV_TIDDIT.out.versions) CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6bc1ccbba..8733edab0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -78,7 +78,6 @@ workflow CALL_SV_MT { ch_mt_lastdb ) - ch_versions = ch_versions.mix(SEQTK_SAMPLE.out.versions) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index fc3b79817..ac3d457fd 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -29,9 +29,6 @@ workflow CALL_SV_TIDDIT { SVDB_MERGE_TIDDIT ( merge_input_vcfs, [], true ) - ch_versions = TIDDIT_SV.out.versions - emit: vcf = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index 4a72744eb..d0f1a472b 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -17,7 +17,6 @@ workflow GENERATE_CYTOSURE_FILES { val_sample_id_map // string: path to sample_id_map file main: - ch_versions = channel.empty() ch_reheader_out = channel.empty() TIDDIT_COV_VCF2CYTOSURE (ch_bam, [[],[]]) @@ -87,9 +86,4 @@ workflow GENERATE_CYTOSURE_FILES { [[:], []], [[:], []], ch_blacklist ) - - ch_versions = ch_versions.mix(TIDDIT_COV_VCF2CYTOSURE.out.versions) - - emit: - versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index ac06731a5..ebfb7b3c1 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -92,7 +92,7 @@ workflow PREPARE_REFERENCES { // Genome indices // if (!val_fai) { - SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[:],[]], true) + SAMTOOLS_FAIDX_GENOME(ch_genome_fasta.map{meta, fasta -> return [meta,fasta,[]]}, true) ch_genome_fai = SAMTOOLS_FAIDX_GENOME.out.fai.collect() ch_chrom_sizes = SAMTOOLS_FAIDX_GENOME.out.sizes.map {_meta, sizes -> sizes}.collect() } else { @@ -128,7 +128,6 @@ workflow PREPARE_REFERENCES { if (!val_bwamem2 && val_aligner.equals("bwameme")) { ch_genome_bwameme_index = BWAMEME_INDEX_GENOME(ch_genome_fasta).index.collect() - ch_versions = ch_versions.mix(BWAMEME_INDEX_GENOME.out.versions) } else if (val_bwameme) { ch_genome_bwameme_index = channel.fromPath(val_bwameme).map {it -> [[id:it.simpleName], it]}.collect() } @@ -137,12 +136,12 @@ workflow PREPARE_REFERENCES { // if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { if (!val_mtfasta) { - ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta, ch_genome_fai, false).fa.collect() + ch_mt_fasta = SAMTOOLS_EXTRACT_MT(ch_genome_fasta.join(ch_genome_fai), false).fa.collect() } else { ch_mt_fasta = channel.fromPath(val_mtfasta).map { it -> [[id:it.simpleName], it] }.collect() } - ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta, [[:],[]], false).fai.collect() + ch_mt_fai = SAMTOOLS_FAIDX_MT(ch_mt_fasta.map{meta, fasta -> return [meta, fasta,[]]}, false).fai.collect() ch_mt_dict = GATK_SD_MT(ch_mt_fasta).dict.collect() ch_genome_hisat2_index = HISAT2_INDEX_GENOME(ch_genome_fasta,[[:],[]], [[:],[]]).index.collect() @@ -166,8 +165,6 @@ workflow PREPARE_REFERENCES { } .set {ch_shiftfasta_mtintervals} - ch_versions = ch_versions.mix (HISAT2_INDEX_GENOME.out.versions, - LAST_INDEX_MT.out.versions) } // // MT alignment indices @@ -268,7 +265,6 @@ workflow PREPARE_REFERENCES { ch_genome_fasta.map { meta, fasta -> return [meta, fasta, [], [] ] } .set {ch_rtgformat_in} ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf - ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) } emit: diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 89aceb143..1484b0f76 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -43,7 +43,6 @@ workflow QC_BAM { main: ch_cov = channel.empty() ch_cov_y = channel.empty() - ch_versions = channel.empty() ch_hsmetrics = channel.empty() ch_qualimap = channel.empty() ch_ngsbits = channel.empty() @@ -60,7 +59,6 @@ workflow QC_BAM { } if (!skip_qualimap) { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results - ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions) } TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input @@ -93,15 +91,11 @@ workflow QC_BAM { if (!skip_ngsbits) { NGSBITS_SAMPLEGENDER(ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_ngsbits_method) ch_ngsbits = NGSBITS_SAMPLEGENDER.out.tsv - ch_versions = ch_versions.mix(NGSBITS_SAMPLEGENDER.out.versions) } // Check contamination ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) - ch_versions = ch_versions.mix(TIDDIT_COV.out.versions) - ch_versions = ch_versions.mix(UCSC_WIGTOBIGWIG.out.versions) - emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] @@ -114,5 +108,4 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 798b5ac62..6ac7c6c98 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -30,6 +30,6 @@ workflow SUBSAMPLE_MT_FRAC { } .set { ch_subsample_in } - SAMTOOLS_VIEW(ch_subsample_in, [[:],[]], [], 'bai') + SAMTOOLS_VIEW(ch_subsample_in, [[:],[],[]], [], 'bai') } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 52ae75a9a..e141eaea3 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -14,15 +14,15 @@ workflow SUBSAMPLE_MT_READS { ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] main: - SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[]], [], '') + SAMTOOLS_VIEW(ch_mt_bam_bai, [[:],[],[]], [], '') - SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[]]) + SAMTOOLS_COLLATE(SAMTOOLS_VIEW.out.bam, [[:],[],[]]) GAWK(SAMTOOLS_COLLATE.out.sam, [], false) GAWK.out.output.map {meta, sam -> return [meta, sam, []] }.set {ch_convert_to_bam} - SAM_TO_BAM(ch_convert_to_bam, [[:],[]], [], '') + SAM_TO_BAM(ch_convert_to_bam, [[:],[],[]], [], '') SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') diff --git a/subworkflows/local/variant_evaluation.nf b/subworkflows/local/variant_evaluation.nf index f4f0e4027..5aa8f526b 100644 --- a/subworkflows/local/variant_evaluation.nf +++ b/subworkflows/local/variant_evaluation.nf @@ -14,8 +14,6 @@ workflow VARIANT_EVALUATION { ch_snv_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: - ch_versions = channel.empty() - ch_rtg_truthvcfs .splitCsv ( header:true ) .map { row -> @@ -42,9 +40,4 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) - ch_versions = ch_versions.mix(TABIX_TRUTHVCF.out.versions) - ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 9b64191c5..b73fabfc3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -219,14 +219,11 @@ workflow RAREDISEASE { // Just one fastq.gz.spring-file with both R1 and R2 ch_one_fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(ch_input_by_sample_type.interleaved_spring, false).fastq - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_FQ_PAIR.out.versions) // Two fastq.gz.spring-files - one for R1 and one for R2 ch_r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[0] ]}, true).fastq ch_r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(ch_input_by_sample_type.separate_spring.map{ meta, files -> [meta, files[1] ]}, true).fastq ch_two_fastq_gz_from_spring = ch_r1_fastq_gz_from_spring.join(ch_r2_fastq_gz_from_spring).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]} - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R1_FQ.out.versions) - ch_versions = ch_versions.mix(SPRING_DECOMPRESS_TO_R2_FQ.out.versions) ch_input_fastqs = ch_input_by_sample_type.fastq_gz.mix(ch_one_fastq_gz_pair_from_spring).mix(ch_two_fastq_gz_from_spring) @@ -317,8 +314,6 @@ workflow RAREDISEASE { skip_ngsbits, skip_qualimap ) - ch_versions = ch_versions.mix(QC_BAM.out.versions) - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -446,7 +441,6 @@ workflow RAREDISEASE { ch_ann_csq_snv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_SNV.out.versions) ANN_CSQ_PLI_SNV.out.vcf_ann .filter { meta, _vcf -> @@ -518,7 +512,6 @@ workflow RAREDISEASE { ch_ann_csq_mtsnv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_MT.out.versions) ANN_CSQ_PLI_MT.out.vcf_ann .filter { meta, _vcf -> @@ -613,7 +606,6 @@ workflow RAREDISEASE { ch_ann_csq_sv_in, false ) - ch_versions = ch_versions.mix(ANN_CSQ_PLI_SV.out.versions) ANN_CSQ_PLI_SV.out.vcf_ann .filter { meta, _vcf -> @@ -723,7 +715,6 @@ workflow RAREDISEASE { ch_ann_csq_me_in, true ) - ch_versions = ch_versions.mix( ANN_CSQ_PLI_ME.out.versions ) } } @@ -754,7 +745,6 @@ workflow RAREDISEASE { SMNCOPYNUMBERCALLER ( ch_bams_bais ) - ch_versions = ch_versions.mix(SMNCOPYNUMBERCALLER.out.versions) } /* @@ -784,7 +774,6 @@ workflow RAREDISEASE { ch_sv_annotate.vcf_ann, val_sample_id_map ) - ch_versions = ch_versions.mix(GENERATE_CYTOSURE_FILES.out.versions) } /* @@ -818,7 +807,6 @@ workflow RAREDISEASE { ch_sdf, CALL_SNV.out.genome_vcf_tabix ) - ch_versions = ch_versions.mix(VARIANT_EVALUATION.out.versions) } /* From 4fd9ff32b1060c407472274d00258b57c06393d8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 19:34:10 +0100 Subject: [PATCH 382/872] update subworkflows and snapshots --- CHANGELOG.md | 28 +- main.nf | 1 - miss | 0 subworkflows/local/align/main.nf | 1 - subworkflows/local/align/tests/main.nf.test | 8 +- .../local/align/tests/main.nf.test.snap | 69 +- .../local/align_MT/tests/main.nf.test.snap | 20 +- .../tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 32 +- .../align_sentieon/tests/main.nf.test.snap | 4 +- .../local/annotate_structural_variants.nf | 3 - .../tests/main.nf.test.snap | 4 +- subworkflows/local/call_snv.nf | 1 - .../local/call_snv_deepvariant/main.nf | 3 +- subworkflows/local/call_sv_MT/main.nf | 2 - subworkflows/local/generate_cytosure_files.nf | 8 +- subworkflows/local/prepare_references/main.nf | 3 - .../tests/main.nf.test.snap | 26 +- subworkflows/local/qc_bam/main.nf | 2 +- .../local/qc_bam/tests/main.nf.test.snap | 16 +- subworkflows/local/rank_variants.nf | 3 - .../scatter_genome/tests/main.nf.test.snap | 4 +- test.sh | 2 + tests/default.nf.test.snap | 45 +- tests/test_bam.nf.test.snap | 34 +- tests/test_singleton.nf.test.snap | 41 +- wflog1 | 6024 +++++++++ wflog2 | 10617 ++++++++++++++++ workflows/raredisease.nf | 7 +- 29 files changed, 16781 insertions(+), 233 deletions(-) create mode 100644 miss create mode 100644 test.sh create mode 100644 wflog1 create mode 100644 wflog2 diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f074e9ce..f59f96ce1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -54,25 +54,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | --------------------- | ----------- | ----------- | | bcftools | 1.20 | 1.21 | -| haplocheck | 1.3.3 | | -| htslib | 1.20 | 1.21 | -| mosdepth | 0.3.8 | 0.3.11 | -| ngs-bits | 2023_02 | 2024_11 | -| gatk4 | 4.5.0.0 | 4.6.2.0 | -| gens-preproc | 1.0.11 | 1.1.2 | -| pigz | 2.3.4 | 2.8 | -| samtools | 1.21 | 1.22.1 | -| sambamba | | 1.0.1 | +| bwa | 0.7.18 | 0.7.19 | +| deepvariant | 1.8.0 | 1.9.0 | +| eKLIPse | 1.8 | | | ensemblverp/filtervep | 113 | 115.2 | | fastp | 0.23.4 | 1.0.1 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | | genmod | 3.9 | 3.10.2 | +| gens-preproc | 1.0.11 | 1.1.2 | +| htslib | 1.20 | 1.21 | +| MitoSalt | | 1.1.1 | +| mosdepth | 0.3.8 | 0.3.11 | | multiqc | 1.32 | 1.33 | +| ngsbits | 202411 | 202512 | | picard | 3.3.0 | 3.4.0 | +| pigz | 2.3.4 | 2.8 | +| sambamba | | 1.0.1 | +| samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | -| deepvariant | 1.8.0 | 1.9.0 | -| MitoSalt | | 1.1.1 | -| eKLIPse | 1.8 | | +| tiddit | 3.6.1 | 3.9.4 | +| ucsc | 447 | 482 | +| vcfanno | 0.3.5 | 0.3.7 | +| vcf2cytosure | 0.9.1 | 0.9.3 | ## 2.6.0 - Cacofonix [2025-06-25] diff --git a/main.nf b/main.nf index c1c42455f..5346dbd30 100644 --- a/main.nf +++ b/main.nf @@ -183,7 +183,6 @@ workflow NFCORE_RAREDISEASE { ch_target_intervals = ch_references.target_intervals ch_vcfanno_extra = ch_references.vcfanno_extra ch_vep_cache = ch_references.vep_resources - ch_versions = ch_versions.mix(ch_references.versions) // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) ch_cadd_resources = channelFromPath(val_cadd_resources, true) diff --git a/miss b/miss new file mode 100644 index 000000000..e69de29bb diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index c946c1d18..327ade6e6 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -107,7 +107,6 @@ workflow ALIGN { ) ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai - ch_versions = ch_versions.mix(ALIGN_SENTIEON.out.versions) } ch_genome_marked_bam = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 32c053815..dce17b191 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -123,8 +123,7 @@ nextflow_workflow { workflow.out.mt_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } ) @@ -224,7 +223,7 @@ nextflow_workflow { workflow.out.mt_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, ).match() } ) @@ -314,8 +313,7 @@ nextflow_workflow { workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.versions + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } ) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 07d7157f9..ceb34df54 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -236,30 +236,13 @@ "427b5e476d84c5277d2d24210800ad60", "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" ] - ], - [ - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T14:52:33.087126495", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T16:47:38.865548433" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwameme - wgs": { "content": [ @@ -383,30 +366,13 @@ ], [ - ], - [ - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3524532e0d268745c6d6c785bc7e734e", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,aef5efcb8852a854022d16b939b52d17", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,b9749a7d836c638ad5deb0f8b208c7ec", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T15:06:13.790400908", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:31:32.266454329" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwamem2 - wes": { "content": [ @@ -477,23 +443,12 @@ ], [ - ], - [ - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,3efddfe43fdf9bf446e23d1526a3973a", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,8191c0426b9e36d914ea3f63bf2428e9", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7", - "versions.yml:md5,c31eb465488334212645bd43296d8bd7" ] ], + "timestamp": "2026-02-17T14:53:17.634008549", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T16:48:59.035282254" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 7537c0bd6..2108f323f 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -103,9 +103,7 @@ ] ], "2": [ - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" + ], "marked_bai": [ [ @@ -208,17 +206,15 @@ ] ], "versions": [ - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04", - "versions.yml:md5,84869ed38f4bfecb303ea73297f03a04" + ] } ], + "timestamp": "2026-02-17T11:24:25.300014158", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:37:55.606130634" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align mt - bwa": { "content": [ @@ -435,10 +431,10 @@ ] } ], + "timestamp": "2026-02-06T17:44:37.818378883", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:44:37.818378883" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index a9d3a12f1..cdde33d3e 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -56,8 +56,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, - workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, - workflow.out.versions + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() } ) @@ -113,8 +112,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, - workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, - workflow.out.versions + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() } ) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 3b33ea9a7..d73f1f5fe 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "da588ff12491da491e3059326ffef0de" + "24b5799be5403926a272596963f9683f" ] ], [ @@ -30,19 +30,13 @@ }, "af8628d9df18b2d3d4f6fd47ef2bb872" ] - ], - [ - "versions.yml:md5,6046f0e9edf48b8d3bd335da75134ee4", - "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], + "timestamp": "2026-02-17T15:13:51.33678644", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:47:53.965738943" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "align bwameme": { "content": [ @@ -58,7 +52,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "91efdc668b5f6e075743e414c7afd0f8" + "b9b01b7ac356afa64bc411d6f10e741" ] ], [ @@ -75,18 +69,12 @@ }, "af8628d9df18b2d3d4f6fd47ef2bb872" ] - ], - [ - "versions.yml:md5,390a09ae83280da84de93856149cc3a1", - "versions.yml:md5,952f0145e6a0a3d1dbd70aac2edf4ced", - "versions.yml:md5,dea31a20732d740f0c824b01226c1dab", - "versions.yml:md5,f56a243ff21d59d873e0d0a3d3ee441d" ] ], + "timestamp": "2026-02-17T15:14:44.637382457", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-06T17:50:27.94216545" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 61e2f2be2..79a96bf5a 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -244,10 +244,10 @@ ] } ], + "timestamp": "2026-01-26T23:22:09.03170299", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-26T23:22:09.03170299" + } } } \ No newline at end of file diff --git a/subworkflows/local/annotate_structural_variants.nf b/subworkflows/local/annotate_structural_variants.nf index 63cd40b07..aa29499df 100644 --- a/subworkflows/local/annotate_structural_variants.nf +++ b/subworkflows/local/annotate_structural_variants.nf @@ -25,8 +25,6 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { val_vep_cache_version // string: [mandatory] default: 107 main: - ch_versions = channel.empty() - if (val_svdb_query_dbs) { ch_svdb_dbs .multiMap { file, in_freq_info_key, in_allele_count_info_key, out_freq_info_key, out_allele_count_info_key -> @@ -101,5 +99,4 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { emit: tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index da37ecae6..685492b45 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -4,10 +4,10 @@ "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], + "timestamp": "2025-10-14T14:06:58.984015651", "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" - }, - "timestamp": "2025-10-14T14:06:58.984015651" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf index 1e0fc8047..adcf63fa6 100644 --- a/subworkflows/local/call_snv.nf +++ b/subworkflows/local/call_snv.nf @@ -71,7 +71,6 @@ workflow CALL_SNV { ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix - ch_versions = ch_versions.mix(CALL_SNV_DEEPVARIANT.out.versions) } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 96c8ec4f7..897cc7373 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -25,7 +25,6 @@ workflow CALL_SNV_DEEPVARIANT { val_analysis_type // boolean main: - ch_versions = channel.empty() if (val_analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) @@ -48,6 +47,7 @@ workflow CALL_SNV_DEEPVARIANT { ch_case_info .combine(ch_file_list) + .map {meta, gvcf -> return [meta, gvcf, []]} .set { ch_gvcfs } GLNEXUS ( ch_gvcfs, [[:],[]] ) @@ -87,5 +87,4 @@ workflow CALL_SNV_DEEPVARIANT { gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] tabix = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 8733edab0..f24d752fc 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -36,7 +36,6 @@ workflow CALL_SV_MT { val_split_length // string: [mandatory] mitosalt_split_length main: - ch_versions = Channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -85,5 +84,4 @@ workflow CALL_SV_MT { mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/generate_cytosure_files.nf b/subworkflows/local/generate_cytosure_files.nf index d0f1a472b..18f6ed80a 100644 --- a/subworkflows/local/generate_cytosure_files.nf +++ b/subworkflows/local/generate_cytosure_files.nf @@ -9,7 +9,7 @@ include { VCF2CYTOSURE } from '../../modules/nf workflow GENERATE_CYTOSURE_FILES { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_blacklist // channel: [optional] [path(blacklist)] ch_sample_id_map // channel: [optional] [val(id), val(id)] ch_tbi // channel: [mandatory] [ val(meta), path(vcf_index) ] @@ -19,15 +19,15 @@ workflow GENERATE_CYTOSURE_FILES { main: ch_reheader_out = channel.empty() - TIDDIT_COV_VCF2CYTOSURE (ch_bam, [[],[]]) + TIDDIT_COV_VCF2CYTOSURE (ch_bam_bai, [[],[]]) // Build channel: [val(sample_meta), path(vcf), path(vcf_index)] ch_vcf.join( ch_tbi, failOnMismatch: true ) .set { ch_vcf_tbi } - ch_bam.combine(ch_vcf_tbi) + ch_bam_bai.combine(ch_vcf_tbi) .map { - meta_sample, _bam, _meta_case, vcf, tbi -> + meta_sample, _bam, _bai, _meta_case, vcf, tbi -> def id_meta = ['id':meta_sample.sample] def sex_meta = ['sex':meta_sample.sex] return [ id_meta, sex_meta, vcf, tbi ] diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index ebfb7b3c1..096e644d9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -59,7 +59,6 @@ workflow PREPARE_REFERENCES { main: - ch_versions = channel.empty() ch_bait_intervals = channel.empty() ch_bwa = channel.empty() ch_genome_bwameme_index = channel.empty() @@ -299,6 +298,4 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] - versions = ch_versions // channel:[ path(versions.yml) ] - } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 0a020cfba..ccd669709 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -422,15 +422,6 @@ ] ] ], - "31": [ - "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,1b3327823f65f68efc82043fc802a384", - "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", - "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" - ], "4": [ [ { @@ -960,22 +951,13 @@ "spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi:md5,3fab1357156412ca02b2bdf075e97382" ] ] - ], - "versions": [ - "versions.yml:md5,12e18a91d3ec0da87543f9fded01f1c1", - "versions.yml:md5,1b3327823f65f68efc82043fc802a384", - "versions.yml:md5,447a22450289bba28dd03ae4f4f92774", - "versions.yml:md5,7479477c0c4b6eb043c58bc40ee41198", - "versions.yml:md5,b9ba5dac48d896837b097c56bcdd768c", - "versions.yml:md5,bdda7848a0b1aaf27939782b868ad9c5", - "versions.yml:md5,f5568ab78d420d74714985cdae832a6e" ] } ], + "timestamp": "2026-02-17T15:18:47.287844356", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-16T23:13:28.796983269" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 1484b0f76..d2edb0da1 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -61,7 +61,7 @@ workflow QC_BAM { ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results } - TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input + TIDDIT_COV (ch_bam_bai, [[],[]]) // 2nd pos. arg is req. only for cram input UCSC_WIGTOBIGWIG (TIDDIT_COV.out.wig, ch_genome_chrsizes) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index b1d3ef2cf..aa697e3ef 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -72,11 +72,11 @@ ] ] ], + "timestamp": "2026-02-17T15:20:57.570426841", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-27T10:15:41.947673274" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "QC_BAM - test, sentieon": { "content": [ @@ -151,10 +151,10 @@ ] ] ], + "timestamp": "2026-02-17T15:21:49.953972761", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-27T10:17:32.616739257" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/rank_variants.nf b/subworkflows/local/rank_variants.nf index 7dc4589b7..92fc42819 100644 --- a/subworkflows/local/rank_variants.nf +++ b/subworkflows/local/rank_variants.nf @@ -19,8 +19,6 @@ workflow RANK_VARIANTS { process_with_sort // Boolean main: - ch_versions = channel.empty() - GENMOD_ANNOTATE(ch_vcf) ch_models_in = GENMOD_ANNOTATE.out.vcf.combine(ch_pedfile) @@ -41,5 +39,4 @@ workflow RANK_VARIANTS { emit: vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 8c25c199f..0e41bad3f 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -144,10 +144,10 @@ ] } ], + "timestamp": "2026-02-09T10:18:23.261854", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T10:18:23.261854" + } } } \ No newline at end of file diff --git a/test.sh b/test.sh new file mode 100644 index 000000000..c76b0b687 --- /dev/null +++ b/test.sh @@ -0,0 +1,2 @@ +nf-test test subworkflows/local/ --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >wflog 2>&1 +nf-test test tests --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >>wflog 2>&1 diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4cb1b4477..565ba07c8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -67,15 +67,13 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -118,11 +116,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -217,7 +215,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" @@ -256,7 +254,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -310,10 +308,10 @@ "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "0.5.1" + "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -325,10 +323,13 @@ "samtools": "1.22.1" }, "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" }, "SAMTOOLS_SORT": { "samtools": "1.22.1" @@ -349,7 +350,7 @@ "seqtk": "1.4-r122" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -444,16 +445,16 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 @@ -465,13 +466,13 @@ "upd": 0.1 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -1089,7 +1090,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T10:21:06.035670185", + "timestamp": "2026-02-19T10:01:20.665806391", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 3adea4c33..a8ce102ed 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -68,11 +68,10 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -115,11 +114,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -208,7 +207,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" @@ -241,7 +240,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -309,6 +308,9 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" + }, "SAMTOOLS_SORT": { "samtools": "1.22.1" }, @@ -322,7 +324,7 @@ "samtools": "1.22.1" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -414,16 +416,16 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 @@ -435,13 +437,13 @@ "upd": 0.1 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -1018,7 +1020,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T10:27:29.654590007", + "timestamp": "2026-02-19T15:08:50.558312851", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f54271b71..6bdc802f6 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -65,15 +65,13 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1", - "samtools": "1.19.2" + "bwamem2": "2.2.1" }, "BWA_INDEX_GENOME": { - "bwa": "0.7.18-r1243-dirty" + "bwa": "0.7.19-r1273" }, "CAT_CAT_BAIT": { "pigz": 2.8 @@ -110,11 +108,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "add_most_severe_consequence": 1.1, + "addmostsevereconsequence": 1.1, "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "add_most_severe_pli": 1.1, + "addmostseverepli": 1.1, "bgzip": 1.21 }, "DEEPVARIANT": { @@ -209,7 +207,7 @@ "coreutils": 9.5 }, "GLNEXUS": { - "glnexus": "1.4.1-0-g68e25e5" + "glnexus": "1.4.1" }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" @@ -248,7 +246,7 @@ "samtools": 1.23 }, "NGSBITS_SAMPLEGENDER": { - "ngs-bits": 202411 + "ngsbits": 202512 }, "PEDDY": { "peddy": "0.4.8" @@ -317,10 +315,13 @@ "samtools": "1.22.1" }, "SAMTOOLS_INDEX_ALIGN": { - "samtools": 1.21 + "samtools": "1.22.1" }, "SAMTOOLS_INDEX_MARKDUP": { - "samtools": 1.21 + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" }, "SAMTOOLS_SORT": { "samtools": "1.22.1" @@ -341,7 +342,7 @@ "seqtk": "1.4-r122" }, "SMNCOPYNUMBERCALLER": { - "SMNCopyNumberCaller": "1.1.2" + "smncopynumbercaller": "1.1.2" }, "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 @@ -433,28 +434,28 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "TIDDIT_SV": { - "tiddit": "3.6.1" + "tiddit": "3.9.4" }, "UCSC_WIGTOBIGWIG": { - "ucsc": 447 + "ucsc": 482 }, "UNTAR_VEP_CACHE": { "untar": 1.34 }, "VCF2CYTOSURE": { - "vcf2cytosure": "0.9.1" + "vcf2cytosure": "0.9.3" }, "VCFANNO": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "VCFANNO_MT": { - "vcfanno": "0.3.5" + "vcfanno": "0.3.7" }, "Workflow": { "nf-core/raredisease": "v2.7.0dev" @@ -708,7 +709,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-03T10:31:17.265377549", + "timestamp": "2026-02-19T18:45:40.125652788", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/wflog1 b/wflog1 new file mode 100644 index 000000000..d4a1be1a7 --- /dev/null +++ b/wflog1 @@ -0,0 +1,6024 @@ +Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp + +🚀 nf-test 0.9.4 +https://www.nf-test.com +(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr + +Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar +Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar +Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar +Warning: every snapshot that fails during this test run is re-recorded. + +Test Workflow ALIGN + + Test [9e55951e] 'align bwamem2 - wgs' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 76951fb0df + [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) + [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) + [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) + [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) + [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) + [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e0/2e14cf254f7fbb4dc949380310a337/earlycasualcaiman.fastp.json" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/98/26e65c7abf446866ff37cbbd541717/hugelymodelbat.fastp.json" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/f5/98f07ad89689da1a3f1100da58ed14/slowlycivilbuck.fastp.json" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/bf/df3174d0c94ba9bcfdf3f79ac94aff/earlycasualcaiman.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/24/2893d5535a534aa7039df0a5261eea/earlycasualcaiman.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/c4c15846708fac2faff4a670b81503/hugelymodelbat.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/12/26927042b8031768ba14d2a75910f5/hugelymodelbat.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/9b/c35b8bf43ad637c89a38893c11055e/slowlycivilbuck.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/8c/d4a49d10b0869d21d9186339b356b8/slowlycivilbuck.bam.bai" + ] + ], + "6": [ + [ + { + 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"id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] + ], + "versions": [ + + ] + } +PASSED (5684.323s) + Test [59260ec0] 'align bwamem2 - wes' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: db2dc4c6c7 + [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) + [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) + [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) + [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) + [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) + [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) + [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) + [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) + [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/b8/4d574f613662456c74c71fbcd5c43a/earlycasualcaiman.fastp.json" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/51/29cdff1116f2d5e95019c51dfab7ad/hugelymodelbat.fastp.json" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/41/6ea3afbfecf3264f36467ff22e97cd/slowlycivilbuck.fastp.json" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": 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+ "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "mt_bam_bai": [ + + ], + "mt_bam_bai_gatksubwf": [ + + ], + "mtshift_bam_bai_gatksubwf": [ + + ], + "versions": [ + + ] + } +PASSED (422.715s) + Test [412be509] 'align bwameme - wgs' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 615692c6bf + [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) + [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) + [5a/738041] Submitted process > GENOME_MEME (reference.fasta) + [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) + [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) + [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) + [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) + [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) + [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) + [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) + [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) + [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) + [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) + [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) + [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) + [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.bam" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/44/50914a860567366221acc4e448aaff/earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/86/bd7aff1284232cbe15e2675b533a8b/hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/14/875b8f9dc9717693a954a75ae4724f/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/14/875b8f9dc9717693a954a75ae4724f/slowlycivilbuck_sorted_md.bam.bai" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/1c/c18c9f8144f9b0182f1cb5b0130123/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/bf/44a690def20faf7781982c3680f13d/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/d2/6a6294cdd434779a02a95f9887d407/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "mtshift_bam_bai_gatksubwf": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/67/6149f3bcd6867a446f82667a477995/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] + ], + "versions": [ + + ] + } +PASSED (4812.56s) + +Test Workflow ALIGN_MT + + Test [b23715c6] 'align mt - bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: b10847aa0f + [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) + [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam + [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "2": [ + + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "versions": [ + + ] + } +PASSED (1439.157s) + Test [846f97b8] 'align mt - bwa' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: f6ad620135 + [09/f02677] Submitted process > MT_BWA (reference_mt.fa) + [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) + [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) + [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) + [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "2": [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" + ] + ], + "versions": [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" + ] + } +PASSED (1343.021s) + +Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME + + Test [dfe67d65] 'align bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 399b5fe8cb + [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) + [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) + [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" + ] + ], + "4": [ + + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" + ] + ], + "versions": [ + + ] + } +PASSED (296.275s) + Test [6b77a48f] 'align bwameme' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 9f7b282f72 + [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) + [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) + [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) + [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) + [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) + [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) + [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) + [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" + ] + ], + "4": [ + + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" + ] + ], + "versions": [ + + ] + } +PASSED (321.442s) + +Test Workflow ALIGN_SENTIEON + + Test [b3f3ddb4] 'align sentieon' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 2840f9cc33 + [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) + [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) + [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) + [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" + ] + ], + "6": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" + ] + ], + "7": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" + ] + ], + "aln_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" + ] + ], + "gc_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" + ] + ], + "gc_summary": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" + ] + ], + "is_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" + ] + ], + "mq_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" + ] + ], + "qd_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" + ] + ] + } +PASSED (340.075s) + +Test Workflow CALL_REPEAT_EXPANSIONS + + Test [9ebd2699] 'CALL_REPEAT_EXPANSIONS' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value + > WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value + WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 5dde73596c + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam + [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" + ] + ] + } +PASSED (518.242s) + +Test Workflow PREPARE_REFERENCES + + Test [8ce0dfef] 'Should run without failures' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 + > [HISAT2 index build] Available memory: 15 GB + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 + [HISAT2 index build] Available memory: 15 GB + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 458de812a0 + [HISAT2 index build] Available memory: 15 GB + [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index + [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) + [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) + [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) + [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) + [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) + [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) + [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" + ] + ], + "1": [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ], + "10": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" + ] + ], + "11": [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" + ] + ], + "12": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" + ] + ], + "13": [ + + ], + "14": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" + ] + ], + "15": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" + ] + ], + "16": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" + ] + ], + "17": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" + ] + ], + "18": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" + ] + ], + "19": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" + ] + ], + "2": [ + [ + { + "id": "dbsnp_-138-" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" + ] + ], + "20": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" + ] + ], + "21": [ + + ], + "22": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" + ] + ], + "23": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" + ] + ], + "24": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" + ] + ], + "25": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" + ] + ], + "26": [ + + ], + "27": [ + [ + { + "id": "target" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" + ] + ], + "28": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" + ] + ], + "29": [ + [ + [ + + ] + ] + ], + "3": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" + ] + ], + "30": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" + ] + ], + "4": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" + ] + ], + "5": [ + + ], + "6": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" + ] + ], + "7": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" + ] + ], + "8": [ + [ + { + "id": "reference" + }, + "/nf-core/test-datasets/raredisease/reference/reference.fasta" + ] + ], + "9": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" + ] + ], + "bait_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" + ] + ], + "dbsnp": [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ], + "dbsnp_tbi": [ + [ + { + "id": "dbsnp_-138-" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" + ] + ], + "genome_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" + ] + ], + "genome_bwamem2_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" + ] + ], + "genome_bwameme_index": [ + + ], + "genome_chrom_sizes": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" + ] + ], + "genome_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" + ] + ], + "genome_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" + ] + ], + "genome_fasta": [ + [ + { + "id": "reference" + }, + "/nf-core/test-datasets/raredisease/reference/reference.fasta" + ] + ], + "genome_hisat2_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" + ] + ], + "gnomad_af_idx": [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" + ] + ], + "mt_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" + ] + ], + "mt_bwamem2_index": [ + + ], + "mt_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" + ] + ], + "mt_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" + ] + ], + "mt_fasta": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" + ] + ], + "mt_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" + ] + ], + "mt_last_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" + ] + ], + "mtshift_backchain": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" + ] + ], + "mtshift_bwa_index": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" + ] + ], + "mtshift_bwamem2_index": [ + + ], + "mtshift_dict": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" + ] + ], + "mtshift_fai": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" + ] + ], + "mtshift_fasta": [ + [ + { + "id": "reference" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" + ] + ], + "mtshift_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" + ] + ], + "sdf": [ + + ], + "target_bed": [ + [ + { + "id": "target" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" + ] + ], + "target_intervals": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" + ] + ], + "vcfanno_extra": [ + [ + [ + + ] + ] + ], + "vep_resources": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" + ] + ] + } +PASSED (1793.716s) + +Test Workflow QC_BAM + + Test [afc7bf7a] 'QC_BAM - test, bwamem2' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: ad4f64ff7c + [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "10": [ + + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" + ] + ], + "4": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" + ] + ], + "5": [ + + ], + "6": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "bigwig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" + ] + ], + "cov": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "cov_y": [ + + ], + "d4": [ + + ], + "global_dist": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ] + ], + "hs_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "multiple_metrics": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "qualimap_results": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" + ] + ], + "self_sm": [ + + ], + "sex_check": [ + + ], + "tiddit_wig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" + ] + ] + } +PASSED (291.083s) + Test [f2c7c2bb] 'QC_BAM - test, sentieon' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 60d4a16c8e + [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) + [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) + [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) + [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] + ], + "10": [ + + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" + ] + ], + "4": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" + ] + ], + "5": [ + + ], + "6": [ + [ + { + "id": "earlycasualcaiman", + "sample": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] + ], + "qualimap_results": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" + ] + ], + "self_sm": [ + + ], + "sex_check": [ + + ], + "tiddit_wig": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" + ] + ] + } +PASSED (214.248s) + +Test Workflow SCATTER_GENOME + + Test [ad40db63] 'Should run without failures' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/trace.csv -w 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value + [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 5c5d631253 + [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) + [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) + Stop plugin 'nf-schema@2.5.1' + + Output Channels: + { + "0": [ + [ + { + "id": "genome" + }, + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" + ] + ], + "1": [ + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" + ], + [ + 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" + ], + [ + "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" + ] + ] + } +PASSED (512.277s) + + +SUCCESS: Executed 13 tests in 17995.327s + diff --git a/wflog2 b/wflog2 new file mode 100644 index 000000000..4f05bdf51 --- /dev/null +++ b/wflog2 @@ -0,0 +1,10617 @@ +Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp + +🚀 nf-test 0.9.4 +https://www.nf-test.com +(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr + +Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar +Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar +Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar +Warning: every snapshot that fails during this test run is re-recorded. + +Test pipeline + + Test [6304aa7b] '-profile test' + + Profiles: [test, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - default + > config_profile_description : Minimal test dataset to check pipeline function + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_00-58-31 + > + > Core Nextflow options + > runName : zen_franklin + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - default + config_profile_description : Minimal test dataset to check pipeline function + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_00-58-31 + + Core Nextflow options + runName : zen_franklin + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) + [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) + [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) + [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) + [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz + [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) + [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) + [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) + [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) + [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) + [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) + [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) + [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) + [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) + [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) + [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) + [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) + [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) + [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) + [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) + [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) + [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) + [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) + [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) + [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) + [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) + [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] + [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) + [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (32575.636s) + Snapshots: + 1 updated [-profile test] + +Test pipeline + + Test [df780376] '-profile test_bam' + + Profiles: [test_bam, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/params.json -ansi-log false -profile test_bam,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > ngsbits_samplegender_method : sry + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - bam + > config_profile_description : Minimal test dataset to check pipeline function + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_10-01-37 + > + > Core Nextflow options + > runName : gloomy_newton + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test_bam,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + ngsbits_samplegender_method : sry + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - bam + config_profile_description : Minimal test dataset to check pipeline function + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_10-01-37 + + Core Nextflow options + runName : gloomy_newton + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test_bam,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) + [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) + [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) + [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) + [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) + [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) + [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) + [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) + [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) + [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) + [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) + [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) + [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) + [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) + [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) + [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) + [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) + [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) + [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) + [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) + [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) + [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) + [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) + [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) + [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) + [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) + [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) + [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) + [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) + [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) + [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) + [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) + [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) + [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) + [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) + [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) + [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) + [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) + [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) + [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) + [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) + [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) + [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) + [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) + [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) + [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) + [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) + [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) + [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) + [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) + [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) + [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) + [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) + [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) + [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) + [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) + [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) + [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) + [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) + [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) + [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) + [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) + [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) + [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) + [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) + [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) + [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) + [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) + [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) + [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) + [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) + [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) + [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) + [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) + [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) + [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) + [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) + [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) + [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) + [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) + [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) + [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) + [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) + [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) + [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) + [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) + [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) + [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) + [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) + [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) + [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) + [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) + [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) + [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) + [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) + [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) + [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) + [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) + [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) + [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) + [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) + [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) + [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) + [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) + [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) + [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) + [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) + [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) + [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) + [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) + [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) + [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) + [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) + [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) + [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) + [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) + [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) + [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) + [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) + [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) + [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) + [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) + [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) + [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) + [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) + [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) + [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) + [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) + [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) + [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) + [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) + [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) + [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) + [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) + [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) + [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) + [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) + [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) + [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) + [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) + [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) + [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) + [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) + [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) + [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) + [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) + [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) + [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) + [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) + [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) + [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (18448.933s) + Snapshots: + 1 updated [-profile test_bam] + +Test pipeline + + Test [577d1960] '-profile test_singleton' + + Profiles: [test_singleton, singularity] + Configs: [nextflow.config, tests/nextflow.config] + Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/params.json -ansi-log false -profile test_singleton,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work -stub + > N E X T F L O W ~ version 25.10.4 + > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 + > + > ------------------------------------------------------ + > ,--./,-. + >  ___ __ __ __ ___ /,-._.--~' + >  |\ | |__ __ / ` / \ |__) |__ } { + >  | \| | \__, \__/ | \ |___ \`-._,-`-, + > `._,._,' + >  nf-core/raredisease 2.7.0dev + > ------------------------------------------------------ + > + > Input/output options + > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv + > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output + > + > Reference file options + > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + > genome : GRCh37 + > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + > igenomes_ignore : true + > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + > mito_name : MT + > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + > + > Analysis options + > homoplasmy_af_threshold : 1 + > skip_tools : germlinecnvcaller,gens + > + > Annotation options + > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + > vep_cache_version : 107 + > + > Institutional config options + > config_profile_name : Test profile - singleton + > config_profile_description : Minimal test dataset to check pipeline function using a single sample + > + > Generic options + > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + > trace_report_suffix : 2026-02-19_15-09-08 + > + > Core Nextflow options + > runName : zen_hugle + > containerEngine : singularity + > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 + > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work + > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + > userName : ramprasad.neethiraj + > profile : test_singleton,singularity + > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + > + > !! Only displaying parameters that differ from the pipeline defaults !! + > ------------------------------------------------------ + > + > * The pipeline + > https://doi.org/10.5281/zenodo.7995798 + > + > * The nf-core framework + > https://doi.org/10.1038/s41587-020-0439-x + > + > * Software dependencies + > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + > + > WARN: The following invalid input values have been detected: + > + > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + > + > + > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + > + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + > [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + > -[nf-core/raredisease] Pipeline completed successfully- + + Stdout: + N E X T F L O W ~ version 25.10.4 + Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 + + ------------------------------------------------------ + ,--./,-. +  ___ __ __ __ ___ /,-._.--~' +  |\ | |__ __ / ` / \ |__) |__ } { +  | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' +  nf-core/raredisease 2.7.0dev + ------------------------------------------------------ + + Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv + outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output + + Reference file options + fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai + fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta + genome : GRCh37 + gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz + igenomes_ignore : true + intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list + intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list + known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz + mito_name : MT + mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv + mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv + score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini + score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini + svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv + target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed + variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json + vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt + vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml + vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua + vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz + vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv + vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt + + Analysis options + homoplasmy_af_threshold : 1 + skip_tools : germlinecnvcaller,gens + + Annotation options + variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt + vep_cache_version : 107 + + Institutional config options + config_profile_name : Test profile - singleton + config_profile_description : Minimal test dataset to check pipeline function using a single sample + + Generic options + pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ + trace_report_suffix : 2026-02-19_15-09-08 + + Core Nextflow options + runName : zen_hugle + containerEngine : singularity + container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 + launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 + workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work + projectDir : /home/ramprasad.neethiraj/nextflow/raredisease + userName : ramprasad.neethiraj + profile : test_singleton,singularity + configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config + + !! Only displaying parameters that differ from the pipeline defaults !! + ------------------------------------------------------ + + * The pipeline + https://doi.org/10.5281/zenodo.7995798 + + * The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + + * Software dependencies + https://github.com/nf-core/raredisease/blob/master/CITATIONS.md + + WARN: The following invalid input values have been detected: + + * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ + + + WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. + HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. + + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value + [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + + Stderr: + + Nextflow Output: + N E X T F L O W ~ version 25.10.4 + Enabled plugins: [] + Disabled plugins: [] + PF4J version 3.12.0 in 'deployment' mode + No plugins + Plugin 'nf-schema@2.5.1' resolved + Start plugin 'nf-schema@2.5.1' + revision: 0e8c7493e0 + + Input/output options + + Plugin 'nf-amazon@3.4.4' resolved + Start plugin 'nf-amazon@3.4.4' + [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) + [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) + [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) + [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) + [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) + [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) + [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) + [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) + [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) + [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) + [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) + [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) + [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) + [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) + [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) + [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) + [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) + [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) + [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) + [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) + [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) + [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) + [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) + [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) + [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) + [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) + [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) + [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) + [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) + [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) + [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) + [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) + [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) + [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) + [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) + [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) + [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) + [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) + [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) + [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) + [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) + [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) + [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) + [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) + [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) + [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) + [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) + [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) + [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) + [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) + [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) + [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) + [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) + [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) + [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) + [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) + [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) + [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) + [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) + [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) + [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) + [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) + [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) + [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) + [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) + [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) + [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) + [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) + [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) + [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) + [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) + [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) + [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) + [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) + [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) + [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) + [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) + [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) + [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) + [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) + [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) + [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) + [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) + [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) + [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) + [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) + [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) + [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) + [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) + [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) + [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) + [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) + [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) + [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) + [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) + [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) + [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) + [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) + [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) + [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) + [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) + [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) + [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) + [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) + [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) + [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) + [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) + [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) + [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) + [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) + [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) + [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) + [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) + [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) + [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) + [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) + [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) + [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) + [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) + [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) + [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) + [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) + [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) + [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) + [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz + Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz + [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) + [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) + [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) + [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) + [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) + [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) + [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) + [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) + [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) + [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) + [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) + [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) + [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) + [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) + [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) + [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) + [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) + [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) + [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) + [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) + [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) + [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) + [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) + [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) + [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) + [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) + [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) + [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) + [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) + [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) + [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) + [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) + [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) + [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) + [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) + [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) + [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) + [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) + [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) + [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) + [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) + [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) + [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) + [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) + [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) + [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) + [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) + [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) + [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) + [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) + [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) + [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) + [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) + [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) + [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) + [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) + [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) + [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) + [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) + [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) + [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) + [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) + [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC + -[nf-core/raredisease] Pipeline completed successfully- + Stop plugin 'nf-amazon@3.4.4' + Stop plugin 'nf-schema@2.5.1' + + PASSED (13011.306s) + Snapshots: + 1 updated [-profile test_singleton] + + +Snapshot Summary: + 3 updated + +SUCCESS: Executed 3 tests in 64038.604s + diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b73fabfc3..997d91530 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -458,7 +458,6 @@ workflow RAREDISEASE { ch_ranksnv_nuclear_in, false ) - ch_versions = ch_versions.mix(RANK_VARIANTS_SNV.out.versions) } // @@ -529,7 +528,6 @@ workflow RAREDISEASE { ch_ranksnv_mt_in, false ) - ch_versions = ch_versions.mix(RANK_VARIANTS_MT.out.versions) } } @@ -578,7 +576,6 @@ workflow RAREDISEASE { val_genome, val_vep_cache_version ).set { ch_sv_annotate } - ch_versions = ch_versions.mix(ch_sv_annotate.versions) ch_sv_annotate.vcf_ann .multiMap { meta, vcf -> @@ -623,7 +620,6 @@ workflow RAREDISEASE { ch_ranksnv_sv_in, true ) - ch_versions = ch_versions.mix(RANK_VARIANTS_SV.out.versions) } } /* @@ -659,7 +655,6 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) - ch_versions = ch_versions.mix(CALL_SV_MT.out.versions) } /* @@ -767,7 +762,7 @@ workflow RAREDISEASE { */ if (!skip_vcf2cytosure && val_analysis_type.equals("wgs") && !skip_sv_calling && !skip_sv_annotation) { GENERATE_CYTOSURE_FILES ( - ch_mapped.genome_marked_bam, + ch_mapped.genome_marked_bam_bai, ch_vcf2cytosure_blacklist, ch_sample_id_map, ch_sv_annotate.tbi, From 546639adf538527ee462aba8b82b08a24731bbc7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 19:35:20 +0100 Subject: [PATCH 383/872] remove logs --- miss | 0 test.sh | 2 - wflog1 | 6024 ------------------------------- wflog2 | 10617 ------------------------------------------------------ 4 files changed, 16643 deletions(-) delete mode 100644 miss delete mode 100644 test.sh delete mode 100644 wflog1 delete mode 100644 wflog2 diff --git a/miss b/miss deleted file mode 100644 index e69de29bb..000000000 diff --git a/test.sh b/test.sh deleted file mode 100644 index c76b0b687..000000000 --- a/test.sh +++ /dev/null @@ -1,2 +0,0 @@ -nf-test test subworkflows/local/ --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >wflog 2>&1 -nf-test test tests --profile test,singularity --verbose --debug --update-snapshot --clean-snapshot >>wflog 2>&1 diff --git a/wflog1 b/wflog1 deleted file mode 100644 index d4a1be1a7..000000000 --- a/wflog1 +++ /dev/null @@ -1,6024 +0,0 @@ -Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp - -🚀 nf-test 0.9.4 -https://www.nf-test.com -(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr - -Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar -Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar -Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar -Warning: every snapshot that fails during this test run is re-recorded. - -Test Workflow ALIGN - - Test [9e55951e] 'align bwamem2 - wgs' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9e55951e6d05e70586045920c57dd99f.nf` [dreamy_jepsen] DSL2 - revision: 76951fb0df - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 76951fb0df - [2f/b8eb7e] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [8d/a40861] Submitted process > MT_MEM2 (reference_mt.fa) - [d4/e7d392] Submitted process > GENOME_MEM2 (reference.fasta) - [e0/2e14cf] Submitted process > ALIGN:FASTP (earlycasualcaiman) - [f5/98f07a] Submitted process > ALIGN:FASTP (slowlycivilbuck) - [98/26e65c] Submitted process > ALIGN:FASTP (hugelymodelbat) - [b1/375670] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - [d7/f0f56c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - [ae/fed8d4] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - [76/92d1b7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [42/529b85] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [96/c152d6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [07/88a55a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [11/664df9] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [d7/167408] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [c8/338927] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [5e/7c9a5a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [38/4319cc] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [e7/cd3273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [64/346b5e] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - [9b/c35b8b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [ea/581707] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [23/e5f981] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [cb/77f4cc] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - [05/c4c158] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [c2/09f965] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - [bf/df3174] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [12/269270] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [15/3691aa] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [8c/d4a49d] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [3e/981042] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [a2/8e9876] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [24/2893d5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [97/bcf1a6] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [03/c6555b] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [ad/209e67] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [00/1ab319] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [9c/ec60cc] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [6e/1ec166] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [71/786301] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [30/c6f451] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [f2/dc4352] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [16/e3916d] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [82/107b31] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [3b/95f593] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [96/8b79b5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [11/d683e9] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [24/601f09] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [13/b187c4] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [b9/fb418d] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [d0/b30509] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/8d6b0b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [07/372e48] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [a3/f65cdd] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [ed/c8b594] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [ac/fcf922] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [7b/281732] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [3a/83f3c2] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [a7/4c8fbb] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c8/40fe69] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [16/84a7c8] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [a1/caaca6] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [05/83a7b2] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [4f/399cf0] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [ae/1bd8a1] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [38/908410] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e0/2e14cf254f7fbb4dc949380310a337/earlycasualcaiman.fastp.json" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/98/26e65c7abf446866ff37cbbd541717/hugelymodelbat.fastp.json" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/f5/98f07ad89689da1a3f1100da58ed14/slowlycivilbuck.fastp.json" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/23/e5f9815152c618b55fef4dee3d1ed5/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/11/664df9ca532aff0813088c9ec0ef4c/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ea/581707852cadbced290f23957bbf88/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/42/529b855dabc7c35e72af35da8c5b42/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/e7/cd3273c9383242c1c33b781d1847dc/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/c8/338927c9e617b5f9eddb41c0e1c927/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": 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"mt_bam_bai_gatksubwf": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/38/908410bfc3d6b21a01178d2fff1ae4/earlycasualcaiman_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/38/908410bfc3d6b21a01178d2fff1ae4/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/83a7b2f1f57b0d1ca7ae28dde0fa2c/hugelymodelbat_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/05/83a7b2f1f57b0d1ca7ae28dde0fa2c/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/a1/caaca66e607db2356b239ec7eac182/slowlycivilbuck_sorted_merged_md_sorted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/a1/caaca66e607db2356b239ec7eac182/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "mtshift_bam_bai_gatksubwf": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ae/1bd8a1f66e7867f907762839b1e897/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/ae/1bd8a1f66e7867f907762839b1e897/earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/4f/399cf0cf99d1f59a4a56b6109a8af0/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9e55951e6d05e70586045920c57dd99f/work/16/84a7c8da7f0b7b2f8318f7b7b02ee6/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] - ], - "versions": [ - - ] - } -PASSED (5684.323s) - Test [59260ec0] 'align bwamem2 - wes' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-59260ec0911f4e1a7b93a03dbf80f47b.nf` [focused_volhard] DSL2 - revision: db2dc4c6c7 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: db2dc4c6c7 - [88/2672e2] Submitted process > MT_MEM2 (reference_mt.fa) - [1f/a6c70a] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [77/cffae5] Submitted process > GENOME_MEM2 (reference.fasta) - [51/29cdff] Submitted process > ALIGN:FASTP (hugelymodelbat) - [b8/4d574f] Submitted process > ALIGN:FASTP (earlycasualcaiman) - [41/6ea3af] Submitted process > ALIGN:FASTP (slowlycivilbuck) - [68/1bcbd6] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck) - [72/5badd7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat) - [6c/aceea0] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman) - [d4/c17e33] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [0c/e07c27] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [3b/76815e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [57/b63d69] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [a8/d15e6c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [f8/8bdfa1] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [70/bf093e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [2a/3bdec7] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [15/6ad41f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [7b/06938d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [32/3edfa5] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [f2/65cf0c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/b8/4d574f613662456c74c71fbcd5c43a/earlycasualcaiman.fastp.json" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/51/29cdff1116f2d5e95019c51dfab7ad/hugelymodelbat.fastp.json" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/41/6ea3afbfecf3264f36467ff22e97cd/slowlycivilbuck.fastp.json" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": 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"/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f2/65cf0c9c0309a9469e27227422711b/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/32/3edfa5656fa9bb7fd16b4d3c42d88b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/7b/06938df4fb34e93a22a96fb3ba2217/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "markdup_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/f8/8bdfa1c82af79bcf5b464aacd992e0/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/0c/e07c27d00fefd24d3e6e7d42fd06fe/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/59260ec0911f4e1a7b93a03dbf80f47b/work/57/b63d691d9036ba6933cdf3eae6d970/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "mt_bam_bai": [ - - ], - "mt_bam_bai_gatksubwf": [ - - ], - "mtshift_bam_bai_gatksubwf": [ - - ], - "versions": [ - - ] - } -PASSED (422.715s) - Test [412be509] 'align bwameme - wgs' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-412be5094492a1a9fce41065fb7d3c20.nf` [lethal_wiles] DSL2 - revision: 615692c6bf - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 615692c6bf - [82/c2b849] Submitted process > SHIFTMT_MEM2 (reference_shift.fasta) - [46/0af46a] Submitted process > MT_MEM2 (reference_mt.fa) - [5a/738041] Submitted process > GENOME_MEME (reference.fasta) - [55/4e3044] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (slowlycivilbuck) - [df/4f9975] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (earlycasualcaiman) - [8f/99f625] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (hugelymodelbat) - [bb/d49273] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman) - [6d/76a64d] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [68/94532c] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat) - [e1/95f571] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [11/6a3afd] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck) - [fc/9c557e] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [f6/42e118] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman) - [e6/6bcdbe] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat) - [4d/b76183] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck) - [14/875b8f] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [44/50914a] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [86/bd7aff] Submitted process > ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [54/629774] Submitted process > ALIGN:SAMTOOLS_VIEW (earlycasualcaiman) - [a4/7b57bc] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [33/c99941] Submitted process > ALIGN:SAMTOOLS_VIEW (hugelymodelbat) - [6e/1e98c8] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [96/d05400] Submitted process > ALIGN:SAMTOOLS_VIEW (slowlycivilbuck) - [b6/94d269] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [06/a0bcb0] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [67/6b8624] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [e6/cf9dfb] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [8f/07d888] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [7a/e1e0a5] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [12/8072e1] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [b2/7493da] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [2b/bb8b72] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [da/c2b911] Submitted process > ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [04/ecdb5b] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [57/def9e0] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [c1/1ec0fb] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [69/cfd046] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [f7/21fa37] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [cc/e55a09] Submitted process > ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [2c/2b45a1] Submitted process > ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [10/dd873a] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [c4/0aeed5] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [11/3bf5a8] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [8c/e64ba0] Submitted process > ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [6e/23cbbf] Submitted process > ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b0/88e254] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [52/e702c1] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [43/baf87e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [32/934e6e] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [17/0c81a2] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [8b/126580] Submitted process > ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [59/25a10b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c0/b427f4] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [a4/a209d0] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [ff/634e8b] Submitted process > ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [6c/70bb77] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [da/a9282c] Submitted process > ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [67/6149f3] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [d2/6a6294] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cb/c5bb27] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [15/de50bf] Submitted process > ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [bf/44a690] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [1c/c18c9f] Submitted process > ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.bam" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/44/50914a860567366221acc4e448aaff/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/86/bd7aff1284232cbe15e2675b533a8b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/14/875b8f9dc9717693a954a75ae4724f/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/44/50914a860567366221acc4e448aaff/earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/86/bd7aff1284232cbe15e2675b533a8b/hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/14/875b8f9dc9717693a954a75ae4724f/slowlycivilbuck_sorted_md.bam.bai" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/6d/76a64d8beccaaec58b731a0d2def95/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/e1/95f57162c11c4633b1711b981613ca/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/fc/9c557e263569b320cd35fcd3a83db4/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/a4/7b57bc11845f5bc4733ece4b94487c/earlycasualcaiman.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/8f/07d888a3a1a96250875143512851fc/earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - 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}, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/15/de50bfd0a1a7d13aa0e0171abadd23/hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/412be5094492a1a9fce41065fb7d3c20/work/cb/c5bb2737454504bf4336ac64e20b27/slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] - ], - "versions": [ - - ] - } -PASSED (4812.56s) - -Test Workflow ALIGN_MT - - Test [b23715c6] 'align mt - bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b23715c6714600940ebae2595444b020.nf` [happy_stone] DSL2 - revision: b10847aa0f - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: b10847aa0f - [a2/59bfd9] Submitted process > MT_MEM2 (reference_mt.fa) - [a4/47dca1] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [79/437c37] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [96/ea10c4] Submitted process > ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [bf/67fbd6] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [a7/84716b] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/slowlycivilbuck_mtreverted.bam - [4a/cc09bd] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [58/cc550a] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [86/122190] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [63/347368] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [74/76f506] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [81/2477c7] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [3d/ac25b1] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [2c/a85d01] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [5b/fd3ca3] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [8a/fc7d03] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "2": [ - - ], - "marked_bai": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/8a/fc7d0356091733e9a8c03109b7134a/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/5b/fd3ca38890f6ce66b055ef3b022493/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b23715c6714600940ebae2595444b020/work/2c/a85d01bd602e48b6ca1c7c8251aa16/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "versions": [ - - ] - } -PASSED (1439.157s) - Test [846f97b8] 'align mt - bwa' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_MT/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-846f97b87defe1bc0c31ab878122be89.nf` [berserk_fermat] DSL2 - revision: f6ad620135 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: f6ad620135 - [09/f02677] Submitted process > MT_BWA (reference_mt.fa) - [0a/d3c16c] Submitted process > ALIGN_MT:BWA_MEM_MT (slowlycivilbuck) - [80/b53f33] Submitted process > ALIGN_MT:BWA_MEM_MT (hugelymodelbat) - [19/82ba22] Submitted process > ALIGN_MT:BWA_MEM_MT (earlycasualcaiman) - [0a/ff65d4] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [00/8f44e2] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b1/a67329] Submitted process > ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [d8/4d4e6d] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [b7/1ca4eb] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [f9/ee9d61] Submitted process > ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [75/8e0609] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [18/c5da1d] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [d8/098178] Submitted process > ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [14/79dbb2] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cf/bc3d65] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [71/cec937] Submitted process > ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "2": [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" - ], - "marked_bai": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam.bai" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/71/cec93735b9521d0ef834bb2b25f4cf/earlycasualcaiman_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/cf/bc3d656e47703744319b92f2127550/hugelymodelbat_sorted_merged_md_sorted.bam" - ], - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/14/79dbb2160288a970154fe5a72e5dc4/slowlycivilbuck_sorted_merged_md_sorted.bam" - ] - ], - "versions": [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/0a/d3c16c7c6dd5ed7799a4d8a475026e/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/80/b53f33e44b9bf5bc3495475e0a8a32/versions.yml", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/846f97b87defe1bc0c31ab878122be89/work/19/82ba22d06a43fed9916a9a5826ceb8/versions.yml" - ] - } -PASSED (1343.021s) - -Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME - - Test [dfe67d65] 'align bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-dfe67d6565de3968b09cdd238ec5bea6.nf` [lonely_bhaskara] DSL2 - revision: 399b5fe8cb - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 399b5fe8cb - [94/9cf1bc] Submitted process > BWAMEM2_INDEX (genome.fasta) - [f2/9fbbe0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (test) - [43/2a7f03] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - [0c/885b4b] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - [b8/3c7799] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - [f5/7214a2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - [55/4c7de2] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - [24/9694ab] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "3": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" - ] - ], - "4": [ - - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/24/9694abf7b65938d90b3a3b9ad88453/test_sorted_md.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.bam" - ] - ], - "metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/55/4c7de2a1b1ca50a15e0a344249ff8c/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "stats": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/dfe67d6565de3968b09cdd238ec5bea6/work/f5/7214a2e9bc41799235b44611141fde/test.stats" - ] - ], - "versions": [ - - ] - } -PASSED (296.275s) - Test [6b77a48f] 'align bwameme' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_bwa_bwamem2_bwameme/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-6b77a48fd341e9b3c377db84f8fea2d2.nf` [jovial_fermat] DSL2 - revision: 9f7b282f72 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 9f7b282f72 - [80/a2e931] Submitted process > BWAMEME_INDEX (genome.fasta) - [95/522acf] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM (test) - [39/5a6b69] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (test) - [52/ae1364] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_EXTRACT (test) - [c2/379548] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:EXTRACT_ALIGNMENTS (test) - [bb/1f2371] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (test) - [03/25446e] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (test) - [8c/c960a0] Submitted process > ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "3": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" - ] - ], - "4": [ - - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/8c/c960a0791228f55032d088d0360010/test_sorted_md.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.bam" - ] - ], - "metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/03/25446e678b4ddbc78d1af044db4d5b/test_sorted_md.MarkDuplicates.metrics.txt" - ] - ], - "stats": [ - [ - { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6b77a48fd341e9b3c377db84f8fea2d2/work/bb/1f237117e15e7bc83beb8e6a59fb91/test.stats" - ] - ], - "versions": [ - - ] - } -PASSED (321.442s) - -Test Workflow ALIGN_SENTIEON - - Test [b3f3ddb4] 'align sentieon' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/align_sentieon/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-b3f3ddb494b75fd3e58fa5747b9af08e.nf` [marvelous_wing] DSL2 - revision: 2840f9cc33 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 2840f9cc33 - [67/5ad7ae] Submitted process > SENTIEON_BWAINDEX (genome.fasta) - [59/b15e37] Submitted process > ALIGN_SENTIEON:SENTIEON_BWAMEM (test) - [3c/9e3cac] Submitted process > ALIGN_SENTIEON:SENTIEON_DEDUP (test) - [8f/ebbca7] Submitted process > ALIGN_SENTIEON:SENTIEON_DATAMETRICS (test) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_aln_metrics.txt" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_metrics.txt" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_gc_summary.txt" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_is_metrics.txt" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam.bai" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/3c/9e3cac80f7ce77c7bbb01d9d285a9d/test_dedup.bam" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_mq_metrics.txt" - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/b3f3ddb494b75fd3e58fa5747b9af08e/work/8f/ebbca70a7bc53eeeb951df8de77afd/test_datametrics_qd_metrics.txt" - ] - ] - } -PASSED (340.075s) - -Test Workflow CALL_REPEAT_EXPANSIONS - - Test [9ebd2699] 'CALL_REPEAT_EXPANSIONS' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/call_repeat_expansions/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value - > WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-9ebd2699e9b89a8b0a3abc4583d4718b.nf` [desperate_salas] DSL2 - revision: 5dde73596c - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Process `CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT` publishDir path contains a variable with a null value - WARN: Process `CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP` publishDir path contains a variable with a null value - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 5dde73596c - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/earlycasualcaiman_sorted_md.bam - [3d/43188f] Submitted process > CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [99/80e4ee] Submitted process > CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [c4/3b191e] Submitted process > CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [ec/375090] Submitted process > CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [d1/252afb] Submitted process > CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [39/b7605b] Submitted process > CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [dc/2daad2] Submitted process > CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" - ] - ], - "vcf": [ - [ - { - "id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/9ebd2699e9b89a8b0a3abc4583d4718b/work/dc/2daad215ed4f624836b62af98bf35d/justhusky.vcf.gz" - ] - ] - } -PASSED (518.242s) - -Test Workflow PREPARE_REFERENCES - - Test [8ce0dfef] 'Should run without failures' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/prepare_references/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 - > [HISAT2 index build] Available memory: 15 GB - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-8ce0dfefeaa4cb24b9b0365d78505ebd.nf` [big_fermat] DSL2 - revision: 458de812a0 - [HISAT2 index build] Available memory: 15 GB - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 458de812a0 - [HISAT2 index build] Available memory: 15 GB - [HISAT2 index build] At least 0 GB available, so using splice sites and exons to build HISAT2 index - [2e/26d380] Submitted process > PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [43/c0e479] Submitted process > PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [5a/f3ca41] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_GENOME (reference.fasta) - [a6/48292d] Submitted process > PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [d5/4a8372] Submitted process > PREPARE_REFERENCES:GATK_SD (reference.fasta) - [a7/755fac] Submitted process > PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [93/7124a8] Submitted process > PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [d2/b3e0e8] Submitted process > PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [8b/d610cd] Submitted process > PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [fd/9a6556] Submitted process > PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [d7/62eb1c] Submitted process > PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [80/a17259] Submitted process > PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [c0/5b5688] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT (reference_mt.fa) - [1a/33bc09] Submitted process > PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [47/7e70a6] Submitted process > PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [0c/1e4f86] Submitted process > PREPARE_REFERENCES:GATK_BILT (target) - [3e/e65b8b] Submitted process > PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [d9/cbfa2f] Submitted process > PREPARE_REFERENCES:GATK_ILT (target) - [da/895cbb] Submitted process > PREPARE_REFERENCES:BWA_INDEX_MT_SHIFT (reference_shift.fasta) - [b0/f7d59b] Submitted process > PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" - ] - ], - "1": [ - [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" - ] - ], - "10": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" - ] - ], - "11": [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" - ] - ], - "12": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" - ] - ], - "13": [ - - ], - "14": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" - ] - ], - "15": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" - ] - ], - "16": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" - ] - ], - "17": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" - ] - ], - "18": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" - ] - ], - "19": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" - ] - ], - "2": [ - [ - { - "id": "dbsnp_-138-" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" - ] - ], - "20": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" - ] - ], - "21": [ - - ], - "22": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" - ] - ], - "23": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" - ] - ], - "24": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" - ] - ], - "25": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" - ] - ], - "26": [ - - ], - "27": [ - [ - { - "id": "target" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" - ] - ], - "28": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" - ] - ], - "29": [ - [ - [ - - ] - ] - ], - "3": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" - ] - ], - "30": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" - ] - ], - "4": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" - ] - ], - "5": [ - - ], - "6": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" - ] - ], - "7": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" - ] - ], - "8": [ - [ - { - "id": "reference" - }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" - ] - ], - "9": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" - ] - ], - "bait_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/b0/f7d59b6caec3f9ab91d6f940c19360/target_bait.intervals_list" - ] - ], - "dbsnp": [ - [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" - ] - ], - "dbsnp_tbi": [ - [ - { - "id": "dbsnp_-138-" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/2e/26d3808fbba5f72502f99be5be7040/dbsnp_-138-.vcf.gz.tbi" - ] - ], - "genome_bwa_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a7/755facbf0cad1cd612932567c8450e/bwa" - ] - ], - "genome_bwamem2_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/a6/48292dacda8344deb0291f7ba8d01f/bwamem2" - ] - ], - "genome_bwameme_index": [ - - ], - "genome_chrom_sizes": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.sizes" - ] - ], - "genome_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d5/4a8372e7bd8b28c82a45d4a08fbe70/reference.dict" - ] - ], - "genome_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/5a/f3ca4114dccb9f1d0173090a80ea6b/reference.fasta.fai" - ] - ], - "genome_fasta": [ - [ - { - "id": "reference" - }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" - ] - ], - "genome_hisat2_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/93/7124a8c8645770b98208a097646eac/hisat2" - ] - ], - "gnomad_af_idx": [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/43/c0e4791cee2cbe51048f96bb124c99/gnomad_reformated.tab.gz.tbi" - ] - ], - "mt_bwa_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/c0/5b5688954c235a6795485f0a4d02bb/bwa" - ] - ], - "mt_bwamem2_index": [ - - ], - "mt_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/1a/33bc092b22c32f57d5af9e043f06f2/reference_mt.dict" - ] - ], - "mt_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/80/a17259351ab93f9fae66c40843f91a/reference_mt.fa.fai" - ] - ], - "mt_fasta": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/8b/d610cd9a341e354cf1d8a215e9c85d/reference_mt.fa" - ] - ], - "mt_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.intervals" - ] - ], - "mt_last_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/47/7e70a62b86ed25e033fbd95ac72341/lastdb" - ] - ], - "mtshift_backchain": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.back_chain" - ] - ], - "mtshift_bwa_index": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/da/895cbb846124f8cf358d10bd8e09f1/bwa" - ] - ], - "mtshift_bwamem2_index": [ - - ], - "mtshift_dict": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.dict" - ] - ], - "mtshift_fai": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta.fai" - ] - ], - "mtshift_fasta": [ - [ - { - "id": "reference" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_shift.fasta" - ] - ], - "mtshift_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/3e/e65b8b203de8584180589df9f1e95a/reference_mt.shifted.intervals" - ] - ], - "sdf": [ - - ], - "target_bed": [ - [ - { - "id": "target" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d7/62eb1c3acc19b027cbad5b63644d4c/target_pad100.bed.gz.tbi" - ] - ], - "target_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/0c/1e4f862e897fb6e9dbd835df6dfe8c/target_target.interval_list" - ] - ], - "vcfanno_extra": [ - [ - [ - - ] - ] - ], - "vep_resources": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/8ce0dfefeaa4cb24b9b0365d78505ebd/work/d2/b3e0e86b6243a5c3b8dea3e477a13c/vep_cache" - ] - ] - } -PASSED (1793.716s) - -Test Workflow QC_BAM - - Test [afc7bf7a] 'QC_BAM - test, bwamem2' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-afc7bf7ad225d9b0b9ee431dd55d4499.nf` [grave_agnesi] DSL2 - revision: ad4f64ff7c - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: ad4f64ff7c - [88/a55d00] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - [a3/5fe8f6] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [99/f92d39] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - [0b/378d69] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [c1/1cf56a] Submitted process > QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [b8/e56399] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [85/99d68e] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [ac/af6f79] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "10": [ - - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" - ] - ], - "3": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" - ] - ], - "4": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" - ] - ], - "5": [ - - ], - "6": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" - ] - ], - "bigwig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/ac/af6f794aea8379d0d6e938759292fb/earlycasualcaiman_tidditcov.bw" - ] - ], - "cov": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/c1/1cf56a56140efafe7d4f995a17d948/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" - ] - ], - "cov_y": [ - - ], - "d4": [ - - ], - "global_dist": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/99/f92d395eb67adb85bf20ec8d66960c/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "hs_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/b8/e5639936765d769758a99f5bd3ef69/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "multiple_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/0b/378d69b1860cdbda6ea4533d3c9353/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "qualimap_results": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/a3/5fe8f6d6bc4fd8b58724235a685d99/earlycasualcaiman_qualimap" - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/afc7bf7ad225d9b0b9ee431dd55d4499/work/88/a55d007d46cfeb70ffc12fab18fa3a/earlycasualcaiman_tidditcov.wig" - ] - ] - } -PASSED (291.083s) - Test [f2c7c2bb] 'QC_BAM - test, sentieon' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/qc_bam/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-f2c7c2bbc63f5d1d3e599d69dbda20d3.nf` [small_cori] DSL2 - revision: 60d4a16c8e - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 60d4a16c8e - [4f/f37ece] Submitted process > QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [35/d4334d] Submitted process > QC_BAM:TIDDIT_COV (earlycasualcaiman) - [d5/687117] Submitted process > QC_BAM:MOSDEPTH (earlycasualcaiman) - [0d/0ba645] Submitted process > QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [89/e64816] Submitted process > QC_BAM:SENTIEON_WGSMETRICS_WG (earlycasualcaiman) - [8d/74f582] Submitted process > QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [87/bc8fd6] Submitted process > QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [e6/5a33a9] Submitted process > QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "10": [ - - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" - ] - ], - "3": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" - ] - ], - "4": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" - ] - ], - "5": [ - - ], - "6": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" - ] - ], - "bigwig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/e6/5a33a9c0d67f765040cf8e54c60678/earlycasualcaiman_tidditcov.bw" - ] - ], - "cov": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/89/e64816628e50a65a93876aab03719d/earlycasualcaiman_wgsmetrics.txt" - ] - ], - "cov_y": [ - - ], - "d4": [ - - ], - "global_dist": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/d5/6871170c9cebe736b62b7e9d3f5a38/earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" - ] - ], - "hs_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/0d/0ba645537c7b448ca2f8021d1988e2/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" - ] - ], - "multiple_metrics": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/8d/74f58240d2d66ce1a2759eda55cd45/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] - ] - ], - "qualimap_results": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/4f/f37ece6d30d84745e98c509dcc0956/earlycasualcaiman_qualimap" - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/f2c7c2bbc63f5d1d3e599d69dbda20d3/work/35/d4334d969f70672045031a7e4158d9/earlycasualcaiman_tidditcov.wig" - ] - ] - } -PASSED (214.248s) - -Test Workflow SCATTER_GENOME - - Test [ad40db63] 'Should run without failures' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/subworkflows/local/scatter_genome/tests/./nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test-ad40db631cc506424fde3f421cb6171f.nf` [sleepy_leavitt] DSL2 - revision: 5c5d631253 - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 5c5d631253 - [1e/2ac886] Submitted process > SCATTER_GENOME:GAWK (genome) - [b9/29c1ee] Submitted process > SCATTER_GENOME:GATK4_SPLITINTERVALS (genome) - Stop plugin 'nf-schema@2.5.1' - - Output Channels: - { - "0": [ - [ - { - "id": "genome" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" - ] - ], - "1": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" - ] - ], - "bed": [ - [ - { - "id": "genome" - }, - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/1e/2ac88621b9464b2d9116e81a64084b/genome.bed" - ] - ], - "split_intervals": [ - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0000-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0001-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0002-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0003-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0004-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0005-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0006-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0007-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0008-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0009-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0010-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0011-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0012-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0013-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0014-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0015-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0016-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0017-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0018-scattered.interval_list" - ], - [ - "/home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/ad40db631cc506424fde3f421cb6171f/work/b9/29c1ee72539fbdf30d4a72767e61ba/genome_intervals/0019-scattered.interval_list" - ] - ] - } -PASSED (512.277s) - - -SUCCESS: Executed 13 tests in 17995.327s - diff --git a/wflog2 b/wflog2 deleted file mode 100644 index 4f05bdf51..000000000 --- a/wflog2 +++ /dev/null @@ -1,10617 +0,0 @@ -Picked up JAVA_TOOL_OPTIONS: -Djava.io.tmpdir=/home/ramprasad.neethiraj/tmp - -🚀 nf-test 0.9.4 -https://www.nf-test.com -(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr - -Load .nf-test/plugins/nft-utils/0.0.3/nft-utils-0.0.3.jar -Load .nf-test/plugins/nft-bam/0.6.0/nft-bam-0.6.0.jar -Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar -Warning: every snapshot that fails during this test run is re-recorded. - -Test pipeline - - Test [6304aa7b] '-profile test' - - Profiles: [test, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/params.json -ansi-log false -profile test,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - default - > config_profile_description : Minimal test dataset to check pipeline function - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_00-58-31 - > - > Core Nextflow options - > runName : zen_franklin - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_franklin] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_fq_spring.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - default - config_profile_description : Minimal test dataset to check pipeline function - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_00-58-31 - - Core Nextflow options - runName : zen_franklin - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4 - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/6304aa7ba78073b590a03c9431c889a4/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [fb/ea3c15] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [19/c3d34f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [65/82aeb7] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [91/0a6559] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [40/80614e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [d5/040b87] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [6c/9bb245] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [82/8ea253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SPRING_DECOMPRESS_TO_FQ_PAIR (earlycasualcaiman_LNUMBER1) - [2f/f25e12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER3) - [50/982250] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER3) - [29/4335aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER3) - [a9/13e4ea] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [3a/8ede16] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [64/8b381d] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [27/ec7384] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [4c/37a851] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz - [ad/8743ee] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [18/a402ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (slowlycivilbuck_LNUMBER2) - [2a/9f7ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (slowlycivilbuck_LNUMBER2) - [7a/12d1df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (slowlycivilbuck_LNUMBER2) - [d0/30653c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [3f/370a12] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [93/30573b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [88/90b4a1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [98/406073] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [63/04e13c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (earlycasualcaiman_LNUMBER1) - [11/27e0a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (earlycasualcaiman_LNUMBER1) - [50/606745] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (earlycasualcaiman_LNUMBER1) - [02/a024e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [53/bf5496] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [7c/63d5a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (slowlycivilbuck_LNUMBER2) - [8d/cd3bcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER3) - [59/24c7d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (earlycasualcaiman_LNUMBER1) - [20/5ddc63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER3) - [65/9927b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [ca/61bf7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (slowlycivilbuck_LNUMBER2) - [a2/913579] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (slowlycivilbuck) - [a8/e07046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER3) - [ae/48f4db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (slowlycivilbuck_LNUMBER2) - [ce/c8b2b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (earlycasualcaiman_LNUMBER1) - [3c/f001fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (earlycasualcaiman) - [3e/86e1cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [bf/90f1b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (earlycasualcaiman_LNUMBER1) - [ac/47c02e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (slowlycivilbuck_LNUMBER2) - [50/aebe5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER3) - [d3/162f12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (earlycasualcaiman_LNUMBER1) - [97/4b2ee1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - [cf/0785c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (slowlycivilbuck) - [ab/d41f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - [1f/053106] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [f5/86f0e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [87/fb9dab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [56/05572f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - [dc/1881eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - [4d/16af5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - [e3/ddd20f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - [59/582712] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d3/57f53f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fb/fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474/data [cache /home/ramprasad.neethiraj/nextflow/singularity_cache_nf/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-fb-fbf8cfd89c36e9a18a895066bb1da04b93ef585a593b0821ec7037aba6c03474-data.img] - [a6/f4f421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - [6a/d1915d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [be/6c2089] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - [13/fbf054] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [de/e9b839] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [31/dc1b6c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [aa/39ce86] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - [18/471e0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [83/3fc3a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [74/f03782] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [ee/0f8a7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [79/e734da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - [69/c567de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - [ee/23b79b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [ff/9ecbba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [e8/ab5fcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [17/9a0d5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [ec/950346] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [49/6ab2ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [9f/26d944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d2/013233] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [15/eac957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [67/49b805] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [e9/fe4f09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [a0/c6d3d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [64/02c8b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [ed/9136cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [d9/279850] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [55/0a06a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [4a/c8f25d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [1b/78140d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - [17/534d0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (earlycasualcaiman) - [04/64665a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [2b/e76a3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [bf/58f8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [7b/9519f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [50/1e10a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [03/6de6da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/8685ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [be/ba06f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [dc/c0dd26] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [98/df77d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [03/7bdded] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4d/4a4c83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4a/0d7072] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [08/2e17c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [63/12dda6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [74/a24a53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e9/8ee681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [55/21ced3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [96/7426ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [f8/546dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b6/4a339a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [a1/053bc2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2c/221586] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [76/b1c937] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - [e5/bde72a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [51/1d13be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [5b/189667] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [72/da1878] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2d/979871] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [50/b6bc54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1e/cb81cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [e3/ede9c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [9f/3bc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [96/2f13fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [4b/7dd676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [09/b10058] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [97/d57364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - [01/673342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ad/88e63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - [d4/92faf0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - [a6/ed544b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [8b/32f7ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - [6b/8ecf15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - [4c/4ac2e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - [f0/b8cf88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [f8/249323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [77/49dbf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - [f8/6b6553] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - [76/297771] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f9/1c5833] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [84/c4e425] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [35/102c84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [b0/c41318] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [3c/c7fc88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [6c/7679af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [8f/883c4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [8f/6629be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [a8/d339da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [b8/9c0923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - [3d/c0d6dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [62/d68ce2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [01/fd923c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [7e/07833f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - [c5/9ad444] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [ee/cbc1a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [22/9f4b7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [d8/5f3e4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [2d/973c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1b/e1ac28] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [28/d6543b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [81/b900b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [85/629e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [bf/16eaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - [c5/5293b1] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [dd/78cf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f0/ba3323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [1f/ac807e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [04/734aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [df/fafebe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [3a/fe4b69] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [3c/d4953d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [87/35203d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [5b/b381ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - [49/410f2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [d0/3c9cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a1/77b0fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [ee/219466] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [39/22f215] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [81/b46b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [2d/80990b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [07/1f970f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [13/30242c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [75/1bcfc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [5e/1e1950] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c8/5372f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - [44/ea496e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [f3/2c52ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [9b/35335f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [77/ece410] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [78/b3b55b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a3/df4ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c6/0d13b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [9a/d3873a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [db/f4d19b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [8a/445c0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c7/5eac3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - [6a/35b76a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e2/a1f90a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [f7/fd3293] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [34/cfab95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [21/e682af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [74/3ddf07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [2c/558fb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [24/85e814] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9c/7bce6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/45ad4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - [82/8e060e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d1/6a20d2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [92/ae623e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - [d2/859d0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e7/96fd75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - [0c/755907] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [0b/b58fc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5c/b54cee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [36/33dd06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9e/e25e04] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [12/49b9b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [91/9bd212] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [37/f86528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [b8/0721f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a2/cd9a50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - [97/da7653] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [b0/819c2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d4/f50f17] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [f5/1208d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [da/8fbec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [c5/773197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e3/847fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [07/477983] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [80/2ad385] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [06/8625e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [eb/58fefe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a1/63d42e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [c3/cc82ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a0/4cefa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [66/a4d1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5d/a44135] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - [b4/3aa193] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - [9c/0c8936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [d3/c2081e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [15/382903] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - [5f/e6fc3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [7e/340bcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [7f/d8b746] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5f/a70c92] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [9d/47a27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [4e/002bdd] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [47/1649e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [24/0fdec5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [59/e08197] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [f0/b7116a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [71/b91312] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f5/f59711] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [57/7c9d8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [51/f7ce54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [52/5bb8b9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - [b4/f49588] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5c/aa8008] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f6/f6be34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [76/659e7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [a2/e06344] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - [51/dd7aaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b7/db4884] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [06/c989b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [27/f79927] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [05/6195b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - [cc/1a1d15] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [b5/8d7df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [d1/367d4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [9f/a2993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [51/d4948d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [b7/b81b3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [a8/701361] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - [44/b20c16] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [5b/8af426] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [58/d16ec0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ca/a6c948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [cc/dea762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [1a/461300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4e/4ec77a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [49/7e1a99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [7f/56f92f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [41/a1047e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - [71/4f36f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [9c/eb9e73] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [ba/dd4b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [91/8ff479] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [a6/0b9845] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [9a/26d481] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [5e/479ea0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [fd/77deca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - [4a/761b1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f3/b44b78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [2b/7ed957] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5d/f6665c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [25/e3a375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [e5/a1f0be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [72/b5dd0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [2e/e0e3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [11/602d84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6d/dc0147] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [87/56feb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [8a/bc51b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [0b/97f4d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [01/727ee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6e/1aab89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e4/3680a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c5/b1a0a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [2f/cd947f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [55/72ba1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - [28/cf65cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [09/0fa85c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2f/a60fca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2e/b4fa60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [50/fc8a1b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [f6/1f818b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [84/a6993f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2a/626517] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [86/2f923e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ae/956db6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5b/b9d2c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [52/b60f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [d1/b6d9b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [08/54bc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [b6/f5186b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [39/5318b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [a6/f7b55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e7/d25908] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [10/a6efdd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [f4/da5c0a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [b2/fb1f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [7f/ea9629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [6e/59c840] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [8e/4eaf41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [4f/3a94a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [5e/edc317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [61/780de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4b/bb493e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [00/4c1dd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [eb/79c3b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e8/d8f70d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [09/e37d8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [53/8daf0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [83/e8341c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [8f/81db15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [c5/43fab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [46/f2ecd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [a2/5591c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [5d/123564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [13/550914] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - [e9/d5de9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [dc/24d607] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [d0/aa963f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [e0/b83b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [6e/61eef5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [22/358de3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [13/b5aaf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [02/a4045d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [a4/73bbaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [87/300b24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [63/ae74b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4c/aa4fb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [50/980cf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a1/ce44b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7b/7bc596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [96/f632cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [31/aaf606] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [cf/0016a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - [96/544a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [4e/7d9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [33/f18885] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [8c/2378a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [57/33ff08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [30/915a78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [34/5450bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [d0/c17cb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [53/a7583f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [d3/27a740] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [6e/85898e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [29/7f3e3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [8a/4ce75d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [40/cf20d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [e2/454c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [6f/2c0ce3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [17/d46dc9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [b8/6e38a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [bd/4c2e9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [78/6caf13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [85/285a9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [57/dadf9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [25/f7e7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [c7/c268d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3e/c2a77b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - [e8/d41806] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [79/3f8c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [95/036b58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [38/1097a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [6f/31e6df] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ee/1f12d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f8/d800a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f7/71fab3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [8b/e5ffd8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [31/e5238b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e1/baf880] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - [e3/776858] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [46/c4dbaa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [26/b24944] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [f8/baab7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - [58/b1f012] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - [93/98e998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [54/31b68f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [28/6e2113] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [8c/0f270a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [4f/3e629a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [09/b8ace7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [98/ac1e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [ea/0d0e73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ee/2729d3] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [e0/fe9d34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - [b2/706345] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [b3/298149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [b2/b63181] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [49/e15f0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [81/47a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [58/a01573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1c/a02988] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ef/f023a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [38/d21a4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [13/75a08c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d0/9b50fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - [d4/85c8dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [60/bdcb6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f0/c937a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [be/062f25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [13/46100b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [2f/ef3ac6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [98/983793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d7/a363b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a4/f17640] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [bf/75bbc5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [b4/670b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [67/d8aee9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [72/0b4018] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [10/68bc4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [19/749300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [4f/e366e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ee/f1acaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c6/541527] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [7d/c7bd47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ab/22c80d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [fc/38c51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - [ac/df04ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9d/523473] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [67/df6bb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [da/50550f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - [10/819695] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [15/831b19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [9f/527af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [e6/9f0c7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [61/2204f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [57/fd1daf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [6e/323ce8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [20/7d450b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [3d/478f9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [f6/3d66f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [52/19b661] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [87/a385ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [f4/3ddcf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [df/87aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [d2/5b17da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9b/551487] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b8/194c68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9e/3c7fab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [1f/6ceb9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [a4/68f418] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [11/481162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [4a/17dfd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [1c/8e2002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [da/940d96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c3/b655c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [3d/2b04ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [9c/2f0a54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [df/1257bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ce/3e79ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9d/31f7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [8a/4a2141] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [34/4d1152] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [bf/73d335] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [ea/5c9192] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [6e/594ed8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [04/4c2774] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a9/144bcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [8c/a8527f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [dc/32afbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [75/f376a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [da/faad96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e5/77bb74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e8/d1aa8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [1e/0ac33a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [59/dbd528] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [dc/842f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [84/a9a3bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bb/0e805d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [3c/5bc676] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ee/a9f300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [6b/3c3040] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - [88/100750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [41/ebb7da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [80/7c0f61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [d2/8485c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [11/d3437c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [71/e8432b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - [fa/b257c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e6/b0016b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [ba/1b60d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [de/e09ecc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/e7b5aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [78/0ab2d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - [43/27585f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [39/b22a40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b9/dc8162] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [af/59c0f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [a4/0db872] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [24/219521] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [fa/ea8b98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [2a/023f76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [5a/d532fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [62/955915] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [7b/3b95fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [c9/b621c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b5/70d802] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [d3/7f8dfa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [f9/daf76d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5c/bd1ef9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [3d/cc16ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [9b/27a416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [4b/2ccbdf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [43/182a9c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b8/2f56c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [1e/7362c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6f/6e8b9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [eb/a49c61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [69/a663fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [b6/0cfadf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [72/9d9f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [94/b9afc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [3c/16c42a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [63/8cc064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [8c/dbaeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e0/9c9391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [37/69eb56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [96/a30cca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6a/11b0e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [66/2f5617] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [c6/e21cbd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e1/532d9f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a7/e49566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [5c/bf6cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [ac/292b08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ed/a4f599] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [71/6542c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [bf/5a4300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a5/6f88ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [d4/ccb1b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - [31/fc2d6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [49/ebe75a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [00/922f71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - [08/0ca7eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [92/59f12e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [f8/6a377c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [33/bcda3b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ae/d2f6ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [50/6a10ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [87/97b094] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [eb/b3eb4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [4b/397a75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - [98/a0ec52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [43/2ea0ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6c/83f2d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [79/4133d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [37/0f42db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ca/e82531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [b0/3c369d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6d/73d951] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [66/eb0faf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [c2/3884be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [93/3766a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [22/99505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6c/288092] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [39/a96ac4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5f/40c634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6a/55045e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e8/8938d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [24/94185f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [5d/a238ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [63/5cf9bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ce/d39305] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e2/e2529b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d8/5687f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6f/b85fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ef/51adc7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [04/eaad6b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [60/58b5cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [1c/685bd3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e4/bce705] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [3d/abd6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d4/cba286] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [2f/4f4670] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [68/03f063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [6d/5ae279] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - [bb/b683db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [33/8939e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [2b/9e25d0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [b6/eae088] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [3b/36d45b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [4d/d02755] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - [79/bf8a35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - [a5/3c2928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [22/097b54] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [fe/1294e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [12/d160f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [80/3cdba0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [04/cfc4c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [1c/6611c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [f5/96a74d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [67/c90811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [ea/e77965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - [d8/1e7531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - [ef/7b3777] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [cc/e41ef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [cf/8dad84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - [ff/fcc63a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [09/54fcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [9a/51d5b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [42/5b8e2c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [5c/a8fde9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [cb/6a08f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [18/9a33f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [8c/8c299e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [bb/e00669] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [f7/55667c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [dc/eef8fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [db/1768a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [17/0b8411] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [73/4f7f32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [98/118cde] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [4b/a2bf0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [da/53d276] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [4f/fe8dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [1f/53dff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [2b/d7723f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [49/4aa483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [71/a05cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [4a/4dff53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [1b/87a848] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [57/eb9cf9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [d1/e10f8c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [b3/0275cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - [04/3819a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - [b6/94b7b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [a1/7332a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [05/4cca4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [57/a65f34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [09/e26db2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [0c/a3aa12] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [35/32e5ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [77/5740fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [7e/112b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - [87/b59820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - [19/0d98a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [f4/7eae51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [19/510aa2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [ed/a574ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [17/fe2263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [cf/f4c660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [c6/35d0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [c1/53d1ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [1a/7aa767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [ed/53d2f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [0d/d2e29f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [e6/4e8239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [7c/ae7359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [f4/f85958] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [67/2643fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [c6/ee018d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [b8/11aaee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [0f/18cc05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [23/508928] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [55/7261be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [b2/81899d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [e4/597be9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [7d/92bb0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [88/1a919f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [ee/5e5273] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [8e/024d08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [d2/e19326] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [06/ccae18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [ab/e8a593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [bb/056402] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [14/733751] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [8a/32cf05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [56/52556a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - [04/cec32c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - [0b/5c99af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - [3c/0d498b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - [a5/37b52a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [dc/9c64dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [08/3d1c62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [ae/dbae5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [96/c223d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [00/b071d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [e6/83f8c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [9a/69aae2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [fb/406cb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [7f/cac57b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [ef/a103b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - [62/a91e79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [f6/818122] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [6c/face5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [b6/58eac7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [e8/cfa812] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - [91/cc2f2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [72/041e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [96/c92e2b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [66/85faee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [24/0f636a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [ee/a24dbf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [d7/a28d56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [3a/0931f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [34/b594d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [f2/101f20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [a5/145219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [db/a454be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [89/f445a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [59/201070] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - [e8/d3c03a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - [89/57309f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bf/d8e01b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - [0c/7c9cae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - [3b/6b3d0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - [ea/c9a5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [40/0f838b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - [76/ba2c5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [0f/a3dab7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [b0/50233d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - [a2/b23b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - [5c/15def1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [a2/740433] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - [4c/1d7183] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - [27/b2d2fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - [38/d8ece3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - [57/772ad8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [c3/fcf035] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [82/557d50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [0c/90a2be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [ab/139c1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [89/37e593] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - [a7/7fd77e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - [41/74e820] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - [ae/a3ab18] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [50/97afa3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - [4f/01542f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [64/74ffba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [54/5d0532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - [21/f4fc40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - [f6/b7e12b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [21/aee079] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [90/84caf2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [bf/079e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [c1/6b85da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [02/d843e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [86/911afb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - [8a/490e91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [3c/2c5adf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [45/2f2f1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - [31/79b0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [ca/57886b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [3c/026c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [6b/6ac891] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [54/18eff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [61/f10149] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [11/14a7ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - [ef/fe6ffb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - [34/f4d8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [3e/8f1364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - [1e/3ba582] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - [00/3c4ca5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - [35/195017] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [bf/dd829e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - [b0/f8f0ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [c4/0c7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - [38/807e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - [4d/80c32a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - [82/200b39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [fa/fbd916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - [57/63168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - [b7/dd42bc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [6d/87ffc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [95/256924] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [f9/039114] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [85/4d5a15] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [de/10ecbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [0b/8ad08a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [64/71aa13] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [4d/3048bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [3c/d33592] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [a9/6e6826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [c8/3f9548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [15/41853f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [ac/0eb09c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [ea/3eadb7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [c6/c5615b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [65/5016ea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [74/3fd1d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [d6/9adb64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [b5/8f4fa7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [85/144ad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [fc/1fa69f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [01/b8e20b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [7a/51ad68] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [f4/c9fdb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [df/9683c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [42/137648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (32575.636s) - Snapshots: - 1 updated [-profile test] - -Test pipeline - - Test [df780376] '-profile test_bam' - - Profiles: [test_bam, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/params.json -ansi-log false -profile test_bam,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > ngsbits_samplegender_method : sry - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - bam - > config_profile_description : Minimal test dataset to check pipeline function - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_10-01-37 - > - > Core Nextflow options - > runName : gloomy_newton - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test_bam,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [gloomy_newton] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_bam.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - ml_model : https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.1.model - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - ngsbits_samplegender_method : sry - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - bam - config_profile_description : Minimal test dataset to check pipeline function - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_10-01-37 - - Core Nextflow options - runName : gloomy_newton - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/df78037639a996485dcdc07f3e0ffe1a/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test_bam,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [9a/ed92a4] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [e6/c57941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (earlycasualcaiman) - [f1/851bcd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [d6/102143] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [6f/3b12db] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [c4/c2a34e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [9e/f21314] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [3f/942263] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (slowlycivilbuck) - [2a/01c235] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [1c/7df80f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [67/fbaec1] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [76/fbc951] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [16/1adc03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (slowlycivilbuck) - [9b/eed519] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (slowlycivilbuck) - [9a/8e1560] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [20/88ae99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (slowlycivilbuck) - [ba/2387f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [dd/575538] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [d1/56930a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [7b/42660c] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [6b/9a6005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (slowlycivilbuck) - [b6/a1b571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (slowlycivilbuck) - [d9/0e3ee7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [3d/bbfcaf] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [8e/de4534] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [24/5277e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [86/f2b96f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (earlycasualcaiman) - [06/0b6d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (earlycasualcaiman) - [13/bb5f53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (earlycasualcaiman) - [d3/48964d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (slowlycivilbuck) - [14/d7b2cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (slowlycivilbuck) - [cd/0e438e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [73/da0282] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (earlycasualcaiman) - [66/07c016] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (earlycasualcaiman) - [74/2a6db7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (earlycasualcaiman) - [c7/fbe7f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (slowlycivilbuck) - [2d/1d3b0f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (slowlycivilbuck) - [d2/1799a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [9c/05f235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [9a/c0b2b9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [6f/a5f1e4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [88/f87b88] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [1e/43d078] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [80/99dafa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [a1/fed5b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [44/50281a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [69/5da0fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [cb/2af6f6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [92/4793e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fc/29742f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [5c/15afd6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [8c/6437fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [87/455511] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [7c/2d81e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [e6/d62f41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [7b/d313ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (slowlycivilbuck) - [f9/424622] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [5c/86ca62] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [aa/84d0bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [88/0239fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [00/d76aaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c1/fa3fe9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fa/29aa4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1e/472317] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e7/a418db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [07/88a40f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [74/fa149e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [0d/c9f6f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [0d/3298d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [60/21b194] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [29/efc5a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (slowlycivilbuck) - [05/dd88e5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [d9/4655aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [2a/bb9ed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [7b/45cd42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (earlycasualcaiman) - [f1/1e4602] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [8c/e0293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [16/884477] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [eb/0729b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [8b/fcf55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [ce/89f2b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (earlycasualcaiman) - [1b/dc9619] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [18/bec953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [68/688911] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c7/37c022] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a0/058f7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [48/87a8f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [71/df9a20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [34/c5213f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (earlycasualcaiman) - [4d/f681a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (earlycasualcaiman) - [47/cc8b36] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (slowlycivilbuck) - [98/fc4635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [eb/25b747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [98/fc1a23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [47/17c440] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b2/6f1bc3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [c3/464c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [e8/11cc30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [b6/c672e7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [76/ba3ae0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [09/4adc95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b3/d7ad7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [88/02bbfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [68/f028c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [19/4f5a66] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (earlycasualcaiman) - [1c/bf9675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [fe/3265ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [c1/490a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [94/b67747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [1f/8af428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [d5/2c2f8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [25/3a0c49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [e5/00c72f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [4b/0db11c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [af/d93865] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [fe/506309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c0/4f868c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [32/2368d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [49/26b98c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [6a/e44a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [f2/447bf4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [3b/1af19f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [78/f53b3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) - [ab/a4cb58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [e9/25b00c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [dd/3211e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (slowlycivilbuck) - [28/599e39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [25/ab49f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [fd/3a8158] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [ed/887df7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [a4/b0b6c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [57/9cbf84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [57/987750] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (slowlycivilbuck) - [0c/8f6df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (earlycasualcaiman) - [84/0ea5e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [fb/22aeb3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (slowlycivilbuck) - [51/af5be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [ed/75a0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (earlycasualcaiman) - [d9/258ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (earlycasualcaiman) - [b8/18dcbe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3f/0f39c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [cf/7336ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [19/39a556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [89/7e8b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [9b/4e5025] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (earlycasualcaiman) - [35/fb8bed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (slowlycivilbuck) - [5e/f57080] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [19/ac9976] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ab/50f992] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a8/247e47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [95/bebd74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5c/e6031b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [80/edaa3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [d7/dd245b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [12/44ff23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [21/87b9e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [af/b87585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (slowlycivilbuck) - [30/0f62f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [91/fecefb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [df/a8d4ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [a1/30f0d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [10/61fad7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [82/02cee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [63/da59a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [12/bd8391] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [a6/70cdce] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [df/fcfcf3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [f4/3aa1f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (slowlycivilbuck) - [d3/18808a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [1d/b70f4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (earlycasualcaiman) - [96/4e2c66] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [d5/0ffd01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [df/01a029] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [45/4ae4e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [92/ff47d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [dd/fb09d1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [85/e720fc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [52/3ed494] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [27/9ae7a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [8e/920df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [34/b385f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (earlycasualcaiman) - [6e/014374] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (slowlycivilbuck) - [42/7133e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [87/7b1448] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ef/5bcfef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [12/35fdc0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [68/d8a571] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5b/53bae4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [db/e4ede9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1d/04e8f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [bf/bcb9a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (earlycasualcaiman) - [33/01bb52] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [81/683f3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [64/3b7a63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [43/95c31e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [6c/8988c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f1/f5bf3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [2d/e9d672] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [1f/46521a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3c/4d22d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [1a/93b89a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d3/f44d3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [f3/341856] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [42/ed0675] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [7a/31f351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [0d/f7d12a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [62/15d875] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [94/2b29e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d8/8923a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d1/573a94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [38/2ef1b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [1e/594c6a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [f5/c132a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [ed/e68db3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [52/68fdc1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4b/1ce395] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [39/cd99d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [1b/fb87d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [dd/9ad157] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [4a/03380d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [99/49a9e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [42/d11842] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (slowlycivilbuck) - [88/cb91e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [30/09db38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (earlycasualcaiman) - [2c/fb503d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [5d/037a3f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (slowlycivilbuck) - [e7/1a30a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [47/cc2c5c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [5f/c514a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [ef/a848c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a5/ee9d09] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (slowlycivilbuck) - [35/a16258] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (earlycasualcaiman) - [84/6c3758] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [ab/4fa860] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/738861] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [05/d70db8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [14/45a4ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (earlycasualcaiman) - [28/961a51] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (slowlycivilbuck) - [40/7f1e98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [16/25390f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [06/21d8c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (earlycasualcaiman) - [89/695267] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [25/d99c3c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [34/b21021] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (earlycasualcaiman) - [43/457b5d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [80/f1be89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (slowlycivilbuck) - [75/ba8a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [67/c29d0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [13/e88d6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [d1/2e582d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (earlycasualcaiman) - [60/626d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [da/9966de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f4/6b7130] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a9/fa6762] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [cb/3ab362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [fe/e186e5] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [2f/aa2ead] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e8/81dc72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [85/462ff3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [57/006398] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (slowlycivilbuck) - [d4/982a3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [96/f68421] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [bb/7292a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (slowlycivilbuck) - [b0/2e3ca1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [bb/5103c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [3d/e06663] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [24/03732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [66/653ca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [4a/feb573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [30/7fd2fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a9/058757] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [38/f1a65d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (earlycasualcaiman) - [58/c6efa6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4f/1707a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [36/899d1e] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [26/6d1e9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [ff/ced7ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [7c/84cfc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (slowlycivilbuck) - [16/78382b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [3c/a87bd2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (earlycasualcaiman) - [64/0e6002] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4c/d38f4a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [5f/cdcd7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [63/aa9f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [75/e80362] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [50/9e64ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [bd/8c340c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7e/405397] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [fb/6e5c70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [1b/186300] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [40/e2a126] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [b0/411dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [f5/a8c8b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [c3/fa889a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b2/694e6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [6e/ddab6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [01/4b452c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [2a/f7dd83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2d/983dcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [55/9cf78a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ea/44c6e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [9c/301442] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [7d/53293d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [d8/3effa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [90/107f5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [d4/ad9295] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a7/d66560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5b/bea0f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [f7/167d4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [5d/2c0f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (slowlycivilbuck) - [a5/e83259] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [44/d14a4e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [71/e5a996] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [72/a15a6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a0/04bc8e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [36/02fd91] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [e2/a50cc8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [b6/28594b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9e/bb22c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [35/35cb73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [a0/2acfe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [84/11f3be] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [4b/68a76e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [b6/c8ed96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c4/9dfbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (earlycasualcaiman) - [e3/16f382] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [bf/ae3393] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [eb/d25547] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (slowlycivilbuck) - [83/98961e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (slowlycivilbuck) - [bb/75753d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (earlycasualcaiman) - [7e/0b93b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (earlycasualcaiman) - [39/fba795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9a/4c4a58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [0f/57d18e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [27/50041f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (earlycasualcaiman) - [90/cff1da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (slowlycivilbuck) - [a8/5f9565] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [20/585df6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e7/5ea381] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [75/371704] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dd/56a548] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [db/36a64b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [8d/00a336] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (slowlycivilbuck) - [06/955a32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [84/342596] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [36/2fb64a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [27/3504f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [07/87f83f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d1/fbb658] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5f/fa1df2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [ef/2e4794] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [11/5295de] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dd/5dd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [03/8ed37a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [f4/c32163] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [db/5323b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3a/78ca79] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b2/982ea5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [35/325324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [63/47c918] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [7c/b2d605] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [45/64e0c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [96/fd47a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [6f/00917b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (earlycasualcaiman) - [8a/e0a4f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [83/39ff96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [2c/cfbff8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [62/10df53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [dd/890a3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [ee/dfb134] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (earlycasualcaiman) - [9c/4f32ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (slowlycivilbuck) - [07/4601a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [94/897d81] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [d6/2b10dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [88/2c283d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f2/473cbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [44/ca5916] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [c2/4cb0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [03/6a53a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [3d/338948] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1a/670b89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [dc/569b61] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [0b/fe0652] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [81/e96445] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [e0/e09cec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [00/345ae8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [fa/86921e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [af/6bebbc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a8/3bf9e6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [30/ac0083] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [60/740aa0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f6/563536] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [69/a3b9ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [42/29a36a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (earlycasualcaiman) - [26/363fc6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ab/8d8c21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [7d/038573] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [02/dbb5c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [32/4910ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5a/22e4d8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (slowlycivilbuck) - [2a/779464] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [d8/b76eab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [1f/cddfd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b8/829064] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [cd/e49998] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [bd/90aab1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (slowlycivilbuck) - [66/654439] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [fc/57ad40] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [0a/c55206] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [74/7eed0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (earlycasualcaiman) - [23/437179] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [66/bb4c96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [b5/4af359] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [03/0574cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [f1/3166e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3b/3017c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [e2/fe1f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [a5/6a3f96] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [86/b3f27c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [e0/4d7b63] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [32/938d4d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [5d/150a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [87/3b0d10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (earlycasualcaiman) - [1a/1221c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (slowlycivilbuck) - [3b/a6b629] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [44/02112c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (earlycasualcaiman) - [2c/b34b3e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [e1/a1505c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (slowlycivilbuck) - [82/ed3cf8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [db/56777f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [17/3a2ee4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [59/1bbbb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [fa/da6b7e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [91/562a76] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [ba/062c7d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [78/9159bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (slowlycivilbuck) - [66/1eb526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [fb/d914f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [40/f6aa71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [fe/136657] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e1/6a7a08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [93/fc615e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [04/ffe0f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a5/699c80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e0/b557a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b2/a3fb35] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [00/ccaa37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e3/c4ce03] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [ae/ce288a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a1/6e1731] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e1/3af82b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [10/19d08f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [e8/41f5b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1e/00c10a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [2c/798b57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ec/0eb5b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [cb/01ee97] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [61/800b87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5a/de4eb0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0f/d28fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e4/a58c77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [15/5e1fe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (earlycasualcaiman) - [14/2c7a60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [57/7aed4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [ce/b9aca8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b3/9314c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [e1/86d748] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [99/ab7488] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [64/fa2566] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [5d/226cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [31/eda633] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (slowlycivilbuck) - [d8/2451c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (earlycasualcaiman) - [28/96bcdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [4b/6f5c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [49/6950d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [fe/2758b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [6c/f98e8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [f8/037af9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [a3/fc6169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [67/27bb06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [27/b3c966] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [4e/731fd0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [7a/6adb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [58/d13b20] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [fe/66fa23] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [9f/792895] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [39/24e9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [a6/588375] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [3f/471aff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [11/9e956a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [c8/370de2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [78/3c035f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [d0/9c8793] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [73/49ffe4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [01/ca303c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [5f/de886f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [5b/ceba3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [9c/b02b50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [44/883e85] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4f/ece202] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [38/9608eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [c1/c1371f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [83/e38690] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [90/5c2d01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4d/e72b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [cd/b377a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [8f/8a3520] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7d/c8b6d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [74/0453c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [e5/44da1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [72/6ebe0e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5b/4a0a59] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [61/cdbaa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [b7/3d70fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [26/e8e3c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f8/c35a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [c2/079ccb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [40/d0c5a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [21/c7fd31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [bc/e0e31a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [a9/bc2fa1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [99/0e24d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7b/b23caf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [56/09657e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [b3/9e9715] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [25/00313d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [af/e4d3a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [aa/a25d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (slowlycivilbuck) - [9c/352364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (earlycasualcaiman) - [c2/5574d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [93/79d7dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [e9/4180c8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [bd/9d3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [87/d9bc1d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [d1/464555] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [7e/3812ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [16/ef453b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b6/f43c0c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [77/e0f526] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [20/8bcf2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [d8/937531] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [33/b9a1a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [b8/b3f8ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [93/a6463c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [de/80908e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [49/99cd33] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [11/c901ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [0f/d76f42] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e0/ee4c78] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [1c/3a1767] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [62/30dfcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [f7/7869e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [7f/b87af1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [c6/95a04f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e6/3b27f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a9/415bdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [62/70bb49] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [47/5d27ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1b/a9edf1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (slowlycivilbuck) - [cc/31a13b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (earlycasualcaiman) - [32/b01642] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1d/4a168c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [65/160ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [96/3c0641] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [19/c49d55] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/991dfe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0a/dbf826] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [55/e1fc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [bc/750443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [95/0b6980] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [56/8ece95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (earlycasualcaiman) - [e6/3d1923] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (slowlycivilbuck) - [a5/9934aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [b9/4fa1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [d8/0671b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [c9/fe1e07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [a2/782235] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [b0/bccf34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [76/855133] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [b2/2cd71f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (slowlycivilbuck) - [76/849d83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [2f/c74474] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [f6/1ee503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [91/ffc369] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (earlycasualcaiman) - [e7/09f897] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ed/849257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [ee/aa081a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ef/46d0b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [07/5baa01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [22/e600db] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [cd/3f2ed3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (slowlycivilbuck) - [58/0109a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [4f/ce452a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [ea/36ecd9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (earlycasualcaiman) - [22/30a7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [98/4f2bac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (earlycasualcaiman) - [68/b2a55e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (slowlycivilbuck) - [28/d89c24] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [67/6251ee] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (slowlycivilbuck) - [ab/bc4854] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (earlycasualcaiman) - [ce/8856cf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [11/c9dc44] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [33/bf3117] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [c6/875cad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [8b/cd04f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [17/503296] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [02/e33028] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [81/6a6609] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [97/270a5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (slowlycivilbuck) - [88/a13b5f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (slowlycivilbuck) - [1f/14d635] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [ff/0da274] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (earlycasualcaiman) - [99/09e1ae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (earlycasualcaiman) - [13/ec02d7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [3a/1008f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [9e/60c21d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [3e/215ad1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (slowlycivilbuck) - [b5/b9e07f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [03/2e81f7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (earlycasualcaiman) - [11/62a8f2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [15/d300ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [69/5c03bf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [b5/12f1ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [20/9324eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [28/3523a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [3e/5e610c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (earlycasualcaiman) - [08/275014] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [db/7f1d73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (slowlycivilbuck) - [fd/5a00b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [9b/7d4aba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (earlycasualcaiman) - [39/20fb94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [17/ab7afe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (slowlycivilbuck) - [cf/11a8a5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [fb/b99e84] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [f0/81e33c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [da/3d47a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [29/a8b8ba] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [83/ec0322] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [99/ac2351] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [44/7e59ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [43/60fcd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [3a/3dd51f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [37/883e2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [a6/08c93e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [8a/9c0a2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [4d/9cc446] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [f7/29d57e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [b4/fefd56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [d4/cdb9dc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [e8/9c95e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/693fed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [f5/2a9634] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [99/ed1403] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [11/cb92cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [58/5b53f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [90/9757d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [72/8e950f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [54/cdc6e0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [0b/ae75ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (slowlycivilbuck) - [71/c52721] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [7a/39c659] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [11/581af6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (earlycasualcaiman) - [b1/fdd07a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [17/a668f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [2a/4745b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [58/785fb6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [a3/7fbce9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [e4/9aaa07] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [ce/34136b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (slowlycivilbuck) - [19/9ff6b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [26/8ba356] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (earlycasualcaiman) - [d6/47b625] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [3a/128c98] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [95/bc609f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [09/d56a1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [38/1172b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [49/778452] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [cb/da0f9d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (slowlycivilbuck) - [84/e1bed2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [9c/81c86a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (earlycasualcaiman) - [11/e4af29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (slowlycivilbuck) - [bc/815a64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (earlycasualcaiman) - [26/aece05] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (slowlycivilbuck) - [60/c1a503] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (earlycasualcaiman) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - [5c/ac4df3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [e1/be2c02] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [ec/71b811] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [dc/14461d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [94/65e696] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [ff/18c4ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [90/b677b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [7d/f8839f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [7b/7fc28c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [5e/afd505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [39/d73514] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [cd/aea940] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (slowlycivilbuck) - [cb/0655c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [68/5caf9b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [e0/87d483] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (earlycasualcaiman) - [44/dc4735] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (earlycasualcaiman) - [ee/939f94] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (slowlycivilbuck) - [d3/85cf3d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [e9/3c3137] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [fe/24d700] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [57/5cfd4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [d8/8dc0ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_SITES (justhusky) - [d5/c4270f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:UPD_REGIONS (justhusky) - [53/7595e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [a2/ab80c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [a1/9e7034] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS (hugelymodelbat) - [9b/e0c123] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES (hugelymodelbat) - [cd/4b2ccd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (slowlycivilbuck) - [91/8f1e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [81/980115] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (earlycasualcaiman) - [17/3bcbe8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [f0/a3ebc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (slowlycivilbuck) - [d9/54d1d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [99/394d37] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (earlycasualcaiman) - [13/c26ecd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [a1/f820c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (earlycasualcaiman) - [0b/0dbd30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (earlycasualcaiman) - [46/3d736a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (slowlycivilbuck) - [eb/d9de6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (slowlycivilbuck) - [1b/41da8a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [7e/68414e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [74/774b4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [26/d6265b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (earlycasualcaiman) - [fe/5e9b8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (slowlycivilbuck) - [df/044c53] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [d7/9e87e4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [d3/4ccaea] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (earlycasualcaiman) - [31/eebc06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (earlycasualcaiman) - [2f/be2b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (slowlycivilbuck) - [27/d00e5a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (slowlycivilbuck) - [69/f082e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [50/d68f08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [15/e5690f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [23/b04b2f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [b9/4aa06f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [e1/1bf945] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [05/2a8ae9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [1c/6b5046] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [4b/ffba21] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [b0/d13567] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [b0/61f965] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [de/3c1f8b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (earlycasualcaiman) - [30/0af3c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (slowlycivilbuck) - [73/1241bd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [54/8f23ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [ff/5617a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (earlycasualcaiman) - [6f/9469e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (slowlycivilbuck) - [92/cd5e93] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [82/dba773] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [d2/5b75eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (slowlycivilbuck) - [06/51e438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (earlycasualcaiman) - [21/2a70c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [13/b95cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [d3/1b3aa4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [6f/1e2a87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (earlycasualcaiman) - [b7/916a5e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (slowlycivilbuck) - [c4/653257] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [41/758c4b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (earlycasualcaiman) - [b1/a33ec8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (slowlycivilbuck) - [a2/22e973] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (earlycasualcaiman) - [ab/e308eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (slowlycivilbuck) - [75/598b32] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (earlycasualcaiman) - [60/7024a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (slowlycivilbuck) - [08/d00aa9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT (justhusky) - [45/0d4edd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [b6/2f2522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [ea/c6aa1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [68/88caf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [35/0e4a72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [f6/0e8d72] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [87/6e9fb9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [da/51971c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [1c/750d19] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [c9/759648] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [f9/c81132] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [ba/4e0a6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [64/5ad9fb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [59/73e87d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [90/9e7242] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [95/2cf2b3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [b2/33732e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [c7/302428] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [4c/2f99a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [ad/fa9b0b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [84/455ea7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [00/93a2da] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [8e/17c662] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [9f/eac62e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [14/c8e1fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [51/9e1b9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [97/d24643] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (18448.933s) - Snapshots: - 1 updated [-profile test_bam] - -Test pipeline - - Test [577d1960] '-profile test_singleton' - - Profiles: [test_singleton, singularity] - Configs: [nextflow.config, tests/nextflow.config] - Command: /home/ramprasad.neethiraj/nextflow/.pixi/envs/default/bin/nextflow -log /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/nextflow.log run /home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf -c /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config -c /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config -params-file /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/params.json -ansi-log false -profile test_singleton,singularity -with-trace /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/meta/trace.csv -w /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work -stub - > N E X T F L O W ~ version 25.10.4 - > Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 - > - > ------------------------------------------------------ - > ,--./,-. - >  ___ __ __ __ ___ /,-._.--~' - >  |\ | |__ __ / ` / \ |__) |__ } { - >  | \| | \__, \__/ | \ |___ \`-._,-`-, - > `._,._,' - >  nf-core/raredisease 2.7.0dev - > ------------------------------------------------------ - > - > Input/output options - > input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv - > outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output - > - > Reference file options - > fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - > fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - > genome : GRCh37 - > gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - > igenomes_ignore : true - > intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - > intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - > known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - > mito_name : MT - > mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - > mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - > score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - > score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - > svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - > target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - > variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - > vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - > vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - > vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - > vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - > vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - > vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - > - > Analysis options - > homoplasmy_af_threshold : 1 - > skip_tools : germlinecnvcaller,gens - > - > Annotation options - > variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - > vep_cache_version : 107 - > - > Institutional config options - > config_profile_name : Test profile - singleton - > config_profile_description : Minimal test dataset to check pipeline function using a single sample - > - > Generic options - > pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - > trace_report_suffix : 2026-02-19_15-09-08 - > - > Core Nextflow options - > runName : zen_hugle - > containerEngine : singularity - > container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - > launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 - > workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work - > projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - > userName : ramprasad.neethiraj - > profile : test_singleton,singularity - > configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - > - > !! Only displaying parameters that differ from the pipeline defaults !! - > ------------------------------------------------------ - > - > * The pipeline - > https://doi.org/10.5281/zenodo.7995798 - > - > * The nf-core framework - > https://doi.org/10.1038/s41587-020-0439-x - > - > * Software dependencies - > https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - > - > WARN: The following invalid input values have been detected: - > - > * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - > - > - > WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - > HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - > - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - > WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - > Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - > WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - > [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - > -[nf-core/raredisease] Pipeline completed successfully- - - Stdout: - N E X T F L O W ~ version 25.10.4 - Launching `/home/ramprasad.neethiraj/nextflow/raredisease/tests/../main.nf` [zen_hugle] DSL2 - revision: 0e8c7493e0 - - ------------------------------------------------------ - ,--./,-. -  ___ __ __ __ ___ /,-._.--~' -  |\ | |__ __ / ` / \ |__) |__ } { -  | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' -  nf-core/raredisease 2.7.0dev - ------------------------------------------------------ - - Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_single.csv - outdir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/output - - Reference file options - fai : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai - fasta : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta - genome : GRCh37 - gnomad_af : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz - igenomes_ignore : true - intervals_wgs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list - intervals_y : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list - known_dbsnp : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz - mito_name : MT - mobile_element_references : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv - mobile_element_svdb_annotations: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - modules_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - reduced_penetrance : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv - score_config_mt : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini - score_config_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini - svdb_query_dbs : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv - target_bed : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed - variant_catalog : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json - vcfanno_resources : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt - vcfanno_toml : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml - vcfanno_lua : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua - vep_cache : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz - vep_plugin_files : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv - vep_filters : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt - - Analysis options - homoplasmy_af_threshold : 1 - skip_tools : germlinecnvcaller,gens - - Annotation options - variant_consequences_snv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - variant_consequences_sv : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt - vep_cache_version : 107 - - Institutional config options - config_profile_name : Test profile - singleton - config_profile_description : Minimal test dataset to check pipeline function using a single sample - - Generic options - pipelines_testdata_base_path : https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/ - trace_report_suffix : 2026-02-19_15-09-08 - - Core Nextflow options - runName : zen_hugle - containerEngine : singularity - container.ENSEMBLVEP.* : biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0 - launchDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66 - workDir : /home/ramprasad.neethiraj/nextflow/raredisease/.nf-test/tests/577d1960ac9623233fa5c4207d4c9b66/work - projectDir : /home/ramprasad.neethiraj/nextflow/raredisease - userName : ramprasad.neethiraj - profile : test_singleton,singularity - configFiles : /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/nextflow.config, /home/ramprasad.neethiraj/nextflow/raredisease/tests/nextflow.config - - !! Only displaying parameters that differ from the pipeline defaults !! - ------------------------------------------------------ - - * The pipeline - https://doi.org/10.5281/zenodo.7995798 - - * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - - * Software dependencies - https://github.com/nf-core/raredisease/blob/master/CITATIONS.md - - WARN: The following invalid input values have been detected: - - * --sarscov_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ - - - WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. - HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`. - - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - WARN: Access to undefined parameter `hisat2_build_memory` -- Initialise it to a default value eg. `params.hisat2_build_memory = some_value` - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - WARN: Environment variable `SENTIEON_LICENSE` evaluates to an empty value - [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - - Stderr: - - Nextflow Output: - N E X T F L O W ~ version 25.10.4 - Enabled plugins: [] - Disabled plugins: [] - PF4J version 3.12.0 in 'deployment' mode - No plugins - Plugin 'nf-schema@2.5.1' resolved - Start plugin 'nf-schema@2.5.1' - revision: 0e8c7493e0 - - Input/output options - - Plugin 'nf-amazon@3.4.4' resolved - Start plugin 'nf-amazon@3.4.4' - [2c/6c30c3] Submitted process > NFCORE_RAREDISEASE:CREATE_PEDIGREE_FILE (pedigree) - [2f/255a73] Submitted process > NFCORE_RAREDISEASE:CREATE_HGNCIDS_FILE (standard) - [24/bc22fe] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GET_CHROM_SIZES (reference.fasta.fai) - [de/6a7846] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GAWK (reference) - [ec/aef308] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_GNOMAD_AF (gnomad_reformated) - [89/9c333b] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BEDTOOLS_PAD_TARGET_BED (target) - [46/b3afa9] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_DBSNP (dbsnp_-138-) - [d4/bba127] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD (reference.fasta) - [92/53db33] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWA_INDEX_GENOME (reference.fasta) - [d2/7b4c82] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_GENOME (reference.fasta) - [22/ffbb34] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT (reference.fasta) - [aa/ccc062] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:HISAT2_INDEX_GENOME (reference.fasta) - [c3/b05921] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:FASTQC (hugelymodelbat_LNUMBER1) - [95/fa3d9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:SEQTK_SAMPLE (hugelymodelbat_LNUMBER1) - [31/37c3ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:FASTP (hugelymodelbat_LNUMBER1) - [59/893222] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:UNTAR_VEP_CACHE (vep_cache_and_plugins.tar.gz) - [8b/0b5721] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:TABIX_BGZIPINDEX_PADDED_BED (target) - [8c/f633e2] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SD_MT (reference_mt.fa) - [b4/7d0328] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT (reference_mt.fa) - [2a/0936d8] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT (reference_mt.fa) - [20/74e5b4] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:LAST_INDEX_MT (reference) - [aa/5be5cd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:ADD_VARCALLER_TO_BED (mutect2) - [70/8c6cfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:ADD_VARCALLER_TO_BED (deepvariant) - [91/be5dcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM (hugelymodelbat_LNUMBER1) - [0d/cb8bf7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_ALIGN (hugelymodelbat_LNUMBER1) - [8e/fe8a73] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES (hugelymodelbat) - [09/bff3b1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_STATS (hugelymodelbat_LNUMBER1) - [31/045fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:PREP_MITOSALT (reference) - [ce/e581eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MITOSALT (hugelymodelbat_LNUMBER1) - [34/a618a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP (hugelymodelbat) - [e8/e6d72e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:QUALIMAP_BAMQC (hugelymodelbat) - [85/be21a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAM (hugelymodelbat) - [3d/132829] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RENAME_BAI (hugelymodelbat) - [2d/5b4253] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:TIDDIT_COV_VCF2CYTOSURE (hugelymodelbat) - [97/c10c2e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:TIDDIT_COV (hugelymodelbat) - [83/a15f7b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [92/fc5af4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [8c/e4e013] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [e9/1d5853] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4c/20cde2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2f/84ed7a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [2c/51bc7f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/e224c7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [04/71e4ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [52/07fbc4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [24/d6f323] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [08/26b169] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [4c/ead49e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [b5/e707ec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [18/d2e195] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [36/2009aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_RD (hugelymodelbat) - [c1/f8ca5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SV_MT:MT_DELETION (hugelymodelbat) - [bf/afb364] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [a7/ee86c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [f1/1ae187] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTMULTIPLEMETRICS (hugelymodelbat) - [d0/34976f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [90/21f6b8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [37/ed2508] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [72/0b3b34] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [71/99b9a4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [02/daabae] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [df/87defe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:ME_SPLIT_ALIGNMENT (hugelymodelbat) - [c9/8c8063] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:TIDDIT_SV (hugelymodelbat) - [94/5e122c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_WG (hugelymodelbat) - [fb/5e83ad] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:NGSBITS_SAMPLEGENDER (hugelymodelbat) - [ed/9848a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTWGSMETRICS_Y (hugelymodelbat) - [96/d5762a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:MOSDEPTH (hugelymodelbat) - [ab/ebf7bb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [1e/803f8d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [88/adaa80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [01/39a554] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e7/552f1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (hugelymodelbat) - [03/3bbf77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA (justhusky) - [c5/2ae486] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a2/0c03c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [2c/8c62af] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:UCSC_WIGTOBIGWIG (hugelymodelbat) - [00/e9c9f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [27/e6f6f1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:CHROMOGRAPH_COV (hugelymodelbat) - [0c/9d389e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [ea/664fe6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:INDEX_TIDDIT (hugelymodelbat) - [16/18ea4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7c/2607e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [a0/33f747] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [ae/e3e674] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [e5/d6790e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [cc/0d6238] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [53/11298e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [fe/c9a51e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [54/f0a6f4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [45/a9e0c1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER (justhusky) - [5e/b69fcb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER (hugelymodelbat) - [0f/005a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [d6/f2cfec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [3d/afd36c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/0fdf10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7f/a345fa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [94/a9f522] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [8d/e20a11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_DISCOVER (hugelymodelbat) - [7c/343938] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA (justhusky) - [be/68e795] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [e3/77aa58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [fe/a0fa29] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2b/9a0844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2f/2061a7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT (hugelymodelbat) - [29/778979] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST (hugelymodelbat) - [62/6df6ab] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [13/8ef8e1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [83/a2368f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [54/5d8f5b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [9c/fc0604] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_BILT (target) - [c3/3b353b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [ad/e085b0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [c3/93b499] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/c5407c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [14/dd3d58] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [18/0282d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [3b/bf3c8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [7c/c2bef7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [28/304a9e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [91/574478] Submitted process > NFCORE_RAREDISEASE:SCATTER_GENOME:GATK4_SPLITINTERVALS (reference) - [23/afd556] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT (hugelymodelbat) - [79/e2c784] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [72/730be2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [b4/14a6b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [75/64959d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [0c/cc4019] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_SHIFTFASTA (reference) - [fa/de5019] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT (justhusky) - [3c/2f6c99] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [52/cbd67d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [88/b7d010] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP (hugelymodelbat) - [a1/509337] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:RETROSEQ_CALL (hugelymodelbat) - [2c/ccf7c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [72/7afaaf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [eb/16b16e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [52/d02d47] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [77/151b3a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [40/43ace4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5d/c47f6f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [6d/bfbca0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [4b/8896e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d7/df32c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ad/e796b7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:RENAMESAMPLE_EXP (hugelymodelbat) - [62/e52458] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [3a/313217] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [63/84d987] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [12/73d1d2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT (hugelymodelbat) - [11/7657a2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [f5/1f1416] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5c/43d3b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [28/fb2443] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [29/a514a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [5b/3b03d4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [ac/1ae239] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d2/7f9311] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [7f/6fff80] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [1f/b6685b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [d0/ff9691] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME (hugelymodelbat) - [50/01b47d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT (hugelymodelbat) - [9e/5ae9ce] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:GLNEXUS (justhusky) - [2f/647d39] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [85/c9725a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [54/b16400] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [32/b79324] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bd/0aa55a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/fb5a88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [15/1b8118] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:TABIX_EXP_RENAME (hugelymodelbat) - [3a/02143e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [0c/a47453] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [54/b3d5f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [bb/0ea509] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [99/5167c0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0f/00d409] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/bb814a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [98/ab63a6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [e4/148e6d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [45/82bd82] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [07/387699] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [38/a1d9cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [a4/031055] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [39/bc49b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [08/96bfe7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [4e/6f5e45] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [f1/61aa25] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [e4/35115d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [43/c4b234] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [97/af8c30] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [5f/fdde9a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [98/f06681] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [dc/007a10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [d5/fb48eb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [94/c2f7ca] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [72/9e24cb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_SORT_ME (hugelymodelbat) - [45/e267a1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP (hugelymodelbat) - [1b/9ad844] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:SPLIT_MULTIALLELICS_GL (justhusky) - [be/66de67] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [ab/6a10f9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [66/cb4562] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5c/1e1c74] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [65/82ff88] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [1c/8b4bd1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [5d/8cc953] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [74/08ef27] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [7b/a45660] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [d4/1b4d4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0b/ba9146] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [63/5092c9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [70/51315b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION (hugelymodelbat) - [f6/34529f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [0b/aa92e2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [38/579edb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [69/5b1386] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_REPEAT_EXPANSIONS:SVDB_MERGE_REPEATS (justhusky) - [9b/35a43e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME_SPLIT (hugelymodelbat) - [6b/ef22a8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL (justhusky) - [51/a8b8ef] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:BCFTOOLS_CONCAT_ME (hugelymodelbat) - [63/e7bad6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_GL (justhusky) - [20/e8f8c6] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:GATK_ILT (target) - [78/5011d5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (justhusky) - [e8/fcc396] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:STRANGER (justhusky) - [b9/bf2342] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE (justhusky) - [8c/e2c218] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:TABIX_ANNOTATE (justhusky) - [98/c301c5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT (hugelymodelbat) - [79/6e5d71] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:SAMTOOLS_INDEX_MT (hugelymodelbat) - [a3/ed844e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_VIEW (hugelymodelbat) - [cd/c7ea8f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:TABIX_ME (justhusky) - [83/ef440b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:SVDB_QUERY_DB (justhusky) - [b1/597fb1] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:GATK4_SELECTVARIANTS (justhusky) - [e5/6ee828] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_COLLATE (hugelymodelbat) - [09/b95518] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:GAWK (hugelymodelbat) - [70/bcad4f] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT (reference_shift.fasta) - [1b/ed84cc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAM_TO_BAM (hugelymodelbat) - [b5/49e354] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:SUBSAMPLE_MT_READS:SAMTOOLS_SORT (hugelymodelbat) - [de/5f84c6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL (hugelymodelbat) - [24/cd5309] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:PICARD_SORTVCF (justhusky) - [48/673161] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:ENSEMBLVEP_ME (justhusky) - [92/a44b1e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF (hugelymodelbat) - [ea/bde0d6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MOBILE_ELEMENTS:BCFTOOLS_VIEW_FILTER (justhusky) - [b8/389a70] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP (justhusky) - [8f/8741b5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [46/9b0f89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [7b/70db8a] Submitted process > NFCORE_RAREDISEASE:PREPARE_REFERENCES:CAT_CAT_BAIT (target_bait.intervals_list) - [ce/949a06] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:QC_BAM:PICARD_COLLECTHSMETRICS (hugelymodelbat) - [e0/8203c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [dd/fb6799] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:INDEX_CNVNATOR (hugelymodelbat) - [f4/923ba3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_ME:TABIX_BGZIPTABIX (justhusky) - [e9/faad1a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bb/10abdc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR (hugelymodelbat) - [22/0433f5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT (hugelymodelbat) - [f9/e69d77] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:PEDDY (justhusky) - [48/88b532] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_ROH (justhusky) - [71/1efa83] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR (justhusky) - [16/0ebad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [22/044dec] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:RHOCALL_ANNOTATE (justhusky) - [a4/57b936] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_ROHCALL (justhusky) - [f9/79e560] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_ME:TABIX_TABIX (justhusky) - [ed/aea404] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [10/69bdac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:GATK4_SELECTVARIANTS (justhusky) - [73/58f26b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:SVDB_MERGE (justhusky) - [01/3380e8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:TABIX_TABIX (justhusky) - [25/8687b6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:SVDB_QUERY_DB (justhusky) - [ad/30e71d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:PICARD_SORTVCF (justhusky) - [97/e8ca6e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:BCFTOOLS_VIEW (justhusky) - [b6/25824c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:ENSEMBLVEP_SV (justhusky) - [53/4bc17d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:BWAMEM2_MEM_MT (hugelymodelbat) - [1f/728c22] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:BWAMEM2_MEM_MT (hugelymodelbat) - [4d/5886aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [08/63cc1f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT (hugelymodelbat) - [b7/40a941] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP (justhusky) - [8b/741ae5] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP (justhusky) - [fa/918585] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [f2/054808] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:SPLIT_AND_FILTER_SV_VCF (hugelymodelbat) - [9c/393fd4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_cadd.tsv.gz - Staging foreign file: https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz - [c6/e80a95] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [b0/7b39ff] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:VCFANNO (justhusky) - [a2/fc9f0d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CYTOSURE_FILES:VCF2CYTOSURE (hugelymodelbat) - [0d/fdca11] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [48/020f43] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO (justhusky) - [b4/fee414] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [e0/d7fbdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [39/a9cb89] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW (justhusky) - [14/b117d9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SV:TABIX_BGZIPTABIX (justhusky) - [2a/4989a9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [99/f44f10] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [c5/6dd88e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV (justhusky) - [fa/a79e38] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [6f/5c18b4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [54/5b8219] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [02/066fcf] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_ANNOTATE (justhusky) - [24/49a42b] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [97/c629fe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [6b/13ff7c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_VEP (justhusky) - [21/06e6ed] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_MODELS (justhusky) - [83/7e26fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT (justhusky) - [44/64c893] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [21/19d995] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT (justhusky) - [7d/1ca679] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP (justhusky) - [9b/5a18a0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [2b/d68e2d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_SCORE (justhusky) - [de/b02d31] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL (hugelymodelbat) - [19/039796] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [38/3732b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:TABIX_TABIX (hugelymodelbat) - [98/893e87] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:GENMOD_COMPOUND (justhusky) - [3a/da9ab4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [52/edff41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH (hugelymodelbat) - [d2/9184f0] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_UNCOMPRESS (hugelymodelbat) - [b0/07bbcc] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SV:BCFTOOLS_SORT (justhusky) - [45/c0e564] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [4d/9cd67e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ (hugelymodelbat) - [f2/249bb4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_SNV:TABIX_BGZIPTABIX (justhusky) - [15/85aafe] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_ADDORREPLACEREADGROUPS_MT (hugelymodelbat) - [42/e57dbb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [d6/1d9505] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [3e/65a456] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG (hugelymodelbat) - [c3/04795d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG (hugelymodelbat) - [d1/0b8502] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [2f/1c0b4f] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_SNV:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [8b/5317c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [97/1e5e1c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT (hugelymodelbat) - [d9/63e5ac] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_ANNOTATE (justhusky) - [3e/ecdec2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [7f/b80c50] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT_SHIFT:SAMTOOLS_SORT_MT (hugelymodelbat) - [97/e8d327] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_MODELS (justhusky) - [cc/28af57] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_MUTECT2_MT (hugelymodelbat) - [af/d685a3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_MT:SAMTOOLS_SORT_MT (hugelymodelbat) - [3f/a5d97c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [96/57970c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_MUTECT2_MT (hugelymodelbat) - [ec/a8830d] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_SCORE (justhusky) - [cc/43a5b2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:GENMOD_COMPOUND (justhusky) - [a5/f5053e] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_SNV:TABIX_BGZIPTABIX (justhusky) - [54/a15cd7] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT_SHIFT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [63/03c876] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:HAPLOCHECK_MT (hugelymodelbat) - [3c/1a7acb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_MT:GATK4_FILTERMUTECTCALLS_MT (hugelymodelbat) - [0e/872688] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:PICARD_LIFTOVERVCF (hugelymodelbat) - [64/2479f8] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT (hugelymodelbat) - [a3/271f60] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT (hugelymodelbat) - [86/d122c4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_MT (hugelymodelbat) - [9f/bddb4c] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT (hugelymodelbat) - [32/dae5e9] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:REMOVE_DUPLICATES_MT (hugelymodelbat) - [57/862c08] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MT2 (hugelymodelbat) - [c2/0807f3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_TABIX_MERGE (justhusky) - [f8/705ad3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE (justhusky) - [04/d3dda4] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:POSTPROCESS_MT_CALLS:TABIX_ANNOTATE (justhusky) - [c5/b6d438] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HMTNOTE_ANNOTATE (justhusky) - [d6/fa0e41] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:REPLACE_SPACES_IN_VCFINFO (justhusky) - [81/9d9b00] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_HMTNOTE_MT (justhusky) - [86/808b64] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:VCFANNO_MT (justhusky) - [dd/2f7713] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ZIP_TABIX_VCFANNO_MT (justhusky) - [5c/8a9cf6] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT (justhusky) - [45/fa64aa] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:ENSEMBLVEP_MT (justhusky) - [8b/0af1fd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT (justhusky) - [f2/232005] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:GENERATE_CLINICAL_SET_MT:BCFTOOLS_VIEW (justhusky) - [25/0787c3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [bc/a7ac01] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVERECONSEQUENCE (justhusky) - [83/c43551] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [f0/7f08d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:ANN_CSQ_PLI_MT:CUSTOM_ADDMOSTSEVEREPLI (justhusky) - [ba/07ad75] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [bb/353bb2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_ANNOTATE (justhusky) - [dc/86bbfd] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [b9/f7c203] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_MODELS (justhusky) - [9e/72c2c2] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [02/cdc9e3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_SCORE (justhusky) - [bf/7ae5d3] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [81/2dc216] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:GENMOD_COMPOUND (justhusky) - [fa/58a99a] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [91/da1a56] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:RANK_VARIANTS_MT:TABIX_BGZIPTABIX (justhusky) - [1a/697cdb] Submitted process > NFCORE_RAREDISEASE:RAREDISEASE:MULTIQC - -[nf-core/raredisease] Pipeline completed successfully- - Stop plugin 'nf-amazon@3.4.4' - Stop plugin 'nf-schema@2.5.1' - - PASSED (13011.306s) - Snapshots: - 1 updated [-profile test_singleton] - - -Snapshot Summary: - 3 updated - -SUCCESS: Executed 3 tests in 64038.604s - From c479c99be43fbfaa586ce8d4d0589da03e871889 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Feb 2026 16:53:15 +0100 Subject: [PATCH 384/872] update more modules --- modules.json | 16 +- modules/nf-core/bwa/mem/environment.yml | 11 +- modules/nf-core/bwa/mem/main.nf | 21 +- modules/nf-core/bwa/mem/meta.yml | 108 +++-- modules/nf-core/bwa/mem/tests/main.nf.test | 15 +- .../nf-core/bwa/mem/tests/main.nf.test.snap | 212 +++++++--- modules/nf-core/bwa/mem/tests/tags.yml | 3 - modules/nf-core/cat/cat/main.nf | 4 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/last/lastdb/main.nf | 1 - modules/nf-core/peddy/environment.yml | 2 + modules/nf-core/peddy/main.nf | 52 +-- modules/nf-core/peddy/meta.yml | 195 +++++++-- modules/nf-core/peddy/tests/main.nf.test | 84 +++- modules/nf-core/peddy/tests/main.nf.test.snap | 377 ++++++++++++++++-- modules/nf-core/peddy/tests/nextflow.config | 5 + modules/nf-core/peddy/tests/tags.yml | 2 - .../nf-core/rhocall/annotate/environment.yml | 2 + modules/nf-core/rhocall/annotate/main.nf | 20 +- modules/nf-core/rhocall/annotate/meta.yml | 46 ++- .../rhocall/annotate/tests/main.nf.test | 87 ++++ .../rhocall/annotate/tests/main.nf.test.snap | 62 +++ modules/nf-core/rhocall/viz/environment.yml | 4 +- modules/nf-core/rhocall/viz/main.nf | 16 +- modules/nf-core/rhocall/viz/meta.yml | 42 +- .../rhocall/viz/tests/main.nf.test.snap | 20 +- modules/nf-core/rhocall/viz/tests/tags.yml | 2 - modules/nf-core/svdb/merge/main.nf | 8 +- subworkflows/local/align/main.nf | 5 - subworkflows/local/align_MT/main.nf | 3 - .../local/align_bwa_bwamem2_bwameme/main.nf | 4 - subworkflows/local/annotate_genome_snvs.nf | 3 - .../local/annotate_rhocallviz/main.nf | 6 - workflows/raredisease.nf | 2 - 34 files changed, 1139 insertions(+), 303 deletions(-) delete mode 100644 modules/nf-core/bwa/mem/tests/tags.yml create mode 100644 modules/nf-core/peddy/tests/nextflow.config delete mode 100644 modules/nf-core/peddy/tests/tags.yml create mode 100644 modules/nf-core/rhocall/annotate/tests/main.nf.test create mode 100644 modules/nf-core/rhocall/annotate/tests/main.nf.test.snap delete mode 100644 modules/nf-core/rhocall/viz/tests/tags.yml diff --git a/modules.json b/modules.json index 9bba47184..a2c443e83 100644 --- a/modules.json +++ b/modules.json @@ -72,7 +72,7 @@ }, "bwa/mem": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", "installed_by": ["modules"] }, "bwamem2/index": { @@ -102,7 +102,7 @@ }, "cat/cat": { "branch": "master", - "git_sha": "69614d4579a6bd9b8a2ecffb35959809d9c36559", + "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a", "installed_by": ["modules"] }, "chromograph": { @@ -158,7 +158,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "5bdb098216aaf5df9c3b6343e6204cd932503c16", + "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { @@ -304,7 +304,7 @@ }, "last/lastdb": { "branch": "master", - "git_sha": "d92ad4055433d66d3e3eb4fd8d729d6ae9f75693", + "git_sha": "a54953d05812af249d40ffaccb5b8ee371a75866", "installed_by": ["modules"] }, "manta/germline": { @@ -329,7 +329,7 @@ }, "peddy": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { @@ -379,12 +379,12 @@ }, "rhocall/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "rhocall/viz": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", "installed_by": ["modules"] }, "rtgtools/format": { @@ -499,7 +499,7 @@ }, "svdb/merge": { "branch": "master", - "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", + "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", "installed_by": ["modules"] }, "svdb/query": { diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index ef7b966c0..54e679492 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,8 +1,13 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bwa=0.7.18 - - htslib=1.20.0 - - samtools=1.20 + # renovate: datasource=conda depName=bioconda/bwa + - bioconda::bwa=0.7.19 + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.22.1 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.22.1 diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf index 9c815f0c8..e3732673e 100644 --- a/modules/nf-core/bwa/mem/main.nf +++ b/modules/nf-core/bwa/mem/main.nf @@ -4,8 +4,8 @@ process BWA_MEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0' : - 'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:1bd8542a8a0b42e0981337910954371d0230828e-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d7/d7e24dc1e4d93ca4d3a76a78d4c834a7be3985b0e1e56fddd61662e047863a8a/data' : + 'community.wave.seqera.io/library/bwa_htslib_samtools:83b50ff84ead50d0' }" input: tuple val(meta) , path(reads) @@ -18,7 +18,8 @@ process BWA_MEM { tuple val(meta), path("*.cram") , emit: cram, optional: true tuple val(meta), path("*.csi") , emit: csi, optional: true tuple val(meta), path("*.crai") , emit: crai, optional: true - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bwa'), eval('bwa 2>&1 | sed -n "s/^Version: //p"'), topic: versions, emit: versions_bwa + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools when: task.ext.when == null || task.ext.when @@ -44,19 +45,11 @@ process BWA_MEM { \$INDEX \\ $reads \\ | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ stub: - def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def samtools_command = sort_bam ? 'sort' : 'view' def extension = args2.contains("--output-fmt sam") ? "sam" : args2.contains("--output-fmt cram") ? "cram": sort_bam && args2.contains("-O cram")? "cram": @@ -66,11 +59,5 @@ process BWA_MEM { touch ${prefix}.${extension} touch ${prefix}.csi touch ${prefix}.crai - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index 37467d291..450a3fe99 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -16,8 +16,9 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 - licence: ["GPL-3.0-or-later"] - identifier: "" + licence: + - "GPL-3.0-or-later" + identifier: "biotools:bwa" input: - - meta: type: map @@ -29,6 +30,9 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1930" - - meta2: type: map description: | @@ -38,6 +42,8 @@ input: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + ontologies: + - edam: "http://edamontology.org/data_3210" - - meta3: type: map description: | @@ -47,52 +53,92 @@ input: type: file description: Reference genome in FASTA format pattern: "*.{fasta,fa}" - - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + ontologies: + - edam: "http://edamontology.org/data_2044" + - edam: "http://edamontology.org/format_1929" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - bam: - - meta: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + bam: + - - meta: + type: map + description: Groovy Map containing sample information - "*.bam": type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - cram: - - meta: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + ontologies: + - edam: "http://edamontology.org/format_2572" + cram: + - - meta: + type: map + description: Groovy Map containing sample information - "*.cram": type: file description: Output CRAM file containing read alignments pattern: "*.{cram}" - - csi: - - meta: - type: file - description: Optional index file for BAM file - pattern: "*.{csi}" + ontologies: + - edam: "http://edamontology.org/format_3462" + csi: + - - meta: + type: map + description: Groovy Map containing sample information - "*.csi": type: file description: Optional index file for BAM file pattern: "*.{csi}" - - crai: - - meta: - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + ontologies: [] + crai: + - - meta: + type: map + description: Groovy Map containing sample information - "*.crai": type: file description: Optional index file for CRAM file pattern: "*.{crai}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_bwa: + - - ${task.process}: + type: string + description: The name of the process + - bwa: + type: string + description: The name of the tool + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: eval + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwa: + type: string + description: The name of the tool + - 'bwa 2>&1 | sed -n "s/^Version: //p"': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test index 5de2c2f45..6486ab000 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test +++ b/modules/nf-core/bwa/mem/tests/main.nf.test @@ -48,8 +48,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -83,8 +82,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -119,8 +117,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -155,8 +152,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } @@ -191,8 +187,7 @@ nextflow_process { process.out.cram, process.out.csi, process.out.crai, - process.out.versions, - bam(process.out.bam[0][1]).getHeaderMD5(), + process.out.findAll { key, val -> key.startsWith("versions") }, bam(process.out.bam[0][1]).getReadsMD5() ).match() } diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap index 2079ea224..8aca4b234 100644 --- a/modules/nf-core/bwa/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/mem/tests/main.nf.test.snap @@ -10,17 +10,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "b6d9cb250261a4c125413c5d867d87a7", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "798439cbd7fd81cbcc5078022dc5479d" ], + "timestamp": "2026-02-18T12:42:52.901827", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:28.051598" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Single-End Sort": { "content": [ @@ -33,17 +45,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "848434ae4b79cfdcb2281c60b33663ce", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "94fcf617f5b994584c4e8d4044e16b4f" ], + "timestamp": "2026-02-18T12:43:01.149915", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:39.671154" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End": { "content": [ @@ -56,17 +80,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "5b34d31be84478761f789e3e2e805e31", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], + "timestamp": "2026-02-18T12:43:09.528042", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:22:51.919479" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End Sort": { "content": [ @@ -79,17 +115,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "69003376d9a8952622d8587b39c3eaae", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "af8628d9df18b2d3d4f6fd47ef2bb872" ], + "timestamp": "2026-02-18T12:43:17.876121", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:23:00.833562" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Single-end - stub": { "content": [ @@ -125,7 +173,18 @@ ] ], "4": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "5": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -157,16 +216,27 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-18T12:43:33.853248", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:31:29.46282" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-End - no fasta": { "content": [ @@ -179,17 +249,29 @@ [ ], - [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" - ], - "5b34d31be84478761f789e3e2e805e31", + { + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] + ] + }, "57aeef88ed701a8ebc8e2f0a381b2a6" ], + "timestamp": "2026-02-18T12:43:26.121474", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:23:09.942545" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Paired-end - stub": { "content": [ @@ -225,7 +307,18 @@ ] ], "4": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "5": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ], "bam": [ [ @@ -257,15 +350,26 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,478b816fbd37871f5e8c617833d51d80" + "versions_bwa": [ + [ + "BWA_MEM", + "bwa", + "0.7.19-r1273" + ] + ], + "versions_samtools": [ + [ + "BWA_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-18T12:43:42.119907", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-02T12:31:37.757037" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/bwa/mem/tests/tags.yml b/modules/nf-core/bwa/mem/tests/tags.yml deleted file mode 100644 index 82992d1f0..000000000 --- a/modules/nf-core/bwa/mem/tests/tags.yml +++ /dev/null @@ -1,3 +0,0 @@ -bwa/mem: - - modules/nf-core/bwa/index/** - - modules/nf-core/bwa/mem/** diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index aa72fc4d9..15274c4ce 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -20,7 +20,7 @@ process CAT_CAT { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def file_list = files_in.collect { it.toString() } + def file_list = files_in.collect { file -> file.toString() } // choose appropriate concatenation tool depending on input and output format @@ -55,7 +55,7 @@ process CAT_CAT { """ stub: - def file_list = files_in.collect { it.toString() } + def file_list = files_in.collect { file -> file.toString() } prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" if(file_list.contains(prefix.trim())) { error "The name of the input file can't be the same as for the output prefix in the " + diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 4b3041dc5..f5629527d 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -1,6 +1,6 @@ process FASTQC { tag "${meta.id}" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index 43d84750b..8f5b5c27e 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -31,7 +31,6 @@ process LAST_LASTDB { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir lastdb diff --git a/modules/nf-core/peddy/environment.yml b/modules/nf-core/peddy/environment.yml index 8d7fa2b6a..2bb1deb8e 100644 --- a/modules/nf-core/peddy/environment.yml +++ b/modules/nf-core/peddy/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 0e533ec3b..0090f4e28 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -4,26 +4,35 @@ process PEDDY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' : - 'biocontainers/peddy:0.4.8--pyh5e36f6f_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a1f7f39ed4c0e429d5a5805cdfa5251cbe56d4f2cf9cf4257172db1a56ab6bf/data' : + 'community.wave.seqera.io/library/peddy:0.4.8--e3cef30bae621593' }" input: tuple val(meta), path(vcf), path(vcf_tbi) - path ped + tuple val(meta2), path(ped) + tuple val(meta3), path(sites) output: - tuple val(meta), path("*.html") , emit: html - tuple val(meta), path("*.csv") , emit: csv - tuple val(meta), path("*.peddy.ped"), emit: ped - tuple val(meta), path("*.png") , optional: true, emit: png - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vs.html") , emit: vs_html + tuple val(meta), path("${prefix}.html") , emit: html + tuple val(meta), path("${prefix}.peddy.ped") , emit: ped + tuple val(meta), path("${prefix}.het_check.png") , optional: true, emit: het_check_png + tuple val(meta), path("${prefix}.ped_check.png") , optional: true, emit: ped_check_png + tuple val(meta), path("${prefix}.sex_check.png") , optional: true, emit: sex_check_png + tuple val(meta), path("${prefix}.het_check.csv") , optional: true, emit: het_check_csv + tuple val(meta), path("${prefix}.ped_check.csv") , optional: true, emit: ped_check_csv + tuple val(meta), path("${prefix}.sex_check.csv") , optional: true, emit: sex_check_csv + tuple val(meta), path("${prefix}.ped_check.rel-difference.csv") , optional: true, emit: ped_check_rel_difference_csv + tuple val("${task.process}"), val("peddy"), eval("peddy --version | sed 's/peddy, version //'"), topic: versions, emit: versions_peddy when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def sites_arg = sites ? "--sites $sites" : '' + if (sites && args.contains('--sites')) error "Double definition of --sites (in sites channel and in ext.args)" """ peddy \\ $args \\ @@ -31,27 +40,24 @@ process PEDDY { --plot \\ -p $task.cpus \\ $vcf \\ + $sites_arg \\ $ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' ) - END_VERSIONS """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + if (sites && args.contains('--sites')) error "Double definition of --sites (in sites channel and in ext.args)" """ - touch ${prefix}.ped_check.csv touch ${prefix}.vs.html + touch ${prefix}.html + touch ${prefix}.peddy.ped touch ${prefix}.het_check.csv + touch ${prefix}.ped_check.csv touch ${prefix}.sex_check.csv - touch ${prefix}.peddy.ped - touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - peddy: \$( peddy --version 2>&1 | tail -1 | sed 's/peddy, version //' ) - END_VERSIONS + touch ${prefix}.het_check.png + touch ${prefix}.ped_check.png + touch ${prefix}.sex_check.png + touch ${prefix}.ped_check.rel-difference.csv """ } diff --git a/modules/nf-core/peddy/meta.yml b/modules/nf-core/peddy/meta.yml index 6b6b7347d..b503b76b9 100644 --- a/modules/nf-core/peddy/meta.yml +++ b/modules/nf-core/peddy/meta.yml @@ -6,13 +6,14 @@ keywords: - family tools: - peddy: - description: genotype, ped correspondence check, ancestry check, sex check. directly, - quickly on VCF + description: genotype, ped correspondence check, ancestry check, sex check. + directly, quickly on VCF homepage: https://github.com/brentp/peddy documentation: https://peddy.readthedocs.io/en/latest/ tool_dev_url: https://github.com/brentp/peddy doi: "10.1016/j.ajhg.2017.01.017" - licence: ["MIT"] + licence: + - "MIT" identifier: "" input: - - meta: @@ -23,61 +24,195 @@ input: - vcf: type: file description: VCF file - pattern: "*.{vcf.gz}" + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 - vcf_tbi: type: file description: TBI file - pattern: "*.{vcf.gz.tbi}" - - - ped: + pattern: "*.vcf.gz.tbi" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ped: type: file description: PED/FAM file pattern: "*.{ped,fam}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: sites file. By defaults peddy uses hg19/GRCh37, "--sites + hg38" can be specified in the process argument or a custom file + following syntax + https://github.com/brentp/peddy/blob/master/peddy/GRCH37.sites can be + provided + pattern: "*.sites" + ontologies: [] output: - - html: - - meta: + vs_html: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.html": + - ${prefix}.vs.html: type: file - description: HTML file - pattern: "*.{html}" - - csv: - - meta: + description: HTML file comparison between reported and inferred sex + pattern: "*.vs.html" + ontologies: [] + html: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.csv": + - ${prefix}.html: type: file - description: CSV file - pattern: "*.{csv}" - - ped: - - meta: + description: HTML report + pattern: "*.html" + ontologies: [] + ped: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.peddy.ped": + - ${prefix}.peddy.ped: type: file - description: PED/FAM file - pattern: "*.peddy.{ped}" - - png: - - meta: + description: Inferred PED file + pattern: "*.peddy.ped" + ontologies: [] + het_check_png: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.png": + - ${prefix}.het_check.png: type: file - description: PNG file - pattern: "*.{png}" - - versions: - - versions.yml: + description: | + PNG file containing heterozygosity check. + Rate of het calls, allele-balance at het calls, + mean and median depth, and a PCA projection onto thousand + genomes. + pattern: "*.het_check.png" + ontologies: [] + ped_check_png: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.png: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + PNG file containing pedigree check between reported + and inferred sex + pattern: "*.het_check.png" + ontologies: [] + sex_check_png: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sex_check.png: + type: file + description: | + PNG file with sex check performs a comparison + between the sex reported in the ped file and that + inferred from the genotypes on the non-PAR regions + of the X chromosome. + pattern: "*.sex_check.png" + ontologies: [] + het_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.het_check.csv: + type: file + description: | + CSV file containing heterozygosity check. + Rate of het calls, allele-balance at het calls, + mean and median depth, and a PCA projection onto thousand + genomes. + pattern: "*.het_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + ped_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.csv: + type: file + description: | + CSV file containing pedigree check between reported + and inferred sex + pattern: "*.het_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + sex_check_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sex_check.csv: + type: file + description: | + CSV file with sex check performs a comparison + between the sex reported in the ped file and that + inferred from the genotypes on the non-PAR regions + of the X chromosome. + pattern: "*.sex_check.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + ped_check_rel_difference_csv: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ped_check.rel-difference.csv: + type: file + description: | + CSV file with the comparison between inferred and given relatedness + pattern: "*.ped_check.rel-difference.csv" + ontologies: + - edam: http://edamontology.org/format_3752 + versions_peddy: + - - ${task.process}: + type: string + description: The name of the process + - peddy: + type: string + description: The name of the tool + - peddy --version | sed 's/peddy, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - peddy: + type: string + description: The name of the tool + - peddy --version | sed 's/peddy, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@rannick" maintainers: diff --git a/modules/nf-core/peddy/tests/main.nf.test b/modules/nf-core/peddy/tests/main.nf.test index 21ff538d1..f52d22919 100644 --- a/modules/nf-core/peddy/tests/main.nf.test +++ b/modules/nf-core/peddy/tests/main.nf.test @@ -8,6 +8,70 @@ nextflow_process { tag "modules_nfcore" tag "peddy" + test("test - peddy") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + + ) + } + + } + + test("test - peddy - double_sites") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert !process.success }, + { assert process.exitStatus != 0 } + ) + } + } + test("test - peddy - stub") { options "-stub" @@ -17,19 +81,27 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM_snvs_annotated_ranked.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'ped_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/FAM.ped', checkIfExists: true) + ] + input[2] = [ + [ id:'sites_file' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/peddy.sites', checkIfExists: true) ] - input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) """ } } then { - assert process.success - assert snapshot(process.out).match() + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) } } - } diff --git a/modules/nf-core/peddy/tests/main.nf.test.snap b/modules/nf-core/peddy/tests/main.nf.test.snap index 5de593f1d..c122208ad 100644 --- a/modules/nf-core/peddy/tests/main.nf.test.snap +++ b/modules/nf-core/peddy/tests/main.nf.test.snap @@ -8,10 +8,7 @@ "id": "test", "single_end": false }, - [ - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -20,11 +17,14 @@ "id": "test", "single_end": false }, - [ - "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + "PEDDY", + "peddy", + "0.4.8" ] ], "2": [ @@ -37,22 +37,84 @@ ] ], "3": [ - + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "4": [ - "versions.yml:md5,d3587e67aded68bcf24c47542efe012f" + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], - "csv": [ + "5": [ [ { "id": "test", "single_end": false }, - [ - "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sex_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "het_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "het_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "html": [ @@ -61,10 +123,7 @@ "id": "test", "single_end": false }, - [ - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "ped": [ @@ -76,18 +135,278 @@ "test.peddy.ped:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "png": [ - + "ped_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ped_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ped_check_rel_difference_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sex_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sex_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_peddy": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "vs_html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-02-18T10:39:07.038845862", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test - peddy": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,a749380edef4653dade663534ddcfbd6" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,e3af87096747a19966222a74242943b6" + ] + ], + "10": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.peddy.ped:md5,8378f6599ee4ad6a9db42bfe226968a6" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,ce21f5e727cc6b4346d407d2963b0442" + ] ], - "versions": [ - "versions.yml:md5,d3587e67aded68bcf24c47542efe012f" + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,861d8b204d78a22a59b0cedafd8d4a16" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,b2ff9afe9f596dee5a22431ba920980c" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,b8623fa750218dade5468542d459fafe" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,21dded6c03dab39859d2936d4820c426" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,763950d0eff48b64da29a6a883d6b11c" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,b59f50df00b5b3af6e71e774d8b99103" + ] + ], + "het_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.csv:md5,b8623fa750218dade5468542d459fafe" + ] + ], + "het_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.het_check.png:md5,ce21f5e727cc6b4346d407d2963b0442" + ] + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,e3af87096747a19966222a74242943b6" + ] + ], + "ped": [ + [ + { + "id": "test", + "single_end": false + }, + "test.peddy.ped:md5,8378f6599ee4ad6a9db42bfe226968a6" + ] + ], + "ped_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.csv:md5,21dded6c03dab39859d2936d4820c426" + ] + ], + "ped_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.png:md5,861d8b204d78a22a59b0cedafd8d4a16" + ] + ], + "ped_check_rel_difference_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped_check.rel-difference.csv:md5,b59f50df00b5b3af6e71e774d8b99103" + ] + ], + "sex_check_csv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.csv:md5,763950d0eff48b64da29a6a883d6b11c" + ] + ], + "sex_check_png": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sex_check.png:md5,b2ff9afe9f596dee5a22431ba920980c" + ] + ], + "versions_peddy": [ + [ + "PEDDY", + "peddy", + "0.4.8" + ] + ], + "vs_html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vs.html:md5,a749380edef4653dade663534ddcfbd6" + ] ] } ], + "timestamp": "2026-02-18T10:44:20.669530641", "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T09:28:05.418978589" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/peddy/tests/nextflow.config b/modules/nf-core/peddy/tests/nextflow.config new file mode 100644 index 000000000..bca49c052 --- /dev/null +++ b/modules/nf-core/peddy/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'PEDDY' { + ext.args = '--sites --hg38' + } +} diff --git a/modules/nf-core/peddy/tests/tags.yml b/modules/nf-core/peddy/tests/tags.yml deleted file mode 100644 index d8324a74c..000000000 --- a/modules/nf-core/peddy/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -mosdepth: - - "modules/nf-core/peddy/**" diff --git a/modules/nf-core/rhocall/annotate/environment.yml b/modules/nf-core/rhocall/annotate/environment.yml index ba95c3cbe..8a0fe435e 100644 --- a/modules/nf-core/rhocall/annotate/environment.yml +++ b/modules/nf-core/rhocall/annotate/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/rhocall/annotate/main.nf b/modules/nf-core/rhocall/annotate/main.nf index 78de45c18..070d37c1c 100644 --- a/modules/nf-core/rhocall/annotate/main.nf +++ b/modules/nf-core/rhocall/annotate/main.nf @@ -4,8 +4,8 @@ process RHOCALL_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - 'biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7d/7dbf7021085cfea72a20cafffe57fcf47392706d9a433f1143f1e60b389b85ae/data': + 'community.wave.seqera.io/library/rhocall:0.5.1--a7eced77e39d2b82' }" input: tuple val(meta), path(vcf), path(tbi) @@ -14,7 +14,7 @@ process RHOCALL_ANNOTATE { output: tuple val(meta), path("*_rhocall.vcf"), emit: vcf - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("rhocall"), eval("rhocall --version | sed 's/rhocall, version //'"), topic: versions, emit: versions_rhocall when: task.ext.when == null || task.ext.when @@ -24,6 +24,8 @@ process RHOCALL_ANNOTATE { def prefix = task.ext.prefix ?: "${meta.id}" def az_bed = bed ? "-b ${bed}" : '' """ + export MPLCONFIGDIR=\$PWD + rhocall \\ annotate \\ $args \\ @@ -31,21 +33,13 @@ process RHOCALL_ANNOTATE { -r $roh \\ -o ${prefix}_rhocall.vcf \\ $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}_rhocall.vcf + export MPLCONFIGDIR=\$PWD - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS + touch ${prefix}_rhocall.vcf """ } diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml index fb041cae8..4df7c6d6e 100644 --- a/modules/nf-core/rhocall/annotate/meta.yml +++ b/modules/nf-core/rhocall/annotate/meta.yml @@ -10,7 +10,8 @@ tools: homepage: "https://github.com/dnil/rhocall" documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" input: - - meta: @@ -22,10 +23,12 @@ input: type: file description: vcf file pattern: "*.{vcf,vcf.gz}" + ontologies: [] - tbi: type: file description: vcf index file pattern: "*.{tbi}" + ontologies: [] - - meta2: type: map description: | @@ -35,13 +38,15 @@ input: type: file description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL pattern: "*.{roh}" - - - bed: - type: file - description: BED file with AZ windows. - pattern: "*.{bed}" + ontologies: [] + - bed: + type: file + description: BED file with AZ windows. + pattern: "*.{bed}" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,11 +55,28 @@ output: type: file description: vcf file pattern: "*.{vcf,vcf.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rhocall: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/annotate/tests/main.nf.test b/modules/nf-core/rhocall/annotate/tests/main.nf.test new file mode 100644 index 000000000..fafd3826d --- /dev/null +++ b/modules/nf-core/rhocall/annotate/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process RHOCALL_ANNOTATE" + + script "../main.nf" + process "RHOCALL_ANNOTATE" + + tag "modules" + tag "modules_nfcore" + tag "rhocall" + tag "rhocall/annotate" + tag "bcftools" + tag "bcftools/roh" + + setup { + run("BCFTOOLS_ROH") { + script "../../../bcftools/roh/main.nf" + + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true) + ] + input[1] = [[],[]] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + } + + test("sarscov2") { + + when { + params { + module_args = '' + } + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true) + ] + input[1] = BCFTOOLS_ROH.out.roh + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.findAll {key, value -> key.startsWith("versions")} + ).match() } + ) + } + } + + test("sarscov2 - stub") { + options '-stub' + when { + params { + module_args = '' + } + process { + """ + input[0] = [[id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists:true)] + input[1] = BCFTOOLS_ROH.out.roh + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap b/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap new file mode 100644 index 000000000..44987e7fd --- /dev/null +++ b/modules/nf-core/rhocall/annotate/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "sarscov2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_rhocall.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_rhocall.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_rhocall": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ] + } + ], + "timestamp": "2026-02-18T10:11:48.513471", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2": { + "content": [ + "bc7bf3ee9e8430e064c539eb81e59bf9", + { + "versions_rhocall": [ + [ + "RHOCALL_ANNOTATE", + "rhocall", + "0.5.1" + ] + ] + } + ], + "timestamp": "2026-02-18T10:14:26.928869", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/rhocall/viz/environment.yml b/modules/nf-core/rhocall/viz/environment.yml index 538db5092..8a0fe435e 100644 --- a/modules/nf-core/rhocall/viz/environment.yml +++ b/modules/nf-core/rhocall/viz/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::rhocall=0.5.1" + - bioconda::rhocall=0.5.1 diff --git a/modules/nf-core/rhocall/viz/main.nf b/modules/nf-core/rhocall/viz/main.nf index 4191ef3bc..78c048ede 100644 --- a/modules/nf-core/rhocall/viz/main.nf +++ b/modules/nf-core/rhocall/viz/main.nf @@ -4,8 +4,8 @@ process RHOCALL_VIZ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0': - 'biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7d/7dbf7021085cfea72a20cafffe57fcf47392706d9a433f1143f1e60b389b85ae/data': + 'community.wave.seqera.io/library/rhocall:0.5.1--a7eced77e39d2b82' }" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process RHOCALL_VIZ { output: tuple val(meta), path("${prefix}/${prefix}.bed"), emit: bed tuple val(meta), path("${prefix}/${prefix}.wig"), emit: wig - path "versions.yml" , emit: versions + tuple val("${task.process}"), val("rhocall"), eval("rhocall --version | sed 's/rhocall, version //'"), topic: versions, emit: versions_rhocall when: task.ext.when == null || task.ext.when @@ -32,11 +32,6 @@ process RHOCALL_VIZ { mv ${prefix}/output.bed ${prefix}/${prefix}.bed mv ${prefix}/output.wig ${prefix}/${prefix}.wig - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ stub: @@ -45,10 +40,5 @@ process RHOCALL_VIZ { mkdir ${prefix} touch ${prefix}/${prefix}.bed touch ${prefix}/${prefix}.wig - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' ) - END_VERSIONS """ } diff --git a/modules/nf-core/rhocall/viz/meta.yml b/modules/nf-core/rhocall/viz/meta.yml index 7efcab02a..5911cae46 100644 --- a/modules/nf-core/rhocall/viz/meta.yml +++ b/modules/nf-core/rhocall/viz/meta.yml @@ -10,9 +10,9 @@ tools: homepage: "https://github.com/dnil/rhocall" documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: "" - input: - - meta: type: map @@ -23,6 +23,7 @@ input: type: file description: VCF file pattern: "*.{vcf}" + ontologies: [] - - meta2: type: map description: | @@ -32,9 +33,10 @@ input: type: file description: Input RHO file produced from rhocall pattern: "*.{roh}" + ontologies: [] output: - - bed: - - meta: + bed: + - - meta: type: map description: | Groovy Map containing sample information @@ -43,8 +45,9 @@ output: type: file description: Bed file containing roh calls pattern: "*.{bed}" - - wig: - - meta: + ontologies: [] + wig: + - - meta: type: map description: | Groovy Map containing sample information @@ -53,11 +56,28 @@ output: type: file description: Wig file containing roh calls pattern: "*.{wig}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions_rhocall: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - rhocall: + type: string + description: The name of the tool + - rhocall --version | sed 's/rhocall, version //': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/viz/tests/main.nf.test.snap b/modules/nf-core/rhocall/viz/tests/main.nf.test.snap index cba4067f2..c7c75a230 100644 --- a/modules/nf-core/rhocall/viz/tests/main.nf.test.snap +++ b/modules/nf-core/rhocall/viz/tests/main.nf.test.snap @@ -19,7 +19,11 @@ ] ], "2": [ - "versions.yml:md5,079291120b14dd6b9368dd1cff72518e" + [ + "RHOCALL_VIZ", + "rhocall", + "0.5.1" + ] ], "bed": [ [ @@ -29,8 +33,12 @@ "test.bed:md5,4579710bbd8e1e4449274d261c439891" ] ], - "versions": [ - "versions.yml:md5,079291120b14dd6b9368dd1cff72518e" + "versions_rhocall": [ + [ + "RHOCALL_VIZ", + "rhocall", + "0.5.1" + ] ], "wig": [ [ @@ -42,6 +50,10 @@ ] } ], - "timestamp": "2024-02-05T17:57:24.70125206" + "timestamp": "2026-02-18T10:11:58.070955", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/rhocall/viz/tests/tags.yml b/modules/nf-core/rhocall/viz/tests/tags.yml deleted file mode 100644 index bc2d74a70..000000000 --- a/modules/nf-core/rhocall/viz/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -rhocall/viz: - - "modules/nf-core/rhocall/viz/**" diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 8779a2ce4..88002c962 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -37,10 +37,10 @@ process SVDB_MERGE { if (input_priority) { if (vcfs.collect().size() > 1 && sort_inputs) { // make vcf-priority pairs and sort on VCF name, so priority is also sorted the same - def pairs = vcfs.indices.collect { [vcfs[it], input_priority[it]] } + def pairs = vcfs.indices.collect { index -> [vcfs[index], input_priority[index]] } pairs = pairs.sort { a, b -> a[0].name <=> b[0].name } - vcfs = pairs.collect { it[0] } - priority = pairs.collect { it[1] } + vcfs = pairs.collect { vcf -> vcf[0] } + priority = pairs.collect { pair -> pair[1] } } else { priority = input_priority } @@ -54,7 +54,7 @@ process SVDB_MERGE { } else { // if there's no priority input just sort the vcfs by name if possible - input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { it.name } : vcfs + input = (vcfs.collect().size() > 1 && sort_inputs) ? vcfs.sort { vcf_file -> vcf_file.name } : vcfs } def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" : diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 327ade6e6..cc9cf0b9f 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -51,7 +51,6 @@ workflow ALIGN { ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() - ch_versions = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) @@ -95,7 +94,6 @@ workflow ALIGN { ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics - ch_versions = ch_versions.mix(ALIGN_BWA_BWAMEM2_BWAMEME.out.versions) } else if (val_aligner.equals("sentieon")) { ALIGN_SENTIEON ( ch_genome_bwaindex, @@ -150,8 +148,6 @@ workflow ALIGN { .join(ALIGN_MT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling ch_mtshift_bam_bai_gatksubwf = ALIGN_MT_SHIFT.out.marked_bam .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling - ch_versions = ch_versions - .mix(ALIGN_MT.out.versions, ALIGN_MT_SHIFT.out.versions) } if (val_save_mapped_as_cram) { @@ -167,5 +163,4 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index da40874e9..17de7f7c1 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -22,7 +22,6 @@ workflow ALIGN_MT { val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' main: - ch_versions = channel.empty() if (val_mt_aligner.equals("bwamem2")) { BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, ch_fasta, true) @@ -33,7 +32,6 @@ workflow ALIGN_MT { } else if (val_mt_aligner.equals("bwa")) { BWA_MEM_MT ( ch_fastq, ch_bwaindex, ch_fasta, true ) ch_align = BWA_MEM_MT.out.bam - ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions) } ch_align .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true) @@ -50,5 +48,4 @@ workflow ALIGN_MT { emit: marked_bai = SAMTOOLS_SORT_MT.out.bai // channel: [ val(meta), path(bai) ] marked_bam = SAMTOOLS_SORT_MT.out.bam // channel: [ val(meta), path(bam) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 42a19c489..65e7b1256 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -29,13 +29,10 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { val_sort_threads // integer: [mandatory] default: 4 main: - ch_versions = channel.empty() - // Map, sort, and index if (val_aligner.equals("bwa")) { BWA ( ch_input_reads, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam - ch_versions = ch_versions.mix(BWA.out.versions) } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam @@ -85,5 +82,4 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_genome_snvs.nf b/subworkflows/local/annotate_genome_snvs.nf index e0f30eb91..f5a1ef3e9 100644 --- a/subworkflows/local/annotate_genome_snvs.nf +++ b/subworkflows/local/annotate_genome_snvs.nf @@ -194,9 +194,6 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) - ch_versions = ch_versions.mix(RHOCALL_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(ANNOTATE_RHOCALLVIZ.out.versions) - emit: tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 120f36013..d2a2a52da 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -18,8 +18,6 @@ workflow ANNOTATE_RHOCALLVIZ { ch_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] main: - ch_versions = channel.empty() - ch_vcf_tbi .combine(ch_samples) .map {_meta, vcf, tbi, meta2 -> return [meta2,vcf,tbi]} @@ -54,8 +52,4 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_versions = ch_versions.mix(RHOCALL_VIZ.out.versions) - - emit: - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 997d91530..a6460fd6e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -273,7 +273,6 @@ workflow RAREDISEASE { val_save_mapped_as_cram ) .set { ch_mapped } - ch_versions = ch_versions.mix(ALIGN.out.versions) if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { if (val_mt_subsample_approach.equals("fraction")) { @@ -752,7 +751,6 @@ workflow RAREDISEASE { CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), ch_pedfile ) - ch_versions = ch_versions.mix(PEDDY.out.versions) } /* From 021fb3c6a748a10030aab8cdc6170ea787df7912 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 20:27:24 +0100 Subject: [PATCH 385/872] update modules --- modules.json | 6 +- modules/nf-core/bwamem2/mem/main.nf | 49 ++++---- modules/nf-core/bwamem2/mem/meta.yml | 19 +++ .../nf-core/bwamem2/mem/tests/main.nf.test | 8 +- .../bwamem2/mem/tests/main.nf.test.snap | 109 +++++++++--------- .../ensemblvep/filtervep/environment.yml | 4 +- modules/nf-core/ensemblvep/filtervep/main.nf | 5 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 37 ++++-- .../filtervep/tests/main.nf.test.snap | 14 +++ .../vcf_filter_bcftools_ensemblvep/main.nf | 1 - 10 files changed, 152 insertions(+), 100 deletions(-) diff --git a/modules.json b/modules.json index a2c443e83..1217dc026 100644 --- a/modules.json +++ b/modules.json @@ -82,7 +82,7 @@ }, "bwamem2/mem": { "branch": "master", - "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", + "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a", "installed_by": ["modules"] }, "bwameme/index": { @@ -137,7 +137,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "f50d3c606dbc7e5af367cce070d824b796872ed2", + "git_sha": "09ea5d9fcd6eda714f148e0f3b6a4920b2091f41", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { @@ -583,7 +583,7 @@ }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", - "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", + "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf index d1c0ac8f6..b8ac263b5 100644 --- a/modules/nf-core/bwamem2/mem/main.nf +++ b/modules/nf-core/bwamem2/mem/main.nf @@ -1,25 +1,26 @@ process BWAMEM2_MEM { - tag "$meta.id" + tag "${meta.id}" label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' : - 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e0/e05ce34b46ad42810eb29f74e4e304c0cb592b2ca15572929ed8bbaee58faf01/data' + : 'community.wave.seqera.io/library/bwa-mem2_htslib_samtools:db98f81f55b64113'}" input: tuple val(meta), path(reads) tuple val(meta2), path(index) tuple val(meta3), path(fasta) - val sort_bam + val sort_bam output: - tuple val(meta), path("*.sam") , emit: sam , optional:true - tuple val(meta), path("*.bam") , emit: bam , optional:true - tuple val(meta), path("*.cram") , emit: cram, optional:true - tuple val(meta), path("*.crai") , emit: crai, optional:true - tuple val(meta), path("*.csi") , emit: csi , optional:true + tuple val(meta), path("*.sam"), emit: sam, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true tuple val("${task.process}"), val('bwamem2'), eval('bwa-mem2 version | grep -o -E "[0-9]+(\\.[0-9]+)+"'), emit: versions_bwamem2, topic: versions + tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), emit: versions_samtools, topic: versions when: task.ext.when == null || task.ext.when @@ -31,39 +32,41 @@ process BWAMEM2_MEM { def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" - if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" - + def reference = fasta && extension == "cram" ? "--reference ${fasta}" : "" + if (!fasta && extension == "cram") { + error("Fasta reference is required for CRAM output") + } """ INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` bwa-mem2 \\ mem \\ - $args \\ - -t $task.cpus \\ + ${args} \\ + -t ${task.cpus} \\ \$INDEX \\ - $reads \\ - | samtools $samtools_command $args2 -@ $task.cpus ${reference} -o ${prefix}.${extension} - + ${reads} \\ + | samtools ${samtools_command} ${args2} -@ ${task.cpus} ${reference} -o ${prefix}.${extension} - """ stub: - def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args2 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" - if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" + if (!fasta && extension == "cram") { + error("Fasta reference is required for CRAM output") + } def create_index = "" if (extension == "cram") { create_index = "touch ${prefix}.crai" - } else if (extension == "bam") { + } + else if (extension == "bam") { create_index = "touch ${prefix}.csi" } - """ touch ${prefix}.${extension} ${create_index} diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index bcfd006df..a60d67889 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -129,6 +129,16 @@ output: - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": type: eval description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -140,6 +150,15 @@ topics: - bwa-mem2 version | grep -o -E "[0-9]+(\.[0-9]+)+": type: eval description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools version | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test b/modules/nf-core/bwamem2/mem/tests/main.nf.test index 20e372545..be33a3a7e 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test @@ -50,7 +50,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - fastq, index, fasta, true") { @@ -79,7 +78,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, false") { @@ -111,7 +109,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, true") { @@ -143,7 +140,6 @@ nextflow_process { ).match() } ) } - } test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") { @@ -170,10 +166,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap index 74763935c..06d854b00 100644 --- a/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap @@ -10,52 +10,25 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:27.481278728", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:00.500092" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - "BWAMEM2_MEM", - "bwamem2", - "2.2.1" - ] - ], "bam": [ [ { @@ -89,14 +62,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:54:06.902806102", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:22.004027" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - [fastq1, fastq2], index, fasta, true": { "content": [ @@ -109,14 +89,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:40.483217643", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:25:14.131056" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq, index, fasta, false": { "content": [ @@ -129,14 +116,21 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:02.459481643", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:24:34.624533" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - fastq, index, fasta, true": { "content": [ @@ -149,13 +143,20 @@ "bwamem2", "2.2.1" ] + ], + "versions_samtools": [ + [ + "BWAMEM2_MEM", + "samtools", + "1.22.1" + ] ] } ], + "timestamp": "2026-02-19T11:51:15.170720681", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-09T16:24:47.191245" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index d9ed9b6bd..7e60f7f95 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - # renovate: datasource=conda depName=bioconda/ensembl-vep - - bioconda::ensembl-vep=115.2=pl5321h2a3209d_1 + - bioconda::ensembl-vep=115.2 + - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index dcf0148ef..ed561b023 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_FILTERVEP { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4b/4b5a8c173dc9beaa93effec76b99687fc926b1bd7be47df5d6ce19d7d6b4d6b7/data' - : 'community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" input: tuple val(meta), path(input) @@ -14,6 +14,7 @@ process ENSEMBLVEP_FILTERVEP { output: tuple val(meta), path("*.${extension}"), emit: output tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index 68928cfc8..6c6641597 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_filtervep -description: Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations. +description: Filter variants based on Ensembl Variant Effect Predictor (VEP) + annotations. keywords: - annotation - vcf @@ -12,7 +13,8 @@ tools: or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html - licence: ["Apache-2.0"] + licence: + - "Apache-2.0" identifier: "" input: - - meta: @@ -25,11 +27,11 @@ input: description: VCF/TAB file annotated with vep pattern: "*.{vcf,tab,tsv,txt}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 - feature_file: type: file - description: File containing features on separate lines. To be used with --filter - option. + description: File containing features on separate lines. To be used with + --filter option. ontologies: [] output: output: @@ -43,7 +45,7 @@ output: description: VCF/TAB file pattern: "*.{vcf,tab,txt,tsv}" ontologies: - - edam: http://edamontology.org/format_3475 # TSV + - edam: http://edamontology.org/format_3475 versions_ensemblvep: - - ${task.process}: type: string @@ -52,8 +54,18 @@ output: type: string description: The tool name - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string + type: eval description: The command used to generate the version of the tool + versions_perlmathcdf: + - - ${task.process}: + type: string + description: The process the versions were collected from + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -63,8 +75,17 @@ topics: type: string description: The tool name - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: string + type: eval description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process the versions were collected from + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 1559d7e79..0bd02680e 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -8,6 +8,13 @@ "ensemblvep", "115.2" ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_FILTERVEP", + "perl-math-cdf", + "" + ] ] } ], @@ -26,6 +33,13 @@ "ensemblvep", "115.2" ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_FILTERVEP", + "perl-math-cdf", + "" + ] ] } ], diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf index 33b4d9a8d..00c752502 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf @@ -11,7 +11,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { filter_with_filter_vep // bool: should filter_vep be run main: - ch_versions = channel.empty() ch_tbi = channel.empty() // Since bcftools is likely much faster than filter_vep, From 7d01ba0e09c6270125762ff77a70861a8fe6ad1b Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 20:57:44 +0100 Subject: [PATCH 386/872] update vep --- modules.json | 474 +++++++++++++----- .../ensemblvep/vep/ensemblvep-vep.diff | 61 +-- .../nf-core/ensemblvep/vep/environment.yml | 8 + modules/nf-core/ensemblvep/vep/main.nf | 69 +-- modules/nf-core/ensemblvep/vep/meta.yml | 227 +++++++-- .../nf-core/ensemblvep/vep/tests/main.nf.test | 89 ++++ .../ensemblvep/vep/tests/main.nf.test.snap | 69 +++ .../ensemblvep/vep/tests/nextflow.config | 5 + .../ensemblvep/vep/tests/tab.gz.config | 5 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + 10 files changed, 774 insertions(+), 238 deletions(-) create mode 100644 modules/nf-core/ensemblvep/vep/environment.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config diff --git a/modules.json b/modules.json index 1217dc026..4d01e7c44 100644 --- a/modules.json +++ b/modules.json @@ -8,559 +8,791 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/index": { "branch": "master", "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/mem": { "branch": "master", "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "chromograph": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostseverepli": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/filtervep": { "branch": "master", "git_sha": "09ea5d9fcd6eda714f148e0f3b6a4920b2091f41", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", - "installed_by": ["modules"], + "git_sha": "34505e1fc5e9f4fd641210ca440acff6bd33b842", + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "expansionhunter": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastp": { "branch": "master", "git_sha": "a331ecfd1aa48b2b2298aab23bb4516c800e410b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", - 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"installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -569,25 +801,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index f141ba410..b94671e36 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -1,51 +1,34 @@ Changes in component 'nf-core/ensemblvep/vep' +Changes in 'ensemblvep/vep/environment.yml': +--- modules/nf-core/ensemblvep/vep/environment.yml ++++ modules/nf-core/ensemblvep/vep/environment.yml +@@ -4,5 +4,5 @@ + - conda-forge + - bioconda + dependencies: +- - bioconda::ensembl-vep=115.2 ++ - bioconda::ensembl-vep=110.1 + - bioconda::perl-math-cdf=0.1 + 'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf +++ modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ - conda "bioconda::ensembl-vep=110.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : -- 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : -+ 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container +- ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' +- : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" ++ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' ++ : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" input: tuple val(meta), path(vcf), path(custom_extra_files) -@@ -20,8 +20,8 @@ - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json -- path "*.summary.html" , emit: report -- path "versions.yml" , emit: versions -+ tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true -+ tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - - when: - task.ext.when == null || task.ext.when -@@ -48,11 +48,6 @@ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ - -- -- cat <<-END_VERSIONS > versions.yml -- "${task.process}": -- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') -- END_VERSIONS - """ - - stub: -@@ -63,9 +58,5 @@ - touch ${prefix}.json.gz - touch ${prefix}.summary.html - -- cat <<-END_VERSIONS > versions.yml -- "${task.process}": -- ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') -- END_VERSIONS - """ - } +'modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap' is unchanged +'modules/nf-core/ensemblvep/vep/tests/tab.gz.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/vcf.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/nextflow.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml new file mode 100644 index 000000000..744ccc71c --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::ensembl-vep=110.1 + - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 61da45d06..2e79210f3 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -1,62 +1,67 @@ process ENSEMBLVEP_VEP { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' - conda "bioconda::ensembl-vep=110.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f79e4fcf077482a6f17596bd68f7ba5a8c1972a439a5b7899549bc33baed8c9d/data' : - 'community.wave.seqera.io/library/ensembl-vep:110.0--cf66340b49c82813' }" + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" input: tuple val(meta), path(vcf), path(custom_extra_files) - val genome - val species - val cache_version - path cache + val genome + val species + val cache_version + path cache tuple val(meta2), path(fasta) - path extra_files + path extra_files output: - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json + tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf, optional: true + tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.tab.gz"), emit: tab, optional: true + tuple val(meta), path("${prefix}.json.gz"), emit: json, optional: true tuple val(meta), val("${task.process}"), val('ensemblvep'), path("*.html"), topic: multiqc_files, emit: report, optional: true tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep + tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \\\$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' + def args2 = task.ext.args2 ?: '' + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" - def reference = fasta ? "--fasta $fasta" : "" + def reference = fasta ? "--fasta ${fasta}" : "" + def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : "" """ vep \\ - -i $vcf \\ + -i ${vcf} \\ -o ${prefix}.${file_extension}.gz \\ - $args \\ - $compress_cmd \\ - $reference \\ - --assembly $genome \\ - --species $species \\ + ${args} \\ + ${compress_cmd} \\ + ${reference} \\ + --assembly ${genome} \\ + --species ${species} \\ --cache \\ - --cache_version $cache_version \\ - --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --cache_version ${cache_version} \\ + --dir_cache ${dir_cache} \\ + --fork ${task.cpus} + ${create_index} """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json") ? 'json' : args.contains("--tab") ? 'tab' : 'vcf' + def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : "" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz - touch ${prefix}.summary.html - + echo "" | gzip > ${prefix}.${file_extension}.gz + ${create_index} + touch ${prefix}_summary.html """ } diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847dc..48f025495 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ -name: ENSEMBLVEP_VEP -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +name: ensemblvep_vep +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is + controlled through `task.ext.args`. keywords: - annotation - vcf @@ -12,22 +13,26 @@ tools: or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html - licence: ["Apache-2.0"] + licence: + - "Apache-2.0" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + ontologies: [] + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + ontologies: [] - genome: type: string description: | @@ -44,45 +49,167 @@ input: type: file description: | path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + ontologies: [] - extra_files: type: file description: | path to file(s) needed for plugins (optional) + ontologies: [] output: - - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" - - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" - - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" - - report: - type: file - description: VEP report file - pattern: "*.html" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + vcf: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.vcf.gz: + type: file + description: | + annotated vcf (optional) + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + tbi: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.vcf.gz.tbi: + type: file + description: | + annotated vcf index (optional) + pattern: "*.vcf.gz.tbi" + ontologies: [] + tab: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.tab.gz: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + json: + - - meta: + type: map + description: | + Map with sample information + - ${prefix}.json.gz: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + ontologies: + - edam: http://edamontology.org/format_3989 + report: + - - meta: + type: map + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions_ensemblvep: + - - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: eval + description: The command used to generate the version of the tool + versions_tabix: + - - ${task.process}: + type: string + description: The process + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + versions_perlmathcdf: + - - ${task.process}: + type: string + description: The process + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool +topics: + multiqc_files: + - - meta: + type: string + description: | + Map with sample information + - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "*.html": + type: file + description: VEP report file + pattern: "*.html" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process + - ensemblvep: + type: string + description: The tool name + - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": + type: eval + description: The command used to generate the version of the tool + - - ${task.process}: + type: string + description: The process + - tabix: + type: string + description: The tool name + - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The process + - perl-math-cdf: + type: string + description: The tool name + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': + type: eval + description: The expression to obtain the version of the tool authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 000000000..374f840cf --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + + test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") { + config "./vcf.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.vcf[0][1]).name + ",variantsMD5:" + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + when { + process { + """ + vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() + + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = vep_cache + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + file(process.out.tab[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") + }).match() }, + { assert path(process.out.tab[0][1]).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 000000000..96c18d9cd --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + "test.tab.gz", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_VEP", + "perl-math-cdf", + "0.1" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-06T12:47:57.03116265" + }, + "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { + "content": [ + "test.vcf.gz,variantsMD5:d41d8cd98f00b204e9800998ecf8427e", + "test.vcf.gz.tbi", + { + "versions_ensemblvep": [ + [ + "ENSEMBLVEP_VEP", + "ensemblvep", + "115.2" + ] + ], + "versions_perlmathcdf": [ + [ + "ENSEMBLVEP_VEP", + "perl-math-cdf", + "0.1" + ] + ], + "versions_tabix": [ + [ + "ENSEMBLVEP_VEP", + "tabix", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-06T12:47:34.421995264" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 000000000..8e68fe24a --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,5 @@ +params { + vep_cache_version = "115" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 000000000..40eb03e59 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 000000000..ad8955a37 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} From 50664b36545c9c2f6921c11ad8fbb35c49753433 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Feb 2026 21:00:20 +0100 Subject: [PATCH 387/872] Update modules.json --- modules.json | 469 +++++++++++++-------------------------------------- 1 file changed, 117 insertions(+), 352 deletions(-) diff --git a/modules.json b/modules.json index 4d01e7c44..6e017be96 100644 --- a/modules.json +++ b/modules.json @@ -8,791 +8,564 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - 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"modules" - ] + "installed_by": ["modules"] }, "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upd": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2cytosure": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -801,33 +574,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 452e8d9cbb1b9dc66b6174c08ee52d1de6199ebd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 11:51:15 +0100 Subject: [PATCH 388/872] update snapshots --- conf/test.config | 6 --- conf/test_bam.config | 6 --- conf/test_full.config | 6 --- conf/test_sentieon.config | 6 --- conf/test_singleton.config | 6 --- modules.json | 2 +- modules/nf-core/ensemblvep/filtervep/main.nf | 2 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 4 +- .../filtervep/tests/main.nf.test.snap | 20 ++++----- .../ensemblvep/filtervep/tests/tab.gz.config | 2 +- .../ensemblvep/filtervep/tests/vcf.config | 2 +- .../local/align_MT/tests/main.nf.test.snap | 24 ++--------- tests/default.nf.test.snap | 41 ++++++++++++------- tests/test_bam.nf.test.snap | 34 ++++++++++----- tests/test_singleton.nf.test.snap | 37 +++++++++++------ workflows/raredisease.nf | 7 +++- 16 files changed, 100 insertions(+), 105 deletions(-) diff --git a/conf/test.config b/conf/test.config index dc6dd262e..ee863b84e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '2.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_bam.config b/conf/test_bam.config index 0173ea483..8e90c1a5b 100644 --- a/conf/test_bam.config +++ b/conf/test_bam.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_full.config b/conf/test_full.config index cca2a2463..ff2c306c8 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config index e34a7f9c1..330be5a04 100644 --- a/conf/test_sentieon.config +++ b/conf/test_sentieon.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/conf/test_singleton.config b/conf/test_singleton.config index 180bfc0a1..559e1d6da 100644 --- a/conf/test_singleton.config +++ b/conf/test_singleton.config @@ -16,12 +16,6 @@ process { memory: '15.GB', time: '1.h' ] - - withName: 'ENSEMBLVEP.*' { - container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' } - } } env { diff --git a/modules.json b/modules.json index 6e017be96..9ae2f6592 100644 --- a/modules.json +++ b/modules.json @@ -137,7 +137,7 @@ }, "ensemblvep/filtervep": { "branch": "master", - "git_sha": "09ea5d9fcd6eda714f148e0f3b6a4920b2091f41", + "git_sha": "2e751c119b5e6e9c7ecda7a682e157aabb57a812", "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "ensemblvep/vep": { diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf index ed561b023..d9deff488 100644 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ b/modules/nf-core/ensemblvep/filtervep/main.nf @@ -14,7 +14,7 @@ process ENSEMBLVEP_FILTERVEP { output: tuple val(meta), path("*.${extension}"), emit: output tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf + tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \\\$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index 6c6641597..20239ba91 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -63,7 +63,7 @@ output: - perl-math-cdf: type: string description: The tool name - - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': type: eval description: The expression to obtain the version of the tool topics: @@ -83,7 +83,7 @@ topics: - perl-math-cdf: type: string description: The tool name - - perl -MMath::CDF -e 'print \$Math::CDF::VERSION': + - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': type: eval description: The expression to obtain the version of the tool authors: diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap index 0bd02680e..6ed6da27b 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap @@ -13,16 +13,16 @@ [ "ENSEMBLVEP_FILTERVEP", "perl-math-cdf", - "" + "0.1" ] ] } ], + "timestamp": "2026-02-25T10:48:08.943902", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-07T17:41:53.157363596" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test_ensemblvep_filtervep_tab_gz": { "content": [ @@ -38,15 +38,15 @@ [ "ENSEMBLVEP_FILTERVEP", "perl-math-cdf", - "" + "0.1" ] ] } ], + "timestamp": "2026-02-25T10:48:20.24913", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-07T17:42:10.309756999" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index f1eb11d65..ace089baa 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -7,7 +7,7 @@ process { withName: ENSEMBLVEP_VEP { - ext.args = '--tab' + ext.args = '--tab --offline' ext.prefix = { "${meta.id}_vep" } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index a737274ef..9f34e2a90 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -7,7 +7,7 @@ process { withName: ENSEMBLVEP_VEP { - ext.args = '--vcf' + ext.args = '--vcf --offline' ext.prefix = { "${meta.id}_vep" } } diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 2108f323f..978d90592 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -101,9 +101,6 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] - ], - "2": [ - ], "marked_bai": [ [ @@ -204,13 +201,10 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-02-17T11:24:25.300014158", + "timestamp": "2026-02-20T00:15:07.330482228", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -319,11 +313,6 @@ "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] ], - "2": [ - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" - ], "marked_bai": [ [ { @@ -423,18 +412,13 @@ }, "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" ] - ], - "versions": [ - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c", - "versions.yml:md5,74b9e9afccf630be329f7c6cbd9e077c" ] } ], - "timestamp": "2026-02-06T17:44:37.818378883", + "timestamp": "2026-02-20T00:32:17.118099572", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 565ba07c8..32005ed3c 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -67,10 +67,12 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -127,19 +129,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -308,10 +319,10 @@ "retroseq": 1.5 }, "RHOCALL_ANNOTATE": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "RHOCALL_VIZ": { - "rhocall": "Matplotlib is building the font cache; this may take a moment. 0.5.1" + "rhocall": "0.5.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -658,11 +669,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -708,10 +717,14 @@ "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -1090,10 +1103,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-19T10:01:20.665806391", + "timestamp": "2026-02-24T17:18:24.169571113", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index a8ce102ed..80b1b4ff8 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -68,7 +68,8 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -125,19 +126,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -620,11 +630,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -654,10 +662,14 @@ "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -1020,10 +1032,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-19T15:08:50.558312851", + "timestamp": "2026-02-24T23:58:33.320173721", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 6bdc802f6..7b2ddcf52 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -65,10 +65,12 @@ "bwamem2": "2.2.1" }, "BWAMEM2_MEM": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWAMEM2_MEM_MT": { - "bwamem2": "2.2.1" + "bwamem2": "2.2.1", + "samtools": "1.22.1" }, "BWA_INDEX_GENOME": { "bwa": "0.7.19-r1273" @@ -119,19 +121,28 @@ "deepvariant": "1.9.0" }, "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 110.0 + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 }, "ENSEMBLVEP_ME": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_MT": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SNV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "ENSEMBLVEP_SV": { - "ensemblvep": 110.0 + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 }, "EXPANSIONHUNTER": { "bgzip": "1.22.1", @@ -523,11 +534,9 @@ "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", - "annotate_sv/justhusky_svdbquery_vep.json.gz", - "annotate_sv/justhusky_svdbquery_vep.summary.html", - "annotate_sv/justhusky_svdbquery_vep.tab.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", "call_mobile_elements", "call_mobile_elements/justhusky_mobile_elements.vcf.gz", "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", @@ -559,10 +568,14 @@ "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", "peddy/justhusky.html", "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", "peddy/justhusky.peddy.ped", "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", "peddy/justhusky.vs.html", "pedigree", "pedigree/justhusky.ped", @@ -709,10 +722,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-02-19T18:45:40.125652788", + "timestamp": "2026-02-25T02:33:23.251038469", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} \ No newline at end of file +} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a6460fd6e..418d634b0 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -749,7 +749,8 @@ workflow RAREDISEASE { if (!skip_peddy) { PEDDY ( CALL_SNV.out.genome_vcf.join(CALL_SNV.out.genome_tabix, failOnMismatch:true, failOnDuplicate:true), - ch_pedfile + ch_pedfile.map{ped -> return[[id:"pedigree"], ped]}, + [[:],[]] ) } @@ -884,7 +885,9 @@ workflow RAREDISEASE { if (!skip_peddy) { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.het_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.sex_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) } MULTIQC ( From 7c46ae3b9b5c3fa56acb570592248b9d8e4f060f Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:25:04 +0100 Subject: [PATCH 389/872] update modules --- modules.json | 23 +-- .../picard/addorreplacereadgroups/main.nf | 3 - .../picard/addorreplacereadgroups/meta.yml | 1 - .../addorreplacereadgroups/tests/bam.config | 1 - .../addorreplacereadgroups/tests/cram.config | 1 - .../addorreplacereadgroups/tests/main.nf.test | 23 +-- .../tests/main.nf.test.snap | 37 +--- .../nf-core/picard/collecthsmetrics/main.nf | 43 ++-- .../nf-core/picard/collecthsmetrics/meta.yml | 4 +- .../collecthsmetrics/tests/main.nf.test | 25 +-- .../collecthsmetrics/tests/main.nf.test.snap | 44 ++-- .../picard/collectmultiplemetrics/main.nf | 29 ++- .../picard/collectmultiplemetrics/meta.yml | 4 +- .../collectmultiplemetrics/tests/main.nf.test | 144 +++++++++---- .../tests/main.nf.test.snap | 156 ++++++++++++++- .../nf-core/picard/collectwgsmetrics/main.nf | 33 ++- .../nf-core/picard/collectwgsmetrics/meta.yml | 5 +- .../collectwgsmetrics/tests/main.nf.test | 119 ++++++++--- .../collectwgsmetrics/tests/main.nf.test.snap | 74 ++++++- modules/nf-core/picard/liftovervcf/main.nf | 29 ++- modules/nf-core/picard/liftovervcf/meta.yml | 6 +- .../picard/liftovervcf/tests/main.nf.test | 65 +++--- .../liftovervcf/tests/main.nf.test.snap | 32 ++- modules/nf-core/picard/markduplicates/main.nf | 46 +++-- .../nf-core/picard/markduplicates/meta.yml | 6 +- .../picard/markduplicates/tests/main.nf.test | 6 +- .../markduplicates/tests/main.nf.test.snap | 189 ++++-------------- .../markduplicates/tests/nextflow.config | 2 +- .../nf-core/picard/renamesampleinvcf/main.nf | 26 ++- .../nf-core/picard/renamesampleinvcf/meta.yml | 6 +- .../renamesampleinvcf/tests/main.nf.test | 29 ++- .../renamesampleinvcf/tests/main.nf.test.snap | 30 ++- modules/nf-core/picard/sortvcf/main.nf | 32 +-- modules/nf-core/picard/sortvcf/meta.yml | 5 +- .../nf-core/picard/sortvcf/tests/main.nf.test | 47 +++-- .../picard/sortvcf/tests/main.nf.test.snap | 30 ++- 36 files changed, 793 insertions(+), 562 deletions(-) diff --git a/modules.json b/modules.json index 9ae2f6592..d90a2bf82 100644 --- a/modules.json +++ b/modules.json @@ -286,11 +286,6 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, - "haplocheck": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", @@ -303,7 +298,7 @@ }, "hmtnote/annotate": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"], "patch": "modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff" }, @@ -339,42 +334,42 @@ }, "picard/addorreplacereadgroups": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collecthsmetrics": { "branch": "master", - "git_sha": "976ed20e328a92cb24ab6c63a8983ed31bf48469", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectmultiplemetrics": { "branch": "master", - "git_sha": "74ec93d00bef147da3fb1f2262e8d31c14108f88", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/liftovervcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/renamesampleinvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "picard/sortvcf": { "branch": "master", - "git_sha": "66d5808eaaabd9de8997c4c31a9e8cdd3b56c080", + "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, "qualimap/bamqc": { diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 5ef3b7d8e..7261dc8e2 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -34,7 +34,6 @@ process PICARD_ADDORREPLACEREADGROUPS { } if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ picard \\ -Xmx${avail_mem}M \\ @@ -43,7 +42,6 @@ process PICARD_ADDORREPLACEREADGROUPS { $reference \\ --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} - """ stub: @@ -52,6 +50,5 @@ process PICARD_ADDORREPLACEREADGROUPS { if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.${suffix} - """ } diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index 6c3ed7599..b26a1c508 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -90,7 +90,6 @@ output: - "picard AddOrReplaceReadGroups --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config index 3f37c2fd9..132cc0f7c 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/bam.config @@ -9,5 +9,4 @@ process { "-SM ${meta.id}" ].join(' ').trim()} } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config index 966c14d79..be92e72bb 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/cram.config @@ -9,5 +9,4 @@ process { ].join(' ').trim()} ext.suffix = { "cram" } } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test index 45729f3b5..5586ab469 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test @@ -27,14 +27,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.bam[0][1]).name, - file(process.out.bai[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.bam[0][1]).name, + file(process.out.bai[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("homo_sapiens - cram") { @@ -58,19 +56,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.cram[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - }, + file(process.out.cram[0][1]).name, + process.out.findAll { key, val -> key.startsWith("versions") } + ).match()} ) } - } test("sarscov2 - bam - stub") { config "./bam.config" options "-stub" - when { process { """ @@ -84,10 +79,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } - } diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index d2a99ee27..7ec99fbb5 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -12,36 +12,15 @@ ] } ], + "timestamp": "2026-02-02T09:36:16.966842212", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:16.966842212" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - - }, - "null.replaced.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - "PICARD_ADDORREPLACEREADGROUPS", - "picard", - "3.4.0" - ] - ], "bai": [ ], @@ -65,11 +44,11 @@ ] } ], + "timestamp": "2026-02-19T17:34:40.3572859", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:29.861163004" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam": { "content": [ @@ -85,10 +64,10 @@ ] } ], + "timestamp": "2026-02-02T09:36:00.935196996", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T09:36:00.935196996" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index b13871f8c..96045b5dd 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -1,22 +1,22 @@ process PICARD_COLLECTHSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') tuple val(meta2), path(ref) tuple val(meta3), path(ref_fai) tuple val(meta4), path(ref_dict) - tuple val(meta5), path(ref_gzi) // ref_gzi only required if reference is gzipped + tuple val(meta5), path(ref_gzi) output: - tuple val(meta), path("*_metrics") , emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*_metrics"), emit: metrics + tuple val("${task.process}"), val('picard'), eval("picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -28,41 +28,38 @@ process PICARD_COLLECTHSMETRICS { def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } def bait_interval_list = bait_intervals def bait_intervallist_cmd = "" - if (bait_intervals =~ /.(bed|bed.gz)$/){ + if (bait_intervals =~ /.(bed|bed.gz)$/) { bait_interval_list = bait_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") bait_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${bait_intervals} --OUTPUT ${bait_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } def target_interval_list = target_intervals def target_intervallist_cmd = "" - if (target_intervals =~ /.(bed|bed.gz)$/){ + if (target_intervals =~ /.(bed|bed.gz)$/) { target_interval_list = target_intervals.toString().replaceAll(/.(bed|bed.gz)$/, ".interval_list") target_intervallist_cmd = "picard -Xmx${avail_mem}M BedToIntervalList --INPUT ${target_intervals} --OUTPUT ${target_interval_list} --SEQUENCE_DICTIONARY ${ref_dict} --TMP_DIR ." } - - """ - - $bait_intervallist_cmd - $target_intervallist_cmd + ${bait_intervallist_cmd} + ${target_intervallist_cmd} picard \\ -Xmx${avail_mem}M \\ CollectHsMetrics \\ - $args \\ - $reference \\ - --BAIT_INTERVALS $bait_interval_list \\ - --TARGET_INTERVALS $target_interval_list \\ - --INPUT $bam \\ + ${args} \\ + ${reference} \\ + --BAIT_INTERVALS ${bait_interval_list} \\ + --TARGET_INTERVALS ${target_interval_list} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics - """ stub: diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index a21aa6ecd..89bc502c9 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -106,7 +106,7 @@ output: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -118,7 +118,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectHsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test index 07a9ccf42..d73661111 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test @@ -40,11 +40,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - gzippedfa") { @@ -78,17 +76,13 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - stub") { - options "-stub" - when { process { """ @@ -110,10 +104,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } test("sarscov2 - bam - nofasta") { @@ -147,11 +140,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - bed") { @@ -186,11 +177,9 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } test("sarscov2 - bam - samebed") { @@ -225,10 +214,8 @@ nextflow_process { size, lines, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } - } } diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 74d9441fa..43385314a 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -115,31 +115,15 @@ ] } ], + "timestamp": "2026-01-05T17:03:29.566021877", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:29.566021877" + } }, "sarscov2 - bam - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "PICARD_COLLECTHSMETRICS", - "picard", - "3.4.0" - ] - ], "metrics": [ [ { @@ -158,11 +142,11 @@ ] } ], + "timestamp": "2026-02-19T17:36:03.822502867", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:13.333276975" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam - gzippedfa": { "content": [ @@ -280,11 +264,11 @@ ] } ], + "timestamp": "2026-01-05T17:03:04.382110367", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:03:04.382110367" + } }, "sarscov2 - bam - samebed": { "content": [ @@ -402,11 +386,11 @@ ] } ], + "timestamp": "2026-01-05T17:13:22.872920293", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:22.872920293" + } }, "sarscov2 - bam": { "content": [ @@ -524,11 +508,11 @@ ] } ], + "timestamp": "2026-01-05T17:02:47.615784738", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:02:47.615784738" + } }, "sarscov2 - bam - bed": { "content": [ @@ -646,10 +630,10 @@ ] } ], + "timestamp": "2026-01-05T17:13:02.812282052", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-05T17:13:02.812282052" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index 3c6152e5f..9de927e69 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -1,21 +1,21 @@ process PICARD_COLLECTMULTIPLEMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: - tuple val(meta) , path(bam), path(bai) + tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val(meta), path("*.pdf") , emit: pdf, optional: true - tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val(meta), path("*.pdf"), emit: pdf, optional: true + tuple val("${task.process}"), val('picard'), eval("picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,19 +26,19 @@ process PICARD_COLLECTMULTIPLEMETRICS { def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectMultipleMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectMultipleMetrics \\ - $reference - + ${reference} """ stub: @@ -54,6 +54,5 @@ process PICARD_COLLECTMULTIPLEMETRICS { touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics - """ } diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 1ea47244c..213d600be 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -81,7 +81,7 @@ output: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool @@ -93,7 +93,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectMultipleMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test index 08456941b..0037acab6 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test @@ -16,16 +16,15 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [[id:'genome'],[]] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] """ } } @@ -37,8 +36,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -49,13 +47,12 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [[id:'genome'],[]] + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] input[2] = [[id:'genome'],[]] - """ } } @@ -67,8 +64,7 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -79,19 +75,18 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] """ } } @@ -103,10 +98,89 @@ nextflow_process { process.out.metrics[0][1].collect { file(it).name }.toSorted(), process.out.pdf[0][1].collect { file(it).name }.toSorted(), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} + ) + } + } + + test("test-picard-collectmultiplemetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectmultiplemetrics-nofasta - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [[id:'genome'],[]] + input[2] = [[id:'genome'],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } + test("test-picard-collectmultiplemetrics-cram - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index 1acf37765..393ed1003 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -25,11 +25,107 @@ ] } ], + "timestamp": "2026-02-02T10:22:21.230301646", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:22:21.230301646" + } + }, + "test-picard-collectmultiplemetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:38.701455244", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectmultiplemetrics-nofasta - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:48.923918624", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -57,11 +153,11 @@ ] } ], + "timestamp": "2026-02-02T10:23:52.23446844", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:52.23446844" + } }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -89,10 +185,58 @@ ] } ], + "timestamp": "2026-02-02T10:23:27.387621193", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T10:23:27.387621193" + } + }, + "test-picard-collectmultiplemetrics-cram - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "pdf": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTMULTIPLEMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:32:57.11686549", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index aa77100c7..a5db512c0 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -1,51 +1,50 @@ process PICARD_COLLECTWGSMETRICS { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) - path intervallist + path intervallist output: tuple val(meta), path("*_metrics"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 - def interval = intervallist ? "--INTERVALS ${intervallist}" : '' + def interval = intervallist ? "--INTERVALS ${intervallist}" : '' if (!task.memory) { - log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ CollectWgsMetrics \\ - $args \\ - --INPUT $bam \\ + ${args} \\ + --INPUT ${bam} \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --REFERENCE_SEQUENCE ${fasta} \\ - $interval - + ${interval} """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.CollectWgsMetrics.coverage_metrics - """ } diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index c59811d58..c5afe2e7c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -76,10 +76,9 @@ output: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -88,7 +87,7 @@ topics: - picard: type: string description: The tool name - - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard CollectWgsMetrics --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test index d6a60e6bf..1bda5980a 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test @@ -16,19 +16,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] """ } } @@ -37,10 +36,9 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } @@ -51,19 +49,18 @@ nextflow_process { process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - [] - ] - input[1] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) """ } } @@ -72,12 +69,70 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), + file(process.out.metrics[0][1]).text.contains('coverage high_quality_coverage_count'), process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-collectwgsmetrics - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } + + test("test-picard-collectwgsmetrics-with-interval - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + [] + ] + input[1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index 375c2ef9d..79f1145ff 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -1,7 +1,34 @@ { + "test-picard-collectwgsmetrics-with-interval - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:35:04.636691319", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-collectwgsmetrics-with-interval": { "content": [ - true, + false, { "versions_picard": [ [ @@ -12,15 +39,42 @@ ] } ], + "timestamp": "2026-02-20T10:34:45.059411647", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "test-picard-collectwgsmetrics - stub": { + "content": [ + { + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CollectWgsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_picard": [ + [ + "PICARD_COLLECTWGSMETRICS", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:34:54.347278951", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:55.091876466" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-collectwgsmetrics": { "content": [ - true, + false, { "versions_picard": [ [ @@ -31,10 +85,10 @@ ] } ], + "timestamp": "2026-02-20T10:34:25.744978033", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T14:52:11.334274481" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index 186afc50f..da025c9b6 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -1,11 +1,11 @@ process PICARD_LIFTOVERVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(input_vcf) @@ -14,9 +14,9 @@ process PICARD_LIFTOVERVCF { tuple val(meta4), path(chain) output: - tuple val(meta), path("*.lifted.vcf.gz") , emit: vcf_lifted + tuple val(meta), path("*.lifted.vcf.gz"), emit: vcf_lifted tuple val(meta), path("*.unlifted.vcf.gz"), emit: vcf_unlifted - tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -26,21 +26,21 @@ process PICARD_LIFTOVERVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard LiftoverVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } """ picard \\ -Xmx${avail_mem}M \\ LiftoverVcf \\ - $args \\ - --INPUT $input_vcf \\ + ${args} \\ + --INPUT ${input_vcf} \\ --OUTPUT ${prefix}.lifted.vcf.gz \\ - --CHAIN $chain \\ + --CHAIN ${chain} \\ --REJECT ${prefix}.unlifted.vcf.gz \\ - --REFERENCE_SEQUENCE $fasta - + --REFERENCE_SEQUENCE ${fasta} """ stub: @@ -48,6 +48,5 @@ process PICARD_LIFTOVERVCF { """ echo | gzip > ${prefix}.lifted.vcf.gz echo | gzip > ${prefix}.unlifted.vcf.gz - """ } diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index bc4baf2da..24253b41f 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -79,10 +79,9 @@ output: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -91,10 +90,9 @@ topics: - picard: type: string description: The tool name - - "picard LiftoverVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard LiftoverVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test b/modules/nf-core/picard/liftovervcf/tests/main.nf.test index d0e35b45d..8317403ca 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test @@ -17,18 +17,17 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -37,33 +36,31 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf_lifted[0][1]).vcf.summary, - path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, + path(process.out.vcf_lifted[0][1]).vcf.summary, + path(process.out.vcf_unlifted[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } - test("test-picard-liftovervcf-stubs") { - options '-stub' + test("test-picard-liftovervcf - stub") { + options "-stub" when { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[3] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[3] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.chain.gz', checkIfExists: true) + ] """ } } @@ -71,14 +68,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.vcf_lifted[0][1]).name, - file(process.out.vcf_unlifted[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } - } diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index 9bb324bbe..c17b69349 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -1,9 +1,23 @@ { - "test-picard-liftovervcf-stubs": { + "test-picard-liftovervcf - stub": { "content": [ - "test.lifted.vcf.gz", - "test.unlifted.vcf.gz", { + "vcf_lifted": [ + [ + { + "id": "test" + }, + "test.lifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_unlifted": [ + [ + { + "id": "test" + }, + "test.unlifted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], "versions_picard": [ [ "PICARD_LIFTOVERVCF", @@ -13,11 +27,11 @@ ] } ], + "timestamp": "2026-02-20T10:38:09.430447871", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:41:30.546426132" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-picard-liftovervcf": { "content": [ @@ -33,10 +47,10 @@ ] } ], + "timestamp": "2026-02-02T11:40:19.064084452", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:40:19.064084452" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 10621e019..17bcf27ba 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -1,11 +1,11 @@ process PICARD_MARKDUPLICATES { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(reads) @@ -13,11 +13,11 @@ process PICARD_MARKDUPLICATES { tuple val(meta3), path(fai) output: - tuple val(meta), path("*.bam") , emit: bam, optional: true - tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.metrics.txt"), emit: metrics - tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -25,37 +25,39 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ picard \\ -Xmx${avail_mem}M \\ MarkDuplicates \\ - $args \\ - --INPUT $reads \\ + ${args} \\ + --INPUT ${reads} \\ --OUTPUT ${prefix}.${suffix} \\ - $reference \\ - --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - + ${reference} \\ + --METRICS_FILE ${prefix}.metrics.txt """ stub: def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.suffix ?: "${reads.getExtension()}" - if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + if ("${reads}" == "${prefix}.${suffix}") { + error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!") + } """ touch ${prefix}.${suffix} touch ${prefix}.${suffix}.bai - touch ${prefix}.MarkDuplicates.metrics.txt - + touch ${prefix}.metrics.txt """ } diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 0ec99c7f1..aa0ddbdba 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -100,10 +100,9 @@ output: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -112,10 +111,9 @@ topics: - picard: type: string description: The tool name - - "picard MarkDuplicates --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard MarkDuplicates --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index e18723be0..4d0064531 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -114,7 +114,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -137,7 +137,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 848013849..4ea479a32 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -2,50 +2,13 @@ "sarscov2 [sorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -54,7 +17,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -66,7 +29,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -78,59 +41,22 @@ ] } ], + "timestamp": "2026-02-19T17:43:13.544887277", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:02.077382134" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam] - stub": { "content": [ { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -139,7 +65,7 @@ "id": "test", "single_end": false }, - "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "cram": [ @@ -151,7 +77,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -163,18 +89,18 @@ ] } ], + "timestamp": "2026-02-19T17:43:06.193033248", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:49.985589186" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [unsorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -187,18 +113,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:40.574463587", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:42:49.704752548" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [sorted bam]": { "content": [ - "test.marked.bam", + "test.md.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.md.bam --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -211,18 +137,18 @@ ] } ], + "timestamp": "2026-02-19T17:42:49.374645492", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:44:17.407572621" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram]": { "content": [ - "test.marked.cram", + "test.md.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.md.cram --METRICS_FILE test.md.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], { @@ -235,59 +161,22 @@ ] } ], + "timestamp": "2026-02-19T17:42:59.07843756", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:45:33.412603893" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "homo_sapiens [cram] - stub": { "content": [ { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "PICARD_MARKDUPLICATES", - "picard", - "3.4.0" - ] - ], "bai": [ [ { "id": "test", "single_end": false }, - "test.marked.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam": [ @@ -299,7 +188,7 @@ "id": "test", "single_end": false }, - "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.cram:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "metrics": [ @@ -308,7 +197,7 @@ "id": "test", "single_end": false }, - "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_picard": [ @@ -320,10 +209,10 @@ ] } ], + "timestamp": "2026-02-19T17:43:20.676018462", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:46:18.599127485" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config index 02818dd6e..f8dd0f1ca 100644 --- a/modules/nf-core/picard/markduplicates/tests/nextflow.config +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -1,6 +1,6 @@ process { withName: PICARD_MARKDUPLICATES { - ext.prefix = { "${meta.id}.marked" } + ext.prefix = { "${meta.id}.md" } ext.args = '--ASSUME_SORT_ORDER queryname' } } diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 6b02886bf..801ed9f26 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -1,19 +1,18 @@ - process PICARD_RENAMESAMPLEINVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -24,19 +23,18 @@ process PICARD_RENAMESAMPLEINVCF { def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard RenameSampleInVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - RenameSampleInVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ + RenameSampleInVcf \\ + --INPUT ${vcf} \\ --OUTPUT ${prefix}_renam.vcf.gz \\ - $extended_args - + ${extended_args} """ stub: diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 762780bd0..2b757b19d 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -44,10 +44,9 @@ output: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -56,10 +55,9 @@ topics: - picard: type: string description: The tool name - - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard RenameSampleInVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test index 42e127a01..3e59c23bc 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test @@ -16,9 +16,8 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] """ } } @@ -27,12 +26,30 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).vcf.variantsMD5, + path(process.out.vcf[0][1]).vcf.variantsMD5, process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-renamesampleinvcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index 86626ce81..2b6367ae7 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -12,10 +12,36 @@ ] } ], + "timestamp": "2026-02-02T15:51:56.010473", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T15:51:56.010473" + } + }, + "test-picard-renamesampleinvcf - stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_renam.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_RENAMESAMPLEINVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:39:17.132250662", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 782deba2b..92286e8a7 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -1,11 +1,11 @@ process PICARD_SORTVCF { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' : - 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' + : 'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6'}" input: tuple val(meta), path(vcf) @@ -14,7 +14,7 @@ process PICARD_SORTVCF { output: tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'"), topic: versions, emit: versions_picard + tuple val("${task.process}"), val('picard'), eval("picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'"), topic: versions, emit: versions_picard when: task.ext.when == null || task.ext.when @@ -22,23 +22,23 @@ process PICARD_SORTVCF { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def seq_dict = dict ? "--SEQUENCE_DICTIONARY $dict" : "" - def reference = fasta ? "--REFERENCE_SEQUENCE $fasta" : "" + def seq_dict = dict ? "--SEQUENCE_DICTIONARY ${dict}" : "" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { - log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() + log.info('[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.') + } + else { + avail_mem = (task.memory.mega * 0.8).intValue() } - """ picard \\ - SortVcf \\ -Xmx${avail_mem}M \\ - --INPUT $vcf \\ - $args \\ - $seq_dict \\ - $reference \\ + SortVcf \\ + --INPUT ${vcf} \\ + ${args} \\ + ${seq_dict} \\ + ${reference} \\ --OUTPUT ${prefix}_sorted.vcf.gz """ diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index f6e327ff9..6cbe6b724 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -62,10 +62,9 @@ output: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool - topics: versions: - - ${task.process}: @@ -74,7 +73,7 @@ topics: - picard: type: string description: The tool name - - "picard SortVcf --version 2>&1 | sed -n 's/^Version:*//p'": + - "picard SortVcf --version 2>&1 | sed -n 's/.*Version://p'": type: string description: The command used to generate the version of the tool authors: diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test b/modules/nf-core/picard/sortvcf/tests/main.nf.test index e8ef67501..a594b011b 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test @@ -16,15 +16,14 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ [ id:'genome' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - ] - + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] """ } } @@ -33,12 +32,36 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).linesGzip[3..7], + path(process.out.vcf[0][1]).linesGzip[3..7], process.out.findAll { key, val -> key.startsWith("versions") } - ).match() - } + ).match()} ) } } + test("test-picard-sortvcf stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + input[1] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() } + ) + } + } } diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index 9db773653..25dcb7ef6 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -1,4 +1,30 @@ { + "test-picard-sortvcf stub": { + "content": [ + { + "vcf": [ + [ + { + "id": "test" + }, + "test_sorted.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_picard": [ + [ + "PICARD_SORTVCF", + "picard", + "3.4.0" + ] + ] + } + ], + "timestamp": "2026-02-20T10:40:26.218029661", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "test-picard-sortvcf": { "content": [ [ @@ -18,10 +44,10 @@ ] } ], + "timestamp": "2026-02-02T11:47:50.61817621", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-02-02T11:47:50.61817621" + } } } \ No newline at end of file From a86d5a25b622dea264a1fd32cac8a09b1e8a59fe Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:11:33 +0100 Subject: [PATCH 390/872] update modules --- modules.json | 2 +- modules/nf-core/cadd/environment.yml | 2 + modules/nf-core/cadd/main.nf | 46 +++++++-------- modules/nf-core/cadd/meta.yml | 59 +++++++++++++++----- modules/nf-core/cadd/tests/main.nf.test | 37 ++++++++++++ modules/nf-core/cadd/tests/main.nf.test.snap | 48 ++++++++++++++++ 6 files changed, 154 insertions(+), 40 deletions(-) create mode 100644 modules/nf-core/cadd/tests/main.nf.test create mode 100644 modules/nf-core/cadd/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index d90a2bf82..dcf570b57 100644 --- a/modules.json +++ b/modules.json @@ -97,7 +97,7 @@ }, "cadd": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "1d40acd9f567cea7ccdd4b6211310d4e94356357", "installed_by": ["modules"] }, "cat/cat": { diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml index 4477e16e5..d98de6522 100644 --- a/modules/nf-core/cadd/environment.yml +++ b/modules/nf-core/cadd/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf index 0af87f6e5..94aa19796 100644 --- a/modules/nf-core/cadd/main.nf +++ b/modules/nf-core/cadd/main.nf @@ -1,53 +1,47 @@ process CADD { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1' - containerOptions { - (workflow.containerEngine == 'singularity') ? + containerOptions "${ prescored_dir ? + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? + "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -B ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : + "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -v ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" : - "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" - } + "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" }" input: tuple val(meta), path(vcf) - path(annotation_dir) + tuple val(meta2), path(annotation_dir) + tuple val(meta3), path(prescored_dir) output: - tuple val(meta), path("*.tsv.gz"), emit: tsv - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.tsv.gz"), emit: tsv + tuple val("${task.process}"), val("cadd"), val("1.6.post1"), emit: versions_cadd, topic: versions + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ + export XDG_CACHE_HOME=\$PWD/snakemake_cache + mkdir -p \$XDG_CACHE_HOME + cadd.sh \\ -o ${prefix}.tsv.gz \\ - $args \\ - $vcf - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cadd: $VERSION - END_VERSIONS + ${args} \\ + ${vcf} """ stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.tsv.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - cadd: $VERSION - END_VERSIONS + echo "" | gzip > ${prefix}.tsv.gz """ } diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml index 751bea454..b70cb7d9c 100644 --- a/modules/nf-core/cadd/meta.yml +++ b/modules/nf-core/cadd/meta.yml @@ -1,6 +1,6 @@ name: "cadd" -description: CADD is a tool for scoring the deleteriousness of single nucleotide variants - as well as insertion/deletions variants in the human genome. +description: CADD is a tool for scoring the deleteriousness of single nucleotide + variants as well as insertion/deletions variants in the human genome. keywords: - cadd - annotate @@ -25,28 +25,61 @@ input: type: file description: Input file for annotation in vcf or vcf.gz format pattern: "*.{vcf,vcf.gz}" - - - annotation_dir: - type: file + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - annotation_dir: + type: directory description: | Path to folder containing the vcf files with precomputed CADD scores. This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. - pattern: "*.{vcf,vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - prescored_dir: + type: directory + description: | + Path to folder containing prescored files. + This folder contains the uncompressed files that would otherwise be in data/prescored/${GENOME_BUILD}_${VERSION}/ folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. output: - - tsv: - - meta: + tsv: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tsv.gz": + - ${prefix}.tsv.gz: type: file description: Annotated tsv file pattern: "*.{tsv,tsv.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3475 + versions_cadd: + - - ${task.process}: + type: string + description: The name of the process + - cadd: + type: string + description: The name of the tool + - 1.6.post1: + type: string + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - cadd: + type: string + description: The name of the tool + - 1.6.post1: + type: string + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cadd/tests/main.nf.test b/modules/nf-core/cadd/tests/main.nf.test new file mode 100644 index 000000000..cc36d0cdd --- /dev/null +++ b/modules/nf-core/cadd/tests/main.nf.test @@ -0,0 +1,37 @@ +nextflow_process { + + name "Test Process CADD" + + script "../main.nf" + process "CADD" + + tag "modules" + tag "modules_nfcore" + tag "cadd" + + test("test_cadd - stub") { + options '-stub' + when { + + process { + """ + input[0] = [ + [id:'test',single_end:false],// meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf',checkIfExists:true) + ] + input[1] = Channel.from("\$PWD").map { dir -> [ [ id: dir ], dir ] } + input[2] = Channel.from("/").map { dir -> [ [ id: dir ], dir ] } + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out, + process.out.versions.collect{ path(it).yaml } + ).match() } + ) + } + } +} diff --git a/modules/nf-core/cadd/tests/main.nf.test.snap b/modules/nf-core/cadd/tests/main.nf.test.snap new file mode 100644 index 000000000..de4c6dc7c --- /dev/null +++ b/modules/nf-core/cadd/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test_cadd - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CADD", + "cadd", + "1.6.post1" + ] + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_cadd": [ + [ + "CADD", + "cadd", + "1.6.post1" + ] + ] + }, + [ + + ] + ], + "timestamp": "2026-02-19T20:06:20.885977", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 3efe9fe605f33ced8498ae2a701bc94a551cd8f1 Mon Sep 17 00:00:00 2001 From: ramprasadn <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Feb 2026 14:36:58 +0100 Subject: [PATCH 391/872] add haplocheck back --- modules.json | 5 + modules/nf-core/haplocheck/environment.yml | 7 ++ modules/nf-core/haplocheck/main.nf | 43 ++++++++ modules/nf-core/haplocheck/meta.yml | 65 ++++++++++++ modules/nf-core/haplocheck/tests/main.nf.test | 56 ++++++++++ .../haplocheck/tests/main.nf.test.snap | 100 ++++++++++++++++++ 6 files changed, 276 insertions(+) create mode 100644 modules/nf-core/haplocheck/environment.yml create mode 100644 modules/nf-core/haplocheck/main.nf create mode 100644 modules/nf-core/haplocheck/meta.yml create mode 100644 modules/nf-core/haplocheck/tests/main.nf.test create mode 100644 modules/nf-core/haplocheck/tests/main.nf.test.snap diff --git a/modules.json b/modules.json index dcf570b57..3417c5ac5 100644 --- a/modules.json +++ b/modules.json @@ -286,6 +286,11 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, + "haplocheck": { + "branch": "master", + "git_sha": "dbc43f924a7410a2b828f2a022305f1d6e71ed84", + "installed_by": ["modules"] + }, "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml new file mode 100644 index 000000000..d74b4d7ed --- /dev/null +++ b/modules/nf-core/haplocheck/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplocheck/main.nf b/modules/nf-core/haplocheck/main.nf new file mode 100644 index 000000000..443156309 --- /dev/null +++ b/modules/nf-core/haplocheck/main.nf @@ -0,0 +1,43 @@ +process HAPLOCHECK { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/haplocheck:1.3.3--h4a94de4_0': + 'biocontainers/haplocheck:1.3.3--h4a94de4_0' }" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("*.txt") , emit: txt + tuple val(meta), path("*.html"), emit: html + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + haplocheck --raw --out $prefix $vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.raw.txt + touch ${prefix}.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml new file mode 100644 index 000000000..692f7c5d7 --- /dev/null +++ b/modules/nf-core/haplocheck/meta.yml @@ -0,0 +1,65 @@ +name: "haplocheck" +description: | + Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing + the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides + users a graphical report to investigate the contamination further. Internally, it uses the + Haplogrep tool, that supports rCRS and RSRS mitochondrial versions. +keywords: + - mitochondrial + - mtDNA + - contamination +tools: + - "haplocheck": + description: "Detects in-sample contamination in mtDNA or WGS sequencing studies + by analyzing the mitochondrial content." + homepage: "https://github.com/genepi/haplocheck" + documentation: "https://github.com/genepi/haplocheck" + tool_dev_url: "https://github.com/genepi/haplocheck" + doi: 10.1101/gr.256545.119 + licence: ["MIT"] + identifier: biotools:haplocheck +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + ontologies: [] +output: + txt: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Raw report in txt format + pattern: "*.{txt}" + ontologies: [] + html: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Haplocheck HTML report + pattern: "*.{html}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML +authors: + - "@lmtani" +maintainers: + - "@lmtani" diff --git a/modules/nf-core/haplocheck/tests/main.nf.test b/modules/nf-core/haplocheck/tests/main.nf.test new file mode 100644 index 000000000..8957d02e2 --- /dev/null +++ b/modules/nf-core/haplocheck/tests/main.nf.test @@ -0,0 +1,56 @@ + +nextflow_process { + + name "Test Process HAPLOCHECK" + script "../main.nf" + process "HAPLOCHECK" + + tag "modules" + tag "modules_nfcore" + tag "haplocheck" + + test("test-haplocheck") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-haplocheck-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/haplocheck/tests/main.nf.test.snap b/modules/nf-core/haplocheck/tests/main.nf.test.snap new file mode 100644 index 000000000..abe1eab56 --- /dev/null +++ b/modules/nf-core/haplocheck/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "test-haplocheck-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ], + "html": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:41:40.703528" + }, + "test-haplocheck": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.html:md5,59d69052c86edff0301816956eaf4d5f" + ] + ], + "2": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ], + "html": [ + [ + { + "id": "test" + }, + "test.html:md5,59d69052c86edff0301816956eaf4d5f" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.raw.txt:md5,69f4e5b28a59b97fc19eb8e8b650d9d5" + ] + ], + "versions": [ + "versions.yml:md5,ff75b052ef552a4c9cecf3f60403af9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:43:05.761086" + } +} \ No newline at end of file From c31204a6068582e580baffcbab218ab018897e08 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Feb 2026 13:23:52 +0100 Subject: [PATCH 392/872] update_snapshots --- tests/default.nf.test.snap | 17 ++++++++++++----- tests/test_bam.nf.test.snap | 11 +++++++++-- tests/test_singleton.nf.test.snap | 11 ++++++++--- 3 files changed, 29 insertions(+), 10 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 32005ed3c..e96bb52a5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -228,6 +228,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -505,19 +508,19 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.MarkDuplicates.metrics.txt", "alignment/earlycasualcaiman_sorted_md.bam", "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.MarkDuplicates.metrics.txt", "alignment/slowlycivilbuck_sorted_md.bam", "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -706,6 +709,10 @@ "fastqc/slowlycivilbuck_LNUMBER2", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", + "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", + "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1103,10 +1110,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-24T17:18:24.169571113", + "timestamp": "2026-02-27T12:45:44.180676148", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 80b1b4ff8..677a2294a 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -219,6 +219,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -651,6 +654,10 @@ "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "haplocheck", + "haplocheck/earlycasualcaiman.raw.txt", + "haplocheck/hugelymodelbat.raw.txt", + "haplocheck/slowlycivilbuck.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1032,10 +1039,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-02-24T23:58:33.320173721", + "timestamp": "2026-02-27T12:52:01.429826076", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 7b2ddcf52..92b111f83 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -220,6 +220,9 @@ "GLNEXUS": { "glnexus": "1.4.1" }, + "HAPLOCHECK_MT": { + "haplocheck": "1.3.3" + }, "HAPLOGREP3_CLASSIFY_MT": { "haplogrep3": "3.2.2" }, @@ -488,9 +491,9 @@ "alignment", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.MarkDuplicates.metrics.txt", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -559,6 +562,8 @@ "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "haplocheck", + "haplocheck/hugelymodelbat.raw.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -722,10 +727,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-02-25T02:33:23.251038469", + "timestamp": "2026-02-27T12:55:52.928711503", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } } -} +} \ No newline at end of file From e6ab91d0ad444af7bcf9abe2595206fbbdcd918d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Feb 2026 15:52:45 +0100 Subject: [PATCH 393/872] update subworkflow snapshots --- .../local/align_MT/tests/main.nf.test.snap | 52 +++++++++---------- .../tests/main.nf.test.snap | 8 +-- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 978d90592..53cd47acd 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,aa29752265d70e5c2ed10de503fa8b33" ], [ { @@ -33,7 +33,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,011888be5d5c6e77b48d8b8fd81155a4" ], [ { @@ -49,7 +49,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,9934e5e180a1760490bc36aaf23ec10c" ] ], "1": [ @@ -67,7 +67,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d4ea71dac6170a728c27457e4d042a17" ], [ { @@ -83,7 +83,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,eba491066ead408a1cdfd13fd353fc1d" ], [ { @@ -99,7 +99,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,3263f88b4f8987f16b81a5980bf26aad" ] ], "marked_bai": [ @@ -117,7 +117,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,f4c756c6781d6af030fbd473fff01fe0" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,aa29752265d70e5c2ed10de503fa8b33" ], [ { @@ -133,7 +133,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,1cd5ba90856d1a311477ff6f0159e734" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,011888be5d5c6e77b48d8b8fd81155a4" ], [ { @@ -149,7 +149,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,65af456a3e4ba9b3b5153a921aa3189d" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,9934e5e180a1760490bc36aaf23ec10c" ] ], "marked_bam": [ @@ -167,7 +167,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,751b43aa7e76f1e5e4915069dce08b95" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d4ea71dac6170a728c27457e4d042a17" ], [ { @@ -183,7 +183,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,c3f5d414669eb47dcca97528c1700786" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,eba491066ead408a1cdfd13fd353fc1d" ], [ { @@ -199,12 +199,12 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,dce10a8f97e471f907785244842eae51" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,3263f88b4f8987f16b81a5980bf26aad" ] ] } ], - "timestamp": "2026-02-20T00:15:07.330482228", + "timestamp": "2026-02-27T15:43:54.097536585", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -228,7 +228,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,bc1e2296080bc0d6d9878d3784892ee0" ], [ { @@ -244,7 +244,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,8df5c65448c3c2f20cd8f574182f5593" ], [ { @@ -260,7 +260,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,de7d63cfa5735162d2274d877bf0b85b" ] ], "1": [ @@ -278,7 +278,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,7ee847d7f586a961a446566f8d473c30" ], [ { @@ -294,7 +294,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d294ef713b4f83c621be387294d7937e" ], [ { @@ -310,7 +310,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,ffe465201f5119c2699a49cd110628d3" ] ], "marked_bai": [ @@ -328,7 +328,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,989cbf1c64cc10b37b6b63c2ef2b069d" + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,bc1e2296080bc0d6d9878d3784892ee0" ], [ { @@ -344,7 +344,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,c883a94cb4854a44b6b6d98142bf8414" + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,8df5c65448c3c2f20cd8f574182f5593" ], [ { @@ -360,7 +360,7 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,a5294589ebe916c77ccee2db46710f9c" + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,de7d63cfa5735162d2274d877bf0b85b" ] ], "marked_bam": [ @@ -378,7 +378,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,0ec18ff7aaec000bebe1297d4bf0ebe1" + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,7ee847d7f586a961a446566f8d473c30" ], [ { @@ -394,7 +394,7 @@ "maternal": "slowlycivilbuck", "case_id": "justhusky" }, - "hugelymodelbat_sorted_merged_md_sorted.bam:md5,2ab1645a9c7ada8c8b16ae4764a11065" + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d294ef713b4f83c621be387294d7937e" ], [ { @@ -410,12 +410,12 @@ "maternal": 0, "case_id": "justhusky" }, - "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,2e37db7571195ad7c38a4ab0cc73f923" + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,ffe465201f5119c2699a49cd110628d3" ] ] } ], - "timestamp": "2026-02-20T00:32:17.118099572", + "timestamp": "2026-02-27T15:45:57.190438488", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index d73f1f5fe..09b3ed99d 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "24b5799be5403926a272596963f9683f" + "72b312c47e502b8272741a40e435b96" ] ], [ @@ -32,7 +32,7 @@ ] ] ], - "timestamp": "2026-02-17T15:13:51.33678644", + "timestamp": "2026-02-27T15:46:37.232286266", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -52,7 +52,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "b9b01b7ac356afa64bc411d6f10e741" + "40408ed51d46ab3f1524be98d6b31441" ] ], [ @@ -71,7 +71,7 @@ ] ] ], - "timestamp": "2026-02-17T15:14:44.637382457", + "timestamp": "2026-02-27T15:47:22.733461874", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 017ecab371e020801bb39a378361f85414d3d7b5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 09:37:42 +0100 Subject: [PATCH 394/872] restore hmtnote/annotate --- .../nf-core/hmtnote/annotate/environment.yml | 6 +++++- .../hmtnote/annotate/hmtnote-annotate.diff | 5 ++++- modules/nf-core/hmtnote/annotate/meta.yml | 18 +++++++++++------- 3 files changed, 20 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/hmtnote/annotate/environment.yml b/modules/nf-core/hmtnote/annotate/environment.yml index 1d9d20e3f..d5e7d3bbc 100644 --- a/modules/nf-core/hmtnote/annotate/environment.yml +++ b/modules/nf-core/hmtnote/annotate/environment.yml @@ -1,5 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::hmtnote=0.7.2 + - conda-forge::pip=21.3.1 + - conda-forge::python=3.6 + - pip: + - hmtnote==0.7.2 diff --git a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff b/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff index 745e98637..21993e931 100644 --- a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff +++ b/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff @@ -1,5 +1,4 @@ Changes in component 'nf-core/hmtnote/annotate' -'modules/nf-core/hmtnote/annotate/environment.yml' is unchanged 'modules/nf-core/hmtnote/annotate/meta.yml' is unchanged Changes in 'hmtnote/annotate/main.nf': --- modules/nf-core/hmtnote/annotate/main.nf @@ -48,4 +47,8 @@ Changes in 'hmtnote/annotate/main.nf': """ } +'modules/nf-core/hmtnote/annotate/environment.yml' is unchanged +'modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/hmtnote/annotate/tests/nextflow.config' is unchanged +'modules/nf-core/hmtnote/annotate/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/hmtnote/annotate/meta.yml b/modules/nf-core/hmtnote/annotate/meta.yml index 661d5cde0..92348f434 100644 --- a/modules/nf-core/hmtnote/annotate/meta.yml +++ b/modules/nf-core/hmtnote/annotate/meta.yml @@ -22,9 +22,10 @@ input: type: file description: vcf file pattern: "*.vcf" + ontologies: [] output: - - vcf: - - meta: + vcf: + - - meta: type: map description: | Groovy Map containing sample information @@ -32,11 +33,14 @@ output: type: file description: annotated vcf pattern: "*_annotated.vcf" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@sysbiocoder" maintainers: From 3353191638bd9cd0888ef4bc9fd3bd479dcff8c7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:08:36 +0100 Subject: [PATCH 395/872] Update CHANGELOG.md --- CHANGELOG.md | 53 ++++++++++++++++++++++++++-------------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f59f96ce1..c208fb469 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -51,32 +51,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| --------------------- | ----------- | ----------- | -| bcftools | 1.20 | 1.21 | -| bwa | 0.7.18 | 0.7.19 | -| deepvariant | 1.8.0 | 1.9.0 | -| eKLIPse | 1.8 | | -| ensemblverp/filtervep | 113 | 115.2 | -| fastp | 0.23.4 | 1.0.1 | -| gatk4 | 4.5.0.0 | 4.6.2.0 | -| genmod | 3.9 | 3.10.2 | -| gens-preproc | 1.0.11 | 1.1.2 | -| htslib | 1.20 | 1.21 | -| MitoSalt | | 1.1.1 | -| mosdepth | 0.3.8 | 0.3.11 | -| multiqc | 1.32 | 1.33 | -| ngsbits | 202411 | 202512 | -| picard | 3.3.0 | 3.4.0 | -| pigz | 2.3.4 | 2.8 | -| sambamba | | 1.0.1 | -| samtools | 1.21 | 1.22.1 | -| sentieon | 202503 | 202503.02 | -| stranger | 0.9.4 | 0.10.0 | -| tiddit | 3.6.1 | 3.9.4 | -| ucsc | 447 | 482 | -| vcfanno | 0.3.5 | 0.3.7 | -| vcf2cytosure | 0.9.1 | 0.9.3 | +| Tool | Old version | New version | +| -------------------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| bwa | 0.7.18 | 0.7.19 | +| deepvariant | 1.8.0 | 1.9.0 | +| eKLIPse | 1.8 | | +| ensemblvep/vep | 110 | 110.1 | +| ensemblvep/filtervep | 113 | 115.2 | +| fastp | 0.23.4 | 1.0.1 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | +| genmod | 3.9 | 3.10.2 | +| gens-preproc | 1.0.11 | 1.1.2 | +| htslib | 1.20 | 1.21 | +| MitoSalt | | 1.1.1 | +| mosdepth | 0.3.8 | 0.3.11 | +| multiqc | 1.32 | 1.33 | +| ngsbits | 202411 | 202512 | +| picard | 3.3.0 | 3.4.0 | +| pigz | 2.3.4 | 2.8 | +| sambamba | | 1.0.1 | +| samtools | 1.21 | 1.22.1 | +| sentieon | 202503 | 202503.02 | +| stranger | 0.9.4 | 0.10.0 | +| tiddit | 3.6.1 | 3.9.4 | +| ucsc | 447 | 482 | +| vcfanno | 0.3.5 | 0.3.7 | +| vcf2cytosure | 0.9.1 | 0.9.3 | ## 2.6.0 - Cacofonix [2025-06-25] From a862e2f6646de5ce7c80ab5874592b1cf5b81a92 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:11:30 +0100 Subject: [PATCH 396/872] run_mt_for_wes to val_run_mt_for_wes --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 418d634b0..8c744d0c3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -626,7 +626,7 @@ workflow RAREDISEASE { CALL MITOCHONDRIAL SVs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - if (val_analysis_type.matches("wgs|mito") || run_mt_for_wes) { + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CALL_SV_MT( ch_mapped.genome_marked_bam_bai, ch_genome_chrsizes, From fd1d2dca3c6f8dfdf579cce2a9930e2fec4f89ac Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 2 Mar 2026 21:22:23 +0100 Subject: [PATCH 397/872] review suggestions and nextflow lint --- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 2 +- subworkflows/local/annotate_cadd/main.nf | 2 +- subworkflows/local/call_structural_variants.nf | 2 -- workflows/raredisease.nf | 2 -- 4 files changed, 2 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 65e7b1256..fb7a850e3 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -62,7 +62,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return[meta,fasta,fai,[]]}) + SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 0d571e48b..33557bea1 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -55,7 +55,7 @@ workflow ANNOTATE_CADD { TABIX_VIEW(BCFTOOLS_VIEW.out.vcf) - CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources) + CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, [[:], []]) TABIX_CADD(CADD.out.tsv) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index f7ff6b90a..8d4cbcf6c 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -15,7 +15,6 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] @@ -27,7 +26,6 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] val_analysis_type // string: "wes", "wgs", or "mito" - run_mt_for_wes // boolean skip_germlinecnvcaller // boolean main: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8c744d0c3..faa5e259c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -541,7 +541,6 @@ workflow RAREDISEASE { ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, ch_mapped.genome_marked_bam_bai, - ch_mapped.mt_bam_bai, ch_genome_bwaindex, ch_genome_fasta, ch_genome_fai, @@ -553,7 +552,6 @@ workflow RAREDISEASE { ch_ploidy_model, ch_gcnvcaller_model, val_analysis_type, - val_run_mt_for_wes, skip_germlinecnvcaller, ) ch_versions = ch_versions.mix(CALL_STRUCTURAL_VARIANTS.out.versions) From 1b21c1159f71b9fe5a99e5ec97722ce120ae15b1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 3 Mar 2026 11:51:08 +0100 Subject: [PATCH 398/872] update output.md --- docs/output.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/docs/output.md b/docs/output.md index 1a9ff5a9e..eea840452 100644 --- a/docs/output.md +++ b/docs/output.md @@ -76,6 +76,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Annotating mobile elements](#annotating-mobile-elements) - [Variant evaluation](#variant-evaluation) - [Gens](#gens) + - [Peddy](#peddy) - [Pipeline information](#pipeline-information) ### Alignment @@ -453,6 +454,7 @@ Based on VEP annotations, custom scripts used by the pipeline further annotate e - `annotate_sv/` - `_svdbquery_vep.vcf.gz`: file containing svdb query, and vep annotations. - `_svdbquery_vep.vcf.gz.tbi`: index of the file containing bcftools roh, vcfanno, and vep annotations. + - `_svdbquery_vep_summary.html`: vep summary.
    @@ -628,6 +630,26 @@ The sequencing data can be prepared for visualization of CNVs in [Gens](https:// +### Peddy + +[Peddy](https://github.com/brentp/peddy) compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF. + +
    +Output files + +- `peddy/` + - `*.het_check.csv` + - `*.het_check.png` + - `*.html` + - `*.pca_check.png` + - `*.ped_check.csv` + - `*.ped_check.png` + - `*.ped_check.rel-difference.csv` + - `*.peddy.ped` + - `*.sex_check.csv` + - `*.sex_check.png` + - `*.vs.html` + ### Pipeline information [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. From fa2c667efd5e78a47441a6da44243bfdc6218bf1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 3 Mar 2026 09:42:38 +0000 Subject: [PATCH 399/872] [automated] Fix code linting --- conf/modules/call_snv_MT.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config index f6a49bf50..72442a992 100644 --- a/conf/modules/call_snv_MT.config +++ b/conf/modules/call_snv_MT.config @@ -43,4 +43,4 @@ process { ext.prefix = { "${meta.id}_filtered_shifted" } } -} \ No newline at end of file +} From 6fbf757661b6350118a3b8ccebb05b7b44dc2780 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Tue, 3 Mar 2026 16:51:55 +0100 Subject: [PATCH 400/872] removed nf core module hmtnote/annotate --- .../nf-core/hmtnote/annotate/environment.yml | 9 ---- .../hmtnote/annotate/hmtnote-annotate.diff | 54 ------------------- modules/nf-core/hmtnote/annotate/main.nf | 45 ---------------- modules/nf-core/hmtnote/annotate/meta.yml | 47 ---------------- 4 files changed, 155 deletions(-) delete mode 100644 modules/nf-core/hmtnote/annotate/environment.yml delete mode 100644 modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff delete mode 100644 modules/nf-core/hmtnote/annotate/main.nf delete mode 100644 modules/nf-core/hmtnote/annotate/meta.yml diff --git a/modules/nf-core/hmtnote/annotate/environment.yml b/modules/nf-core/hmtnote/annotate/environment.yml deleted file mode 100644 index d5e7d3bbc..000000000 --- a/modules/nf-core/hmtnote/annotate/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ -channels: - - conda-forge - - bioconda - -dependencies: - - conda-forge::pip=21.3.1 - - conda-forge::python=3.6 - - pip: - - hmtnote==0.7.2 diff --git a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff b/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff deleted file mode 100644 index 21993e931..000000000 --- a/modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff +++ /dev/null @@ -1,54 +0,0 @@ -Changes in component 'nf-core/hmtnote/annotate' -'modules/nf-core/hmtnote/annotate/meta.yml' is unchanged -Changes in 'hmtnote/annotate/main.nf': ---- modules/nf-core/hmtnote/annotate/main.nf -+++ modules/nf-core/hmtnote/annotate/main.nf -@@ -11,7 +11,7 @@ - tuple val(meta), path(vcf) - - output: -- tuple val(meta), path("*_annotated.vcf"), emit: vcf -+ tuple val(meta), path("${prefix}.vcf"), emit: vcf - path "versions.yml" , emit: versions - - when: -@@ -19,27 +19,27 @@ - - script: - def args = task.ext.args ?: '' -- def prefix = task.ext.prefix ?: "${meta.id}" -+ prefix = task.ext.prefix ?: "${meta.id}" - - """ - hmtnote \\ - annotate \\ - $vcf \\ -- ${prefix}_annotated.vcf \\ -+ ${prefix}.vcf \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": -- hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' )) -+ hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ) - END_VERSIONS - """ - stub: -- def prefix = task.ext.prefix ?: "${meta.id}" -+ prefix = task.ext.prefix ?: "${meta.id}" - """ -- touch ${prefix}_annotated.vcf -+ touch ${prefix}.vcf - cat <<-END_VERSIONS > versions.yml - "${task.process}": -- hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' )) -+ hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ) - END_VERSIONS - """ - } - -'modules/nf-core/hmtnote/annotate/environment.yml' is unchanged -'modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap' is unchanged -'modules/nf-core/hmtnote/annotate/tests/nextflow.config' is unchanged -'modules/nf-core/hmtnote/annotate/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/hmtnote/annotate/main.nf b/modules/nf-core/hmtnote/annotate/main.nf deleted file mode 100644 index a894d0073..000000000 --- a/modules/nf-core/hmtnote/annotate/main.nf +++ /dev/null @@ -1,45 +0,0 @@ -process HMTNOTE_ANNOTATE { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_1': - 'biocontainers/hmtnote:0.7.2--pyhdfd78af_1' }" - - input: - tuple val(meta), path(vcf) - - output: - tuple val(meta), path("${prefix}.vcf"), emit: vcf - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - - """ - hmtnote \\ - annotate \\ - $vcf \\ - ${prefix}.vcf \\ - $args - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ) - END_VERSIONS - """ - stub: - prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.vcf - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/hmtnote/annotate/meta.yml b/modules/nf-core/hmtnote/annotate/meta.yml deleted file mode 100644 index 92348f434..000000000 --- a/modules/nf-core/hmtnote/annotate/meta.yml +++ /dev/null @@ -1,47 +0,0 @@ -name: hmtnote_annotate -description: Human mitochondrial variants annotation using HmtVar. Contains .plk file - with annotation, so can be run offline -keywords: - - hmtnote - - mitochondria - - annotation -tools: - - hmtnote: - description: Human mitochondrial variants annotation using HmtVar. - homepage: https://github.com/robertopreste/HmtNote - documentation: https://hmtnote.readthedocs.io/en/latest/usage.html - doi: "10.1101/600619" - licence: ["MIT"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - - vcf: - type: file - description: vcf file - pattern: "*.vcf" - ontologies: [] -output: - vcf: - - - meta: - type: map - description: | - Groovy Map containing sample information - - "*_annotated.vcf": - type: file - description: annotated vcf - pattern: "*_annotated.vcf" - ontologies: [] - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML -authors: - - "@sysbiocoder" -maintainers: - - "@sysbiocoder" From 1c70d3b6e11eeacb695beb0fe8724f6f8911df13 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Tue, 3 Mar 2026 16:52:33 +0100 Subject: [PATCH 401/872] updated documentation --- CHANGELOG.md | 1 + docs/output.md | 9 +- modules.json | 467 ++++++++++++++++++++++++++++++++++++------------- 3 files changed, 349 insertions(+), 128 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c208fb469..1602266bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Sambamba depth now filters on not duplicates and not failed_quality_control [#768](https://github.com/nf-core/raredisease/pull/768) - Removed eKLIPse [#743](https://github.com/nf-core/raredisease/pull/743) - Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) +- Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) ### `Fixed` diff --git a/docs/output.md b/docs/output.md index eea840452..a0bae4571 100644 --- a/docs/output.md +++ b/docs/output.md @@ -66,7 +66,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [HaploGrep2](#haplogrep2) - [vcfanno](#vcfanno-1) - [CADD](#cadd-1) - - [Hmtnote](#hmtnote) - [VEP](#vep-2) - [Filtering and ranking](#filtering-and-ranking) - [Filter_vep](#filter_vep) @@ -512,10 +511,6 @@ We recommend using vcfanno to annotate SNVs with precomputed CADD scores (files [CADD](https://cadd.gs.washington.edu/) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. In nf-core/raredisease, SNVs can be annotated with precomputed CADD scores using vcfanno. However, for small indels they will be calculated on the fly by CADD. The output files are not published in the output folder, and is passed to VEP for further annotation. -##### Hmtnote - -[HmtNote](https://github.com/robertopreste/HmtNote) annotates vcf containing human mitochondrial variants with HmtVar. It will run offline by default with a database within the container. - ##### VEP [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) determines the effect of your variants on genes, transcripts, and protein sequence, as well as regulatory regions. @@ -524,8 +519,8 @@ We recommend using vcfanno to annotate SNVs with precomputed CADD scores (files Output files - `annotate_snv/mitochondria` - - `_mitochondria_hmtnote_vcfanno_.vcf.gz`: file containing mitochondrial annotations. - - `_mitochondria_hmtnote_vcfanno_.vcf.gz.tbi`: index of the file containing mitochondrial annotations. + - `_mitochondria_vcfanno_.vcf.gz`: file containing mitochondrial annotations. + - `_mitochondria_vcfanno_.vcf.gz.tbi`: index of the file containing mitochondrial annotations.
    diff --git a/modules.json b/modules.json index 3417c5ac5..5627ec509 100644 --- a/modules.json +++ b/modules.json @@ -8,283 +8,397 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/mem": { "branch": "master", "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/index": { "branch": "master", "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwamem2/mem": { "branch": "master", "git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/index": { "branch": "master", "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwameme/mem": { "branch": "master", "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cadd": { "branch": "master", "git_sha": "1d40acd9f567cea7ccdd4b6211310d4e94356357", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "chromograph": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cnvnator/convert2vcf": { "branch": "master", "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostsevereconsequence": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/addmostseverepli": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/filtervep": { "branch": "master", "git_sha": "2e751c119b5e6e9c7ecda7a682e157aabb57a812", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "34505e1fc5e9f4fd641210ca440acff6bd33b842", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "expansionhunter": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastp": { "branch": "master", "git_sha": "a331ecfd1aa48b2b2298aab23bb4516c800e410b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/collectreadcounts": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/denoisereadcounts": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/filtermutectcalls": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/germlinecnvcaller": { "branch": "master", "git_sha": "86308d628760125908c5c77540517effe0f8880f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/mergebamalignment": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "6881702b1f6671b9471e69f4a75ea4e49a0d0349", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/mutect2": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/postprocessgermlinecnvcalls": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/printreads": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/revertsam": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/samtofastq": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/selectvariants": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/shiftfasta": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/splitintervals": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "52b7843bd92ccf833cc12e71cd84aeccf2583852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "76b1f53edcf72798d8515c82f4728ad44b3dd902", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/annotate": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/compound": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/models": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "genmod/score": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "glnexus": { "branch": "master", "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "haplocheck": { "branch": "master", @@ -294,278 +408,381 @@ "haplogrep3/classify": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/build": { "branch": "master", "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c", - "installed_by": ["modules"] - }, - "hmtnote/annotate": { - "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", - "installed_by": ["modules"], - "patch": "modules/nf-core/hmtnote/annotate/hmtnote-annotate.diff" + "installed_by": [ + "modules" + ] }, "last/lastdb": { "branch": "master", "git_sha": "a54953d05812af249d40ffaccb5b8ee371a75866", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "manta/germline": { "branch": "master", "git_sha": "3485512d3930df1fcb66b5f92af639179bdfe4be", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "6832b69ef7f98c54876d6436360b6b945370c615", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ngsbits/samplegender": { "branch": "master", "git_sha": "54c18191be1e99d78832cb62dc6fb9513ed97eae", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "peddy": { "branch": "master", "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/addorreplacereadgroups": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/collecthsmetrics": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/collectmultiplemetrics": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/collectwgsmetrics": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/liftovervcf": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/markduplicates": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/renamesampleinvcf": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/sortvcf": { "branch": "master", "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "qualimap/bamqc": { "branch": "master", "git_sha": "aa50b51492f79e0bf3ca9ca6e34640e3435b60ba", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/annotate": { "branch": "master", "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rhocall/viz": { "branch": "master", "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/format": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sambamba/depth": { "branch": "master", "git_sha": "ca6da11b05740de461b1e2714037345c0f856201", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/collate": { "branch": "master", "git_sha": "18ef126d5c91f6f4ad94fe6b939647771d5bc7b0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwaindex": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/bwamem": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/datametrics": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dedup": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/dnascope": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/readwriter": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/sample": { "branch": "master", "git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "smncopynumbercaller": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spring/decompress": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stranger": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/merge": { "branch": "master", "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] + "installed_by": [ + "modules", + "vcf_filter_bcftools_ensemblvep" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/cov": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tiddit/sv": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/wigtobigwig": { "branch": "master", "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upd": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2cytosure": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "verifybamid/verifybamid2": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -574,25 +791,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file From 7943d14ce095aca13616dd94592fe919e601adc8 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Tue, 3 Mar 2026 17:00:58 +0100 Subject: [PATCH 402/872] fixed formatting --- subworkflows/local/annotate_mt_snvs.nf | 26 ++++---------------------- 1 file changed, 4 insertions(+), 22 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 52aba9ad9..d58756de4 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -2,17 +2,15 @@ // Annotate MT // -//include { REPLACE_SPACES_IN_VCFINFO } from '../../modules/local/replace_spaces_in_vcfinfo' + include { BCFTOOLS_PLUGINSETGT } from '../../modules/nf-core/bcftools/pluginsetgt' include { TABIX_TABIX as TABIX_TABIX_MT } from '../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../modules/nf-core/tabix/tabix/main' -//include { TABIX_BGZIPTABIX as ZIP_TABIX_HMTNOTE_MT } from '../../modules/nf-core/tabix/bgziptabix/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../modules/nf-core/ensemblvep/vep/main' include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../modules/nf-core/haplogrep3/classify/main' include { VCFANNO as VCFANNO_MT } from '../../modules/nf-core/vcfanno/main' include { ANNOTATE_CADD } from './annotate_cadd' include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../modules/nf-core/tabix/bgziptabix/main' -//include { HMTNOTE_ANNOTATE } from '../../modules/nf-core/hmtnote/annotate/main' workflow ANNOTATE_MT_SNVS { take: @@ -37,27 +35,14 @@ workflow ANNOTATE_MT_SNVS { ch_versions = channel.empty() ch_haplog = channel.empty() -/* // add prefix to meta - ch_mt_vcf - .map { meta, vcf -> - return [meta+ [prefix: vcf.simpleName + "_hmtnote"], vcf] - } - .set { ch_hmtnote_in } - - // HMTNOTE ANNOTATE - HMTNOTE_ANNOTATE(ch_hmtnote_in) - REPLACE_SPACES_IN_VCFINFO(HMTNOTE_ANNOTATE.out.vcf) - ZIP_TABIX_HMTNOTE_MT(REPLACE_SPACES_IN_VCFINFO.out.vcf) */ - TABIX_TABIX_MT(ch_mt_vcf) // meta, tbi - // => TABIX_TABIX_MT(ch_mt_vcf) a associer avec ch_mt_vcf [meta, vcf] pour avoir [meta, vcf, tbi] - + // Index vcf + TABIX_TABIX_MT(ch_mt_vcf) ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) // Vcfanno - //ZIP_TABIX_HMTNOTE_MT.out.gz_index // = meta, vcf, tbi ch_mt_vcf_index .combine(ch_vcfanno_extra) - .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} + .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) @@ -129,9 +114,6 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } - ch_versions = ch_versions.mix(VCFANNO_MT.out.versions) - //ch_versions = ch_versions.mix(HMTNOTE_ANNOTATE.out.versions) - emit: haplog = ch_haplog // channel: [ val(meta), path(txt) ] report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] From e78c61e8af5932a89fa75d4e8cc3b9c6559f1ece Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Mar 2026 08:31:36 +0100 Subject: [PATCH 403/872] updated snap --- tests/test_singleton.nf.test.snap | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 1e041cefd..0d010429f 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 368, + 367, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -746,11 +746,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-03T10:31:17.265377549", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, - "timestamp": "2026-03-03T16:11:07.735178695" + "timestamp": "2026-03-04T08:25:27.608017744" } } \ No newline at end of file From a1d4566bdb1c3be9aff3e41d92533979fe7f7b36 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 4 Mar 2026 07:34:38 +0000 Subject: [PATCH 404/872] [automated] Fix code linting --- modules/local/saltshaker/call/environment.yaml | 10 +++++----- modules/local/saltshaker/call/main.nf | 2 +- modules/local/saltshaker/classify/environment.yaml | 10 +++++----- modules/local/saltshaker/plot/environment.yaml | 10 +++++----- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/local/saltshaker/call/environment.yaml b/modules/local/saltshaker/call/environment.yaml index e2f67c93f..57b633f58 100644 --- a/modules/local/saltshaker/call/environment.yaml +++ b/modules/local/saltshaker/call/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- pip -- pip: - - saltshaker==1.0.0 + - pip + - pip: + - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/call/main.nf b/modules/local/saltshaker/call/main.nf index 983b172ce..c3b8c8b09 100644 --- a/modules/local/saltshaker/call/main.nf +++ b/modules/local/saltshaker/call/main.nf @@ -49,7 +49,7 @@ process SALTSHAKER_CALL { """ touch ${prefix}.saltshaker_call_metadata.tsv - + """ } diff --git a/modules/local/saltshaker/classify/environment.yaml b/modules/local/saltshaker/classify/environment.yaml index e2f67c93f..57b633f58 100644 --- a/modules/local/saltshaker/classify/environment.yaml +++ b/modules/local/saltshaker/classify/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- pip -- pip: - - saltshaker==1.0.0 + - pip + - pip: + - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/plot/environment.yaml b/modules/local/saltshaker/plot/environment.yaml index e2f67c93f..57b633f58 100644 --- a/modules/local/saltshaker/plot/environment.yaml +++ b/modules/local/saltshaker/plot/environment.yaml @@ -1,7 +1,7 @@ channels: -- conda-forge -- bioconda + - conda-forge + - bioconda dependencies: -- pip -- pip: - - saltshaker==1.0.0 + - pip + - pip: + - saltshaker==1.0.0 From 3b74a51291b8847535a1231f8d56b9bfad3fa37a Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 4 Mar 2026 09:02:40 +0100 Subject: [PATCH 405/872] update schema --- nextflow_schema.json | 50 ++++++++++++++++++++++---------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5fb2f5035..c9d140bac 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -756,62 +756,62 @@ "hisat2": { "type": "string" }, - "breakspan": { + "mitosalt_breakspan": { "type": "integer", "default": 15, "description": "minimum number of bases a non-split read must span either side of a breakpoint to be considered in the heteroplasmy count" }, - "breakthreshold": { + "mitosalt_breakthreshold": { "type": "integer", "default": 2, "description": "the maximum deviation a given set of split read breakpoints can have to be considered within the same cluster" }, - "cluster_threshold": { + "mitosalt_cluster_threshold": { "type": "integer", "default": 5, "description": "minimum number of reads supporting a cluster" }, - "deletion_threshold_max": { + "mitosalt_deletion_threshold_max": { "type": "integer", "default": 30000, "description": "the maximum size of the gap between fragments of a split read for the split read to be considered as potentially spanning a deletion" }, - "deletion_threshold_min": { + "mitosalt_deletion_threshold_min": { "type": "integer", "default": 30, - "description": "the minimum size of the gap between fragemtns of a split read for the split read to be considered as potentially spanning a deletion" + "description": "the minimum size of the gap between fragments of a split read for the split read to be considered as potentially spanning a deletion" }, - "dom_frac": { + "saltshaker_dominant_fraction": { "type": "number", "default": 0.5, "description": "fraction for dominant fraction for saltshaker classification" }, - "evalue_threshold": { + "mitosalt_evalue_threshold": { "type": "number", "default": 1e-5, "description": "alignment e-value cutoff" }, - "exclude": { + "mitosalt_exclude": { "type": "integer", "default": 5, "description": "filter split reads if both fragments fall within the regions at the start and end to avoid pseudo-gapped alignments due to a circular genome" }, - "flank": { + "mitosalt_flank": { "type": "integer", "default": 15, "description": "basepairs flanking a deletion" }, - "group_radius": { + "saltshaker_group_radius": { "type": "integer", "default": 600, "description": "spatial clustering radius for saltshaker grouping" }, - "high_het": { + "saltshaker_high_heteroplasmy": { "type": "integer", "default": 10, "description": "high heteroplasmy threshold for saltshaker classification" }, - "hplimit": { + "mitosalt_heteroplasmy_limit": { "type": "number", "default": 0.01, "description": "detected heteroplasmy threshold" @@ -826,57 +826,57 @@ "default": 16569, "description": "length of mitochondrial genome" }, - "mult_thresh": { + "saltshaker_multiple_threshold": { "type": "integer", "default": 5, "description": "threshold for multiple saltshaker classification" }, - "noise_thresh": { + "saltshaker_noise_threshold": { "type": "number", "default": 0.3, "description": "heteroplasmy threshold for background noise" }, - "ori_h_start": { + "heavy_strand_origin_start": { "type": "integer", "default": 16081, "description": "start of heavy strand origin" }, - "ori_h_end": { + "heavy_strand_origin_end": { "type": "integer", "default": 407, "description": "end of heavy strand origin" }, - "ori_l_start": { + "light_strand_origin_start": { "type": "integer", "default": 5730, "description": "start of light strand origin" }, - "ori_l_end": { + "light_strand_origin_end": { "type": "integer", "default": 5763, "description": "end of light strand origin" }, - "paired_distance": { + "mitosalt_paired_distance": { "type": "integer", "default": 1000, "description": "the maximum distance of a paired read from its split counterpart for paired support to be considered positive" }, - "score_threshold": { + "mitosalt_score_threshold": { "type": "integer", "default": 80, - "description": "alignemnt score cutoff" + "description": "alignment score cutoff" }, - "sizelimit": { + "mitosalt_sizelimit": { "type": "integer", "default": 10000, "description": "maximum size of deletions tolerated, beyond which they are reclassified as potential duplications in the reverse orientation" }, - "split_distance_threshold": { + "mitosalt_split_distance_threshold": { "type": "integer", "default": 5, "description": "the maximum length of unmapped distance between two fragments of a split read" }, - "split_length": { + "mitosalt_split_length": { "type": "integer", "default": 15, "description": "minimum number of bases in a split read fragment for the read to be considered as potentially spanning a deletion" From 7993d445bba9a3f4580fc32407c071d5e34251e9 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 09:53:39 +0100 Subject: [PATCH 406/872] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 040c57549..a2beacaeb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -65,6 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | genmod | 3.9 | 3.10.2 | | gens-preproc | 1.0.11 | 1.1.2 | | haplocheck | 1.3.3 | | +| hmtnote | 0.7.2 | | | htslib | 1.20 | 1.21 | | MitoSalt | | 1.1.1 | | mosdepth | 0.3.8 | 0.3.11 | From 944317bce5170ff7b24e48353a14f3decd79cd2f Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 09:56:35 +0100 Subject: [PATCH 407/872] fixed formatting --- modules.json | 180 +++++++++++++-------------------------------------- 1 file changed, 45 insertions(+), 135 deletions(-) diff --git a/modules.json b/modules.json index 7a5ff0b97..6e65b78db 100644 --- a/modules.json +++ b/modules.json @@ -8,94 +8,67 @@ "bcftools/annotate": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/filter": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/merge": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginsetgt": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/roh": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/view": { "branch": "master", "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/slop": { "branch": "master", "git_sha": "88d43dad73a675e66bff49ebb57fe657a5909018", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "966ba9887e2b04d89d64db06c01508873bde13b1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", @@ -135,16 +108,12 @@ "chromograph": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvnator/cnvnator": { "branch": "master", "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cnvnator/convert2vcf": { "branch": "master", @@ -164,9 +133,7 @@ "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/filtervep": { "branch": "master", @@ -182,16 +149,12 @@ "expansionhunter": { "branch": "master", "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "a331ecfd1aa48b2b2298aab23bb4516c800e410b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", @@ -201,9 +164,7 @@ "gatk4/bedtointervallist": { "branch": "master", "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", @@ -303,30 +264,22 @@ "genmod/annotate": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/compound": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/models": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "genmod/score": { "branch": "master", "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "glnexus": { "branch": "master", @@ -341,9 +294,7 @@ "hisat2/build": { "branch": "master", "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "last/lastdb": { "branch": "master", @@ -353,16 +304,12 @@ "manta/germline": { "branch": "master", "git_sha": "3485512d3930df1fcb66b5f92af639179bdfe4be", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "6832b69ef7f98c54876d6436360b6b945370c615", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", @@ -472,16 +419,12 @@ "samtools/sort": { "branch": "master", "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", @@ -491,58 +434,42 @@ "sentieon/bwaindex": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/bwamem": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/datametrics": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dedup": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnamodelapply": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/dnascope": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/readwriter": { "branch": "master", "git_sha": "d9c84ed4564744313bb586928885ebf05f40ad98", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "sentieon/wgsmetrics": { "branch": "master", "git_sha": "77fc71f9384035ef6259e0e0519d3406b0cda012", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/sample": { "branch": "master", @@ -562,9 +489,7 @@ "stranger": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "svdb/merge": { "branch": "master", @@ -574,31 +499,22 @@ "svdb/query": { "branch": "master", "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "91a902fb32d6717da38a9694eb4ad3fade53a8db", - "installed_by": [ - "modules", - "vcf_filter_bcftools_ensemblvep" - ] + "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] }, "tabix/tabix": { "branch": "master", "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tiddit/cov": { "branch": "master", @@ -647,23 +563,17 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_filter_bcftools_ensemblvep": { "branch": "master", @@ -674,4 +584,4 @@ } } } -} \ No newline at end of file +} From 5292814947b63fba3bff3633a8d2c8765d4c3f56 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 10:00:33 +0100 Subject: [PATCH 408/872] fixed formatting --- subworkflows/local/annotate_mt_snvs.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index d58756de4..b306feab5 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -36,7 +36,7 @@ workflow ANNOTATE_MT_SNVS { ch_haplog = channel.empty() // Index vcf - TABIX_TABIX_MT(ch_mt_vcf) + TABIX_TABIX_MT(ch_mt_vcf) ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) // Vcfanno From 373c3665f280733eaa9b949ed3d712114e640198 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 10:23:25 +0100 Subject: [PATCH 409/872] fixed bug in output name --- subworkflows/local/annotate_mt_snvs.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index b306feab5..84e38c29f 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -39,10 +39,10 @@ workflow ANNOTATE_MT_SNVS { TABIX_TABIX_MT(ch_mt_vcf) ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) - // Vcfanno + // Vcfanno [meta+ [prefix: vcf.simpleName ch_mt_vcf_index .combine(ch_vcfanno_extra) - .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]} + .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) From 4f52f6d1cc489b3b98846579c21ee51125248532 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 11:04:02 +0100 Subject: [PATCH 410/872] fixed bug in output name --- subworkflows/local/annotate_mt_snvs.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs.nf b/subworkflows/local/annotate_mt_snvs.nf index 84e38c29f..02ffa5cb8 100644 --- a/subworkflows/local/annotate_mt_snvs.nf +++ b/subworkflows/local/annotate_mt_snvs.nf @@ -39,10 +39,10 @@ workflow ANNOTATE_MT_SNVS { TABIX_TABIX_MT(ch_mt_vcf) ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) - // Vcfanno [meta+ [prefix: vcf.simpleName + // Vcfanno ch_mt_vcf_index .combine(ch_vcfanno_extra) - .map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.simpleName + "_vcfanno"], vcf, tbi, resources]} + .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) From 3c579894e74d7ae0a5afe92c7d42ff6516b847c0 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 11:24:02 +0100 Subject: [PATCH 411/872] updated snapshots --- tests/test_bam.nf.test.snap | 2 +- tests/test_singleton.nf.test.snap | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 218b49265..bb374b6e2 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 792, + 790, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index d12c9cea6..42e681d81 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 364, + 362, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, From f3df7dd471b30c8cd6fd00e861b129d18c3ddcb0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 13:11:30 +0100 Subject: [PATCH 412/872] add test for annotate_cadd --- conf/modules/annotate_cadd.config | 2 +- modules.json | 4 +- modules/nf-core/cadd/environment.yml | 4 +- modules/nf-core/cadd/main.nf | 32 +++--- modules/nf-core/cadd/meta.yml | 16 ++- modules/nf-core/cadd/tests/main.nf.test | 2 + modules/nf-core/cadd/tests/main.nf.test.snap | 6 +- modules/nf-core/cadd/tests/nextflow.config | 5 + modules/nf-core/gawk/environment.yml | 2 +- modules/nf-core/gawk/main.nf | 6 +- modules/nf-core/gawk/tests/main.nf.test | 27 +++++ modules/nf-core/gawk/tests/main.nf.test.snap | 101 ++++++++++++------ subworkflows/local/annotate_cadd/main.nf | 23 +--- .../local/annotate_cadd/tests/main.nf.test | 72 +++++++++++++ .../annotate_cadd/tests/main.nf.test.snap | 32 ++++++ .../local/annotate_cadd/tests/nextflow.config | 34 ++++++ 16 files changed, 289 insertions(+), 79 deletions(-) create mode 100644 modules/nf-core/cadd/tests/nextflow.config create mode 100644 subworkflows/local/annotate_cadd/tests/main.nf.test create mode 100644 subworkflows/local/annotate_cadd/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_cadd/tests/nextflow.config diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index d82bdd415..8d47b5543 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -35,7 +35,7 @@ process { } withName: '.*:ANNOTATE_CADD:BCFTOOLS_ANNOTATE' { - ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z" } + ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z --write-index=tbi" } ext.prefix = { "${input.simpleName}_ann" } } diff --git a/modules.json b/modules.json index dcf570b57..7548a1131 100644 --- a/modules.json +++ b/modules.json @@ -97,7 +97,7 @@ }, "cadd": { "branch": "master", - "git_sha": "1d40acd9f567cea7ccdd4b6211310d4e94356357", + "git_sha": "64ab14a6905e5c9d649f61e2757a1e600dbdb8e0", "installed_by": ["modules"] }, "cat/cat": { @@ -258,7 +258,7 @@ }, "gawk": { "branch": "master", - "git_sha": "76b1f53edcf72798d8515c82f4728ad44b3dd902", + "git_sha": "c0da8f3a26835d663873001382a708f75766fec6", "installed_by": ["modules"] }, "genmod/annotate": { diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml index d98de6522..39701b4ab 100644 --- a/modules/nf-core/cadd/environment.yml +++ b/modules/nf-core/cadd/environment.yml @@ -4,6 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::cadd-scripts=1.6.post1 - - conda-forge::conda=4.14.0 - - conda-forge::mamba=1.4.0 + - bioconda::cadd-scripts=1.7.3 diff --git a/modules/nf-core/cadd/main.nf b/modules/nf-core/cadd/main.nf index 94aa19796..771d1445d 100644 --- a/modules/nf-core/cadd/main.nf +++ b/modules/nf-core/cadd/main.nf @@ -3,24 +3,28 @@ process CADD { label 'process_medium' conda "${moduleDir}/environment.yml" - container 'docker.io/biocontainers/cadd-scripts-with-envs:1.6.post1_cv1' - - containerOptions "${ prescored_dir ? - ['singularity', 'apptainer'].contains(workflow.containerEngine) ? - "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -B ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : - "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations -v ${prescored_dir}:/opt/CADD-scripts-1.6.post1/data/prescored" : - ['singularity', 'apptainer'].contains(workflow.containerEngine) ? - "-B ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" : - "-v ${annotation_dir}:/opt/CADD-scripts-1.6.post1/data/annotations" }" + container 'docker.io/clinicalgenomics/cadd-with-scripts:1.7.3' + + containerOptions { + if (prescored_dir) { + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? + "-B ${annotation_dir}:/cadd-scripts/data/annotations -B ${prescored_dir}:/cadd-scripts/data/prescored" : + "-v ${annotation_dir}:/cadd-scripts/data/annotations -v ${prescored_dir}:/cadd-scripts/data/prescored" + } else { + ['singularity', 'apptainer'].contains(workflow.containerEngine) ? + "-B ${annotation_dir}:/cadd-scripts/data/annotations" : + "-v ${annotation_dir}:/cadd-scripts/data/annotations" + } + } input: tuple val(meta), path(vcf) - tuple val(meta2), path(annotation_dir) - tuple val(meta3), path(prescored_dir) + tuple val(meta2), val(annotation_dir) + tuple val(meta3), val(prescored_dir) output: tuple val(meta), path("${prefix}.tsv.gz"), emit: tsv - tuple val("${task.process}"), val("cadd"), val("1.6.post1"), emit: versions_cadd, topic: versions + tuple val("${task.process}"), val("cadd"), val("1.7.3"), emit: versions_cadd, topic: versions // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. when: @@ -31,9 +35,11 @@ process CADD { prefix = task.ext.prefix ?: "${meta.id}" """ export XDG_CACHE_HOME=\$PWD/snakemake_cache + export MPLCONFIGDIR=. mkdir -p \$XDG_CACHE_HOME - cadd.sh \\ + CADD.sh \\ + -m \\ -o ${prefix}.tsv.gz \\ ${args} \\ ${vcf} diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml index b70cb7d9c..1efaa94f0 100644 --- a/modules/nf-core/cadd/meta.yml +++ b/modules/nf-core/cadd/meta.yml @@ -44,8 +44,16 @@ input: - prescored_dir: type: directory description: | - Path to folder containing prescored files. - This folder contains the uncompressed files that would otherwise be in data/prescored/${GENOME_BUILD}_${VERSION}/ folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. + Path to folder containing prescored CADD score files. + Expected structure mirrors data/prescored/ from the CADD-scripts installation: + / + GRCh38_v1.7/ + incl_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores with annotations) + no_anno/ # *.tsv.gz + *.tsv.gz.tbi (scores only) + GRCh37_v1.7/ + incl_anno/ + no_anno/ + See https://github.com/kircherlab/CADD-scripts/#manual-installation for details. output: tsv: - - meta: @@ -66,7 +74,7 @@ output: - cadd: type: string description: The name of the tool - - 1.6.post1: + - 1.7.3: type: string description: The expression to obtain the version of the tool topics: @@ -77,7 +85,7 @@ topics: - cadd: type: string description: The name of the tool - - 1.6.post1: + - 1.7.3: type: string description: The expression to obtain the version of the tool authors: diff --git a/modules/nf-core/cadd/tests/main.nf.test b/modules/nf-core/cadd/tests/main.nf.test index cc36d0cdd..c3287907b 100644 --- a/modules/nf-core/cadd/tests/main.nf.test +++ b/modules/nf-core/cadd/tests/main.nf.test @@ -9,6 +9,8 @@ nextflow_process { tag "modules_nfcore" tag "cadd" + config "./nextflow.config" + test("test_cadd - stub") { options '-stub' when { diff --git a/modules/nf-core/cadd/tests/main.nf.test.snap b/modules/nf-core/cadd/tests/main.nf.test.snap index de4c6dc7c..5e38eeaf5 100644 --- a/modules/nf-core/cadd/tests/main.nf.test.snap +++ b/modules/nf-core/cadd/tests/main.nf.test.snap @@ -15,7 +15,7 @@ [ "CADD", "cadd", - "1.6.post1" + "1.7.3" ] ], "tsv": [ @@ -31,7 +31,7 @@ [ "CADD", "cadd", - "1.6.post1" + "1.7.3" ] ] }, @@ -39,7 +39,7 @@ ] ], - "timestamp": "2026-02-19T20:06:20.885977", + "timestamp": "2026-03-01T12:08:37.372500636", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/modules/nf-core/cadd/tests/nextflow.config b/modules/nf-core/cadd/tests/nextflow.config new file mode 100644 index 000000000..bd24d9f3b --- /dev/null +++ b/modules/nf-core/cadd/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'CADD' { + container = "nf-core/ubuntu:22.04" //Using an basic container because v1.7.3 is too big for CI. + } +} diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index f52109e83..185a0f545 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - conda-forge::gawk=5.3.0 + - conda-forge::gawk=5.3.1 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index a76851dff..33dd24ccd 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -4,8 +4,8 @@ process GAWK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : - 'biocontainers/gawk:5.3.0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a1/a125c778baf3865331101a104b60d249ee15fe1dca13bdafd888926cc5490a34/data' : + 'community.wave.seqera.io/library/gawk:5.3.1--e09efb5dfc4b8156' }" input: tuple val(meta), path(input, arity: '0..*') @@ -51,7 +51,7 @@ process GAWK { stub: prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension()}" + suffix = task.ext.suffix ?: "${input.collect{ file -> file.getExtension()}.get(0)}" def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" """ diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index 5fa9daf16..3bd0a43d6 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -34,6 +34,33 @@ nextflow_process { } } + test("Convert fasta to bed - stub") { + + options "-stub" + + when { + params { + gawk_suffix = "bed" + gawk_args2 = '\'BEGIN { FS = OFS = "\t"}; { print \$1, "0", \$2 }\'' + } + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + input[2] = false + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + } + test("Convert fasta to bed with program file") { when { params { diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index 1444c4688..9d6a36973 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -14,16 +14,16 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:31:50.761549948", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:42:17.741168488" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Convert fasta to bed": { "content": [ @@ -40,16 +40,16 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:30:50.804933797", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:41:46.810784678" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Convert fasta to bed with program file": { "content": [ @@ -66,16 +66,57 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:31:10.838989113", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:41:52.884002736" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "Convert fasta to bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "GAWK", + "gawk", + "5.3.1" + ] + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_gawk": [ + [ + "GAWK", + "gawk", + "5.3.1" + ] + ] + } + ], + "timestamp": "2026-03-04T11:31:00.182649403", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Extract first column from multiple files": { "content": [ @@ -92,16 +133,16 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:31:30.796772884", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:42:05.455428454" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Unzip files before processing": { "content": [ @@ -118,16 +159,16 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:31:40.72259289", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:42:11.976164295" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Convert fasta to bed using awk redirect instead of shell redirect": { "content": [ @@ -144,15 +185,15 @@ [ "GAWK", "gawk", - "5.3.0" + "5.3.1" ] ] } ], + "timestamp": "2026-03-04T11:31:20.33222004", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-05T16:41:58.777371598" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 33557bea1..e8fbc4f66 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -8,9 +8,7 @@ include { BCFTOOLS_ANNOTATE as RENAME_CHRNAMES } from '../../../modules/nf-core include { CADD } from '../../../modules/nf-core/cadd/main' include { GAWK as REFERENCE_TO_CADD_CHRNAMES } from '../../../modules/nf-core/gawk/main' include { GAWK as CADD_TO_REFERENCE_CHRNAMES } from '../../../modules/nf-core/gawk/main' -include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_VIEW } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CADD { @@ -22,7 +20,6 @@ workflow ANNOTATE_CADD { val_genome // string: GRCh37 or GRCh37 main: - ch_versions = channel.empty() ch_rename_chrs = channel.empty() if (val_genome.equals('GRCh38')) { @@ -36,10 +33,10 @@ workflow ANNOTATE_CADD { ch_vcf .map { meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ] } - .set { rename_chrnames_in } + .set { ch_rename_chrnames_in } RENAME_CHRNAMES ( - rename_chrnames_in, + ch_rename_chrnames_in, [], [], REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt } @@ -50,32 +47,20 @@ workflow ANNOTATE_CADD { .set { ch_vcf } } - BCFTOOLS_VIEW(ch_vcf, [], [], []) - TABIX_VIEW(BCFTOOLS_VIEW.out.vcf) - CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, [[:], []]) TABIX_CADD(CADD.out.tsv) ch_vcf .join(CADD.out.tsv) - .join(TABIX_CADD.out.tbi) - .map { meta, vcf, annotations, annotations_index -> [ meta, vcf, [], annotations, annotations_index ] } + .join(TABIX_CADD.out.index) .set { ch_annotate_in } BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_header.map { _meta, header -> header }, ch_rename_chrs) - TABIX_ANNOTATE (BCFTOOLS_ANNOTATE.out.vcf) - - ch_versions = ch_versions.mix(TABIX_VIEW.out.versions) - ch_versions = ch_versions.mix(CADD.out.versions) - ch_versions = ch_versions.mix(TABIX_CADD.out.versions) - ch_versions = ch_versions.mix(TABIX_ANNOTATE.out.versions) - emit: - tbi = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + tbi = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test new file mode 100644 index 000000000..fd7012169 --- /dev/null +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -0,0 +1,72 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_CADD" + script "subworkflows/local/annotate_cadd/main.nf" + workflow "ANNOTATE_CADD" + tag "subworkflows" + tag "annotate_cadd" + config "./nextflow.config" + + test("ANNOTATE_CADD - GRCh37, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[3] = channel.of([ + [id:'test', single_end: false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[4] = 'GRCh37' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } + + test("ANNOTATE_CADD - GRCh38, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[3] = channel.of([ + [id:'test', single_end: false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[4] = 'GRCh38' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } + +} diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap new file mode 100644 index 000000000..9e4755ddf --- /dev/null +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap @@ -0,0 +1,32 @@ +{ + "ANNOTATE_CADD - GRCh37, stub": { + "content": [ + [ + + ], + [ + + ] + ], + "timestamp": "2026-03-04T09:21:01.063197266", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "ANNOTATE_CADD - GRCh38, stub": { + "content": [ + [ + "test_ann_ann.vcf.gz" + ], + [ + "test_ann_ann.vcf.gz.tbi" + ] + ], + "timestamp": "2026-03-04T12:58:16.386863871", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_cadd/tests/nextflow.config b/subworkflows/local/annotate_cadd/tests/nextflow.config new file mode 100644 index 000000000..6b649a5a7 --- /dev/null +++ b/subworkflows/local/annotate_cadd/tests/nextflow.config @@ -0,0 +1,34 @@ +process { + + withName: 'BCFTOOLS_VIEW' { + ext.args = { "--output-type z --types indels,other" } + ext.prefix = { "${vcf.simpleName}_indels" } + } + + withName: 'CADD' { + container = "nf-core/ubuntu:22.04" //Using an basic container because v1.7.3 is too big for CI. + ext.args = { "-g ${params.genome}" } + ext.prefix = { "${vcf.simpleName}_cadd" } + } + + withName: 'TABIX_CADD' { + ext.args = { "--force --sequence 1 --begin 2 --end 2" } + } + + withName: 'BCFTOOLS_ANNOTATE' { + ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z --write-index=tbi" } + ext.prefix = { "${input.simpleName}_ann" } + } + + withName: 'CADD_TO_REFERENCE_CHRNAMES' { + ext.args2 = '\'{original=$1; sub("chr","",$1); print $1, original}\'' + ext.prefix = "cadd_to_reference" + ext.suffix = "txt" + } + + withName: 'REFERENCE_TO_CADD_CHRNAMES' { + ext.args2 = '\'{original=$1; sub("chr","",$1); print original, $1}\'' + ext.prefix = "reference_to_cadd" + ext.suffix = "txt" + } +} From 9d273a63bc27d14387208b4387f26bb1e2fe70ed Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 13:19:55 +0100 Subject: [PATCH 413/872] Update paths --- subworkflows/local/annotate_mt_snvs/main.nf | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 02ffa5cb8..496699da1 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -3,14 +3,14 @@ // -include { BCFTOOLS_PLUGINSETGT } from '../../modules/nf-core/bcftools/pluginsetgt' -include { TABIX_TABIX as TABIX_TABIX_MT } from '../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../modules/nf-core/tabix/tabix/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../modules/nf-core/ensemblvep/vep/main' -include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../modules/nf-core/haplogrep3/classify/main' -include { VCFANNO as VCFANNO_MT } from '../../modules/nf-core/vcfanno/main' -include { ANNOTATE_CADD } from './annotate_cadd' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../modules/nf-core/tabix/bgziptabix/main' +include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt' +include { TABIX_TABIX as TABIX_TABIX_MT } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../../modules/nf-core/tabix/tabix/main' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../modules/nf-core/ensemblvep/vep/main' +include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../../modules/nf-core/haplogrep3/classify/main' +include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' +include { ANNOTATE_CADD } from '../annotate_cadd' +include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow ANNOTATE_MT_SNVS { take: From 8d90541713787fc345126082b15f39d03f55083c Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 13:46:48 +0100 Subject: [PATCH 414/872] updated svdb module --- modules.json | 4 +- modules/nf-core/svdb/merge/environment.yml | 2 +- modules/nf-core/svdb/merge/main.nf | 4 +- .../svdb/merge/tests/main.nf.test.snap | 80 +++++++++---------- modules/nf-core/svdb/query/environment.yml | 2 +- modules/nf-core/svdb/query/main.nf | 4 +- .../svdb/query/tests/main.nf.test.snap | 6 +- 7 files changed, 51 insertions(+), 51 deletions(-) diff --git a/modules.json b/modules.json index 6e65b78db..15191ecc2 100644 --- a/modules.json +++ b/modules.json @@ -493,12 +493,12 @@ }, "svdb/merge": { "branch": "master", - "git_sha": "b75cf1a894cc2d63a81dc3bd58126de7f023acf9", + "git_sha": "7d09b5f86908bdd951e42aef9994ad5bb0f6c307", "installed_by": ["modules"] }, "svdb/query": { "branch": "master", - "git_sha": "7f56b1f1d2e8b7ca92260eb6b3244d26c319a00f", + "git_sha": "7d09b5f86908bdd951e42aef9994ad5bb0f6c307", "installed_by": ["modules"] }, "tabix/bgzip": { diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index dce89b7ea..c64deab4d 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: - bioconda::bcftools=1.23 - - bioconda::svdb=2.8.3 + - bioconda::svdb=2.8.4 diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 88002c962..ab14c8d0f 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -4,8 +4,8 @@ process SVDB_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ff995c756aa8a3c0af13b1d054eacd536a11d35de5fa288dacf558bc21696968/data': - 'community.wave.seqera.io/library/bcftools_svdb:ae3b14d2d608fd81' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f5/f59712ead354411dd8bea4918d777737ca4ef2ad1360289507fe35acb688e74f/data': + 'community.wave.seqera.io/library/bcftools_svdb:12db401acbacc624' }" input: tuple val(meta), path(vcfs) diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test.snap b/modules/nf-core/svdb/merge/tests/main.nf.test.snap index 6e8e14d5e..1312ce744 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/merge/tests/main.nf.test.snap @@ -15,16 +15,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:10.673745" + "timestamp": "2026-03-03T09:17:45.334283313" }, "2 samples, ['tiddit', 'cnvnator'], true - stub": { "content": [ @@ -47,7 +47,7 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ], "4": [ @@ -82,16 +82,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:52:04.81478" + "timestamp": "2026-03-03T09:19:49.291093513" }, "2 samples, ['tiddit', 'cnvnator'], []": { "content": [ @@ -109,16 +109,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:39.788196" + "timestamp": "2026-03-03T09:18:53.242914408" }, "2 samples, [], []": { "content": [ @@ -136,16 +136,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:30.166443" + "timestamp": "2026-03-03T09:18:29.326769277" }, "2 samples, ['tiddit', 'cnvnator'], true": { "content": [ @@ -163,16 +163,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:44.571583" + "timestamp": "2026-03-03T09:19:04.521659905" }, "1 sample, ['tiddit'], []": { "content": [ @@ -190,16 +190,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:20.286591" + "timestamp": "2026-03-03T09:18:07.070476091" }, "1 sample, [], true": { "content": [ @@ -217,16 +217,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:15.445349" + "timestamp": "2026-03-03T09:17:55.505389265" }, "1 sample, ['tiddit'], true": { "content": [ @@ -244,16 +244,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:25.013931" + "timestamp": "2026-03-03T09:18:17.604155783" }, "2 samples, [], true": { "content": [ @@ -271,16 +271,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:35.029226" + "timestamp": "2026-03-03T09:18:41.894600602" }, "2 samples, ['tiddit', 'cnvnator'], [] - stub": { "content": [ @@ -303,7 +303,7 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ], "4": [ @@ -338,16 +338,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:59.208139" + "timestamp": "2026-03-03T09:19:37.850074206" }, "2 samples, [], [] - stub": { "content": [ @@ -370,7 +370,7 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ], "4": [ @@ -405,16 +405,16 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:49.255901" + "timestamp": "2026-03-03T09:19:16.292841025" }, "2 samples, [], true - stub": { "content": [ @@ -437,7 +437,7 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ], "4": [ @@ -472,15 +472,15 @@ [ "SVDB_MERGE", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T09:51:54.851615" + "timestamp": "2026-03-03T09:19:26.851881345" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml index dce89b7ea..c64deab4d 100644 --- a/modules/nf-core/svdb/query/environment.yml +++ b/modules/nf-core/svdb/query/environment.yml @@ -5,4 +5,4 @@ channels: - bioconda dependencies: - bioconda::bcftools=1.23 - - bioconda::svdb=2.8.3 + - bioconda::svdb=2.8.4 diff --git a/modules/nf-core/svdb/query/main.nf b/modules/nf-core/svdb/query/main.nf index 873e0f1c1..3f33d31c0 100644 --- a/modules/nf-core/svdb/query/main.nf +++ b/modules/nf-core/svdb/query/main.nf @@ -4,8 +4,8 @@ process SVDB_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ff995c756aa8a3c0af13b1d054eacd536a11d35de5fa288dacf558bc21696968/data': - 'community.wave.seqera.io/library/bcftools_svdb:ae3b14d2d608fd81' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f5/f59712ead354411dd8bea4918d777737ca4ef2ad1360289507fe35acb688e74f/data': + 'community.wave.seqera.io/library/bcftools_svdb:12db401acbacc624' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/svdb/query/tests/main.nf.test.snap b/modules/nf-core/svdb/query/tests/main.nf.test.snap index 966ea2707..47ccc233f 100644 --- a/modules/nf-core/svdb/query/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/query/tests/main.nf.test.snap @@ -7,15 +7,15 @@ [ "SVDB_QUERY", "svdb", - "2.8.3" + "2.8.4" ] ] } ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-03T10:26:18.573659" + "timestamp": "2026-03-03T09:20:00.331166694" } } \ No newline at end of file From b6cf1573d5d68123eadbbf6b8d06ef3b88715793 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 14:02:36 +0100 Subject: [PATCH 415/872] add rank_variants test --- .../local/annotate_cadd/tests/main.nf.test | 9 +-- .../annotate_cadd/tests/main.nf.test.snap | 68 +++++++++++++++---- .../local/rank_variants/tests/main.nf.test | 63 +++++++++++++++++ .../rank_variants/tests/main.nf.test.snap | 60 ++++++++++++++++ 4 files changed, 179 insertions(+), 21 deletions(-) create mode 100644 subworkflows/local/rank_variants/tests/main.nf.test create mode 100644 subworkflows/local/rank_variants/tests/main.nf.test.snap diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test index fd7012169..7d85b13b6 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -30,10 +30,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, - workflow.out.tbi.collect { meta, tbi -> file(tbi).name } - ).match() } + { assert snapshot(workflow.out).match() } ) } } @@ -62,9 +59,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, - workflow.out.tbi.collect { meta, tbi -> file(tbi).name } - ).match() } + workflow.out).match() } ) } } diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap index 9e4755ddf..de0ebe1cd 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap @@ -1,14 +1,22 @@ { "ANNOTATE_CADD - GRCh37, stub": { "content": [ - [ - - ], - [ - - ] + { + "0": [ + + ], + "1": [ + + ], + "tbi": [ + + ], + "vcf": [ + + ] + } ], - "timestamp": "2026-03-04T09:21:01.063197266", + "timestamp": "2026-03-04T13:59:08.944351192", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -16,14 +24,46 @@ }, "ANNOTATE_CADD - GRCh38, stub": { "content": [ - [ - "test_ann_ann.vcf.gz" - ], - [ - "test_ann_ann.vcf.gz.tbi" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann_ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann_ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann_ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann_ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } ], - "timestamp": "2026-03-04T12:58:16.386863871", + "timestamp": "2026-03-04T13:59:33.695957972", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/rank_variants/tests/main.nf.test b/subworkflows/local/rank_variants/tests/main.nf.test new file mode 100644 index 000000000..0525da75e --- /dev/null +++ b/subworkflows/local/rank_variants/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_workflow { + + name "Test Workflow RANK_VARIANTS" + script "subworkflows/local/rank_variants/main.nf" + workflow "RANK_VARIANTS" + tag "subworkflows" + tag "rank_variants" + + test("RANK_VARIANTS - SNV (process_with_sort = false), stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)) + input[1] = channel.value(file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)) + input[2] = channel.value(file(params.pipelines_testdata_base_path + 'reference/rank_model_snv.ini', checkIfExists: true)) + input[3] = channel.of([ + [id:'justhusky', single_end: false], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true) + ]) + input[4] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("RANK_VARIANTS - SV (process_with_sort = true), stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.value(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true)) + input[1] = channel.value(file(params.pipelines_testdata_base_path + 'reference/reduced_penetrance.tsv', checkIfExists: true)) + input[2] = channel.value(file(params.pipelines_testdata_base_path + 'reference/rank_model_sv.ini', checkIfExists: true)) + input[3] = channel.of([ + [id:'justhusky', single_end: false], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz', checkIfExists: true) + ]) + input[4] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + +} diff --git a/subworkflows/local/rank_variants/tests/main.nf.test.snap b/subworkflows/local/rank_variants/tests/main.nf.test.snap new file mode 100644 index 000000000..77b6eb7ef --- /dev/null +++ b/subworkflows/local/rank_variants/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "RANK_VARIANTS - SV (process_with_sort = true), stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-04T13:56:59.686533478", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "RANK_VARIANTS - SNV (process_with_sort = false), stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-04T13:57:53.225169802", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 70bd30bd79459b1b1de8f2a016ab9fdee00b3602 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 14:17:15 +0100 Subject: [PATCH 416/872] updated snapshots --- tests/default.nf.test.snap | 12 ++++++------ tests/test_bam.nf.test.snap | 12 ++++++------ tests/test_singleton.nf.test.snap | 12 ++++++------ 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index cb38f65c1..2bfad0221 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -384,26 +384,26 @@ }, "SVDB_MERGE": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_CNVNATOR": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_ME": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_REPEATS": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_TIDDIT": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_QUERY_DB": { - "svdb": "2.8.3" + "svdb": "2.8.4" }, "TABIX_ANNOTATE": { "tabix": 1.21 diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index bb374b6e2..00e8f6b85 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -354,26 +354,26 @@ }, "SVDB_MERGE": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_CNVNATOR": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_ME": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_REPEATS": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_TIDDIT": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_QUERY_DB": { - "svdb": "2.8.3" + "svdb": "2.8.4" }, "TABIX_ANNOTATE": { "tabix": 1.21 diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 42e681d81..0e50b6da0 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -373,26 +373,26 @@ }, "SVDB_MERGE": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_CNVNATOR": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_ME": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_REPEATS": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_MERGE_TIDDIT": { "bcftools": 1.23, - "svdb": "2.8.3" + "svdb": "2.8.4" }, "SVDB_QUERY_DB": { - "svdb": "2.8.3" + "svdb": "2.8.4" }, "TABIX_ANNOTATE": { "tabix": 1.21 From 130ac2281d2525c5b36fa434b3ef001699e6ad49 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 14:39:41 +0100 Subject: [PATCH 417/872] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2beacaeb..408666700 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -77,6 +77,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | +| svdb | 2.8.3 | 2.8.4 | | tiddit | 3.6.1 | 3.9.4 | | ucsc | 447 | 482 | | vcfanno | 0.3.5 | 0.3.7 | From 1ec9fde006258b5cdad8dd83348ed6f786828f36 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 4 Mar 2026 16:15:35 +0100 Subject: [PATCH 418/872] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 408666700..16f89fa5f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed eKLIPse [#743](https://github.com/nf-core/raredisease/pull/743) - Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) - Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) +- Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) ### `Fixed` From 416bb62e02b8beac54ca148813606ff2f454e68a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 17:17:37 +0100 Subject: [PATCH 419/872] Review suggestions --- .../tests/main.nf.test | 8 +- .../call_mobile_elements/tests/main.nf.test | 5 +- .../tests/main.nf.test.snap | 42 +++- .../local/call_snv/tests/main.nf.test | 60 +++++- .../local/call_snv/tests/main.nf.test.snap | 180 ++++++++++++++++-- .../local/call_snv_MT/tests/main.nf.test | 30 +++ .../local/call_snv_MT/tests/main.nf.test.snap | 4 +- .../call_snv_deepvariant/tests/main.nf.test | 30 +++ .../local/call_sv_cnvnator/tests/main.nf.test | 32 ++++ .../call_sv_cnvnator/tests/main.nf.test.snap | 8 +- .../local/call_sv_manta/tests/main.nf.test | 3 - .../local/call_sv_tiddit/tests/main.nf.test | 3 - .../subsample_mt_frac/tests/main.nf.test | 5 +- 13 files changed, 364 insertions(+), 46 deletions(-) diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test index eefd009b8..ff2055a66 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -30,8 +30,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - path(workflow.out.vcf_ann[0][1].toString()).vcf.variantsMD5, - path(workflow.out.vcf_ann[0][1].toString()).vcf.summary + path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5, + path(workflow.out.vcf_ann[0][1]).vcf.summary ).match() } ) } @@ -59,8 +59,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - path(workflow.out.vcf_ann[0][1].toString()).vcf.variantsMD5, - path(workflow.out.vcf_ann[0][1].toString()).vcf.summary + path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5, + path(workflow.out.vcf_ann[0][1]).vcf.summary ).match() } ) } diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test b/subworkflows/local/call_mobile_elements/tests/main.nf.test index 58704f076..5655d906b 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test @@ -29,10 +29,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, - workflow.out.tbi.collect { meta, tbi -> file(tbi).name } - ).match() } + { assert snapshot(workflow.out).match() } ) } } diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap index ac97b2c1e..9ce36a3b4 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap @@ -1,14 +1,42 @@ { "CALL_MOBILE_ELEMENTS - stub": { "content": [ - [ - "justhusky_mobile_elements.vcf.gz" - ], - [ - "justhusky_mobile_elements.vcf.gz.tbi" - ] + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } ], - "timestamp": "2026-03-01T17:14:06.948018519", + "timestamp": "2026-03-04T15:43:58.250066806", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index cef6bdfb6..635552bca 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,11 +59,69 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.genome_vcf.collect { meta, vcf -> file(vcf).name }, + path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, + path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, workflow.out.mt_vcf.collect { meta, vcf -> file(vcf).name } ).match() } ) } } + + test("CALL_SNV - deepvariant wgs, stub") { + + when { + workflow { + """ + input[0] = channel.of([[id:'interval'], []]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz', checkIfExists: true)]) + input[3] = channel.of([[id:'genome'], []]) + input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[5] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[9] = channel.of([[id:'model'], []]) + input[10] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[11] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[12] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[13] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[14] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt.intervals', checkIfExists: true)).collect() + input[15] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[16] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.dict', checkIfExists: true)]).collect() + input[17] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.fasta.fai', checkIfExists: true)]).collect() + input[18] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_shift.fasta', checkIfExists: true)]).collect() + input[19] = channel.of(file(params.pipelines_testdata_base_path + 'reference/mt_shift8000.intervals', checkIfExists: true)).collect() + input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/mt_shift8000.back_chain', checkIfExists: true)]).collect() + input[21] = channel.of([[id:'par'], []]) + input[22] = channel.of([[id:'model'], []]) + input[23] = channel.of([[id:'target'], [], []]) + input[24] = 'wgs' + input[25] = false + input[26] = false + input[27] = 'deepvariant' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 5d3984055..95e17a8d1 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -1,9 +1,8 @@ { "CALL_SNV - deepvariant wgs": { "content": [ - [ - "justhusky_snv.vcf.gz" - ], + "dfc0eeae02f4c1f04034e0fff555bf50", + "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ "justhusky_snv.vcf.gz.tbi" ], @@ -11,7 +10,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-03T19:48:35.971369089", + "timestamp": "2026-03-04T15:51:36.199641201", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -19,17 +18,170 @@ }, "CALL_SNV - deepvariant wgs, stub": { "content": [ - [ - "justhusky_snv.vcf.gz" - ], - [ - "justhusky_snv.vcf.gz.tbi" - ], - [ - "justhusky_mitochondria.vcf.gz" - ] + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + ] + ], + "2": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + ] + ], + "3": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34" + ] + ], + "4": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34", + "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + ] + ], + "5": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,ad41a60a92aa9d56f5a08490e4964ae1" + ] + ], + "6": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,2d9e15946c5c4880f98f9fe77258eb84" + ] + ], + "7": [ + + ], + "genome_gtabix": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + ] + ], + "genome_gvcf": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + ] + ], + "genome_tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + ] + ], + "genome_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34" + ] + ], + "genome_vcf_tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34", + "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + ] + ], + "mt_tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,ad41a60a92aa9d56f5a08490e4964ae1" + ] + ], + "mt_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,2d9e15946c5c4880f98f9fe77258eb84" + ] + ], + "versions": [ + + ] + } ], - "timestamp": "2026-03-01T17:27:18.706368747", + "timestamp": "2026-03-04T15:56:34.554829357", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test b/subworkflows/local/call_snv_MT/tests/main.nf.test index 7aada2df4..558a81d49 100644 --- a/subworkflows/local/call_snv_MT/tests/main.nf.test +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test @@ -24,6 +24,36 @@ nextflow_workflow { } } + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + ).match() } + ) + } + } + test("CALL_SNV_MT, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[2] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[4] = channel.of(file('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/reference/mt.intervals', checkIfExists: true)).collect() + """ + } + } + then { assertAll( { assert workflow.success }, diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test.snap b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap index 9de7d0544..63b18c146 100644 --- a/subworkflows/local/call_snv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "CALL_SNV_MT - stub": { + "CALL_SNV_MT, stub": { "content": [ [ "earlycasualcaiman_filtered.vcf.gz" @@ -8,7 +8,7 @@ "earlycasualcaiman_filtered.vcf.gz.tbi" ] ], - "timestamp": "2026-03-01T17:35:07.245240789", + "timestamp": "2026-03-04T17:12:30.676957964", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 0d2b6af03..f24676cb3 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -39,4 +39,34 @@ nextflow_workflow { ) } } + + test("CALL_SNV_DEEPVARIANT - wgs") { + + when { + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of([[id:'par'], []]) + input[7] = channel.of([[id:'target'], [], []]) + input[8] = 'wgs' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test index fc2883e5f..ce9b011e3 100644 --- a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test @@ -37,4 +37,36 @@ nextflow_workflow { ) } } + + test("CALL_SV_CNVNATOR -stub") { + + options "-stub" + + when { + params { + cnvnator_binsize = "10000" + } + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'justhusky']) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.vcf.collect { meta, vcf -> file(vcf).name } + ).match() } + ) + } + } } diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap index 3d3df5679..8f70996f8 100644 --- a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test.snap @@ -1,23 +1,23 @@ { - "CALL_SV_CNVNATOR": { + "CALL_SV_CNVNATOR -stub": { "content": [ [ "justhusky_cnvnator.vcf.gz" ] ], - "timestamp": "2026-03-01T20:36:50.087101237", + "timestamp": "2026-03-04T17:14:53.940820631", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } }, - "CALL_SV_CNVNATOR - stub": { + "CALL_SV_CNVNATOR": { "content": [ [ "justhusky_cnvnator.vcf.gz" ] ], - "timestamp": "2026-03-01T20:22:17.821272901", + "timestamp": "2026-03-01T20:36:50.087101237", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test index 9559081e7..5c93c19f7 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -10,9 +10,6 @@ nextflow_workflow { test("CALL_SV_MANTA - wgs") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = channel.of( diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index e7b28fcf1..0b139f56f 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -24,9 +24,6 @@ nextflow_workflow { } when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = channel.of( diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test b/subworkflows/local/subsample_mt_frac/tests/main.nf.test index 296f122c0..88ff1aec6 100644 --- a/subworkflows/local/subsample_mt_frac/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test @@ -10,13 +10,10 @@ nextflow_workflow { test("SUBSAMPLE_MT_FRAC") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [id:'earlycasualcaiman', seedfrac: 0.1, sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) From 999a840eab9ec6392e678d56aa156041263e074e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 20:31:35 +0100 Subject: [PATCH 420/872] Fix test fails --- .../call_snv_deepvariant/tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 115 ++++++++++++++++++ .../local/call_sv_tiddit/tests/main.nf.test | 2 +- .../call_sv_tiddit/tests/main.nf.test.snap | 4 +- .../call_sv_tiddit/tests/nextflow.config | 1 + 5 files changed, 120 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index f24676cb3..a3e433173 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -40,7 +40,7 @@ nextflow_workflow { } } - test("CALL_SNV_DEEPVARIANT - wgs") { + test("CALL_SNV_DEEPVARIANT - wgs, stub") { when { workflow { diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index 96112588c..f027b6cea 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -1,4 +1,119 @@ { + "CALL_SNV_DEEPVARIANT - wgs, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + ] + ], + "2": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,8283021466e07e50c03a3baba5a195b8" + ] + ], + "3": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,9db1287686ce5b732273da892d8e4613" + ] + ], + "gvcf": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + ] + ], + "gvcf_tabix": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + ] + ], + "tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,8283021466e07e50c03a3baba5a195b8" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,9db1287686ce5b732273da892d8e4613" + ] + ] + } + ], + "timestamp": "2026-03-04T20:01:54.517768538", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CALL_SNV_DEEPVARIANT - wgs": { "content": [ "e4e9e39859d7df52fd955fb32796fdb2", diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index 0b139f56f..7f86ae815 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -48,7 +48,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - path(workflow.out.vcf[0][1]).vcf.summary + path(workflow.out.vcf[0][1]).vcf.chromosomes == ['MT', '21'] as Set ).match() } ) } diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap index 4327bc183..242094c46 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap @@ -1,9 +1,9 @@ { "CALL_SV_TIDDIT": { "content": [ - "VcfFile [chromosomes=[MT, 21], sampleCount=3, variantCount=178, phased=false, phasedAutodetect=false]" + true ], - "timestamp": "2026-03-03T22:37:56.960203544", + "timestamp": "2026-03-04T20:29:06.356832656", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_tiddit/tests/nextflow.config b/subworkflows/local/call_sv_tiddit/tests/nextflow.config index a4f70c367..dc0a83a03 100644 --- a/subworkflows/local/call_sv_tiddit/tests/nextflow.config +++ b/subworkflows/local/call_sv_tiddit/tests/nextflow.config @@ -10,6 +10,7 @@ process { } withName: 'SVDB_MERGE_TIDDIT' { + ext.args = '--notag --pass_only' ext.prefix = { "${meta.id}_svdb_tiddit" } } } From e002163fc53db11dc28b9458d84aab72b01948db Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 21:20:56 +0100 Subject: [PATCH 421/872] Fix DV testx --- .../call_snv_deepvariant/tests/main.nf.test | 2 ++ .../tests/main.nf.test.snap | 18 +++++++++--------- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index a3e433173..c4151469e 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -42,6 +42,8 @@ nextflow_workflow { test("CALL_SNV_DEEPVARIANT - wgs, stub") { + options "-stub" + when { workflow { """ diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index f027b6cea..ded5b9a08 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -17,7 +17,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "1": [ @@ -35,7 +35,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "2": [ @@ -43,7 +43,7 @@ { "id": "justhusky" }, - "justhusky_split_rmdup_info.vcf.gz.tbi:md5,8283021466e07e50c03a3baba5a195b8" + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ @@ -51,7 +51,7 @@ { "id": "justhusky" }, - "justhusky_split_rmdup_info.vcf.gz:md5,9db1287686ce5b732273da892d8e4613" + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "gvcf": [ @@ -69,7 +69,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "gvcf_tabix": [ @@ -87,7 +87,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "tabix": [ @@ -95,7 +95,7 @@ { "id": "justhusky" }, - "justhusky_split_rmdup_info.vcf.gz.tbi:md5,8283021466e07e50c03a3baba5a195b8" + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -103,12 +103,12 @@ { "id": "justhusky" }, - "justhusky_split_rmdup_info.vcf.gz:md5,9db1287686ce5b732273da892d8e4613" + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] } ], - "timestamp": "2026-03-04T20:01:54.517768538", + "timestamp": "2026-03-04T21:10:26.381980616", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From c4b8c09dc94df83e8d28abc20cf3fe3e3ad02c67 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 21:52:28 +0100 Subject: [PATCH 422/872] Update main.nf.test --- subworkflows/local/call_sv_tiddit/tests/main.nf.test | 3 --- 1 file changed, 3 deletions(-) diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index 7f86ae815..ed84df814 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -30,9 +30,6 @@ nextflow_workflow { [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)], - [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true)], [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] From 2bdbdd0ffe7db906c79ec0e6336b3efb4130f44e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 22:07:17 +0100 Subject: [PATCH 423/872] Update num shards --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 907fd6643..6b7dade1f 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -50,7 +50,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 7 + max_shards: 14 - name: debug run: | From c3fcf3dee039d9db62e8f670191fde3910cae454 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 4 Mar 2026 23:41:45 +0100 Subject: [PATCH 424/872] add annotate_genome_snvs test --- .../annotate_genome_snvs/tests/main.nf.test | 50 +++++++++++ .../tests/main.nf.test.snap | 83 +++++++++++++++++++ .../tests/nextflow.config | 73 ++++++++++++++++ 3 files changed, 206 insertions(+) create mode 100644 subworkflows/local/annotate_genome_snvs/tests/main.nf.test create mode 100644 subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_genome_snvs/tests/nextflow.config diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test new file mode 100644 index 000000000..81134bdf0 --- /dev/null +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -0,0 +1,50 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_GENOME_SNVS" + script "subworkflows/local/annotate_genome_snvs/main.nf" + workflow "ANNOTATE_GENOME_SNVS" + tag "subworkflows" + tag "annotate_genome_snvs" + config "./nextflow.config" + + test("ANNOTATE_GENOME_SNVS - GRCh37, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[1] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = channel.value([[],[]]) + input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([ + [id:'justhusky', probands:['earlycasualcaiman'], upd_children:[], mother:'', father:''], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[9] = channel.value([[]]) + input[10] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[11] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[14] = channel.value([]) + input[15] = null + input[16] = 'GRCh37' + input[17] = 107 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap new file mode 100644 index 000000000..c77062433 --- /dev/null +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -0,0 +1,83 @@ +{ + "ANNOTATE_GENOME_SNVS - GRCh37, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "2": [ + + ], + "tbi": [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf_ann": [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + + ] + } + ], + "timestamp": "2026-03-04T23:37:13.141316008", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_genome_snvs/tests/nextflow.config b/subworkflows/local/annotate_genome_snvs/tests/nextflow.config new file mode 100644 index 000000000..ca73a5c7f --- /dev/null +++ b/subworkflows/local/annotate_genome_snvs/tests/nextflow.config @@ -0,0 +1,73 @@ +process { + + withName: 'BCFTOOLS_ROH' { + ext.args = { "--samples ${meta.probands.unique().first()} --skip-indels " } + ext.prefix = { "${meta.id}_roh" } + } + + withName: 'RHOCALL_ANNOTATE' { + ext.args = { "--v14 " } + } + + withName: 'ZIP_TABIX_ROHCALL' { + ext.prefix = { "${input.simpleName}" } + } + + withName: 'GATK4_SELECTVARIANTS' { + ext.prefix = { "${vcf.simpleName}_${intervals.simpleName}" } + } + + withName: 'VCFANNO' { + ext.prefix = { "${meta.prefix}_vcfanno_${meta.scatterid}" } + } + + withName: 'UPD_SITES' { + ext.prefix = { "${meta.upd_child}_upd_sites" } + ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} sites"} + } + + withName: 'UPD_REGIONS' { + ext.prefix = { "${meta.upd_child}_upd_regions" } + ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} regions --min-size 5 --min-sites 1"} + } + + withName: 'CHROMOGRAPH_SITES' { + ext.prefix = { "${meta7.upd_child}_chromograph_sites" } + ext.args = { "--euploid" } + } + + withName: 'CHROMOGRAPH_REGIONS' { + ext.prefix = { "${meta6.upd_child}_chromograph_regions" } + ext.args = { '--euploid' } + } + + withName: 'ZIP_TABIX_VCFANNO' { + ext.prefix = { "${input.simpleName}" } + } + + withName: 'BCFTOOLS_VIEW' { + ext.prefix = { "${meta.prefix}_filter_${meta.scatterid}" } + } + + withName: 'ENSEMBLVEP_SNV' { + ext.prefix = { "${meta.prefix}_vep_${meta.scatterid}" } + ext.args = { [ + '--dir_plugins vep_cache/Plugins', + '--plugin LoFtool,LoFtool_scores.txt', + '--plugin pLI,pLI_values.txt', + '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', + '--distance 5000', + '--buffer_size 20000', + '--format vcf --max_sv_size 248956422', + '--appris --biotype --cache --canonical --ccds --compress_output bgzip', + '--domains --exclude_predicted --force_overwrite', + '--hgvs --humdiv --no_progress --numbers', + '--merged --polyphen p --protein --offline --regulatory --sift p --symbol --tsl', + '--uniprot --vcf' + ].join(' ') } + } + + withName: 'BCFTOOLS_CONCAT' { + ext.args = { "-Oz" } + } +} From 618c3374dc364176cf539a0b9eb624ea24763eee Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 00:18:19 +0100 Subject: [PATCH 425/872] add test for annotate_mobile_elements --- .../tests/main.nf.test | 48 +++++++++++++++++++ .../tests/main.nf.test.snap | 31 ++++++++++++ .../tests/nextflow.config | 20 ++++++++ 3 files changed, 99 insertions(+) create mode 100644 subworkflows/local/annotate_mobile_elements/tests/main.nf.test create mode 100644 subworkflows/local/annotate_mobile_elements/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_mobile_elements/tests/nextflow.config diff --git a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test new file mode 100644 index 000000000..819d2ea98 --- /dev/null +++ b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test @@ -0,0 +1,48 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_MOBILE_ELEMENTS" + script "subworkflows/local/annotate_mobile_elements/main.nf" + workflow "ANNOTATE_MOBILE_ELEMENTS" + tag "subworkflows" + tag "annotate_mobile_elements" + config "./nextflow.config" + + test("ANNOTATE_MOBILE_ELEMENTS - GRCh37, stub") { + + options "-stub" + + when { + params { + bcftools_args = "--output-type z" + } + workflow { + """ + input[0] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[2] = channel.of([ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + 'FRQ', + 'OCC', + 'swegen_FRQ', + 'swegen_OCC' + ]) + input[3] = channel.of([ + [id:'justhusky', single_end:false], + file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true) + ]) + input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[5] = 'GRCh37' + input[6] = 107 + input[7] = channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test.snap new file mode 100644 index 000000000..febc7e5db --- /dev/null +++ b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "ANNOTATE_MOBILE_ELEMENTS - GRCh37, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky_filter.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_ann": [ + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky_filter.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-05T00:16:05.837537418", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_mobile_elements/tests/nextflow.config b/subworkflows/local/annotate_mobile_elements/tests/nextflow.config new file mode 100644 index 000000000..13ccf42dc --- /dev/null +++ b/subworkflows/local/annotate_mobile_elements/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + + withName: 'SVDB_QUERY_DB' { + ext.prefix = { "${meta.id}_me_svdb" } + } + + withName: 'PICARD_SORTVCF' { + ext.prefix = { "${meta.id}_sortvcf" } + } + + withName: 'ENSEMBLVEP_ME' { + ext.prefix = { "${meta.id}_svdbquery_vep" } + } + + withName: 'BCFTOOLS_VIEW_FILTER' { + ext.args = { params.bcftools_args } + ext.prefix = { "${meta.id}_filter" } + } + +} From 77783fee31e8d414b6c4f57f3868b8fbd6b76d2d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 00:26:58 +0100 Subject: [PATCH 426/872] update call snv test --- .../local/call_snv/tests/main.nf.test | 2 ++ .../local/call_snv/tests/main.nf.test.snap | 34 +++++++++---------- 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 635552bca..35cdbda99 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -70,6 +70,8 @@ nextflow_workflow { test("CALL_SNV - deepvariant wgs, stub") { + options "-stub" + when { workflow { """ diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 95e17a8d1..7fa01d040 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -34,7 +34,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "1": [ @@ -52,7 +52,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "2": [ @@ -60,7 +60,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ @@ -68,7 +68,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "4": [ @@ -76,8 +76,8 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34", - "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "5": [ @@ -85,7 +85,7 @@ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz.tbi:md5,ad41a60a92aa9d56f5a08490e4964ae1" + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -93,7 +93,7 @@ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz:md5,2d9e15946c5c4880f98f9fe77258eb84" + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "7": [ @@ -114,7 +114,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1c4a347d20d354e38353bca7d9282522" + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], "genome_gvcf": [ @@ -132,7 +132,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,6e2498db92386f06f95c5f5ea5e7c2f8" + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], "genome_tabix": [ @@ -140,7 +140,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "genome_vcf": [ @@ -148,7 +148,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "genome_vcf_tabix": [ @@ -156,8 +156,8 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,cacbe4a160bdde3667c8706f4aa52e34", - "justhusky_snv.vcf.gz.tbi:md5,901708bdd55d2ef38e56ab74f8619057" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "mt_tabix": [ @@ -165,7 +165,7 @@ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz.tbi:md5,ad41a60a92aa9d56f5a08490e4964ae1" + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "mt_vcf": [ @@ -173,7 +173,7 @@ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz:md5,2d9e15946c5c4880f98f9fe77258eb84" + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ @@ -181,7 +181,7 @@ ] } ], - "timestamp": "2026-03-04T15:56:34.554829357", + "timestamp": "2026-03-05T00:25:20.084209813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 54e4f6b62dd79c4321a60d11ddd8122635487617 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 11:32:14 +0100 Subject: [PATCH 427/872] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2beacaeb..af16c8e27 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1 (homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) - Topic channels to local modules to caputure versions [#774](https://github.com/nf-core/raredisease/pull/774) - MitoSalt to detect mitochondrial deletions [#743](https://github.com/nf-core/raredisease/pull/743) +- Tests to some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) ### `Changed` From fdb8c07d22ddf1570faf14c8116a1b0a6c3f0fea Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 13:08:54 +0100 Subject: [PATCH 428/872] add more tests --- .../tests/main.nf.test | 27 ++++ .../tests/main.nf.test.snap | 27 ++++ .../local/call_sv_manta/tests/main.nf.test | 39 ++++++ .../call_sv_manta/tests/main.nf.test.snap | 123 +++++++++++++++++ .../local/call_sv_tiddit/tests/main.nf.test | 43 ++++++ .../call_sv_tiddit/tests/main.nf.test.snap | 27 ++++ .../tests/main.nf.test | 29 ++++ .../tests/main.nf.test.snap | 129 ++++++++++++++++++ .../subsample_mt_frac/tests/main.nf.test | 23 ++++ .../subsample_mt_reads/tests/main.nf.test | 25 +++- 10 files changed, 491 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test index ff2055a66..1c31b258b 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -65,4 +65,31 @@ nextflow_workflow { ) } } + test("ANNOTATE_CSQ_PLI - with index, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'var_csq'], + file(params.pipelines_testdata_base_path + 'reference/variant_consequences_v2.txt', checkIfExists: true) + ]).collect() + input[1] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) + ]) + input[2] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap index f1765956b..8f9e23930 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap @@ -20,5 +20,32 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "ANNOTATE_CSQ_PLI - with index, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_ann": [ + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-05T12:55:16.985254117", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test index 5c93c19f7..44124b955 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -47,4 +47,43 @@ nextflow_workflow { ) } } + test("CALL_SV_MANTA - wgs, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true)] + ) + input[1] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)], + [[id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:2, paternal:'earlycasualcaiman', maternal:'slowlycivilbuck', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] + ) + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'justhusky']) + input[5] = channel.of([[id:'target'], [], []]) + input[6] = 'wgs' + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test.snap b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap index e7bd2d64a..cbc481726 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap @@ -9,5 +9,128 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "CALL_SV_MANTA - wgs, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_small_indels.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_small_indels.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "justhusky" + }, + "justhusky.diploid_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "justhusky" + }, + "justhusky.diploid_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "justhusky" + }, + "justhusky_manta_filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "candidate_small_indels_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_small_indels.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "candidate_small_indels_vcf_tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_small_indels.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "candidate_sv_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "candidate_sv_vcf_tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky.candidate_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "diploid_sv_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky.diploid_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "diploid_sv_vcf_tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky.diploid_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "filtered_diploid_sv_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_manta_filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-05T12:58:54.578278212", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index ed84df814..6d4bc7f3a 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -50,4 +50,47 @@ nextflow_workflow { ) } } + test("CALL_SV_TIDDIT, stub") { + + options "-stub" + + setup { + run("BWA_INDEX") { + script "modules/nf-core/bwa/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'genome'], + file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + workflow { + """ + input[0] = channel.of( + [[id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)], + [[id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = BWA_INDEX.out.index.collect() + input[3] = channel.of([id:'justhusky']) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap index 242094c46..7d377df60 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test.snap @@ -1,4 +1,31 @@ { + "CALL_SV_TIDDIT, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky_svdb_tiddit.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_svdb_tiddit.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-05T13:01:06.562601729", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CALL_SV_TIDDIT": { "content": [ true diff --git a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test index 57b7c62ad..b7f335fc3 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test +++ b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test @@ -32,4 +32,33 @@ nextflow_workflow { ) } } + + test("CONVERT_MT_BAM_TO_FASTQ - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out + ).match() } + ) + } + } } diff --git a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap index 5851f631c..15bf3061a 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap +++ b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test.snap @@ -1,4 +1,133 @@ { + "CONVERT_MT_BAM_TO_FASTQ - stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "ubam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.reverted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-05T13:04:42.938137711", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CONVERT_MT_BAM_TO_FASTQ": { "content": [ { diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test b/subworkflows/local/subsample_mt_frac/tests/main.nf.test index 88ff1aec6..24c5982d2 100644 --- a/subworkflows/local/subsample_mt_frac/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test @@ -27,4 +27,27 @@ nextflow_workflow { assert workflow.success } } + + test("SUBSAMPLE_MT_FRAC -stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', seedfrac: 0.1, sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = 150 + input[2] = 30 + """ + } + } + + then { + assert workflow.success + } + } } diff --git a/subworkflows/local/subsample_mt_reads/tests/main.nf.test b/subworkflows/local/subsample_mt_reads/tests/main.nf.test index 3a83af0f1..07d84f05c 100644 --- a/subworkflows/local/subsample_mt_reads/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_reads/tests/main.nf.test @@ -12,7 +12,30 @@ nextflow_workflow { when { params { mt_subsample_reads = 18000 - outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assert workflow.success + } + } + + test("SUBSAMPLE_MT_READS -stub") { + + options "-stub" + + when { + params { + mt_subsample_reads = 18000 } workflow { """ From a4651bca9ce91a44b8d366177a90ec0a9934d242 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 14:43:59 +0100 Subject: [PATCH 429/872] Update CHANGELOG.md --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bffd95ff7..abd76d409 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - A parameter `homoplasmy_af_threshold` to set genotypes of MT SNVs to 1/1 (homoplasmic) when AF >=`homoplasmy_af_threshold` [#768](https://github.com/nf-core/raredisease/pull/768) - Topic channels to local modules to caputure versions [#774](https://github.com/nf-core/raredisease/pull/774) - MitoSalt to detect mitochondrial deletions [#743](https://github.com/nf-core/raredisease/pull/743) -- Tests to some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) +- Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) +- Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) ### `Changed` From 901a115541a34eca7d9d5ce012d1e6ff94d08089 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 15:32:02 +0100 Subject: [PATCH 430/872] Update snap --- tests/default.nf.test.snap | 4 ++-- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2bfad0221..d4e118a78 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -208,7 +208,7 @@ "gatk4": "4.6.2.0" }, "GAWK": { - "gawk": "5.3.0" + "gawk": "5.3.1" }, "GENMOD_ANNOTATE": { "genmod": "3.10.2" @@ -1103,7 +1103,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T10:21:06.035670185", + "timestamp": "2026-03-05T15:21:47.257080881", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 00e8f6b85..cb518bd2b 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -199,7 +199,7 @@ "gatk4": "4.6.2.0" }, "GAWK": { - "gawk": "5.3.0" + "gawk": "5.3.1" }, "GENMOD_ANNOTATE": { "genmod": "3.10.2" @@ -1032,7 +1032,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-03T10:27:29.654590007", + "timestamp": "2026-03-05T15:28:02.779912134", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 0e50b6da0..7b7f2890e 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -200,7 +200,7 @@ "gatk4": "4.6.2.0" }, "GAWK": { - "gawk": "5.3.0" + "gawk": "5.3.1" }, "GENMOD_ANNOTATE": { "genmod": "3.10.2" @@ -722,7 +722,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-03T10:31:17.265377549", + "timestamp": "2026-03-05T15:31:47.943426601", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 3002285725f353a01b84f99b59af58fef3f97230 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 5 Mar 2026 16:20:59 +0100 Subject: [PATCH 431/872] Add test for annotate_mt_snvs --- .../local/annotate_mt_snvs/tests/main.nf.test | 47 ++++++++ .../annotate_mt_snvs/tests/main.nf.test.snap | 103 ++++++++++++++++++ .../annotate_mt_snvs/tests/nextflow.config | 39 +++++++ 3 files changed, 189 insertions(+) create mode 100644 subworkflows/local/annotate_mt_snvs/tests/main.nf.test create mode 100644 subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_mt_snvs/tests/nextflow.config diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test new file mode 100644 index 000000000..82626ffff --- /dev/null +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -0,0 +1,47 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_MT_SNVS" + script "subworkflows/local/annotate_mt_snvs/main.nf" + workflow "ANNOTATE_MT_SNVS" + tag "subworkflows" + tag "annotate_mt_snvs" + config "./nextflow.config" + + test("ANNOTATE_MT_SNVS - GRCh37, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[1] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[2] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[4] = channel.of([ + [id:'justhusky', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true) + ]) + input[5] = channel.value([[]]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[7] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[10] = channel.value([]) + input[11] = false + input[12] = null + input[13] = 'GRCh37' + input[14] = 1.0 + input[15] = 107 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap new file mode 100644 index 000000000..84bdc1faf --- /dev/null +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -0,0 +1,103 @@ +{ + "ANNOTATE_MT_SNVS - GRCh37, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + + ], + "haplog": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf_ann": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + + ] + } + ], + "timestamp": "2026-03-05T16:20:14.293268403", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_mt_snvs/tests/nextflow.config b/subworkflows/local/annotate_mt_snvs/tests/nextflow.config new file mode 100644 index 000000000..6d30464f6 --- /dev/null +++ b/subworkflows/local/annotate_mt_snvs/tests/nextflow.config @@ -0,0 +1,39 @@ +process { + + withName: 'VCFANNO_MT' { + ext.prefix = { "${meta.prefix}" } + } + + withName: 'ZIP_TABIX_VCFANNO_MT' { + ext.prefix = { "${meta.prefix}" } + } + + withName: 'ENSEMBLVEP_MT' { + ext.args = { [ + '--dir_plugins vep_cache/Plugins', + '--plugin LoFtool,LoFtool_scores.txt', + '--plugin pLI,pLI_values.txt', + '--plugin SpliceAI,snv=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz,indel=spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', + '--distance 0', + '--buffer_size 20000', + '--format vcf --max_sv_size 248956422', + '--appris --biotype --cache --canonical --ccds --compress_output bgzip', + '--domains --exclude_predicted --force_overwrite', + '--hgvs --humdiv --no_progress --numbers', + '--merged --polyphen p --protein --offline --regulatory --sift p --symbol --tsl --vcf', + '--uniprot' + ].join(' ') } + ext.prefix = { "${meta.prefix}" } + } + + withName: 'HAPLOGREP3_CLASSIFY_MT' { + ext.args = '--tree phylotree-rsrs@17.1' + ext.prefix = { "${meta.prefix}_haplogrep" } + } + + withName: 'BCFTOOLS_PLUGINSETGT' { + ext.prefix = { "${meta.prefix}_mt_modifiedgt" } + ext.args = "--output-type z --write-index=tbi" + ext.args2 = { "-i 'FMT/AF>=${params.homoplasmy_af_threshold} && FMT/DP>=100'" } + } +} From cbf59d2414465767ce3f144f989f1a898515b1c6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 08:54:28 +0100 Subject: [PATCH 432/872] update tests --- conf/modules/annotate_rhocallviz.config | 2 +- .../local/annotate_rhocallviz/main.nf | 5 +- .../annotate_rhocallviz/tests/main.nf.test | 40 ++++++ .../annotate_rhocallviz/tests/nextflow.config | 32 +++++ .../tests/main.nf.test | 85 +++++++++++ .../tests/main.nf.test.snap | 88 ++++++++++++ .../tests/nextflow.config | 24 ++++ .../call_snv_sentieon/tests/main.nf.test | 84 +++++++++++ .../call_snv_sentieon/tests/nextflow.config | 40 ++++++ .../local/call_sv_MT/tests/main.nf.test | 66 +++++++++ .../local/call_sv_MT/tests/main.nf.test.snap | 121 ++++++++++++++++ .../local/call_sv_MT/tests/nextflow.config | 8 ++ .../tests/main.nf.test | 73 ++++++++++ .../tests/nextflow.config | 20 +++ subworkflows/local/gens/tests/main.nf.test | 82 +++++++++++ .../local/gens/tests/main.nf.test.snap | 136 ++++++++++++++++++ subworkflows/local/gens/tests/nextflow.config | 11 ++ .../postprocess_MT_calls/tests/main.nf.test | 42 ++++++ .../tests/main.nf.test.snap | 45 ++++++ subworkflows/local/variant_evaluation/main.nf | 2 +- .../variant_evaluation/tests/main.nf.test | 31 ++++ .../tests/rtg_truthvcfs.csv | 2 + 22 files changed, 1033 insertions(+), 6 deletions(-) create mode 100644 subworkflows/local/annotate_rhocallviz/tests/main.nf.test create mode 100644 subworkflows/local/annotate_rhocallviz/tests/nextflow.config create mode 100644 subworkflows/local/annotate_structural_variants/tests/main.nf.test create mode 100644 subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap create mode 100644 subworkflows/local/annotate_structural_variants/tests/nextflow.config create mode 100644 subworkflows/local/call_snv_sentieon/tests/main.nf.test create mode 100644 subworkflows/local/call_snv_sentieon/tests/nextflow.config create mode 100644 subworkflows/local/call_sv_MT/tests/main.nf.test create mode 100644 subworkflows/local/call_sv_MT/tests/main.nf.test.snap create mode 100644 subworkflows/local/call_sv_MT/tests/nextflow.config create mode 100644 subworkflows/local/generate_cytosure_files/tests/main.nf.test create mode 100644 subworkflows/local/generate_cytosure_files/tests/nextflow.config create mode 100644 subworkflows/local/gens/tests/main.nf.test create mode 100644 subworkflows/local/gens/tests/main.nf.test.snap create mode 100644 subworkflows/local/gens/tests/nextflow.config create mode 100644 subworkflows/local/postprocess_MT_calls/tests/main.nf.test create mode 100644 subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap create mode 100644 subworkflows/local/variant_evaluation/tests/main.nf.test create mode 100644 subworkflows/local/variant_evaluation/tests/rtg_truthvcfs.csv diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config index 82cc1f7bb..c88fa3a33 100644 --- a/conf/modules/annotate_rhocallviz.config +++ b/conf/modules/annotate_rhocallviz.config @@ -19,7 +19,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_VIEW_RHOCALL' { ext.prefix = { "${meta.sample}" } - ext.args = { "--output-type z --min-ac 1 --samples ${meta.sample}" } + ext.args = { "--output-type z --write-index=tbi --min-ac 1 --samples ${meta.sample}" } } withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:BCFTOOLS_ROH' { diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index d2a2a52da..5b24cc641 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -3,7 +3,6 @@ // include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_RHOCALL } from '../../../modules/nf-core/bcftools/view/main' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' include { BCFTOOLS_ROH } from '../../../modules/nf-core/bcftools/roh/main' include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_UNCOMPRESS } from '../../../modules/nf-core/bcftools/view/main' include { RHOCALL_VIZ } from '../../../modules/nf-core/rhocall/viz/main' @@ -25,10 +24,8 @@ workflow ANNOTATE_RHOCALLVIZ { BCFTOOLS_VIEW_RHOCALL(ch_rhocall_viz, [],[],[]) - TABIX_TABIX(BCFTOOLS_VIEW_RHOCALL.out.vcf) - BCFTOOLS_VIEW_RHOCALL.out.vcf - .join(TABIX_TABIX.out.index) + .join(BCFTOOLS_VIEW_RHOCALL.out.tbi) .set {ch_roh_in } BCFTOOLS_ROH(ch_roh_in, [[],[]], [], [], [], []) diff --git a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test new file mode 100644 index 000000000..683898fbd --- /dev/null +++ b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test @@ -0,0 +1,40 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_RHOCALLVIZ" + script "subworkflows/local/annotate_rhocallviz/main.nf" + workflow "ANNOTATE_RHOCALLVIZ" + tag "subworkflows" + tag "annotate_rhocallviz" + config "./nextflow.config" + + test("ANNOTATE_RHOCALLVIZ - stub") { + + options "-stub" + + when { + params { + bcftools_view_rhocall = "--output-type z --write-index=tbi --min-ac 1 --samples test_sample" + bcftools_roh = "--AF-tag GNOMADAF --skip-indels" + bcftools_view_uncompressed = "--output-type v" + rhocall_viz = "--aftag GNOMADAF --wig" + chromograph_autozyg = "--euploid" + ucsc_wigtobigwig = "-clip" + } + workflow { + """ + input[0] = channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)).collect() + input[1] = channel.of([id:'test_sample', sample:'test_sample', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'test_case']) + input[2] = channel.of([ + [id:'test_case', sample:'test_sample'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + """ + } + } + + then { + assert workflow.success + } + } +} diff --git a/subworkflows/local/annotate_rhocallviz/tests/nextflow.config b/subworkflows/local/annotate_rhocallviz/tests/nextflow.config new file mode 100644 index 000000000..3ccb91b06 --- /dev/null +++ b/subworkflows/local/annotate_rhocallviz/tests/nextflow.config @@ -0,0 +1,32 @@ +process { + + withName: 'BCFTOOLS_VIEW_RHOCALL' { + ext.prefix = { "${meta.sample}" } + ext.args = { params.bcftools_view_rhocall } + } + + withName: 'BCFTOOLS_ROH' { + ext.prefix = { "${meta.sample}" } + ext.args = { params.bcftools_roh } + } + + withName: 'BCFTOOLS_VIEW_UNCOMPRESS' { + ext.prefix = { "${meta.sample}" } + ext.args = { params.bcftools_view_uncompressed } + } + + withName: 'RHOCALL_VIZ' { + ext.prefix = { "${meta.sample}_rhocallviz" } + ext.args = { params.rhocall_viz } + } + + withName: 'CHROMOGRAPH_AUTOZYG' { + ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" } + ext.args = { params.chromograph_autozyg } + } + + withName: 'UCSC_WIGTOBIGWIG' { + ext.prefix = { "${meta.sample}_rhocallviz" } + ext.args = { params.ucsc_wigtobigwig } + } +} diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test b/subworkflows/local/annotate_structural_variants/tests/main.nf.test new file mode 100644 index 000000000..d51227ffc --- /dev/null +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_workflow { + + name "Test Workflow ANNOTATE_STRUCTURAL_VARIANTS" + script "subworkflows/local/annotate_structural_variants/main.nf" + workflow "ANNOTATE_STRUCTURAL_VARIANTS" + tag "subworkflows" + tag "annotate_structural_variants" + config "./nextflow.config" + + test("ANNOTATE_STRUCTURAL_VARIANTS - no SVDB queries, stub") { + + options "-stub" + + when { + params { + bcftools_view = "--output-type z" + vep = "--compress_output bgzip --format vcf --vcf" + } + workflow { + """ + input[0] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[2] = channel.empty() + input[3] = channel.empty() + input[4] = channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) + ]) + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[6] = channel.value([]) + input[7] = null + input[8] = null + input[9] = 'GRCh37' + input[10] = 107 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("ANNOTATE_STRUCTURAL_VARIANTS - with SVDB_QUERY_DB, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[2] = channel.empty() + input[3] = channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz', checkIfExists: true), + 'AC', + 'AF', + 'gnomad_svAC', + 'gnomad_svAF' + ]) + input[4] = channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) + ]) + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[6] = channel.value([]) + input[7] = null + input[8] = 'gnomAD.r2.1.1-sv.vcf.gz' + input[9] = 'GRCh37' + input[10] = 107 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap new file mode 100644 index 000000000..038f2516c --- /dev/null +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap @@ -0,0 +1,88 @@ +{ + "ANNOTATE_STRUCTURAL_VARIANTS - no SVDB queries, stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf_ann": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-06T05:42:03.69156986", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "ANNOTATE_STRUCTURAL_VARIANTS - with SVDB_QUERY_DB, stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf_ann": [ + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-06T05:42:35.988656634", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/annotate_structural_variants/tests/nextflow.config b/subworkflows/local/annotate_structural_variants/tests/nextflow.config new file mode 100644 index 000000000..7ff620bd0 --- /dev/null +++ b/subworkflows/local/annotate_structural_variants/tests/nextflow.config @@ -0,0 +1,24 @@ +process { + + withName: 'SVDB_QUERY_DB' { + ext.prefix = { "${meta.id}_vcfdb" } + } + + withName: 'SVDB_QUERY_BEDPE' { + ext.prefix = { "${meta.id}_bedpedb" } + } + + withName: 'PICARD_SORTVCF' { + ext.prefix = { "${meta.id}_svdbquery" } + } + + withName: 'BCFTOOLS_VIEW' { + ext.prefix = { "${meta.id}_view" } + ext.args = { params.bcftools_view } + } + + withName: 'ENSEMBLVEP_SV' { + ext.prefix = { "${meta.id}_svdbquery_vep" } + ext.args = { params.vep } + } +} diff --git a/subworkflows/local/call_snv_sentieon/tests/main.nf.test b/subworkflows/local/call_snv_sentieon/tests/main.nf.test new file mode 100644 index 000000000..4b9ced510 --- /dev/null +++ b/subworkflows/local/call_snv_sentieon/tests/main.nf.test @@ -0,0 +1,84 @@ +nextflow_workflow { + + name "Test Workflow CALL_SNV_SENTIEON" + script "subworkflows/local/call_snv_sentieon/main.nf" + workflow "CALL_SNV_SENTIEON" + tag "subworkflows" + tag "call_snv_sentieon" + config "./nextflow.config" + + test("CALL_SNV_SENTIEON - single sample, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([[id:'interval'], []]) + input[2] = channel.of([id:'justhusky']) + input[3] = channel.of([[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[4] = channel.of([[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) + input[5] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[9] = channel.of([[id:'model'], []]) + input[10] = channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("CALL_SNV_SENTIEON - two samples (merge), stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", lane:1, sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true) + ] + ) + input[1] = channel.of([[id:'interval'], []]) + input[2] = channel.of([id:'justhusky']) + input[3] = channel.of([[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[4] = channel.of([[id:'genome'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) + input[5] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[9] = channel.of([[id:'model'], []]) + input[10] = channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/call_snv_sentieon/tests/nextflow.config b/subworkflows/local/call_snv_sentieon/tests/nextflow.config new file mode 100644 index 000000000..4fd5ffbdc --- /dev/null +++ b/subworkflows/local/call_snv_sentieon/tests/nextflow.config @@ -0,0 +1,40 @@ +process { + + withName: 'SENTIEON_DNASCOPE' { + ext.prefix = { "${meta.id}_dnascope" } + } + + withName: 'SENTIEON_DNAMODELAPPLY' { + ext.prefix = { "${meta.id}_dnamodelapply" } + } + + withName: 'BCF_FILTER_ONE' { + ext.args = "-s 'ML_FAIL' -i 'INFO/ML_PROB <= 0.95' -m x -Oz --write-index=tbi" + ext.prefix = { "${meta.id}_mlfiltered_0.95" } + } + + withName: 'BCF_FILTER_TWO' { + ext.args = "-i FILTER='\"PASS\"' -m x -Oz --write-index=tbi" + ext.prefix = { "${meta.id}_passed" } + } + + withName: 'SPLIT_MULTIALLELICS_SEN' { + ext.args = '--output-type z --multiallelics -both' + ext.prefix = { "${meta.id}_split" } + } + + withName: 'REMOVE_DUPLICATES_SEN' { + ext.args = '--output-type z --rm-dup none' + ext.prefix = { "${meta.id}_split_rmdup" } + } + + withName: 'ADD_VARCALLER_TO_BED' { + ext.args2 = '-s 1 -b 2 -e 3' + } + + withName: 'BCFTOOLS_ANNOTATE' { + ext.args = '-c CHROM,FROM,TO,FOUND_IN --output-type z' + ext.prefix = { "${meta.id}_split_rmdup_info" } + } + +} diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test new file mode 100644 index 000000000..feb8e8f0e --- /dev/null +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -0,0 +1,66 @@ +nextflow_workflow { + + name "Test Workflow CALL_SV_MT" + script "subworkflows/local/call_sv_MT/main.nf" + workflow "CALL_SV_MT" + tag "subworkflows" + tag "call_sv_mt" + config "./nextflow.config" + + test("CALL_SV_MT - stub") { + + options "-stub" + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[4] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[5] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[7] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[8] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[9] = channel.value(10000000) + input[10] = 15 + input[11] = 2 + input[12] = 2 + input[13] = 30000 + input[14] = 30 + input[15] = 0.00001 + input[16] = 5 + input[17] = 15 + input[18] = 0.01 + input[19] = 'chrM' + input[20] = 1000 + input[21] = 80 + input[22] = 10000 + input[23] = 5 + input[24] = 15 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap new file mode 100644 index 000000000..e40ea67d7 --- /dev/null +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -0,0 +1,121 @@ +{ + "CALL_SV_MT - stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mitosalt_breakpoint": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mitosalt_cluster": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mt_del_result": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-06T06:08:49.770501228", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/nextflow.config b/subworkflows/local/call_sv_MT/tests/nextflow.config new file mode 100644 index 000000000..772073c54 --- /dev/null +++ b/subworkflows/local/call_sv_MT/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + + withName: 'MT_DELETION' { + ext.args = {"params.mt_del"} + ext.prefix = { "${meta.id}_mitochondria_deletions" } + } + +} diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test b/subworkflows/local/generate_cytosure_files/tests/main.nf.test new file mode 100644 index 000000000..7934620de --- /dev/null +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test @@ -0,0 +1,73 @@ +nextflow_workflow { + + name "Test Workflow GENERATE_CYTOSURE_FILES" + script "subworkflows/local/generate_cytosure_files/main.nf" + workflow "GENERATE_CYTOSURE_FILES" + tag "subworkflows" + tag "generate_cytosure_files" + config "./nextflow.config" + + test("GENERATE_CYTOSURE_FILES - no sample_id_map, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.value([]) + input[2] = channel.empty() + input[3] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[4] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ]) + input[5] = null + """ + } + } + + then { + assert workflow.success + } + } + + test("GENERATE_CYTOSURE_FILES - with sample_id_map, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.value([]) + input[2] = channel.of([[id:'earlycasualcaiman'], 'CUST_001']) + input[3] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[4] = channel.of([ + [id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ]) + input[5] = 'sample_id_map.csv' + """ + } + } + + then { + assert workflow.success + } + } +} diff --git a/subworkflows/local/generate_cytosure_files/tests/nextflow.config b/subworkflows/local/generate_cytosure_files/tests/nextflow.config new file mode 100644 index 000000000..f4653e109 --- /dev/null +++ b/subworkflows/local/generate_cytosure_files/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + + withName: 'TIDDIT_COV_VCF2CYTOSURE' { + ext.prefix = { "${meta.id}_cov" } + } + + withName: 'SPLIT_AND_FILTER_SV_VCF' { + ext.prefix = { "${meta.id}" } + } + + withName: 'BCFTOOLS_REHEADER_SV_VCF' { + beforeScript = { "echo ${meta.custid} > ${meta.custid}.txt" } + ext.prefix = { "${meta.custid}" } + } + + withName: 'VCF2CYTOSURE' { + ext.prefix = { "${meta.custid}" ? "${meta.custid}" : "${meta.id}" } + } + +} diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test new file mode 100644 index 000000000..ca61de785 --- /dev/null +++ b/subworkflows/local/gens/tests/main.nf.test @@ -0,0 +1,82 @@ +nextflow_workflow { + + name "Test Workflow GENS" + script "subworkflows/local/gens/main.nf" + workflow "GENS" + tag "subworkflows" + tag "gens" + config "./nextflow.config" + + test("GENS - male sample, stub") { + + options "-stub" + + when { + params { + countreadcounts = "--format HDF5" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz', checkIfExists: true)) + input[5] = channel.of([ + [id:'earlycasualcaiman'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[8] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("GENS - female sample, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([ + [id:'slowlycivilbuck', sample:'slowlycivilbuck', sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz', checkIfExists: true)) + input[5] = channel.of([ + [id:'slowlycivilbuck'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[8] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap new file mode 100644 index 000000000..3fb7b91b6 --- /dev/null +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -0,0 +1,136 @@ +{ + "GENS - female sample, stub": { + "content": [ + { + "0": [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gens_baf_bed_gz": [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gens_cov_bed_gz": [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-06T06:32:00.117867897", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "GENS - male sample, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gens_baf_bed_gz": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gens_cov_bed_gz": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-06T06:31:24.998017159", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/gens/tests/nextflow.config b/subworkflows/local/gens/tests/nextflow.config new file mode 100644 index 000000000..bab811d82 --- /dev/null +++ b/subworkflows/local/gens/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + + withName: 'COLLECTREADCOUNTS' { + ext.args = { params.countreadcounts } + } + + withName: 'GENS_GENERATE' { + ext.prefix = { "${meta.id}_gens" } + } + +} diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test new file mode 100644 index 000000000..116242b76 --- /dev/null +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test @@ -0,0 +1,42 @@ +nextflow_workflow { + + name "Test Workflow POSTPROCESS_MT_CALLS" + script "subworkflows/local/postprocess_MT_calls/main.nf" + workflow "POSTPROCESS_MT_CALLS" + tag "subworkflows" + tag "postprocess_MT_calls" + + test("POSTPROCESS_MT_CALLS - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([id:'justhusky']) + input[1] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/foundin.hdr', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[5] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[6] = channel.of([ + [id:'earlycasualcaiman', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true) + ]) + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/mt_shift8000.back_chain', checkIfExists: true)]).collect() + input[8] = channel.of([ + [id:'earlycasualcaiman', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap new file mode 100644 index 000000000..bd5f6421c --- /dev/null +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -0,0 +1,45 @@ +{ + "POSTPROCESS_MT_CALLS - stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-05T22:02:56.111310181", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/variant_evaluation/main.nf b/subworkflows/local/variant_evaluation/main.nf index 73881b50d..63ce6bfd9 100644 --- a/subworkflows/local/variant_evaluation/main.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -28,7 +28,7 @@ workflow VARIANT_EVALUATION { TABIX_TRUTHVCF (BCFTOOLS_REHEADER.out.vcf) BCFTOOLS_REHEADER.out.vcf - .join(TABIX_TRUTHVCF.out.tbi) + .join(TABIX_TRUTHVCF.out.index) .set { ch_truthvcf_tbi } ch_snv_vcf_tbi diff --git a/subworkflows/local/variant_evaluation/tests/main.nf.test b/subworkflows/local/variant_evaluation/tests/main.nf.test new file mode 100644 index 000000000..f08aef3fd --- /dev/null +++ b/subworkflows/local/variant_evaluation/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_workflow { + + name "Test Workflow VARIANT_EVALUATION" + script "subworkflows/local/variant_evaluation/main.nf" + workflow "VARIANT_EVALUATION" + tag "subworkflows" + tag "variant_evaluation" + + test("VARIANT_EVALUATION - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of(file("${projectDir}/subworkflows/local/variant_evaluation/tests/rtg_truthvcfs.csv", checkIfExists: true)).collect() + input[1] = channel.value([[id:'genome'], file("${projectDir}/subworkflows/local/variant_evaluation/tests")]) + input[2] = channel.of([ + [id:'earlycasualcaiman', case_id:'justhusky'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true) + ]) + """ + } + } + + then { + assert workflow.success + } + } +} diff --git a/subworkflows/local/variant_evaluation/tests/rtg_truthvcfs.csv b/subworkflows/local/variant_evaluation/tests/rtg_truthvcfs.csv new file mode 100644 index 000000000..3bfa9483e --- /dev/null +++ b/subworkflows/local/variant_evaluation/tests/rtg_truthvcfs.csv @@ -0,0 +1,2 @@ +samplename,vcf,bedregions,evaluationregions +earlycasualcaiman,https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_gnomad_mt.vcf.gz,, From 657f8466f02d75797d391737aaa80bffe36cf60f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 09:37:07 +0100 Subject: [PATCH 433/872] update cadd test --- subworkflows/local/annotate_cadd/main.nf | 2 +- .../local/annotate_cadd/tests/main.nf.test | 6 ++++ .../annotate_cadd/tests/main.nf.test.snap | 34 ++++++++++++++++--- 3 files changed, 36 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index e8fbc4f66..b5da76182 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -20,7 +20,7 @@ workflow ANNOTATE_CADD { val_genome // string: GRCh37 or GRCh37 main: - ch_rename_chrs = channel.empty() + ch_rename_chrs = channel.value([]) if (val_genome.equals('GRCh38')) { diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test index 7d85b13b6..3dfdf1f18 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -12,6 +12,9 @@ nextflow_workflow { options "-stub" when { + params { + genome = "GRCh37" + } workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } @@ -40,6 +43,9 @@ nextflow_workflow { options "-stub" when { + params { + genome = "GRCh38" + } workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap index de0ebe1cd..6e6570c31 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap @@ -3,20 +3,44 @@ "content": [ { "0": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "tbi": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "vcf": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] } ], - "timestamp": "2026-03-04T13:59:08.944351192", + "timestamp": "2026-03-06T09:35:25.19740914", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 7b08d519be3b3fae885878d4904e1bbfb3efb129 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 09:44:21 +0100 Subject: [PATCH 434/872] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index abd76d409..b78ad5fa3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -65,6 +65,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ensemblvep/filtervep | 113 | 115.2 | | fastp | 0.23.4 | 1.0.1 | | gatk4 | 4.5.0.0 | 4.6.2.0 | +| gawk | 5.3.0 | 5.3.1 | | genmod | 3.9 | 3.10.2 | | gens-preproc | 1.0.11 | 1.1.2 | | haplocheck | 1.3.3 | | From bbfe5b16dac1a21df99d27b0cba9c9613cc677a3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 16:37:07 +0100 Subject: [PATCH 435/872] update bcftools annotate --- modules/nf-core/bcftools/annotate/main.nf | 5 +- modules/nf-core/bcftools/annotate/meta.yml | 26 +-- .../bcftools/annotate/tests/bcf.config | 4 - .../bcftools/annotate/tests/main.nf.test | 158 +++++++++--------- .../bcftools/annotate/tests/main.nf.test.snap | 82 ++++----- .../bcftools/annotate/tests/nextflow.config | 4 + .../bcftools/annotate/tests/vcf.config | 4 - .../annotate/tests/vcf_gz_index.config | 4 - .../annotate/tests/vcf_gz_index_csi.config | 4 - .../annotate/tests/vcf_gz_index_tbi.config | 4 - 10 files changed, 138 insertions(+), 157 deletions(-) delete mode 100644 modules/nf-core/bcftools/annotate/tests/bcf.config create mode 100644 modules/nf-core/bcftools/annotate/tests/nextflow.config delete mode 100644 modules/nf-core/bcftools/annotate/tests/vcf.config delete mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config delete mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config delete mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 28964d2a7..18778cc2b 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -8,10 +8,7 @@ process BCFTOOLS_ANNOTATE { : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: - tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) - path columns - path header_lines - path rename_chrs + tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(columns), path(header_lines), path(rename_chrs) output: tuple val(meta), path("${prefix}.${extension}"), emit: vcf diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index af8bcf84d..863316616 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -36,19 +36,19 @@ input: type: file description: Index of the annotations file ontologies: [] - - columns: - type: file - description: List of columns in the annotations file, one name per row - ontologies: [] - - header_lines: - type: file - description: Contains lines to append to the output VCF header - ontologies: [] - - rename_chrs: - type: file - description: Rename annotations according to this file containing "old_name new_name\n" - pairs separated by whitespaces, each on a separate line. - ontologies: [] + - columns: + type: file + description: List of columns in the annotations file, one name per row + ontologies: [] + - header_lines: + type: file + description: Contains lines to append to the output VCF header + ontologies: [] + - rename_chrs: + type: file + description: Rename annotations according to this file containing "old_name new_name\n" + pairs separated by whitespaces, each on a separate line. + ontologies: [] output: vcf: - - meta: diff --git a/modules/nf-core/bcftools/annotate/tests/bcf.config b/modules/nf-core/bcftools/annotate/tests/bcf.config deleted file mode 100644 index 79d26779d..000000000 --- a/modules/nf-core/bcftools/annotate/tests/bcf.config +++ /dev/null @@ -1,4 +0,0 @@ -process { - ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" - ext.prefix = { "${meta.id}_ann" } -} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 39010bdc3..3e1d25733 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -2,6 +2,7 @@ nextflow_process { name "Test Process BCFTOOLS_ANNOTATE" script "../main.nf" + config "./nextflow.config" process "BCFTOOLS_ANNOTATE" tag "modules" @@ -11,9 +12,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output") { - config "./vcf.config" - when { + params { + args_modules = "-x ID,INFO/DP,FORMAT/DP --output-type z" + } process { """ input[0] = [ @@ -21,11 +23,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -45,9 +45,10 @@ nextflow_process { test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output") { - config "./vcf.config" - when { + params { + args_modules = "-x ID,INFO/DP,FORMAT/DP --output-type z" + } process { """ input[0] = [ @@ -55,11 +56,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -79,9 +78,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index") { - config "./vcf_gz_index.config" - when { + params { + args_modules = "--output-type z --write-index --no-version" + } process { """ input[0] = [ @@ -89,11 +89,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -113,9 +111,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi") { - config "./vcf_gz_index_csi.config" - when { + params { + args_modules = "--output-type z --write-index=csi --no-version" + } process { """ input[0] = [ @@ -123,11 +122,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -147,9 +144,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi") { - config "./vcf_gz_index_tbi.config" - when { + params { + args_modules = "--output-type z --write-index=tbi --no-version" + } process { """ input[0] = [ @@ -157,11 +155,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -181,24 +177,26 @@ nextflow_process { test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output") { - config "./bcf.config" - when { + params { + args_modules = "-x ID,INFO/DP,FORMAT/DP --output-type u" + } process { """ - input[0] = [ + header = channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - input[1] = [] - input[2] = Channel.of( - '##INFO=', - '##INFO=' - ).collectFile(name:"headers.vcf", newLine:true) - input[3] = [] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [] + ]) + .combine(header) + .combine(channel.of([[]])) """ } } @@ -218,21 +216,21 @@ nextflow_process { test("sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output") { - config "./bcf.config" - when { + params { + args_modules = "-x ID,INFO/DP,FORMAT/DP --output-type u" + } process { """ - input[0] = [ + columns = channel.of('INFO/ICB', 'INFO/HOB', 'INFO/DP4').collectFile(name:"columns.txt", newLine:true) + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - input[1] = Channel.of('INFO/ICB', 'INFO/HOB', 'INFO/DP4').collectFile(name:"columns.txt", newLine:true) - input[2] = [] - input[3] = [] + ]).combine(columns) + .combine(channel.of([[], []])) """ } } @@ -252,24 +250,26 @@ nextflow_process { test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index") { - config "./vcf_gz_index.config" - when { + params { + args_modules = "--output-type z --write-index --no-version" + } process { """ - input[0] = [ + headers = channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + rename = channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true) + input[0] = channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - input[1] = [] - input[2] = Channel.of( - '##INFO=', - '##INFO=' - ).collectFile(name:"headers.vcf", newLine:true) - input[3] = Channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [] + ]).combine(headers) + .combine(rename) """ } } @@ -289,10 +289,12 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub") { - config "./vcf.config" options "-stub" when { + params { + args_modules = "-x ID,INFO/DP,FORMAT/DP --output-type z" + } process { """ input[0] = [ @@ -300,11 +302,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -324,10 +324,12 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index - stub") { - config "./vcf_gz_index.config" options "-stub" when { + params { + args_modules = "--output-type z --write-index --no-version" + } process { """ input[0] = [ @@ -335,11 +337,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -359,10 +359,12 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub") { - config "./vcf_gz_index_csi.config" options "-stub" when { + params { + args_modules = "--output-type z --write-index=csi --no-version" + } process { """ input[0] = [ @@ -370,11 +372,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } @@ -394,10 +394,12 @@ nextflow_process { test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub") { - config "./vcf_gz_index_tbi.config" options "-stub" when { + params { + args_modules = "--output-type z --write-index=tbi --no-version" + } process { """ input[0] = [ @@ -405,11 +407,9 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [], [], [] ] - input[1] = [] - input[2] = [] - input[3] = [] """ } } diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index 4d57dfbb1..10af196a1 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.vcf.gz" ] ], [ @@ -19,7 +19,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_ann.vcf.gz.csi" ] ], { @@ -34,9 +34,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:46:28.350541494" + "timestamp": "2026-02-27T15:29:19.618749659" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi": { "content": [ @@ -46,7 +46,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" + "test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] ], [ @@ -55,7 +55,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.tbi" + "test_ann.vcf.gz.tbi" ] ], [ @@ -73,9 +73,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T17:35:23.346991616" + "timestamp": "2026-02-27T15:28:43.350060834" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi": { "content": [ @@ -85,7 +85,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" + "test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] ], [ @@ -97,7 +97,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_ann.vcf.gz.csi" ] ], { @@ -112,9 +112,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T17:35:15.126643898" + "timestamp": "2026-02-27T15:28:36.101003418" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_tbi - stub": { "content": [ @@ -124,7 +124,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.vcf.gz" ] ], [ @@ -133,7 +133,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.tbi" + "test_ann.vcf.gz.tbi" ] ], [ @@ -151,9 +151,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:46:46.844515012" + "timestamp": "2026-02-27T15:29:34.19449127" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index_csi - stub": { "content": [ @@ -163,7 +163,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.vcf.gz" ] ], [ @@ -175,7 +175,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_ann.vcf.gz.csi" ] ], { @@ -190,9 +190,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:46:37.561478889" + "timestamp": "2026-02-27T15:29:26.927815399" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_gz_index": { "content": [ @@ -202,7 +202,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" + "test_ann.vcf.gz:variantsMD5,bc7bf3ee9e8430e064c539eb81e59bf9" ] ], [ @@ -214,7 +214,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_ann.vcf.gz.csi" ] ], { @@ -229,9 +229,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T17:35:06.608740206" + "timestamp": "2026-02-27T15:28:28.891823681" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - stub": { "content": [ @@ -241,7 +241,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.vcf.gz" ] ], [ @@ -262,9 +262,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:46:18.623176402" + "timestamp": "2026-02-27T15:29:12.400301681" }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, [] - bcf_output": { "content": [ @@ -295,9 +295,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:57:59.109447684" + "timestamp": "2026-02-27T15:28:50.375384421" }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" + "test_ann.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" ] ], [ @@ -328,9 +328,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T17:34:58.100296619" + "timestamp": "2026-02-27T15:28:21.320211288" }, "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [], [] - vcf_output": { "content": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" + "test_ann.vcf.gz:variantsMD5,250b64289ab9d48f76359d01699fdf7d" ] ], [ @@ -361,9 +361,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T17:34:49.49779004" + "timestamp": "2026-02-27T15:28:13.274072987" }, "sarscov2 - [vcf, [], annotation, annotation_tbi], [], header, rename_chrs - vcf_gz_index": { "content": [ @@ -373,7 +373,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz" + "test_ann.vcf.gz" ] ], [ @@ -385,7 +385,7 @@ "id": "test", "single_end": false }, - "test_vcf.vcf.gz.csi" + "test_ann.vcf.gz.csi" ] ], { @@ -400,9 +400,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:58:16.686295153" + "timestamp": "2026-02-27T15:29:05.094685409" }, "sarscov2 - [vcf, [], annotation, annotation_tbi], columns, [], [] - bcf_output": { "content": [ @@ -433,8 +433,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.3" }, - "timestamp": "2026-01-15T16:58:07.908352766" + "timestamp": "2026-02-27T15:28:57.906382655" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/nextflow.config b/modules/nf-core/bcftools/annotate/tests/nextflow.config new file mode 100644 index 000000000..102351009 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + ext.args = "${params.args_modules}" + ext.prefix = { "${meta.id}_ann" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf.config b/modules/nf-core/bcftools/annotate/tests/vcf.config deleted file mode 100644 index 611868d55..000000000 --- a/modules/nf-core/bcftools/annotate/tests/vcf.config +++ /dev/null @@ -1,4 +0,0 @@ -process { - ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" - ext.prefix = { "${meta.id}_vcf" } -} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config deleted file mode 100644 index 2fd9a225f..000000000 --- a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config +++ /dev/null @@ -1,4 +0,0 @@ -process { - ext.args = "--output-type z --write-index --no-version" - ext.prefix = { "${meta.id}_vcf" } -} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config deleted file mode 100644 index 512c1dfb0..000000000 --- a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config +++ /dev/null @@ -1,4 +0,0 @@ -process { - ext.args = "--output-type z --write-index=csi --no-version" - ext.prefix = { "${meta.id}_vcf" } -} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config deleted file mode 100644 index 7feb5ebbe..000000000 --- a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config +++ /dev/null @@ -1,4 +0,0 @@ -process { - ext.args = "--output-type z --write-index=tbi --no-version" - ext.prefix = { "${meta.id}_vcf" } -} From 6440af8c2632228b76cc78408812e2f65ddcab14 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 16:41:55 +0100 Subject: [PATCH 436/872] update modules --- conf/modules/call_snv_deepvariant.config | 4 +- conf/modules/call_snv_sentieon.config | 4 +- modules/nf-core/bcftools/merge/main.nf | 6 +- modules/nf-core/bcftools/merge/meta.yml | 20 +- .../nf-core/bcftools/merge/tests/bcf.config | 3 - .../bcftools/merge/tests/bcf_gz.config | 3 - .../nf-core/bcftools/merge/tests/main.nf.test | 342 ++++++------------ .../bcftools/merge/tests/main.nf.test.snap | 141 -------- .../bcftools/merge/tests/nextflow.config | 2 +- .../bcftools/merge/tests/nextflow.gvcf.config | 5 - .../nf-core/bcftools/merge/tests/vcf.config | 3 - .../bcftools/merge/tests/vcf_gz.config | 3 - .../bcftools/merge/tests/vcf_gz_index.config | 3 - .../merge/tests/vcf_gz_index_csi.config | 3 - .../merge/tests/vcf_gz_index_tbi.config | 3 - modules/nf-core/samtools/merge/main.nf | 2 +- modules/nf-core/samtools/merge/meta.yml | 5 + .../nf-core/samtools/merge/tests/main.nf.test | 20 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- subworkflows/local/annotate_cadd/main.nf | 15 +- .../local/call_snv_deepvariant/main.nf | 15 +- .../call_snv_deepvariant/tests/main.nf.test | 5 + .../tests/nextflow.config | 12 + subworkflows/local/call_snv_sentieon/main.nf | 20 +- .../local/postprocess_MT_calls/main.nf | 12 +- 25 files changed, 195 insertions(+), 458 deletions(-) delete mode 100644 modules/nf-core/bcftools/merge/tests/bcf.config delete mode 100644 modules/nf-core/bcftools/merge/tests/bcf_gz.config delete mode 100644 modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config delete mode 100644 modules/nf-core/bcftools/merge/tests/vcf.config delete mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz.config delete mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index.config delete mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config delete mode 100644 modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config create mode 100644 subworkflows/local/call_snv_deepvariant/tests/nextflow.config diff --git a/conf/modules/call_snv_deepvariant.config b/conf/modules/call_snv_deepvariant.config index 140de6d95..93b5b32f6 100644 --- a/conf/modules/call_snv_deepvariant.config +++ b/conf/modules/call_snv_deepvariant.config @@ -34,7 +34,7 @@ process { } withName: '.*CALL_SNV_DEEPVARIANT:REMOVE_DUPLICATES_GL' { - ext.args = '--output-type z --rm-dup none' + ext.args = '--write-index=tbi --output-type z --rm-dup none' ext.prefix = { "${meta.id}_split_rmdup" } } @@ -43,7 +43,7 @@ process { } withName: '.*CALL_SNV_DEEPVARIANT:BCFTOOLS_ANNOTATE' { - ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z" + ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z --write-index=tbi " ext.prefix = { "${meta.id}_split_rmdup_info" } } } diff --git a/conf/modules/call_snv_sentieon.config b/conf/modules/call_snv_sentieon.config index d5f86fb24..0a370e19b 100644 --- a/conf/modules/call_snv_sentieon.config +++ b/conf/modules/call_snv_sentieon.config @@ -44,7 +44,7 @@ process { } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:REMOVE_DUPLICATES_SEN' { - ext.args = '--output-type z --rm-dup none' + ext.args = '--output-type z --rm-dup none --write-index=tbi' ext.prefix = { "${meta.id}_split_rmdup" } } @@ -53,7 +53,7 @@ process { } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:BCFTOOLS_ANNOTATE' { - ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z" + ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type --write-index=tbi" ext.prefix = { "${meta.id}_split_rmdup_info" } } } diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 6c944151b..f1acbd3da 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -8,10 +8,8 @@ process BCFTOOLS_MERGE { : 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}" input: - tuple val(meta), path(vcfs), path(tbis) - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(bed) + tuple val(meta), path(vcfs), path(tbis), path(bed) + tuple val(meta2), path(fasta), path(fai) output: tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index f66b68845..445e5c56b 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -31,6 +31,11 @@ input: List containing the tbi index files corresponding to the vcfs input files e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] ontologies: [] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" + ontologies: [] - - meta2: type: map description: | @@ -42,27 +47,12 @@ input: FILE` parameter)" pattern: "*.{fasta,fa}" ontologies: [] - - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - fai: type: file description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" pattern: "*.fai" ontologies: [] - - - meta4: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'genome' ] - - bed: - type: file - description: "(Optional) The bed regions to merge on" - pattern: "*.bed" - ontologies: [] output: vcf: - - meta: diff --git a/modules/nf-core/bcftools/merge/tests/bcf.config b/modules/nf-core/bcftools/merge/tests/bcf.config deleted file mode 100644 index 4467d07d9..000000000 --- a/modules/nf-core/bcftools/merge/tests/bcf.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = '--output-type u --no-version' -} diff --git a/modules/nf-core/bcftools/merge/tests/bcf_gz.config b/modules/nf-core/bcftools/merge/tests/bcf_gz.config deleted file mode 100644 index 280de8db0..000000000 --- a/modules/nf-core/bcftools/merge/tests/bcf_gz.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = '--output-type b --no-version' -} diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test index e863f1816..3a1f12206 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -2,6 +2,8 @@ nextflow_process { name "Test Process BCFTOOLS_MERGE" script "../main.nf" + config "./nextflow.config" + process "BCFTOOLS_MERGE" tag "modules" @@ -11,9 +13,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], []") { - config "./nextflow.config" - when { + params { + args_modules = "--force-samples --force-single --no-version" + } process { """ input[0] = [ @@ -25,11 +28,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -48,9 +50,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf output") { - config "./vcf.config" - when { + params { + args_modules = "--output-type v --no-version" + } process { """ input[0] = [ @@ -62,11 +65,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -85,9 +87,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output") { - config "./vcf_gz.config" - when { + params { + args_modules = "--output-type z --no-version" + } process { """ input[0] = [ @@ -99,11 +102,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -122,9 +124,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - bcf output") { - config "./bcf.config" - when { + params { + args_modules = "--output-type u --no-version" + } process { """ input[0] = [ @@ -136,11 +139,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -159,9 +161,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output") { - config "./bcf_gz.config" - when { + params { + args_modules = "--output-type b --no-version" + } process { """ input[0] = [ @@ -173,11 +176,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -196,9 +198,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index") { - config "./vcf_gz_index.config" - when { + params { + args_modules = "--output-type z --write-index --no-version" + } process { """ input[0] = [ @@ -210,11 +213,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -235,10 +237,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index") { - config "./vcf_gz_index_csi.config" - when { - + params { + args_modules = "--output-type z --write-index=csi --no-version" + } process { """ input[0] = [ @@ -250,11 +252,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -275,9 +276,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index") { - config "./vcf_gz_index_tbi.config" - when { + params { + args_modules = "--output-type z --write-index=tbi --no-version" + } process { """ input[0] = [ @@ -289,11 +291,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -314,9 +315,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], bed") { - config "./nextflow.config" - when { + params { + args_modules = "--force-samples --force-single --no-version" + } process { """ input[0] = [ @@ -328,14 +330,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] - ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + input[1] = [[],[],[]] """ } } @@ -354,9 +352,10 @@ nextflow_process { test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { - config "./nextflow.gvcf.config" - when { + params { + args_modules = "--force-samples --no-version --output-type z --gvcf genome.fasta" + } process { """ input[0] = [ @@ -368,20 +367,14 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), - ] + ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [ [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ] - input[2] = [ - [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] ] - input[3] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] - ] """ } } @@ -400,8 +393,10 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { - config "./nextflow.config" when { + params { + args_modules = "--force-samples --force-single --no-version" + } process { """ input[0] = [ @@ -411,11 +406,10 @@ nextflow_process { ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -435,9 +429,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - stub") { options "-stub" - config "./nextflow.config" when { + params { + args_modules = "--force-samples --force-single --no-version" + } process { """ input[0] = [ @@ -449,11 +445,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -470,9 +465,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf output - stub") { options "-stub" - config "./vcf.config" when { + params { + args_modules = "--output-type v --no-version" + } process { """ input[0] = [ @@ -484,11 +481,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -505,9 +501,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - stub") { options "-stub" - config "./vcf_gz.config" when { + params { + args_modules = "--output-type z --no-version" + } process { """ input[0] = [ @@ -519,11 +517,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -540,9 +537,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - bcf output - stub") { options "-stub" - config "./bcf.config" when { + params { + args_modules = "--output-type u --no-version" + } process { """ input[0] = [ @@ -554,11 +553,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -575,9 +573,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - bcf.gz output - stub") { options "-stub" - config "./bcf_gz.config" when { + params { + args_modules = "--output-type b --no-version" + } process { """ input[0] = [ @@ -589,11 +589,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -610,9 +609,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index - stub") { options "-stub" - config "./vcf_gz_index.config" when { + params { + args_modules = "--output-type z --write-index --no-version" + } process { """ input[0] = [ @@ -624,11 +625,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -646,9 +646,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - csi index - stub") { options "-stub" - config "./vcf_gz_index_csi.config" when { + params { + args_modules = "--output-type z --write-index=csi --no-version" + } process { """ input[0] = [ @@ -660,11 +662,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] + ], + [] ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] + input[1] = [[],[],[]] """ } } @@ -682,45 +683,11 @@ nextflow_process { test("sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - tbi index - stub") { options "-stub" - config "./vcf_gz_index_tbi.config" when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) - ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] - ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] - """ + params { + args_modules = "--output-type z --write-index=tbi --no-version" } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, - { assert process.out.index.get(0).get(1).endsWith("tbi") }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 - [vcf, tbi], [], [], bed - stub") { - - options "-stub" - config "./nextflow.config" - - when { process { """ input[0] = [ @@ -732,57 +699,10 @@ nextflow_process { [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true), - ] - ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, - { assert snapshot(process.out).match() } - ) - } - } - - test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub") { - - options "-stub" - config "./nextflow.gvcf.config" - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true) ], - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi', checkIfExists: true), - ] - ] - input[1] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ] - input[2] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] - ] - input[3] = [ - [ id:'test' ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + [] ] + input[1] = [[],[],[]] """ } } @@ -791,39 +711,7 @@ nextflow_process { assertAll( { assert process.success }, { assert process.out.vcf.get(0).get(1).endsWith("vcf.gz") }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") { - - options "-stub" - config "./nextflow.config" - - when { - process { - """ - input[0] = [ - [ id:'test' ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - ] - input[1] = [[],[]] - input[2] = [[],[]] - input[3] = [[],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert process.out.index.get(0).get(1).endsWith("tbi") }, { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap index 8f925a8e2..9dd091783 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -351,53 +351,6 @@ }, "timestamp": "2026-01-20T12:04:22.660557224" }, - "sarscov2 - [vcf, tbi], [], [], bed - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ], - "index": [ - - ], - "vcf": [ - [ - { - "id": "test" - }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_bcftools": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:42.799574825" - }, "sarscov2 - [vcf, tbi], [], [], [] - bcf output": { "content": [ "test.bcf", @@ -464,100 +417,6 @@ }, "timestamp": "2026-01-20T12:05:59.932077434" }, - "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ], - "index": [ - - ], - "vcf": [ - [ - { - "id": "test" - }, - "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_bcftools": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:07:00.260709958" - }, - "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - - ], - "2": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ], - "index": [ - - ], - "vcf": [ - [ - { - "id": "test" - }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions_bcftools": [ - [ - "BCFTOOLS_MERGE", - "bcftools", - "1.22" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:06:52.181671234" - }, "sarscov2 - [vcf, tbi], [], [], [] - vcf.gz output - index": { "content": [ "e0de448dc8e712956a03ce68d79a0b3a", diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config index c3f0b7159..36f2fa1a5 100644 --- a/modules/nf-core/bcftools/merge/tests/nextflow.config +++ b/modules/nf-core/bcftools/merge/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: BCFTOOLS_MERGE { - ext.args = '--force-samples --force-single --no-version' + ext.args = "${params.args_modules}" } } diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config b/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config deleted file mode 100644 index 8c457b716..000000000 --- a/modules/nf-core/bcftools/merge/tests/nextflow.gvcf.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: BCFTOOLS_MERGE { - ext.args = { "--force-samples --no-version --output-type z --gvcf $fasta" } - } -} diff --git a/modules/nf-core/bcftools/merge/tests/vcf.config b/modules/nf-core/bcftools/merge/tests/vcf.config deleted file mode 100644 index 759222e58..000000000 --- a/modules/nf-core/bcftools/merge/tests/vcf.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = '--output-type v --no-version' -} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz.config b/modules/nf-core/bcftools/merge/tests/vcf_gz.config deleted file mode 100644 index 8b6ad8b4f..000000000 --- a/modules/nf-core/bcftools/merge/tests/vcf_gz.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = '--output-type z --no-version' -} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config deleted file mode 100644 index 9f1e9b1d8..000000000 --- a/modules/nf-core/bcftools/merge/tests/vcf_gz_index.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-type z --write-index --no-version" -} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config deleted file mode 100644 index 8308ee1ae..000000000 --- a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_csi.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-type z --write-index=csi --no-version" -} diff --git a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config deleted file mode 100644 index 9be4075bc..000000000 --- a/modules/nf-core/bcftools/merge/tests/vcf_gz_index_tbi.config +++ /dev/null @@ -1,3 +0,0 @@ -process { - ext.args = "--output-type z --write-index=tbi --no-version" -} diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 87ebc5014..23aa0d522 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -8,7 +8,7 @@ process SAMTOOLS_MERGE { 'biocontainers/samtools:1.22.1--h96c455f_0' }" input: - tuple val(meta), path(input_files, stageAs: "?/*") + tuple val(meta), path(input_files, stageAs: "?/*"), path(index_files, stageAs: "?/*") tuple val(meta2), path(fasta), path(fai), path(gzi) output: diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 31cc576bc..8a8afca87 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -27,6 +27,11 @@ input: description: BAM/CRAM file pattern: "*.{bam,cram,sam}" ontologies: [] + - index_files: + type: file + description: BAI/CRAI/CSI index file + pattern: "*.{bai,crai,csi}" + ontologies: [] - - meta2: type: map description: | diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index a784c8367..3c2c524fc 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -22,7 +22,8 @@ nextflow_process { [ id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ], + [] ] input[1] = [[],[],[],[]] """ @@ -55,7 +56,9 @@ nextflow_process { input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai', checkIfExists: true) ] ] input[1] = [ [ id:'genome' ], @@ -94,7 +97,9 @@ nextflow_process { input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram', checkIfExists: true) ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai', checkIfExists: true) ] ] input[1] = [ [ id:'genome' ], @@ -132,7 +137,8 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) ] ] input[1] = [[],[],[],[]] """ @@ -168,7 +174,8 @@ nextflow_process { [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ], + [] ] input[1] = [[],[],[],[]] """ @@ -197,7 +204,8 @@ nextflow_process { [ id:'test'], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ], + [] ] input[1] = [[],[],[],[]] """ diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index fb7a850e3..24068cadc 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -62,7 +62,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}) + SAMTOOLS_MERGE ( bams.multiple.map { it -> it + [[]] }, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index b5da76182..ec88166ba 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -32,15 +32,11 @@ workflow ANNOTATE_CADD { .set { ch_rename_chrs } ch_vcf - .map { meta, vcf, tbi -> [ meta, vcf, tbi, [], [] ] } + .map { meta, vcf, tbi -> [ meta, vcf, tbi, [], [], [], [] ] } + .combine(REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt }) .set { ch_rename_chrnames_in } - RENAME_CHRNAMES ( - ch_rename_chrnames_in, - [], - [], - REFERENCE_TO_CADD_CHRNAMES.out.output.map { _meta, txt -> txt } - ) + RENAME_CHRNAMES ( ch_rename_chrnames_in ) RENAME_CHRNAMES.out.vcf .map { meta, vcf -> [ meta, vcf, [] ] } @@ -56,9 +52,12 @@ workflow ANNOTATE_CADD { ch_vcf .join(CADD.out.tsv) .join(TABIX_CADD.out.index) + .map { meta, vcf, tbi, ann, ann_tbi -> [ meta, vcf, tbi, ann, ann_tbi, [] ] } + .combine(ch_header.map { _meta, header -> header }) + .combine(ch_rename_chrs) .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_header.map { _meta, header -> header }, ch_rename_chrs) + BCFTOOLS_ANNOTATE(ch_annotate_in) emit: tbi = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 897cc7373..6e5392da6 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -8,8 +8,6 @@ include { BCFTOOLS_NORM as REMOVE_DUPLICATES_GL } from '../../../modules/nf include { DEEPVARIANT_RUNDEEPVARIANT as DEEPVARIANT } from '../../../modules/nf-core/deepvariant/rundeepvariant/main' include { GLNEXUS } from '../../../modules/nf-core/glnexus/main' include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' -include { TABIX_TABIX as TABIX_GL } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' workflow CALL_SNV_DEEPVARIANT { @@ -62,8 +60,6 @@ workflow CALL_SNV_DEEPVARIANT { return [meta, vcf, []] } REMOVE_DUPLICATES_GL (ch_remove_dup_in, ch_genome_fasta) - TABIX_GL (REMOVE_DUPLICATES_GL.out.vcf) - ch_genome_chrsizes.flatten().map{chromsizes -> return [[id:'deepvariant'], chromsizes] } @@ -74,17 +70,18 @@ workflow CALL_SNV_DEEPVARIANT { .set{ch_varcallerbed} REMOVE_DUPLICATES_GL.out.vcf - .join(TABIX_GL.out.index) + .join(REMOVE_DUPLICATES_GL.out.tbi) .combine(ch_varcallerbed) + .map { it -> it + [[]] } + .combine(ch_foundin_header) + .map { it -> it + [[]] } .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) - - TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) + BCFTOOLS_ANNOTATE(ch_annotate_in) emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] - tabix = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] + tabix = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index c4151469e..74f3c814a 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -6,9 +6,14 @@ nextflow_workflow { tag "subworkflows" tag "call_snv_deepvariant" + config "./nextflow.config" + test("CALL_SNV_DEEPVARIANT - wgs") { when { + params { + bcftools_args = "--write-index=tbi --output-type z" + } workflow { """ input[0] = channel.of( diff --git a/subworkflows/local/call_snv_deepvariant/tests/nextflow.config b/subworkflows/local/call_snv_deepvariant/tests/nextflow.config new file mode 100644 index 000000000..28d487092 --- /dev/null +++ b/subworkflows/local/call_snv_deepvariant/tests/nextflow.config @@ -0,0 +1,12 @@ +process { + + withName: 'REMOVE_DUPLICATES_GL' { + ext.args = { params.bcftools_args } + ext.prefix = { "${meta.id}_split_rmdup" } + } + + withName: 'BCFTOOLS_ANNOTATE' { + ext.args = { params.bcftools_args } + ext.prefix = { "${meta.id}_split_rmdup_info" } + } +} diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 5c982662b..21f5f7731 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -7,11 +7,9 @@ include { SENTIEON_DNAMODELAPPLY } from '../../../modules/nf include { BCFTOOLS_MERGE } from '../../../modules/nf-core/bcftools/merge/main' include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_SEN } from '../../../modules/nf-core/bcftools/norm/main' include { BCFTOOLS_NORM as REMOVE_DUPLICATES_SEN } from '../../../modules/nf-core/bcftools/norm/main' -include { TABIX_TABIX as TABIX_SEN } from '../../../modules/nf-core/tabix/tabix/main' include { BCFTOOLS_FILTER as BCF_FILTER_ONE } from '../../../modules/nf-core/bcftools/filter/main' include { BCFTOOLS_FILTER as BCF_FILTER_TWO } from '../../../modules/nf-core/bcftools/filter/main' include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' workflow CALL_SNV_SENTIEON { @@ -70,7 +68,10 @@ workflow CALL_SNV_SENTIEON { } .set{ ch_vcf_idx_merge_in } - BCFTOOLS_MERGE(ch_vcf_idx_merge_in.multiple, ch_genome_fasta, ch_genome_fai, [[:],[]]) + BCFTOOLS_MERGE( + ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] }, + ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) + ) ch_split_multi_in = BCFTOOLS_MERGE.out.vcf .map{meta, bcf -> @@ -86,8 +87,6 @@ workflow CALL_SNV_SENTIEON { REMOVE_DUPLICATES_SEN(ch_remove_dup_in, ch_genome_fasta) - TABIX_SEN(REMOVE_DUPLICATES_SEN.out.vcf) - ch_genome_chrsizes.flatten().map{chromsizes -> return [[id:'sentieon_dnascope'], chromsizes] } @@ -98,17 +97,18 @@ workflow CALL_SNV_SENTIEON { .set{ch_varcallerbed} REMOVE_DUPLICATES_SEN.out.vcf - .join(TABIX_SEN.out.tbi) + .join(REMOVE_DUPLICATES_SEN.out.tbi) .combine(ch_varcallerbed) + .map { it -> it + [[]] } + .combine(ch_foundin_header) + .map { it -> it + [[]] } .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) - - TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) + BCFTOOLS_ANNOTATE(ch_annotate_in) emit: gvcf = SENTIEON_DNASCOPE.out.gvcf // channel: [ val(meta), path(gvcf) ] gvcf_tbi = SENTIEON_DNASCOPE.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi) ] - tabix = TABIX_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + tabix = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 282d601ad..27769b426 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -89,10 +89,9 @@ workflow POSTPROCESS_MT_CALLS { return [meta, vcf, tbi] }.set { ch_case_vcf } - BCFTOOLS_MERGE_MT( ch_case_vcf.multiple, - ch_genome_fasta, - ch_genome_fai, - [[:],[]] + BCFTOOLS_MERGE_MT( + ch_case_vcf.multiple.map { it -> it + [[]] }, + ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) ) BCFTOOLS_MERGE_MT.out.vcf @@ -113,9 +112,12 @@ workflow POSTPROCESS_MT_CALLS { ch_addfoundintag_in .join(TABIX_TABIX_MERGE.out.index) .combine(ch_varcallerbed) + .map { it -> it + [[]] } + .combine(ch_foundin_header) + .map { it -> it + [[]] } .set { ch_annotate_in } - BCFTOOLS_ANNOTATE(ch_annotate_in, [], ch_foundin_header, []) + BCFTOOLS_ANNOTATE(ch_annotate_in) TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) From 4daeceaa3081063171bd9ee65b9ea6cdac7ab26b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 6 Mar 2026 16:42:06 +0100 Subject: [PATCH 437/872] update modules.json --- modules.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index 85e0c4d13..e66467eb3 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8", "installed_by": ["modules"] }, "bcftools/concat": { @@ -22,7 +22,7 @@ }, "bcftools/merge": { "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", + "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8", "installed_by": ["modules"] }, "bcftools/norm": { @@ -313,7 +313,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b", + "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36", "installed_by": ["modules"] }, "ngsbits/samplegender": { @@ -413,7 +413,7 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a", + "git_sha": "440edf75d8782913115a7b72a88392a227f72cc1", "installed_by": ["modules"] }, "samtools/sort": { From 74cf4a74ace002e590d282685ae1f224622149ca Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Mar 2026 10:11:48 +0100 Subject: [PATCH 438/872] cadd fix --- subworkflows/local/annotate_cadd/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index ec88166ba..03a31d925 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -17,10 +17,10 @@ workflow ANNOTATE_CADD { ch_fai // channel: [optional] [ path(fai) ] ch_header // channel: [mandatory] [ path(txt) ] ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] - val_genome // string: GRCh37 or GRCh37 + val_genome // string: GRCh37 or GRCh38 main: - ch_rename_chrs = channel.value([]) + ch_rename_chrs = channel.value([[]]) if (val_genome.equals('GRCh38')) { From ca1ffd332416781dcbf306e7f1fb2186d2143904 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Mar 2026 11:30:20 +0100 Subject: [PATCH 439/872] Update snaps and remove versions --- subworkflows/local/call_snv/main.nf | 4 ---- subworkflows/local/call_snv/tests/main.nf.test.snap | 8 +------- subworkflows/local/call_snv_MT/main.nf | 4 +--- subworkflows/local/call_structural_variants/main.nf | 3 --- tests/default.nf.test.snap | 5 +---- tests/test_bam.nf.test.snap | 7 ++----- tests/test_singleton.nf.test.snap | 7 ++----- workflows/raredisease.nf | 4 ---- 8 files changed, 7 insertions(+), 35 deletions(-) diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 2c55b6942..dad2ce611 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -42,7 +42,6 @@ workflow CALL_SNV { val_variant_caller // string: 'deepvariant' or 'sentieon' main: - ch_versions = channel.empty() ch_deepvar_vcf = channel.empty() ch_deepvar_tbi = channel.empty() ch_deepvar_gvcf = channel.empty() @@ -137,8 +136,6 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions) - ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions) } if (val_concatenate_snv_calls) { @@ -156,5 +153,4 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 7fa01d040..baf3c72ff 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -95,9 +95,6 @@ }, "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "7": [ - ], "genome_gtabix": [ [ @@ -175,13 +172,10 @@ }, "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-03-05T00:25:20.084209813", + "timestamp": "2026-03-09T11:14:37.035323634", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 14c4c4701..eea854421 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -14,9 +14,8 @@ workflow CALL_SNV_MT { ch_intervals // channel: [mandatory] [ path(interval_list) ] main: - ch_versions = channel.empty() - ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) + ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) @@ -35,5 +34,4 @@ workflow CALL_SNV_MT { stats = GATK4_MUTECT2_MT.out.stats // channel: [ val(meta), path(stats) ] tbi = GATK4_FILTERMUTECTCALLS_MT.out.tbi // channel: [ val(meta), path(tbi) ] vcf = GATK4_FILTERMUTECTCALLS_MT.out.vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index f5565be9d..62ddf1a97 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -29,7 +29,6 @@ workflow CALL_STRUCTURAL_VARIANTS { skip_germlinecnvcaller // boolean main: - ch_versions = channel.empty() ch_merged_svs = channel.empty() ch_merged_tbi = channel.empty() @@ -58,7 +57,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .collect{ _meta, vcf -> vcf } .set { gcnvcaller_vcf } - ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions) } //merge @@ -103,5 +101,4 @@ workflow CALL_STRUCTURAL_VARIANTS { emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d4e118a78..ce8cf8ed1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -425,9 +425,6 @@ "TABIX_EXP_RENAME": { "tabix": 1.21 }, - "TABIX_GL": { - "tabix": 1.21 - }, "TABIX_GNOMAD_AF": { "tabix": 1.21 }, @@ -1103,7 +1100,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-05T15:21:47.257080881", + "timestamp": "2026-03-09T10:37:30.038838422", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index cb518bd2b..dcd91124a 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 790, + 788, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -395,9 +395,6 @@ "TABIX_EXP_RENAME": { "tabix": 1.21 }, - "TABIX_GL": { - "tabix": 1.21 - }, "TABIX_GNOMAD_AF": { "tabix": 1.21 }, @@ -1032,7 +1029,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-05T15:28:02.779912134", + "timestamp": "2026-03-09T10:43:36.178146121", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 7b7f2890e..3aa9924a9 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 362, + 360, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -414,9 +414,6 @@ "TABIX_EXP_RENAME": { "tabix": 1.21 }, - "TABIX_GL": { - "tabix": 1.21 - }, "TABIX_GNOMAD_AF": { "tabix": 1.21 }, @@ -722,7 +719,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-05T15:31:47.943426601", + "timestamp": "2026-03-09T10:47:21.755360364", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index abe8b7398..1119fafb1 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -281,7 +281,6 @@ workflow RAREDISEASE { val_mt_subsample_rd, val_mt_subsample_seed ) - ch_versions = ch_versions.mix(SUBSAMPLE_MT_FRAC.out.versions) } else { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, @@ -385,7 +384,6 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) - ch_versions = ch_versions.mix(CALL_SNV.out.versions) // // ANNOTATE GENOME SNVs @@ -554,8 +552,6 @@ workflow RAREDISEASE { val_analysis_type, skip_germlinecnvcaller, ) - ch_versions = ch_versions.mix(CALL_STRUCTURAL_VARIANTS.out.versions) - // // ANNOTATE STRUCTURAL VARIANTS // From 5716b658a7d470e4f870e53d23030b154fe1fb82 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Mar 2026 11:31:12 +0100 Subject: [PATCH 440/872] precommit fix --- subworkflows/local/call_snv_sentieon/main.nf | 2 +- subworkflows/local/postprocess_MT_calls/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 21f5f7731..7b18ab1a7 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -69,7 +69,7 @@ workflow CALL_SNV_SENTIEON { .set{ ch_vcf_idx_merge_in } BCFTOOLS_MERGE( - ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] }, + ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] }, ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) ) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 27769b426..77d5517f2 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -89,7 +89,7 @@ workflow POSTPROCESS_MT_CALLS { return [meta, vcf, tbi] }.set { ch_case_vcf } - BCFTOOLS_MERGE_MT( + BCFTOOLS_MERGE_MT( ch_case_vcf.multiple.map { it -> it + [[]] }, ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) ) From 5a7ce05abad3024f091ba1860071a3637755f7f0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Mar 2026 12:23:22 +0100 Subject: [PATCH 441/872] fix lint --- modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules.json b/modules.json index e66467eb3..b20d83981 100644 --- a/modules.json +++ b/modules.json @@ -313,7 +313,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36", + "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b", "installed_by": ["modules"] }, "ngsbits/samplegender": { From 935786e73b6aaa0e699c4e63955a8d9c428c94aa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 9 Mar 2026 20:21:39 +0100 Subject: [PATCH 442/872] Remove versions --- subworkflows/local/annotate_genome_snvs/main.nf | 3 --- subworkflows/local/annotate_mt_snvs/main.nf | 3 --- workflows/raredisease.nf | 2 -- 3 files changed, 8 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 5f9088521..82535e9cb 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -45,7 +45,6 @@ workflow ANNOTATE_GENOME_SNVS { main: ch_cadd_vcf = channel.empty() - ch_versions = channel.empty() ch_vcf_scatter_in = channel.empty() ch_vep_in = channel.empty() @@ -122,7 +121,6 @@ workflow ANNOTATE_GENOME_SNVS { val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf - ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) } BCFTOOLS_VIEW.out.vcf @@ -197,5 +195,4 @@ workflow ANNOTATE_GENOME_SNVS { emit: tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 496699da1..0205ea285 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -32,7 +32,6 @@ workflow ANNOTATE_MT_SNVS { val_vep_cache_version // string: vep version ex: 107 main: - ch_versions = channel.empty() ch_haplog = channel.empty() // Index vcf @@ -60,7 +59,6 @@ workflow ANNOTATE_MT_SNVS { val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf - ch_versions = ch_versions.mix(ANNOTATE_CADD.out.versions) } else { ch_cadd_vcf = channel.empty() } @@ -119,5 +117,4 @@ workflow ANNOTATE_MT_SNVS { report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] tbi = ch_tbi // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vcf // channel: [ val(meta), path(vcf) ] - versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 1119fafb1..3d400bd61 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -410,7 +410,6 @@ workflow RAREDISEASE { val_genome, val_vep_cache_version ).set { ch_snv_annotate } - ch_versions = ch_versions.mix(ch_snv_annotate.versions) ch_snv_annotate.vcf_ann .multiMap { meta, vcf -> @@ -480,7 +479,6 @@ workflow RAREDISEASE { val_homoplasmy_af_threshold, val_vep_cache_version ).set { ch_mt_annotate } - ch_versions = ch_versions.mix(ch_mt_annotate.versions) ch_mt_annotate.vcf_ann .multiMap { meta, vcf -> From 8922bb43cb99f71571e3e0f89bc0e9daac3d9c06 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 12:58:42 +0100 Subject: [PATCH 443/872] review --- subworkflows/local/call_snv_deepvariant/main.nf | 3 +-- subworkflows/local/call_snv_sentieon/main.nf | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 6e5392da6..9aadc6aaa 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -72,9 +72,8 @@ workflow CALL_SNV_DEEPVARIANT { REMOVE_DUPLICATES_GL.out.vcf .join(REMOVE_DUPLICATES_GL.out.tbi) .combine(ch_varcallerbed) - .map { it -> it + [[]] } .combine(ch_foundin_header) - .map { it -> it + [[]] } + .map { meta, vcf, vcf_tbi, bed, bed_tbi, hdr -> return [meta, vcf, vcf_tbi, bed, bed_tbi, [], hdr, []] } .set { ch_annotate_in } BCFTOOLS_ANNOTATE(ch_annotate_in) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 7b18ab1a7..6f6e3f643 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -69,7 +69,7 @@ workflow CALL_SNV_SENTIEON { .set{ ch_vcf_idx_merge_in } BCFTOOLS_MERGE( - ch_vcf_idx_merge_in.multiple.map { it -> it + [[]] }, + ch_vcf_idx_merge_in.multiple.map { meta, vcf, idx -> return [meta, vcf, idx, []] }, ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) ) @@ -99,9 +99,8 @@ workflow CALL_SNV_SENTIEON { REMOVE_DUPLICATES_SEN.out.vcf .join(REMOVE_DUPLICATES_SEN.out.tbi) .combine(ch_varcallerbed) - .map { it -> it + [[]] } .combine(ch_foundin_header) - .map { it -> it + [[]] } + .map { meta, vcf, vcf_tbi, bed, bed_tbi, hdr -> return [meta, vcf, vcf_tbi, bed, bed_tbi, [], hdr, []] } .set { ch_annotate_in } BCFTOOLS_ANNOTATE(ch_annotate_in) From 9c44193e54710cb38b48a40f584e0b32a00214af Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 13:22:27 +0100 Subject: [PATCH 444/872] add collect --- subworkflows/local/align_bwa_bwamem2_bwameme/main.nf | 4 ++-- subworkflows/local/align_sentieon/main.nf | 2 +- subworkflows/local/call_snv_sentieon/main.nf | 2 +- subworkflows/local/postprocess_MT_calls/main.nf | 7 +++---- 4 files changed, 7 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 24068cadc..615e6b1ad 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -62,14 +62,14 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { .set{ bams } // If there are no samples to merge, skip the process - SAMTOOLS_MERGE ( bams.multiple.map { it -> it + [[]] }, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}) + SAMTOOLS_MERGE ( bams.multiple.map { it -> it + [[]] }, ch_genome_fasta.join(ch_genome_fai).map{meta,fasta,fai-> return [meta,fasta,fai,[]]}.collect()) prepared_bam = bams.single.mix(SAMTOOLS_MERGE.out.bam) // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { SAMTOOLS_INDEX_EXTRACT ( prepared_bam ) extract_bam_sorted_indexed = prepared_bam.join(SAMTOOLS_INDEX_EXTRACT.out.bai, failOnMismatch:true, failOnDuplicate:true) - EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta.join(ch_genome_fai), [], '') + EXTRACT_ALIGNMENTS( extract_bam_sorted_indexed, ch_genome_fasta.join(ch_genome_fai).collect(), [], '') prepared_bam = EXTRACT_ALIGNMENTS.out.bam } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 31d3541ad..b115efa41 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -40,7 +40,7 @@ workflow ALIGN_SENTIEON { // GET ALIGNMENT FROM SELECTED CONTIGS if (val_extract_alignments) { - EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai), [], 'bai') + EXTRACT_ALIGNMENTS( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai).collect(), [], 'bai') ch_bam_bai = EXTRACT_ALIGNMENTS.out.bam.join(EXTRACT_ALIGNMENTS.out.bai, failOnMismatch:true, failOnDuplicate:true) } diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 6f6e3f643..aacbcab54 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -70,7 +70,7 @@ workflow CALL_SNV_SENTIEON { BCFTOOLS_MERGE( ch_vcf_idx_merge_in.multiple.map { meta, vcf, idx -> return [meta, vcf, idx, []] }, - ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) + ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true).collect() ) ch_split_multi_in = BCFTOOLS_MERGE.out.vcf diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 77d5517f2..388aaab1a 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -90,8 +90,8 @@ workflow POSTPROCESS_MT_CALLS { }.set { ch_case_vcf } BCFTOOLS_MERGE_MT( - ch_case_vcf.multiple.map { it -> it + [[]] }, - ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true) + ch_case_vcf.multiple.map { meta, vcf, tbi -> return [meta, vcf, tbi, []] }, + ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true).collect() ) BCFTOOLS_MERGE_MT.out.vcf @@ -112,9 +112,8 @@ workflow POSTPROCESS_MT_CALLS { ch_addfoundintag_in .join(TABIX_TABIX_MERGE.out.index) .combine(ch_varcallerbed) - .map { it -> it + [[]] } .combine(ch_foundin_header) - .map { it -> it + [[]] } + .map { meta, vcf, vcf_tbi, bed, bed_tbi, hdr -> return [meta, vcf, vcf_tbi, bed, bed_tbi, [], hdr, []] } .set { ch_annotate_in } BCFTOOLS_ANNOTATE(ch_annotate_in) From 6cb16c9f94815b67d6d0bedc2f5271ea85b2268e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 14:42:43 +0100 Subject: [PATCH 445/872] update sentieon snap --- conf/modules/call_snv_sentieon.config | 2 +- .../call_snv_sentieon/tests/main.nf.test.snap | 232 ++++++++++++++++++ .../call_snv_sentieon/tests/nextflow.config | 4 +- 3 files changed, 235 insertions(+), 3 deletions(-) create mode 100644 subworkflows/local/call_snv_sentieon/tests/main.nf.test.snap diff --git a/conf/modules/call_snv_sentieon.config b/conf/modules/call_snv_sentieon.config index 0a370e19b..fcf7b6ef7 100644 --- a/conf/modules/call_snv_sentieon.config +++ b/conf/modules/call_snv_sentieon.config @@ -53,7 +53,7 @@ process { } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:BCFTOOLS_ANNOTATE' { - ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type --write-index=tbi" + ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z--write-index=tbi" ext.prefix = { "${meta.id}_split_rmdup_info" } } } diff --git a/subworkflows/local/call_snv_sentieon/tests/main.nf.test.snap b/subworkflows/local/call_snv_sentieon/tests/main.nf.test.snap new file mode 100644 index 000000000..7002614d1 --- /dev/null +++ b/subworkflows/local/call_snv_sentieon/tests/main.nf.test.snap @@ -0,0 +1,232 @@ +{ + "CALL_SNV_SENTIEON - two samples (merge), stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "gvcf": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-10T14:40:02.625974988", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "CALL_SNV_SENTIEON - single sample, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "gvcf": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_dnascope.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tabix": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-03-10T14:39:28.659577535", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/call_snv_sentieon/tests/nextflow.config b/subworkflows/local/call_snv_sentieon/tests/nextflow.config index 4fd5ffbdc..3cb843d93 100644 --- a/subworkflows/local/call_snv_sentieon/tests/nextflow.config +++ b/subworkflows/local/call_snv_sentieon/tests/nextflow.config @@ -24,7 +24,7 @@ process { } withName: 'REMOVE_DUPLICATES_SEN' { - ext.args = '--output-type z --rm-dup none' + ext.args = '--output-type z --rm-dup none --write-index=tbi' ext.prefix = { "${meta.id}_split_rmdup" } } @@ -33,7 +33,7 @@ process { } withName: 'BCFTOOLS_ANNOTATE' { - ext.args = '-c CHROM,FROM,TO,FOUND_IN --output-type z' + ext.args = '-c CHROM,FROM,TO,FOUND_IN --output-type z --write-index=tbi' ext.prefix = { "${meta.id}_split_rmdup_info" } } From a4cac9b9bf1a5ab7d43a5aa7b5e8f7e39c26f7b5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 14:44:05 +0100 Subject: [PATCH 446/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b78ad5fa3..02b3eedb3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - MitoSalt to detect mitochondrial deletions [#743](https://github.com/nf-core/raredisease/pull/743) - Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) +- Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) ### `Changed` From 68d2e1238f8f438c297bbb32c7fce6bfda234458 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 15:16:18 +0100 Subject: [PATCH 447/872] fix error --- .../local/annotate_genome_snvs/tests/main.nf.test.snap | 8 +------- .../local/annotate_mt_snvs/tests/main.nf.test.snap | 8 +------- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 4 insertions(+), 16 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index c77062433..5c7ae9b36 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -33,9 +33,6 @@ }, "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "2": [ - ], "tbi": [ [ @@ -68,13 +65,10 @@ }, "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-03-04T23:37:13.141316008", + "timestamp": "2026-03-10T15:10:07.607984855", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index 84bdc1faf..1b4910ca6 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -43,9 +43,6 @@ }, "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "4": [ - ], "haplog": [ [ @@ -88,13 +85,10 @@ }, "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - "versions": [ - ] } ], - "timestamp": "2026-03-05T16:20:14.293268403", + "timestamp": "2026-03-10T15:10:49.596531529", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 3aa9924a9..0e6dfba4d 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 360, + 359, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -719,7 +719,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-09T10:47:21.755360364", + "timestamp": "2026-03-10T15:15:02.654289867", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 90cba38fb511fa99cff47afdee3e62b5200aece1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 10 Mar 2026 15:55:57 +0100 Subject: [PATCH 448/872] Update test_bam.nf.test.snap --- tests/test_bam.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index dcd91124a..09737cdd4 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 788, + 785, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -1029,7 +1029,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-09T10:43:36.178146121", + "timestamp": "2026-03-10T15:54:35.091523871", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 20560dff4a83f5a276d0cc773fb3dfed6402c8f0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 11 Mar 2026 16:36:08 +0100 Subject: [PATCH 449/872] Update conf/modules/call_snv_sentieon.config Co-authored-by: Anders Jemt --- conf/modules/call_snv_sentieon.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/call_snv_sentieon.config b/conf/modules/call_snv_sentieon.config index fcf7b6ef7..8ba47353c 100644 --- a/conf/modules/call_snv_sentieon.config +++ b/conf/modules/call_snv_sentieon.config @@ -53,7 +53,7 @@ process { } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:BCFTOOLS_ANNOTATE' { - ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z--write-index=tbi" + ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z --write-index=tbi" ext.prefix = { "${meta.id}_split_rmdup_info" } } } From 933333c4a341b3c7dc10ca939dd94c687fe8a3e0 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 12 Mar 2026 15:57:01 +0100 Subject: [PATCH 450/872] move call_sv_mt into call_structural_variants to merge vcfs --- .../local/call_structural_variants.nf | 110 +++++++++++++++--- workflows/raredisease.nf | 81 ++++++------- 2 files changed, 130 insertions(+), 61 deletions(-) diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf index 8d4cbcf6c..0607025b8 100644 --- a/subworkflows/local/call_structural_variants.nf +++ b/subworkflows/local/call_structural_variants.nf @@ -4,6 +4,7 @@ include { CALL_SV_MANTA } from './call_sv_manta' include { CALL_SV_TIDDIT } from './call_sv_tiddit' +include { CALL_SV_MT } from './call_sv_MT' include { SVDB_MERGE } from '../../modules/nf-core/svdb/merge/main' include { CALL_SV_GERMLINECNVCALLER } from './call_sv_germlinecnvcaller' include { CALL_SV_CNVNATOR } from './call_sv_cnvnator' @@ -12,21 +13,55 @@ include { TABIX_TABIX } from '../../modules/nf-core/tabix/tab workflow CALL_STRUCTURAL_VARIANTS { take: - ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] - ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] - ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] - ch_genome_dictionary // channel: [optional; used by mandatory for GATK's cnvcaller][ val(meta), path(dict) ] - ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] - ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] - ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] - ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] - val_analysis_type // string: "wes", "wgs", or "mito" - skip_germlinecnvcaller // boolean + ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] + ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] + ch_genome_dictionary // channel: [optional; used by mandatory for GATK's cnvcaller][ val(meta), path(dict) ] + ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] + ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] + ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] + ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] + val_analysis_type // string: "wes", "wgs", or "mito" + skip_germlinecnvcaller // boolean + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start + val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end + val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start + val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end + val_mito_length // string: [mandatory] mito_length + val_mito_name // string: [mandatory] mito_name + val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan + val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold + val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold + val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max + val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min + val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold + val_mitosalt_exclude // string: [mandatory] mitosalt_exclude + val_mitosalt_flank // string: [mandatory] mitosalt_flank + val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit + val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance + val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold + val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit + val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold + val_mitosalt_split_length // string: [mandatory] mitosalt_split_length + val_saltshaker_dominant_fraction // string: [mandatory] saltshaker_dominant_fraction + val_saltshaker_group_radius // string: [mandatory] saltshaker_group_radius + val_saltshaker_high_heteroplasmy // string: [mandatory] saltshaker_high_heteroplasmy + val_saltshaker_multiple_threshold // string: [mandatory] saltshaker_multiple_threshold + val_saltshaker_noise_threshold // string: [mandatory] saltshaker_noise_threshold + val_run_mt_for_wes // boolean: [mandatory] run_mt_for_wes main: ch_versions = channel.empty() @@ -61,12 +96,56 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_versions = ch_versions.mix(CALL_SV_GERMLINECNVCALLER.out.versions) } + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { + CALL_SV_MT( + ch_bam_bai, + ch_genome_chrsizes, + ch_genome_fai, + ch_genome_fasta, + ch_genome_hisat2index, + ch_mt_fai, + ch_mt_fasta, + ch_mt_lastdb, + ch_reads, + ch_subdepth, + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end, + val_mito_length, + val_mito_name, + val_mitosalt_breakspan, + val_mitosalt_breakthreshold, + val_mitosalt_cluster_threshold, + val_mitosalt_deletion_threshold_max, + val_mitosalt_deletion_threshold_min, + val_mitosalt_evalue_threshold, + val_mitosalt_exclude, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, + val_mitosalt_paired_distance, + val_mitosalt_score_threshold, + val_mitosalt_sizelimit, + val_mitosalt_split_distance_threshold, + val_mitosalt_split_length, + val_saltshaker_dominant_fraction, + val_saltshaker_group_radius, + val_saltshaker_high_heteroplasmy, + val_saltshaker_multiple_threshold, + val_saltshaker_noise_threshold) + .mitosalt_vcf + .collect{ _meta, vcf -> vcf } + .set { mitosalt_vcf } + } + + //merge if (skip_germlinecnvcaller) { if (val_analysis_type.equals("wgs")) { tiddit_vcf .combine(manta_vcf) .combine(cnvnator_vcf) + .combine(mitosalt_vcf) .toList() .set { vcf_list } } else if (!val_analysis_type.equals("mito")) { @@ -79,6 +158,7 @@ workflow CALL_STRUCTURAL_VARIANTS { .combine(manta_vcf) .combine(gcnvcaller_vcf) .combine(cnvnator_vcf) + .combine(mitosalt_vcf) .toList() .set { vcf_list } } else if (!val_analysis_type.equals("mito")) { diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 63b35e0b1..8ead1795d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -532,7 +532,7 @@ workflow RAREDISEASE { /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CALL AND ANNOTATE NUCLEAR SVs + CALL AND ANNOTATE NUCLEAR AND MITOCHONDRIAL SVs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ @@ -553,6 +553,40 @@ workflow RAREDISEASE { ch_gcnvcaller_model, val_analysis_type, skip_germlinecnvcaller, + ch_mapped.genome_marked_bam_bai, + ch_genome_chrsizes, + ch_genome_hisat2index, + ch_mt_fai, + ch_mt_fasta, + ch_mt_lastdb, + ch_input_fastqs, + ch_subdepth, + params.heavy_strand_origin_start, + params.heavy_strand_origin_end, + params.light_strand_origin_start, + params.light_strand_origin_end, + params.mito_length, + params.mito_name, + params.mitosalt_breakspan, + params.mitosalt_breakthreshold, + params.mitosalt_cluster_threshold, + params.mitosalt_deletion_threshold_max, + params.mitosalt_deletion_threshold_min, + params.mitosalt_evalue_threshold, + params.mitosalt_exclude, + params.mitosalt_flank, + params.mitosalt_heteroplasmy_limit, + params.mitosalt_paired_distance, + params.mitosalt_score_threshold, + params.mitosalt_sizelimit, + params.mitosalt_split_distance_threshold, + params.mitosalt_split_length, + params.saltshaker_dominant_fraction, + params.saltshaker_group_radius, + params.saltshaker_high_heteroplasmy, + params.saltshaker_multiple_threshold, + params.saltshaker_noise_threshold, + val_run_mt_for_wes ) ch_versions = ch_versions.mix(CALL_STRUCTURAL_VARIANTS.out.versions) @@ -620,52 +654,7 @@ workflow RAREDISEASE { } } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CALL MITOCHONDRIAL SVs -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { - CALL_SV_MT( - ch_mapped.genome_marked_bam_bai, - ch_genome_chrsizes, - ch_genome_fai, - ch_genome_fasta, - ch_genome_hisat2index, - ch_mt_fai, - ch_mt_fasta, - ch_mt_lastdb, - ch_input_fastqs, - ch_subdepth, - params.heavy_strand_origin_start, - params.heavy_strand_origin_end, - params.light_strand_origin_start, - params.light_strand_origin_end, - params.mito_length, - params.mito_name, - params.mitosalt_breakspan, - params.mitosalt_breakthreshold, - params.mitosalt_cluster_threshold, - params.mitosalt_deletion_threshold_max, - params.mitosalt_deletion_threshold_min, - params.mitosalt_evalue_threshold, - params.mitosalt_exclude, - params.mitosalt_flank, - params.mitosalt_heteroplasmy_limit, - params.mitosalt_paired_distance, - params.mitosalt_score_threshold, - params.mitosalt_sizelimit, - params.mitosalt_split_distance_threshold, - params.mitosalt_split_length, - params.saltshaker_dominant_fraction, - params.saltshaker_group_radius, - params.saltshaker_high_heteroplasmy, - params.saltshaker_multiple_threshold, - params.saltshaker_noise_threshold - ) - } - -/* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CALL AND ANNOTATE MOBILE ELEMENTS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From d3431c129d28a78092146489d5054590cd2df131 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 12 Mar 2026 21:12:07 +0100 Subject: [PATCH 451/872] migrate to output for align*, qc_bam, and call* --- conf/modules/align.config | 10 ------ conf/modules/align_bwa_bwamem2_bwameme.config | 15 -------- conf/modules/align_sentieon.config | 6 ---- conf/modules/call_mobile_elements.config | 13 ------- conf/modules/call_repeat_expansions.config | 10 ------ conf/modules/call_snv.config | 11 ------ conf/modules/call_structural_variants.config | 13 ------- conf/modules/call_sv_MT.config | 13 ------- conf/modules/postprocess_MT_calls.config | 13 ------- conf/modules/qc_bam.config | 13 ------- main.nf | 10 ++++++ subworkflows/local/align/main.nf | 30 ++++++++++++++-- .../local/align_bwa_bwamem2_bwameme/main.nf | 7 ++++ subworkflows/local/align_sentieon/main.nf | 8 +++++ .../local/call_mobile_elements/main.nf | 5 +++ .../local/call_repeat_expansions/main.nf | 10 ++++-- subworkflows/local/call_snv/main.nf | 14 ++++++++ .../local/call_structural_variants/main.nf | 5 +++ subworkflows/local/call_sv_MT/main.nf | 8 +++++ .../local/postprocess_MT_calls/main.nf | 5 +++ subworkflows/local/qc_bam/main.nf | 34 +++++++++++++++++++ workflows/raredisease.nf | 20 ++++++++++- 22 files changed, 151 insertions(+), 122 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 6df68cb32..7cc52726f 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -19,20 +19,10 @@ process{ '--correction', '--overrepresentation_analysis' ].join(' ').trim() } - publishDir = [ - path: { "${params.outdir}/trimming" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ALIGN:SAMTOOLS_VIEW' { ext.args = { '--output-fmt cram' } ext.prefix = { "${meta.id}_sort_md" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index d3dab330f..da2cd83ff 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -57,20 +57,5 @@ process { withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:MARKDUPLICATES' { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_sorted_md" } - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' { - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config index 9a92b6057..13c051221 100644 --- a/conf/modules/align_sentieon.config +++ b/conf/modules/align_sentieon.config @@ -38,11 +38,5 @@ process { withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' { ext.args4 = { params.rmdup ? "--rmdup" : '' } ext.prefix = { "${meta.id}_dedup.bam" } - publishDir = [ - enabled: !params.save_mapped_as_cram, - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_mobile_elements.config b/conf/modules/call_mobile_elements.config index 6b1346776..dfa59f3fb 100644 --- a/conf/modules/call_mobile_elements.config +++ b/conf/modules/call_mobile_elements.config @@ -50,18 +50,5 @@ process { withName: '.*CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME' { ext.args = { '--bnd_distance 150 --overlap 0.5' } ext.prefix = { "${meta.id}_mobile_elements" } - publishDir = [ - path: { "${params.outdir}/call_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_MOBILE_ELEMENTS:TABIX_ME' { - publishDir = [ - path: { "${params.outdir}/call_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config index 23217bd07..916cff868 100644 --- a/conf/modules/call_repeat_expansions.config +++ b/conf/modules/call_repeat_expansions.config @@ -23,22 +23,12 @@ process { withName: '.*CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT' { ext.prefix = { "${meta.id}_exphunter_sorted" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' { ext.args = "--temp-prefix ." ext.args2 = "-O v" ext.prefix = { "${meta.id}_repeat_expansion" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } withName: '.*CALL_REPEAT_EXPANSIONS:SPLIT_MULTIALLELICS_EXP' { diff --git a/conf/modules/call_snv.config b/conf/modules/call_snv.config index 58ad7b337..2648a2d75 100644 --- a/conf/modules/call_snv.config +++ b/conf/modules/call_snv.config @@ -16,21 +16,10 @@ process { withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' { ext.args = { "--exclude-intervals ${params.mito_name}" } ext.prefix = { "${meta.id}_snv" } - publishDir = [ - path: { "${params.outdir}/call_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*CALL_SNV:BCFTOOLS_CONCAT' { ext.args = { "--write-index=tbi" } ext.prefix = { "${meta.id}_mt_and_nuclear_snvs" } - publishDir = [ - enabled: params.concatenate_snv_calls, - path: { "${params.outdir}/call_snv/concatenated_calls" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_structural_variants.config b/conf/modules/call_structural_variants.config index 23e9325b6..a9fcd660d 100644 --- a/conf/modules/call_structural_variants.config +++ b/conf/modules/call_structural_variants.config @@ -20,18 +20,5 @@ process { withName: '.*CALL_STRUCTURAL_VARIANTS:SVDB_MERGE' { ext.prefix = {"${meta.id}_sv"} ext.args = '--pass_only --same_order' - publishDir = [ - path: { "${params.outdir}/call_sv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_STRUCTURAL_VARIANTS:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/call_sv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index deedd506d..be140cabe 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -20,19 +20,6 @@ process { withName: '.*CALL_SV_MT:MT_DELETION' { ext.args = '-s --insert-size 16000' ext.prefix = { "${meta.id}_mitochondria_deletions" } - publishDir = [ - path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*CALL_SV_MT:MITOSALT' { - publishDir = [ - path: { "${params.outdir}/call_sv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/postprocess_MT_calls.config b/conf/modules/postprocess_MT_calls.config index 61a14131a..f54c383e6 100644 --- a/conf/modules/postprocess_MT_calls.config +++ b/conf/modules/postprocess_MT_calls.config @@ -47,19 +47,6 @@ process { withName: '.*POSTPROCESS_MT_CALLS:BCFTOOLS_ANNOTATE' { ext.args = "-c CHROM,FROM,TO,FOUND_IN --output-type z --include FILTER='\"PASS\"'" ext.prefix = { "${meta.id}_mitochondria" } - publishDir = [ - path: { "${params.outdir}/call_snv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*POSTPROCESS_MT_CALLS:TABIX_ANNOTATE' { - publishDir = [ - path: { "${params.outdir}/call_snv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 0b49f6c80..d0905762b 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -16,14 +16,6 @@ // process { - withName: '.*QC_BAM:.*' { - publishDir = [ - path: { "${params.outdir}/qc_bam" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } - withName: '.*QC_BAM:PICARD_COLLECTMULTIPLEMETRICS' { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_multiplemetrics" } @@ -61,11 +53,6 @@ process { // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } ext.prefix = { "${meta.id}_ngsbits_sex" } - publishDir = [ - path: { "${params.outdir}/ngsbits_samplegender" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_WG' { diff --git a/main.nf b/main.nf index 5346dbd30..58cb974b8 100644 --- a/main.nf +++ b/main.nf @@ -466,6 +466,7 @@ workflow NFCORE_RAREDISEASE { ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + ch_publish = RAREDISEASE.out.ch_publish // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -586,6 +587,15 @@ workflow { params.hook_url, NFCORE_RAREDISEASE.out.multiqc_report ) + + publish: + subworkflow_results = NFCORE_RAREDISEASE.out.ch_publish +} + +output { + subworkflow_results { + path { destination, value -> destination } + } } /* diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index cc9cf0b9f..65b97acf1 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -45,17 +45,26 @@ workflow ALIGN { ch_bwamem2_bam = channel.empty() ch_bwamem2_bai = channel.empty() ch_fastp_json = channel.empty() + ch_fastp_publish = channel.empty() ch_markdup_metrics = channel.empty() ch_mt_bam_bai = channel.empty() ch_mt_bam_bai_gatksubwf = channel.empty() ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() + ch_cram_publish = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) - ch_input_reads = FASTP.out.reads - ch_fastp_json = FASTP.out.json + ch_input_reads = FASTP.out.reads + ch_fastp_json = FASTP.out.json + ch_fastp_publish = FASTP.out.json + .mix(FASTP.out.html) + .mix(FASTP.out.log) + .mix(FASTP.out.reads) + .mix(FASTP.out.reads_fail) + .mix(FASTP.out.reads_merged) + .map { meta, value -> ['trimming/', [meta, value]] } } // @@ -152,8 +161,24 @@ workflow ALIGN { if (val_save_mapped_as_cram) { SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_publish = SAMTOOLS_VIEW.out.cram + .mix(SAMTOOLS_VIEW.out.crai) + .map { meta, value -> ['alignment/', [meta, value]] } } + ch_bam_publish = channel.empty() + if (!val_save_mapped_as_cram) { + if (val_aligner.matches("bwamem2|bwa|bwameme")) { + ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.ch_publish + } else if (val_aligner.equals("sentieon")) { + ch_bam_publish = ALIGN_SENTIEON.out.ch_publish + } + } + + ch_publish = ch_fastp_publish + .mix(ch_bam_publish) + .mix(ch_cram_publish) + emit: fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] @@ -163,4 +188,5 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 615e6b1ad..fda97a2c3 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -77,9 +77,16 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) + ch_publish = MARKDUPLICATES.out.bam + .mix(MARKDUPLICATES.out.metrics) + .mix(SAMTOOLS_INDEX_MARKDUP.out.bai) + .mix(SAMTOOLS_INDEX_MARKDUP.out.csi) + .map { meta, value -> ['alignment/', [meta, value]] } + emit: marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index b115efa41..74b1cc1f2 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -48,6 +48,13 @@ workflow ALIGN_SENTIEON { SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai ) + ch_publish = SENTIEON_DEDUP.out.bam + .mix(SENTIEON_DEDUP.out.bai) + .mix(SENTIEON_DEDUP.out.score) + .mix(SENTIEON_DEDUP.out.metrics) + .mix(SENTIEON_DEDUP.out.metrics_multiqc_tsv) + .map { meta, value -> ['alignment/', [meta, value]] } + emit: marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] marked_bai = SENTIEON_DEDUP.out.bai // channel: [ val(meta), path(bai) ] @@ -57,4 +64,5 @@ workflow ALIGN_SENTIEON { gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 06cd34a5c..80c4bc696 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -119,7 +119,12 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) + ch_publish = SVDB_MERGE_ME.out.vcf + .mix(TABIX_ME.out.index) + .map { meta, value -> ['call_mobile_elements/', [meta, value]] } + emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index 14ec4fb61..ea6d82010 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -57,6 +57,12 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) -emit: - vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish = SAMTOOLS_SORT.out.bam + .mix(SAMTOOLS_SORT.out.bai) + .mix(BCFTOOLS_REHEADER_EXP.out.vcf) + .map { meta, value -> ['repeat_expansions/', [meta, value]] } + + emit: + vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index dad2ce611..acc607efb 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -53,6 +53,8 @@ workflow CALL_SNV { ch_sentieon_tbi = channel.empty() ch_sentieon_gvcf = channel.empty() ch_sentieon_gtbi = channel.empty() + ch_concat_publish = channel.empty() + ch_mt_snv_publish = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( @@ -136,6 +138,7 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) + ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.ch_publish } if (val_concatenate_snv_calls) { @@ -143,8 +146,18 @@ workflow CALL_SNV { BCFTOOLS_CONCAT ( ch_concat_vcf_in ) + ch_concat_publish = BCFTOOLS_CONCAT.out.vcf + .mix(BCFTOOLS_CONCAT.out.tbi) + .mix(BCFTOOLS_CONCAT.out.csi) + .map { meta, value -> ['call_snv/concatenated_calls/', [meta, value]] } } + ch_publish = GATK4_SELECTVARIANTS.out.vcf + .mix(GATK4_SELECTVARIANTS.out.tbi) + .map { meta, value -> ['call_snv/genome/', [meta, value]] } + .mix(ch_concat_publish) + .mix(ch_mt_snv_publish) + emit: genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] @@ -153,4 +166,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 62ddf1a97..49c062ee7 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -98,7 +98,12 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_merged_tbi = TABIX_TABIX.out.index } + ch_publish = ch_merged_svs + .mix(ch_merged_tbi) + .map { meta, value -> ['call_sv/genome/', [meta, value]] } + emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f24d752fc..5c7a97913 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -36,6 +36,7 @@ workflow CALL_SV_MT { val_split_length // string: [mandatory] mitosalt_split_length main: + ch_mitosalt_publish = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -76,12 +77,19 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) + ch_mitosalt_publish = MITOSALT.out.breakpoint + .mix(MITOSALT.out.cluster) } MT_DELETION(ch_bam_bai, ch_genome_fasta) + ch_publish = ch_mitosalt_publish + .mix(MT_DELETION.out.mt_del_result) + .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } + emit: mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 388aaab1a..9f631cd5f 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -120,7 +120,12 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) + ch_publish = BCFTOOLS_ANNOTATE.out.vcf + .mix(TABIX_ANNOTATE.out.index) + .map { meta, value -> ['call_snv/mitochondria/', [meta, value]] } + emit: tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index d2edb0da1..307c51b4e 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -96,6 +96,39 @@ workflow QC_BAM { ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) + ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) + .mix(TIDDIT_COV.out.wig) + .mix(TIDDIT_COV.out.cov) + .mix(UCSC_WIGTOBIGWIG.out.bw) + .mix(CHROMOGRAPH_COV.out.plots) + .mix(MOSDEPTH.out.global_txt) + .mix(MOSDEPTH.out.summary_txt) + .mix(MOSDEPTH.out.per_base_d4) + .mix(MOSDEPTH.out.regions_txt) + .mix(MOSDEPTH.out.per_base_bed) + .mix(MOSDEPTH.out.per_base_csi) + .mix(MOSDEPTH.out.regions_bed) + .mix(MOSDEPTH.out.regions_csi) + .mix(MOSDEPTH.out.quantized_bed) + .mix(MOSDEPTH.out.quantized_csi) + .mix(MOSDEPTH.out.thresholds_bed) + .mix(MOSDEPTH.out.thresholds_csi) + .mix(SAMBAMBA_DEPTH.out.bed) + .mix(VERIFYBAMID_VERIFYBAMID2.out.self_sm) + .mix(VERIFYBAMID_VERIFYBAMID2.out.log) + .mix(VERIFYBAMID_VERIFYBAMID2.out.ud) + .mix(VERIFYBAMID_VERIFYBAMID2.out.bed) + .mix(VERIFYBAMID_VERIFYBAMID2.out.mu) + .mix(VERIFYBAMID_VERIFYBAMID2.out.ancestry) + .mix(ch_hsmetrics) + .mix(ch_qualimap) + .mix(ch_cov) + .mix(ch_cov_y) + .map { meta, value -> ['qc_bam/', [meta, value]] } + .mix(ch_ngsbits + .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] }) + emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] @@ -108,4 +141,5 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] + ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 3d400bd61..e81a3429b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -205,7 +205,12 @@ workflow RAREDISEASE { main: - ch_multiqc_files = channel.empty() + ch_multiqc_files = channel.empty() + ch_call_snv_publish = channel.empty() + ch_call_sv_publish = channel.empty() + ch_call_sv_mt_publish = channel.empty() + ch_call_repeat_expansions_publish = channel.empty() + ch_call_mobile_elements_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -337,6 +342,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) + ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.ch_publish if (!skip_repeat_annotation) { STRANGER ( @@ -384,6 +390,7 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) + ch_call_snv_publish = CALL_SNV.out.ch_publish // // ANNOTATE GENOME SNVs @@ -550,6 +557,8 @@ workflow RAREDISEASE { val_analysis_type, skip_germlinecnvcaller, ) + ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.ch_publish + // // ANNOTATE STRUCTURAL VARIANTS // @@ -646,6 +655,7 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) + ch_call_sv_mt_publish = CALL_SV_MT.out.ch_publish } /* @@ -662,6 +672,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) + ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.ch_publish if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -893,6 +904,13 @@ workflow RAREDISEASE { emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + ch_publish = ALIGN.out.ch_publish + .mix(QC_BAM.out.ch_publish) + .mix(ch_call_snv_publish) + .mix(ch_call_sv_publish) + .mix(ch_call_sv_mt_publish) + .mix(ch_call_repeat_expansions_publish) + .mix(ch_call_mobile_elements_publish) // channel: [ val(destination), val(value) ] } From cbfbb344f9d2e970b4a85b00b590b2aff97ac68e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 12 Mar 2026 22:19:19 +0100 Subject: [PATCH 452/872] updaate changelog --- CHANGELOG.md | 1 + nextflow.config | 2 ++ 2 files changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02b3eedb3..0a0363cc0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) - Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) - Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#784](https://github.com/nf-core/raredisease/pull/784) ### `Fixed` diff --git a/nextflow.config b/nextflow.config index bd520863d..4c212227e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -175,6 +175,8 @@ params { validate_params = true } +workflow.output.mode = 'copy' + // Load base.config by default for all pipelines includeConfig 'conf/base.config' From 072778967ee70d6feb41cd9af403a23335e6538d Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 13 Mar 2026 09:32:32 +0100 Subject: [PATCH 453/872] modules --- modules.json | 593 --------------------------------------------------- 1 file changed, 593 deletions(-) delete mode 100644 modules.json diff --git a/modules.json b/modules.json deleted file mode 100644 index dcf570b57..000000000 --- a/modules.json +++ /dev/null @@ -1,593 +0,0 @@ -{ - "name": "nf-core/raredisease", - "homePage": "https://github.com/nf-core/raredisease", - "repos": { - "https://github.com/nf-core/modules.git": { - "modules": { - "nf-core": { - "bcftools/annotate": { - "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] - }, - "bcftools/concat": { - "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] - }, - "bcftools/filter": { - "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] - }, - "bcftools/merge": { - "branch": "master", - "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6", - "installed_by": ["modules"] - }, - "bcftools/norm": { - "branch": "master", - "git_sha": 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["modules"] - } - } - }, - "subworkflows": { - "nf-core": { - "utils_nextflow_pipeline": { - "branch": "master", - "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", - "installed_by": ["subworkflows"] - }, - "utils_nfcore_pipeline": { - "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", - "installed_by": ["subworkflows"] - }, - "utils_nfschema_plugin": { - "branch": "master", - "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", - "installed_by": ["subworkflows"] - }, - "vcf_filter_bcftools_ensemblvep": { - "branch": "master", - "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": ["subworkflows"] - } - } - } - } - } -} From 9178577eaab61a75ded35e9675e66f332496d149 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 10:09:42 +0100 Subject: [PATCH 454/872] update tests and snaps --- NEXTFLOW_OUTPUT_MIGRATION.md | 162 +++ main.nf | 4 +- subworkflows/local/align/main.nf | 6 +- subworkflows/local/align/tests/main.nf.test | 3 + .../local/align/tests/main.nf.test.snap | 927 +++++++++++++++++- .../local/align_bwa_bwamem2_bwameme/main.nf | 2 +- .../tests/main.nf.test | 2 + .../tests/main.nf.test.snap | 104 +- subworkflows/local/align_sentieon/main.nf | 2 +- .../local/call_mobile_elements/main.nf | 2 +- .../tests/main.nf.test.snap | 42 +- .../local/call_repeat_expansions/main.nf | 2 +- .../call_repeat_expansions/tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 65 +- subworkflows/local/call_snv/main.nf | 4 +- .../local/call_snv/tests/main.nf.test | 1 + .../local/call_snv/tests/main.nf.test.snap | 118 ++- .../local/call_structural_variants/main.nf | 2 +- .../tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 22 +- subworkflows/local/call_sv_MT/main.nf | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 120 ++- .../local/postprocess_MT_calls/main.nf | 2 +- .../tests/main.nf.test.snap | 42 +- subworkflows/local/qc_bam/main.nf | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 2 + tests/default.nf.test.snap | 386 +------- tests/test_bam.nf.test.snap | 355 +------ tests/test_singleton.nf.test.snap | 142 +-- workflows/raredisease.nf | 18 +- 30 files changed, 1627 insertions(+), 916 deletions(-) create mode 100644 NEXTFLOW_OUTPUT_MIGRATION.md diff --git a/NEXTFLOW_OUTPUT_MIGRATION.md b/NEXTFLOW_OUTPUT_MIGRATION.md new file mode 100644 index 000000000..c8a408161 --- /dev/null +++ b/NEXTFLOW_OUTPUT_MIGRATION.md @@ -0,0 +1,162 @@ +--- + +## Centralized Publishing Pattern (nf-core migration approach) + +Instead of using `topic` channels or `publishDir`, we use a **single `ch_publish` channel +per subworkflow** that emits `[destination, value]` tuples. Publishing is handled centrally +in `main.nf`. + +### Pattern Overview + +**Inside each subworkflow**, map every published output into a `[destination, value]` tuple +where `destination` mirrors the original `publishDir` path. Mix all of them into a single +`ch_publish` and emit it: + +```nextflow +// Inside subworkflow +ch_publish = PROCESS_A.out.bam + .map { meta, bam -> ['alignment/', [meta, bam]] } + .mix(PROCESS_B.out.metrics.map { meta, f -> ['qc/', [meta, f]] }) + .mix(PROCESS_C.out.vcf.map { meta, vcf -> ['vcf/', [meta, vcf]] }) + +emit: +ch_publish +``` + +Rules: + +- There must be only **one `ch_publish` emit per subworkflow** +- The destination string should mirror the original `publishDir` path +- Preserve the original channel structure as the second element of the tuple +- Include outputs from processes whose channels are not consumed downstream — + these were previously captured by `publishDir` at the filesystem level + +**In `main.nf`**, collect `ch_publish` from all subworkflows, mix them, and publish +centrally: + +```nextflow +workflow { + main: + SUBWORKFLOW_A(...) + SUBWORKFLOW_B(...) + + publish: + all_outputs = SUBWORKFLOW_A.out.ch_publish + .mix(SUBWORKFLOW_B.out.ch_publish) +} + +output { + all_outputs { + path { destination, value -> destination } + } +} +``` + +### Handling varying channel structures + +Channels with different numbers of elements (e.g. `[meta, bam]` vs `[meta, bam, bai]`) +are handled safely by always wrapping the entire inner tuple as a single second element. +Nextflow recursively scans the value for file objects automatically. + +// CORRECT +.map { meta, bam, bai -> ['alignment/', [meta, bam, bai]] } + +// WRONG — breaks the [destination, value] contract +.map { meta, bam, bai -> ['alignment/', meta, bam, bai] } +``` + +**Your command** — add one line to enforce the wrapping rule: +``` +... + +For each process output that should be published, map it into a tuple of +[destination_path, channel_value] where destination_path mirrors the directory +that publishDir was publishing to. Always wrap the entire channel value as a +single second element regardless of how many elements it contains, e.g. +{ meta, bam, bai -> ['alignment/', [meta, bam, bai]] }. +... + +### Grouping channels by destination before mapping + +Instead of mapping each channel individually, group channels sharing the same destination +using `mix` first, then apply a single `map` per destination group. This reduces repetition +significantly. + +```nextflow +// PREFERRED — one map per destination group +ch_qc_bam = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) + .mix(TIDDIT_COV.out.wig) + .mix(MOSDEPTH.out.global_txt) + .mix(ch_qualimap) + .map { meta, value -> ['qc_bam/', [meta, value]] } + +ch_ngsbits = ch_ngsbits_samplegender + .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] } + +ch_publish = ch_qc_bam.mix(ch_ngsbits) + +// AVOID — one map per channel, very repetitive +ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics + .map { meta, metrics -> ['qc_bam/', [meta, metrics]] } + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf + .map { meta, pdf -> ['qc_bam/', [meta, pdf]] }) + // ... +``` + +Rules: + +- Create one intermediate channel per unique destination directory +- Mix all channels going to the same destination first, then apply a single `map` +- Combine all destination groups into `ch_publish` with a final `mix` + +### Nested subworkflows — bubbling up ch_publish + +When a subworkflow calls other subworkflows, always mix the inner `ch_publish` into the +outer `ch_publish`. This propagates publishing up the call chain to `main.nf`. + +```nextflow +// Inner subworkflow emits its own ch_publish +workflow ALIGN_BWA { + main: + BWA_MEM(...) + SAMTOOLS_SORT(...) + + ch_publish = BWA_MEM.out.bam + .mix(SAMTOOLS_SORT.out.bam) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + ch_publish +} + +// Outer subworkflow mixes in ch_publish from inner subworkflow +workflow ALIGN { + main: + ALIGN_BWA(...) + FASTP(...) + + ch_publish = FASTP.out.reads + .map { meta, value -> ['fastp/', [meta, value]] } + .mix(ALIGN_BWA.out.ch_publish) + + emit: + ch_publish +} +``` + +Rules: + +- Every subworkflow that has publishable outputs must emit `ch_publish` +- If a subworkflow calls inner subworkflows, always mix their `ch_publish` into the + outer `ch_publish` — never discard it +- In `main.nf`, mix `ch_publish` from all top-level subworkflows into one channel + before the `publish:` block + +### Why this approach + +- Subworkflow signatures stay clean — one `ch_publish` emit regardless of how many + output directories exist internally +- Publishing logic is fully centralized in `main.nf` +- No `topic` channel footguns (pipeline hanging forever if a process consumes its own topic) +- Easy to audit all published paths by reading `main.nf` alone diff --git a/main.nf b/main.nf index 58cb974b8..f36c819a1 100644 --- a/main.nf +++ b/main.nf @@ -466,7 +466,7 @@ workflow NFCORE_RAREDISEASE { ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - ch_publish = RAREDISEASE.out.ch_publish // channel: [ val(destination), val(value) ] + publish = RAREDISEASE.out.publish // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -589,7 +589,7 @@ workflow { ) publish: - subworkflow_results = NFCORE_RAREDISEASE.out.ch_publish + subworkflow_results = NFCORE_RAREDISEASE.out.publish } output { diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 65b97acf1..f61c92e04 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -169,9 +169,9 @@ workflow ALIGN { ch_bam_publish = channel.empty() if (!val_save_mapped_as_cram) { if (val_aligner.matches("bwamem2|bwa|bwameme")) { - ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.ch_publish + ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.publish } else if (val_aligner.equals("sentieon")) { - ch_bam_publish = ALIGN_SENTIEON.out.ch_publish + ch_bam_publish = ALIGN_SENTIEON.out.publish } } @@ -188,5 +188,5 @@ workflow ALIGN { mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index dce17b191..06df3a019 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -116,6 +116,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -216,6 +217,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -308,6 +310,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index ceb34df54..93aa1301f 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1,6 +1,371 @@ { "align bwamem2 - wgs": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sort_md.cram:md5,bc7f10d51c282f5632a7fce6a76a891a" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sort_md.cram.crai:md5,b72dd8b4097b1adef34747aa2c53a3ca" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sort_md.cram:md5,6e7b8b26c4e3851fa1f4bf4a629016d9" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sort_md.cram.crai:md5,e39b6adfff50427d53f7e8cd43b1cd26" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sort_md.cram:md5,b34cfc30ca2754d70e69fabadefba4d7" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sort_md.cram.crai:md5,34cc581f4684ba2f403bc1eea3975ad7" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "slowlycivilbuck_R1.fastp.fastq.gz:md5,34b043eb99b2f0f4369079d90dd09b5c", + "slowlycivilbuck_R2.fastp.fastq.gz:md5,54520d9ce8ccd2f54cec2873bbaed0ed" + ] + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.log:md5,17d946e68aee1f92ae5334a74fde8571" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,7ad34e9e48159c794ce777e4e48c0b96" + ] + ], + [ + "trimming/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.html:md5,78c27a84b0667febcb848c83e35eada1" + ] + ], + [ + "trimming/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + 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"sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "trimming/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], [ [ { @@ -445,7 +1366,7 @@ ] ], - "timestamp": "2026-02-17T14:53:17.634008549", + "timestamp": "2026-03-13T09:09:46.038355114", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index fda97a2c3..66eafb804 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -88,5 +88,5 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index cdde33d3e..13fdcdf2a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -55,6 +55,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -111,6 +112,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 09b3ed99d..c61fe2bb9 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -1,6 +1,56 @@ { "align bwamem2": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,171423ac03499a00c4677f8b53771570" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,4730bcc5e26e8f3c29b8fa58f68d43e6" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,b8976cf366140eeee478ee2e9c1cadc9" + ] + ] + ], [ [ { @@ -32,7 +82,7 @@ ] ] ], - "timestamp": "2026-02-27T15:46:37.232286266", + "timestamp": "2026-03-13T09:21:28.631120006", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -40,6 +90,56 @@ }, "align bwameme": { "content": [ + [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,ca247f01365899e07c77c3479fa721b2" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,f5b5580ca2b1035f0cac8ba1db7ab55e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,e1e422e8da8ae8f2fbf0221d29919be0" + ] + ] + ], [ [ { @@ -71,7 +171,7 @@ ] ] ], - "timestamp": "2026-02-27T15:47:22.733461874", + "timestamp": "2026-03-13T09:22:14.004999114", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 74b1cc1f2..2038682b5 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -64,5 +64,5 @@ workflow ALIGN_SENTIEON { gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 80c4bc696..896da1068 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -126,5 +126,5 @@ workflow CALL_MOBILE_ELEMENTS { emit: tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap index 9ce36a3b4..bf9b9c3a3 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap @@ -18,6 +18,46 @@ "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "2": [ + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_mobile_elements/", + [ + { + "id": "justhusky" + }, + "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -36,7 +76,7 @@ ] } ], - "timestamp": "2026-03-04T15:43:58.250066806", + "timestamp": "2026-03-13T09:28:04.925769836", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index ea6d82010..a3bac56e0 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -64,5 +64,5 @@ workflow CALL_REPEAT_EXPANSIONS { emit: vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 75b99f949..8664d596f 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -30,6 +30,7 @@ nextflow_workflow { then { assert workflow.success assert snapshot( + workflow.out.publish, path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 685492b45..a69390d12 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -1,13 +1,72 @@ { "CALL_REPEAT_EXPANSIONS": { "content": [ + [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,9e2d2ec1df32e12dc2e043f7f5dae61c" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,32e22328efec8cdd3c818e18568f2108" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,7cdcf4e866373d4aa0e762acfe0f5d5a" + ] + ] + ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2025-10-14T14:06:58.984015651", + "timestamp": "2026-03-13T09:28:35.853691152", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.04.8" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index acc607efb..266ec9881 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -138,7 +138,7 @@ workflow CALL_SNV { ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.ch_publish + ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.publish } if (val_concatenate_snv_calls) { @@ -166,5 +166,5 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 35cdbda99..727903fdf 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,6 +59,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index baf3c72ff..c8a7b4c10 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -1,6 +1,44 @@ { "CALL_SNV - deepvariant wgs": { "content": [ + [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,b78d7a388ac51028ca8b15474b9efce6" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,81c8e362552865ccdd12941db07bdf6e" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,5b31cdd1aaca1b52aa06ec49b0d3207f" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,057840edb22fe608c7635911a914e9f0" + ] + ] + ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ @@ -10,7 +48,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-04T15:51:36.199641201", + "timestamp": "2026-03-13T09:33:27.081509863", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -96,6 +134,44 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "7": [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "genome_gtabix": [ [ { @@ -172,10 +248,48 @@ }, "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] + ], + "publish": [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-09T11:14:37.035323634", + "timestamp": "2026-03-13T09:34:33.930010907", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 49c062ee7..c6588e55e 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -105,5 +105,5 @@ workflow CALL_STRUCTURAL_VARIANTS { emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 139d26d58..26b2f362b 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -46,6 +46,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 2577e99f7..999d3184e 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -1,6 +1,26 @@ { "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ + [ + [ + "call_sv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_sv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], [ "justhusky_sv.vcf.gz" ], @@ -8,7 +28,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-01T18:18:21.549692378", + "timestamp": "2026-03-13T09:44:18.163494369", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 5c7a97913..5b74b7ba2 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -91,5 +91,5 @@ workflow CALL_SV_MT { mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index e40ea67d7..dc0f6c7af 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -56,6 +56,65 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "3": [ + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "mitosalt_breakpoint": [ [ { @@ -109,10 +168,69 @@ }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "publish": [ + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-06T06:08:49.770501228", + "timestamp": "2026-03-13T09:44:41.052362674", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 9f631cd5f..ef10982ec 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -127,5 +127,5 @@ workflow POSTPROCESS_MT_CALLS { emit: tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap index bd5f6421c..fa37649d4 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -18,6 +18,46 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "2": [ + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "ch_publish": [ + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -36,7 +76,7 @@ ] } ], - "timestamp": "2026-03-05T22:02:56.111310181", + "timestamp": "2026-03-12T23:41:04.472222425", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 307c51b4e..35d00c4d4 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -141,5 +141,5 @@ workflow QC_BAM { self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] cov = ch_cov // channel: [ val(meta), path(metrics) ] cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index f97d7b47a..f354e408c 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -54,6 +54,7 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -132,6 +133,7 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.success }, { assert snapshot( + workflow.out.publish, workflow.out.multiple_metrics .collect {it[1]} .flatten() diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ce8cf8ed1..538aa9fcc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -502,19 +502,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", - "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/hugelymodelbat_sorted_md.metrics.txt", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", - "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -669,30 +660,6 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", - "call_mobile_elements", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -708,10 +675,6 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", - "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", - "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -727,328 +690,6 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", - "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - "qc_bam/earlycasualcaiman/css/minus.png", - "qc_bam/earlycasualcaiman/css/plus.png", - "qc_bam/earlycasualcaiman/css/pygments.css", - "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", - "qc_bam/earlycasualcaiman/css/report.css", - "qc_bam/earlycasualcaiman/css/searchtools.js", - "qc_bam/earlycasualcaiman/css/underscore.js", - "qc_bam/earlycasualcaiman/css/up-pressed.png", - "qc_bam/earlycasualcaiman/css/up.png", - "qc_bam/earlycasualcaiman/css/websupport.js", - "qc_bam/earlycasualcaiman/genome_results.txt", - "qc_bam/earlycasualcaiman/images_qualimapReport", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - 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"qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -1008,17 +664,8 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -1029,7 +676,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-10T15:54:35.091523871", + "timestamp": "2026-03-12T22:43:18.380887473", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 0e6dfba4d..f23ae4108 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -485,9 +485,6 @@ "alignment", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -534,24 +531,6 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", - "call_mobile_elements", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz", - "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", - "call_snv", - "call_snv/genome", - "call_snv/genome/justhusky_snv.vcf.gz", - "call_snv/genome/justhusky_snv.vcf.gz.tbi", - "call_snv/mitochondria", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", - "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", - "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -561,8 +540,6 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", - "ngsbits_samplegender", - "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -578,114 +555,6 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", - "qc_bam", - "qc_bam/hugelymodelbat", - "qc_bam/hugelymodelbat/css", - "qc_bam/hugelymodelbat/css/agogo.css", - "qc_bam/hugelymodelbat/css/ajax-loader.gif", - "qc_bam/hugelymodelbat/css/basic.css", - "qc_bam/hugelymodelbat/css/bgfooter.png", - "qc_bam/hugelymodelbat/css/bgtop.png", - "qc_bam/hugelymodelbat/css/comment-bright.png", - "qc_bam/hugelymodelbat/css/comment-close.png", - "qc_bam/hugelymodelbat/css/comment.png", - "qc_bam/hugelymodelbat/css/doctools.js", - "qc_bam/hugelymodelbat/css/down-pressed.png", - "qc_bam/hugelymodelbat/css/down.png", - "qc_bam/hugelymodelbat/css/file.png", - "qc_bam/hugelymodelbat/css/jquery.js", - "qc_bam/hugelymodelbat/css/minus.png", - "qc_bam/hugelymodelbat/css/plus.png", - "qc_bam/hugelymodelbat/css/pygments.css", - "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", - "qc_bam/hugelymodelbat/css/report.css", - "qc_bam/hugelymodelbat/css/searchtools.js", - "qc_bam/hugelymodelbat/css/underscore.js", - "qc_bam/hugelymodelbat/css/up-pressed.png", - "qc_bam/hugelymodelbat/css/up.png", - "qc_bam/hugelymodelbat/css/websupport.js", - "qc_bam/hugelymodelbat/genome_results.txt", - "qc_bam/hugelymodelbat/images_qualimapReport", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/hugelymodelbat/qualimapReport.html", - "qc_bam/hugelymodelbat/raw_data_qualimapReport", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.per-base.d4", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", - "qc_bam/hugelymodelbat_mosdepth.summary.txt", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", - "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/hugelymodelbat_tidditcov.bed", - "qc_bam/hugelymodelbat_tidditcov.bw", - "qc_bam/hugelymodelbat_tidditcov.wig", - "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", - "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", - "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -700,26 +569,17 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", - "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", - "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-10T15:15:02.654289867", + "timestamp": "2026-03-12T22:47:05.119730547", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e81a3429b..8d78db201 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -206,6 +206,8 @@ workflow RAREDISEASE { main: ch_multiqc_files = channel.empty() + ch_align_publish = channel.empty() + ch_qc_bam_publish = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() ch_call_sv_mt_publish = channel.empty() @@ -278,6 +280,7 @@ workflow RAREDISEASE { val_save_mapped_as_cram ) .set { ch_mapped } + ch_align_publish = ALIGN.out.publish if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { if (val_mt_subsample_approach.equals("fraction")) { @@ -317,6 +320,7 @@ workflow RAREDISEASE { skip_ngsbits, skip_qualimap ) + ch_qc_bam_publish = QC_BAM.out.publish /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -342,7 +346,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) - ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.ch_publish + ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.publish if (!skip_repeat_annotation) { STRANGER ( @@ -390,7 +394,7 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) - ch_call_snv_publish = CALL_SNV.out.ch_publish + ch_call_snv_publish = CALL_SNV.out.publish // // ANNOTATE GENOME SNVs @@ -557,7 +561,7 @@ workflow RAREDISEASE { val_analysis_type, skip_germlinecnvcaller, ) - ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.ch_publish + ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish // // ANNOTATE STRUCTURAL VARIANTS @@ -655,7 +659,7 @@ workflow RAREDISEASE { params.split_distance_threshold, params.split_length ) - ch_call_sv_mt_publish = CALL_SV_MT.out.ch_publish + ch_call_sv_mt_publish = CALL_SV_MT.out.publish } /* @@ -672,7 +676,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) - ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.ch_publish + ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.publish if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -904,8 +908,8 @@ workflow RAREDISEASE { emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] - ch_publish = ALIGN.out.ch_publish - .mix(QC_BAM.out.ch_publish) + publish = ch_align_publish + .mix(ch_qc_bam_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) .mix(ch_call_sv_mt_publish) From 5c40aff2a39592a43a7dc5ef04595e10147c941c Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 13 Mar 2026 10:37:34 +0100 Subject: [PATCH 455/872] add nf-core module --- modules.json | 5 + .../gens/preparecovandbaf/environment.yml | 11 ++ modules/nf-core/gens/preparecovandbaf/main.nf | 46 +++++ .../nf-core/gens/preparecovandbaf/meta.yml | 110 +++++++++++ .../gens/preparecovandbaf/tests/main.nf.test | 66 +++++++ .../preparecovandbaf/tests/main.nf.test.snap | 180 ++++++++++++++++++ .../gens/preparecovandbaf/tests/tags.yml | 2 + 7 files changed, 420 insertions(+) create mode 100644 modules/nf-core/gens/preparecovandbaf/environment.yml create mode 100644 modules/nf-core/gens/preparecovandbaf/main.nf create mode 100644 modules/nf-core/gens/preparecovandbaf/meta.yml create mode 100644 modules/nf-core/gens/preparecovandbaf/tests/main.nf.test create mode 100644 modules/nf-core/gens/preparecovandbaf/tests/main.nf.test.snap create mode 100644 modules/nf-core/gens/preparecovandbaf/tests/tags.yml diff --git a/modules.json b/modules.json index b20d83981..568e1cbf5 100644 --- a/modules.json +++ b/modules.json @@ -281,6 +281,11 @@ "git_sha": "7557033683e4016e7d474a23445f75deae2fb729", "installed_by": ["modules"] }, + "gens/preparecovandbaf": { + "branch": "master", + "git_sha": "8220217c9ccad60dc5b395bd76de4d1ddfb7cd80", + "installed_by": ["modules"] + }, "glnexus": { "branch": "master", "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", diff --git a/modules/nf-core/gens/preparecovandbaf/environment.yml b/modules/nf-core/gens/preparecovandbaf/environment.yml new file mode 100644 index 000000000..47d573b0a --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/environment.yml @@ -0,0 +1,11 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.23 + - conda-forge::pip=26.0.1 + - conda-forge::python=3.14.3 + - pip: + - gens-input-data-tools==2.0.1 diff --git a/modules/nf-core/gens/preparecovandbaf/main.nf b/modules/nf-core/gens/preparecovandbaf/main.nf new file mode 100644 index 000000000..6d4e9a0da --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/main.nf @@ -0,0 +1,46 @@ +process PREPARECOVANDBAF { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/67/67abc0d3d1eaaeaff3eafb36babecf56b5912c2e7b0c5100a9f32eda1c82cb30/data': + 'community.wave.seqera.io/library/htslib_python_pip_gens-input-data-tools:8fd1a0ecd4a60110' }" + + input: + tuple val(meta), path(read_counts), path(gvcf), path(gvcf_tbi) + path baf_positions + + output: + tuple val(meta), path("*.cov.bed.gz") , emit: cov_gz + tuple val(meta), path("*.cov.bed.gz.tbi") , emit: cov_tbi + tuple val(meta), path("*.baf.bed.gz") , emit: baf_gz + tuple val(meta), path("*.baf.bed.gz.tbi") , emit: baf_tbi + tuple val("${task.process}"), val('preparecovandbaf'), eval("generate_cov_and_baf --version"), topic: versions, emit: versions_preparecovandbaf + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + generate_cov_and_baf \\ + --coverage $read_counts \\ + --gvcf $gvcf \\ + --label $prefix \\ + --baf_positions $baf_positions \\ + --bgzip_tabix_output \\ + $args \\ + --outdir . + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.cov.bed.gz + touch ${prefix}.cov.bed.gz.tbi + echo "" | gzip > ${prefix}.baf.bed.gz + touch ${prefix}.baf.bed.gz.tbi + """ +} diff --git a/modules/nf-core/gens/preparecovandbaf/meta.yml b/modules/nf-core/gens/preparecovandbaf/meta.yml new file mode 100644 index 000000000..7de5e1159 --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/meta.yml @@ -0,0 +1,110 @@ +name: "preparecovandbaf" +description: Tools for preparing inputs for visualization in Gens +keywords: + - gens + - preparecovandbaf + - preprocessing + - genomics + - CNV +tools: + - "gens": + description: "Scripts for preparing input data to Gens" + homepage: "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data" + documentation: "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data/README.md" + tool_dev_url: "https://github.com/SMD-Bioinformatics-Lund/Prepare-Gens-input-data" + licence: [MIT] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - read_counts: + type: file + description: Binned coverage calculations from GATK + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - gvcf: + type: file + description: GVCF. It is used to calculate B-allele frequencies at the sites specified in baf_positions. It can be generated using any SNV-caller. + pattern: "*.vcf.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + - gvcf_tbi: + type: file + description: GVCF tabix index + pattern: "*.vcf.gz.tbi" + ontologies: [] + - baf_positions: + type: file + description: Sites to sample for BAF calculations + pattern: "*.{tsv,tsv.gz}" + + ontologies: + - edam: http://edamontology.org/format_3475 # TSV +output: + cov_gz: + - - meta: + type: map + description: | + Groovy Map containing sample information + - "*.cov.bed.gz": + type: file + description: Coverage bed (bgzipped) + + cov_tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + - "*.cov.bed.gz.tbi": + type: file + description: Tabix index for coverage bed + + baf_gz: + - - meta: + type: map + description: | + Groovy Map containing sample information + - "*.baf.bed.gz": + type: file + description: BAF bed (bgzipped) + + baf_tbi: + - - meta: + type: map + description: | + Groovy Map containing sample information + - "*.baf.bed.gz.tbi": + type: file + description: Tabix index for BAF bed + + versions_preparecovandbaf: + - - "${task.process}": + type: string + description: The process the versions were collected from + - "preparecovandbaf": + type: string + description: The tool name + - "generate_cov_and_baf --version": + type: string + description: The command used to generate the version of the tool + +topics: + versions: + - - "${task.process}": + type: string + description: The process the versions were collected from + - "preparecovandbaf": + type: string + description: The tool name + - "generate_cov_and_baf --version": + type: eval + description: The expression used to obtain the tool version +authors: + - "@jakob37" +maintainers: + - "@jakob37" diff --git a/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test b/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test new file mode 100644 index 000000000..f466ecb95 --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test @@ -0,0 +1,66 @@ +nextflow_process { + + name "Test Process PREPARECOVANDBAF" + script "modules/nf-core/gens/preparecovandbaf/main.nf" + process "PREPARECOVANDBAF" + + tag "modules" + tag "modules_nfcore" + tag "gens" + tag "gens/preparecovandbaf" + + test("gens_preparecovandbaf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/hg002_chr20_90000_to_100000.standardizedCR.tsv", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz.tbi", checkIfExists: true), + ] + input[1] = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/tab/gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz", checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("gens_preparecovandbaf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gatk/hg002_chr20_90000_to_100000.standardizedCR.tsv", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz.tbi", checkIfExists: true), + ] + input[1] = [ + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/tab/gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz", checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test.snap b/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test.snap new file mode 100644 index 000000000..f027761d3 --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "gens_preparecovandbaf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "PREPARECOVANDBAF", + "preparecovandbaf", + "1.1.5" + ] + ], + "baf_gz": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "baf_tbi": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cov_gz": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "cov_tbi": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_preparecovandbaf": [ + [ + "PREPARECOVANDBAF", + "preparecovandbaf", + "1.1.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-26T12:47:53.193429367" + }, + "gens_preparecovandbaf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz:md5,2df1734048f1bab141050822a426145e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz.tbi:md5,66025dc44413e9e17c8e11af09e06dbe" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz:md5,ae86e22390df1ba20a931b70be92079f" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz.tbi:md5,442c8518dd2f818757a10ca4f06c1b6c" + ] + ], + "4": [ + [ + "PREPARECOVANDBAF", + "preparecovandbaf", + "1.1.5" + ] + ], + "baf_gz": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz:md5,ae86e22390df1ba20a931b70be92079f" + ] + ], + "baf_tbi": [ + [ + { + "id": "test" + }, + "test.baf.bed.gz.tbi:md5,442c8518dd2f818757a10ca4f06c1b6c" + ] + ], + "cov_gz": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz:md5,2df1734048f1bab141050822a426145e" + ] + ], + "cov_tbi": [ + [ + { + "id": "test" + }, + "test.cov.bed.gz.tbi:md5,66025dc44413e9e17c8e11af09e06dbe" + ] + ], + "versions_preparecovandbaf": [ + [ + "PREPARECOVANDBAF", + "preparecovandbaf", + "1.1.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.3" + }, + "timestamp": "2026-02-26T12:47:42.547489104" + } +} \ No newline at end of file diff --git a/modules/nf-core/gens/preparecovandbaf/tests/tags.yml b/modules/nf-core/gens/preparecovandbaf/tests/tags.yml new file mode 100644 index 000000000..2c5ae0497 --- /dev/null +++ b/modules/nf-core/gens/preparecovandbaf/tests/tags.yml @@ -0,0 +1,2 @@ +gens/preparecovandbaf: + - modules/nf-core/gens/preparecovandbaf/** From aa5f8761cf1eb799367f2a31782c837c67345fbc Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 11:16:12 +0100 Subject: [PATCH 456/872] update snapshot --- .../align_sentieon/tests/main.nf.test.snap | 170 ++++- .../local/qc_bam/tests/main.nf.test.snap | 634 +++++++++++++++++- 2 files changed, 799 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 79a96bf5a..9b1ad860b 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -122,6 +122,88 @@ "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" ] ], + "8": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + ] + ] + ], "aln_metrics": [ [ { @@ -227,6 +309,88 @@ "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" ] ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + ] + ] + ], "qd_metrics": [ [ { @@ -244,10 +408,10 @@ ] } ], - "timestamp": "2026-01-26T23:22:09.03170299", + "timestamp": "2026-03-13T11:07:38.099732631", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index aa697e3ef..4a89b7882 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -1,6 +1,321 @@ { "QC_BAM - test, bwamem2": { "content": [ + [ + [ + "qc_bam/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.summary.txt:md5,5794d9158c08d60cd3fcc27bad005de2" + ] + ], + [ + "qc_bam/", + [ 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"'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics:md5,d4c02430a4ec0dc6c9a1b6b7ad89ac46" + ] + ] + ], [ "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", @@ -151,7 +781,7 @@ ] ] ], - "timestamp": "2026-02-17T15:21:49.953972761", + "timestamp": "2026-03-13T11:15:12.139419029", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From de583b908b6830046d14351b452b29ed16353438 Mon Sep 17 00:00:00 2001 From: peterpru Date: Fri, 13 Mar 2026 11:53:05 +0100 Subject: [PATCH 457/872] replace local module --- conf/modules/gens.config | 16 ---------------- subworkflows/local/gens/main.nf | 21 ++++++++++----------- workflows/raredisease.nf | 1 + 3 files changed, 11 insertions(+), 27 deletions(-) diff --git a/conf/modules/gens.config b/conf/modules/gens.config index 47345b25d..691cacd74 100644 --- a/conf/modules/gens.config +++ b/conf/modules/gens.config @@ -32,20 +32,4 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - - withName: '.*GENS:GENS_GENERATE_BAF_INDEX' { - publishDir = [ - path: { "${params.outdir}/gens" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*GENS:GENS_GENERATE_COV_INDEX' { - publishDir = [ - path: { "${params.outdir}/gens" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } diff --git a/subworkflows/local/gens/main.nf b/subworkflows/local/gens/main.nf index 207d0f6d8..dc8740193 100644 --- a/subworkflows/local/gens/main.nf +++ b/subworkflows/local/gens/main.nf @@ -5,9 +5,7 @@ include { GATK4_COLLECTREADCOUNTS as COLLECTREADCOUNTS } from '../../../modules/nf-core/gatk4/collectreadcounts/main' include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_FEMALE } from '../../../modules/nf-core/gatk4/denoisereadcounts/main' include { GATK4_DENOISEREADCOUNTS as DENOISEREADCOUNTS_MALE } from '../../../modules/nf-core/gatk4/denoisereadcounts/main' -include { GENS as GENS_GENERATE } from '../../../modules/local/gens/main' -include { TABIX_BGZIPTABIX as GENS_GENERATE_BAF_INDEX } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as GENS_GENERATE_COV_INDEX } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { PREPARECOVANDBAF as GENS_GENERATE } from '../../../modules/nf-core/gens/preparecovandbaf/main' workflow GENS { take: @@ -17,6 +15,7 @@ workflow GENS { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_gnomad_pos // channel: [mandatory] [ path(gnomad_pos) ] ch_gvcf // channel: [mandatory] [ val(meta), path(gvcf) ] + ch_gvcf_tbi // channel: [mandatory] [ val(meta), path(gvcf.tbi) ] ch_interval_list // channel: [mandatory] [ path(interval_list) ] ch_pon_female // channel: [mandatory] [ path(pon) ] ch_pon_male // channel: [mandatory] [ path(pon) ] @@ -54,16 +53,16 @@ workflow GENS { .set { ch_denoisereadcounts_out } GENS_GENERATE ( - ch_denoisereadcounts_out, - ch_gvcf, + ch_denoisereadcounts_out + .join(ch_gvcf) + .join(ch_gvcf_tbi) + .map { meta, counts, gvcf, gvcf_tbi -> tuple(meta, counts, gvcf, gvcf_tbi) }, ch_gnomad_pos ) - GENS_GENERATE_BAF_INDEX (GENS_GENERATE.out.baf) - - GENS_GENERATE_COV_INDEX (GENS_GENERATE.out.cov) - emit: - gens_baf_bed_gz = GENS_GENERATE.out.baf // channel: [ val(meta), path(bed) ] - gens_cov_bed_gz = GENS_GENERATE.out.cov // channel: [ val(meta), path(bed) ] + gens_baf_bed_gz = GENS_GENERATE.out.baf_gz // channel: [ val(meta), path(bed.gz) ] + gens_baf_bed_tbi = GENS_GENERATE.out.baf_tbi // channel: [ val(meta), path(tbi) ] + gens_cov_bed_gz = GENS_GENERATE.out.cov_gz // channel: [ val(meta), path(bed.gz) ] + gens_cov_bed_tbi = GENS_GENERATE.out.cov_tbi // channel: [ val(meta), path(tbi) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 1119fafb1..4916fb238 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -777,6 +777,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_gens_gnomad_pos, CALL_SNV.out.genome_gvcf, + CALL_SNV.out.genome_gtabix, ch_gens_interval_list, ch_gens_pon_female, ch_gens_pon_male From 5788ace5b1a381b6a9f7c8dee4d815d343144393 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:02:33 +0100 Subject: [PATCH 458/872] update snapshots --- NEXTFLOW_OUTPUT_MIGRATION.md | 162 --- subworkflows/local/align/tests/main.nf.test | 12 +- .../local/align/tests/main.nf.test.snap | 972 +----------------- .../tests/main.nf.test | 8 +- .../tests/main.nf.test.snap | 106 +- .../call_repeat_expansions/tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 62 +- .../local/call_snv/tests/main.nf.test | 4 +- .../local/call_snv/tests/main.nf.test.snap | 42 +- .../tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 22 +- subworkflows/local/qc_bam/tests/main.nf.test | 8 +- .../local/qc_bam/tests/main.nf.test.snap | 63 +- 13 files changed, 111 insertions(+), 1358 deletions(-) delete mode 100644 NEXTFLOW_OUTPUT_MIGRATION.md diff --git a/NEXTFLOW_OUTPUT_MIGRATION.md b/NEXTFLOW_OUTPUT_MIGRATION.md deleted file mode 100644 index c8a408161..000000000 --- a/NEXTFLOW_OUTPUT_MIGRATION.md +++ /dev/null @@ -1,162 +0,0 @@ ---- - -## Centralized Publishing Pattern (nf-core migration approach) - -Instead of using `topic` channels or `publishDir`, we use a **single `ch_publish` channel -per subworkflow** that emits `[destination, value]` tuples. Publishing is handled centrally -in `main.nf`. - -### Pattern Overview - -**Inside each subworkflow**, map every published output into a `[destination, value]` tuple -where `destination` mirrors the original `publishDir` path. Mix all of them into a single -`ch_publish` and emit it: - -```nextflow -// Inside subworkflow -ch_publish = PROCESS_A.out.bam - .map { meta, bam -> ['alignment/', [meta, bam]] } - .mix(PROCESS_B.out.metrics.map { meta, f -> ['qc/', [meta, f]] }) - .mix(PROCESS_C.out.vcf.map { meta, vcf -> ['vcf/', [meta, vcf]] }) - -emit: -ch_publish -``` - -Rules: - -- There must be only **one `ch_publish` emit per subworkflow** -- The destination string should mirror the original `publishDir` path -- Preserve the original channel structure as the second element of the tuple -- Include outputs from processes whose channels are not consumed downstream — - these were previously captured by `publishDir` at the filesystem level - -**In `main.nf`**, collect `ch_publish` from all subworkflows, mix them, and publish -centrally: - -```nextflow -workflow { - main: - SUBWORKFLOW_A(...) - SUBWORKFLOW_B(...) - - publish: - all_outputs = SUBWORKFLOW_A.out.ch_publish - .mix(SUBWORKFLOW_B.out.ch_publish) -} - -output { - all_outputs { - path { destination, value -> destination } - } -} -``` - -### Handling varying channel structures - -Channels with different numbers of elements (e.g. `[meta, bam]` vs `[meta, bam, bai]`) -are handled safely by always wrapping the entire inner tuple as a single second element. -Nextflow recursively scans the value for file objects automatically. - -// CORRECT -.map { meta, bam, bai -> ['alignment/', [meta, bam, bai]] } - -// WRONG — breaks the [destination, value] contract -.map { meta, bam, bai -> ['alignment/', meta, bam, bai] } -``` - -**Your command** — add one line to enforce the wrapping rule: -``` -... - -For each process output that should be published, map it into a tuple of -[destination_path, channel_value] where destination_path mirrors the directory -that publishDir was publishing to. Always wrap the entire channel value as a -single second element regardless of how many elements it contains, e.g. -{ meta, bam, bai -> ['alignment/', [meta, bam, bai]] }. -... - -### Grouping channels by destination before mapping - -Instead of mapping each channel individually, group channels sharing the same destination -using `mix` first, then apply a single `map` per destination group. This reduces repetition -significantly. - -```nextflow -// PREFERRED — one map per destination group -ch_qc_bam = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) - .mix(TIDDIT_COV.out.wig) - .mix(MOSDEPTH.out.global_txt) - .mix(ch_qualimap) - .map { meta, value -> ['qc_bam/', [meta, value]] } - -ch_ngsbits = ch_ngsbits_samplegender - .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] } - -ch_publish = ch_qc_bam.mix(ch_ngsbits) - -// AVOID — one map per channel, very repetitive -ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - .map { meta, metrics -> ['qc_bam/', [meta, metrics]] } - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf - .map { meta, pdf -> ['qc_bam/', [meta, pdf]] }) - // ... -``` - -Rules: - -- Create one intermediate channel per unique destination directory -- Mix all channels going to the same destination first, then apply a single `map` -- Combine all destination groups into `ch_publish` with a final `mix` - -### Nested subworkflows — bubbling up ch_publish - -When a subworkflow calls other subworkflows, always mix the inner `ch_publish` into the -outer `ch_publish`. This propagates publishing up the call chain to `main.nf`. - -```nextflow -// Inner subworkflow emits its own ch_publish -workflow ALIGN_BWA { - main: - BWA_MEM(...) - SAMTOOLS_SORT(...) - - ch_publish = BWA_MEM.out.bam - .mix(SAMTOOLS_SORT.out.bam) - .map { meta, value -> ['alignment/', [meta, value]] } - - emit: - ch_publish -} - -// Outer subworkflow mixes in ch_publish from inner subworkflow -workflow ALIGN { - main: - ALIGN_BWA(...) - FASTP(...) - - ch_publish = FASTP.out.reads - .map { meta, value -> ['fastp/', [meta, value]] } - .mix(ALIGN_BWA.out.ch_publish) - - emit: - ch_publish -} -``` - -Rules: - -- Every subworkflow that has publishable outputs must emit `ch_publish` -- If a subworkflow calls inner subworkflows, always mix their `ch_publish` into the - outer `ch_publish` — never discard it -- In `main.nf`, mix `ch_publish` from all top-level subworkflows into one channel - before the `publish:` block - -### Why this approach - -- Subworkflow signatures stay clean — one `ch_publish` emit regardless of how many - output directories exist internally -- Publishing logic is fully centralized in `main.nf` -- No `topic` channel footguns (pipeline hanging forever if a process consumes its own topic) -- Easy to audit all published paths by reading `main.nf` alone diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 06df3a019..6efa84853 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -116,7 +116,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -217,7 +219,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -310,7 +314,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 93aa1301f..db6a471d1 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,369 +2,27 @@ "align bwamem2 - wgs": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "slowlycivilbuck_sort_md.cram:md5,bc7f10d51c282f5632a7fce6a76a891a" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "slowlycivilbuck_sort_md.cram.crai:md5,b72dd8b4097b1adef34747aa2c53a3ca" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "hugelymodelbat_sort_md.cram:md5,6e7b8b26c4e3851fa1f4bf4a629016d9" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "hugelymodelbat_sort_md.cram.crai:md5,e39b6adfff50427d53f7e8cd43b1cd26" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "earlycasualcaiman_sort_md.cram:md5,b34cfc30ca2754d70e69fabadefba4d7" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "earlycasualcaiman_sort_md.cram.crai:md5,34cc581f4684ba2f403bc1eea3975ad7" - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "slowlycivilbuck_R1.fastp.fastq.gz:md5,34b043eb99b2f0f4369079d90dd09b5c", - "slowlycivilbuck_R2.fastp.fastq.gz:md5,54520d9ce8ccd2f54cec2873bbaed0ed" - ] - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck.fastp.log:md5,17d946e68aee1f92ae5334a74fde8571" - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "lane": 1, - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck.fastp.json:md5,7ad34e9e48159c794ce777e4e48c0b96" - ] - ], - [ - "trimming/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - 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"single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "trimming/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + "earlycasualcaiman_sorted_md.bam", + "earlycasualcaiman_sorted_md.metrics.txt", + "hugelymodelbat_sorted_md.bam", + "hugelymodelbat_sorted_md.metrics.txt", + "slowlycivilbuck_sorted_md.bam", + "slowlycivilbuck_sorted_md.metrics.txt", + "earlycasualcaiman_sorted_md.bam.bai", + "hugelymodelbat_sorted_md.bam.bai", + "slowlycivilbuck_sorted_md.bam.bai", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck.fastp.log", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat.fastp.log", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.html", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.html" ], [ [ @@ -1366,7 +502,7 @@ ] ], - "timestamp": "2026-03-13T09:09:46.038355114", + "timestamp": "2026-03-13T12:51:28.25179825", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 13fdcdf2a..b0cd92149 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -55,7 +55,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -112,7 +114,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index c61fe2bb9..523ca0a8b 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -2,54 +2,9 @@ "align bwamem2": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,171423ac03499a00c4677f8b53771570" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,4730bcc5e26e8f3c29b8fa58f68d43e6" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,b8976cf366140eeee478ee2e9c1cadc9" - ] - ] + "test_sorted_md.bam", + "test_sorted_md.metrics.txt", + "test_sorted_md.bam.bai" ], [ [ @@ -82,7 +37,7 @@ ] ] ], - "timestamp": "2026-03-13T09:21:28.631120006", + "timestamp": "2026-03-13T13:02:30.573936764", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -91,54 +46,9 @@ "align bwameme": { "content": [ [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,ca247f01365899e07c77c3479fa721b2" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,f5b5580ca2b1035f0cac8ba1db7ab55e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,e1e422e8da8ae8f2fbf0221d29919be0" - ] - ] + "test_sorted_md.bam", + "test_sorted_md.metrics.txt", + "test_sorted_md.bam.bai" ], [ [ @@ -171,7 +81,7 @@ ] ] ], - "timestamp": "2026-03-13T09:22:14.004999114", + "timestamp": "2026-03-13T13:03:18.075557991", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 8664d596f..049378ff5 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -30,7 +30,9 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index a69390d12..ecfabe8f8 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -2,68 +2,14 @@ "CALL_REPEAT_EXPANSIONS": { "content": [ [ - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_repeat_expansion.vcf:md5,9e2d2ec1df32e12dc2e043f7f5dae61c" - ] - ], - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam:md5,32e22328efec8cdd3c818e18568f2108" - ] - ], - [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam.bai:md5,7cdcf4e866373d4aa0e762acfe0f5d5a" - ] - ] + "earlycasualcaiman_repeat_expansion.vcf", + "earlycasualcaiman_exphunter_sorted.bam", + "earlycasualcaiman_exphunter_sorted.bam.bai" ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-13T09:28:35.853691152", + "timestamp": "2026-03-13T12:38:25.736225141", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 727903fdf..87a4fca98 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,7 +59,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index c8a7b4c10..6639eb9bb 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -2,42 +2,10 @@ "CALL_SNV - deepvariant wgs": { "content": [ [ - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,b78d7a388ac51028ca8b15474b9efce6" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,81c8e362552865ccdd12941db07bdf6e" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,5b31cdd1aaca1b52aa06ec49b0d3207f" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,057840edb22fe608c7635911a914e9f0" - ] - ] + "justhusky_snv.vcf.gz.tbi", + "justhusky_snv.vcf.gz", + "justhusky_mitochondria.vcf.gz", + "justhusky_mitochondria.vcf.gz.tbi" ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", @@ -48,7 +16,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-13T09:33:27.081509863", + "timestamp": "2026-03-13T13:11:10.952443789", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 26b2f362b..614370b8c 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -46,7 +46,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 999d3184e..f73f465ab 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -2,24 +2,8 @@ "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ [ - [ - "call_sv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_sv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + "justhusky_sv.vcf.gz", + "justhusky_sv.vcf.gz.tbi" ], [ "justhusky_sv.vcf.gz" @@ -28,7 +12,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-13T09:44:18.163494369", + "timestamp": "2026-03-13T13:21:51.525587168", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index f354e408c..edae66f98 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -54,7 +54,9 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -133,7 +135,9 @@ nextflow_workflow { { assert workflow.success }, { assert workflow.success }, { assert snapshot( - workflow.out.publish, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name }, workflow.out.multiple_metrics .collect {it[1]} .flatten() diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index aa697e3ef..5ecb26245 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -81,77 +81,28 @@ "QC_BAM - test, sentieon": { "content": [ [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ ], [ - "earlycasualcaiman_wgsmetrics.txt" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] + ] ], - "timestamp": "2026-02-17T15:21:49.953972761", + "timestamp": "2026-03-12T23:44:03.5837213", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 88ad0489913a8d0f27513b5beffca441f6cbd281 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:17:15 +0100 Subject: [PATCH 459/872] update sentieon tests --- .../align_sentieon/tests/main.nf.test.snap | 10 +- .../local/qc_bam/tests/main.nf.test.snap | 777 ++++-------------- 2 files changed, 145 insertions(+), 642 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 9b1ad860b..b35de4106 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T11:07:38.099732631", + "timestamp": "2026-03-13T14:06:49.285440618", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 22a3bd5b9..fd4bbf5e2 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,319 +2,50 @@ "QC_BAM - test, bwamem2": { "content": [ [ - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.summary.txt:md5,5794d9158c08d60cd3fcc27bad005de2" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - 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+ "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ ], [ - + "earlycasualcaiman_wgsmetrics.txt" ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] ] ], -<<<<<<< HEAD - "timestamp": "2026-03-12T23:44:03.5837213", -======= - "timestamp": "2026-03-13T11:15:12.139419029", ->>>>>>> aa5f8761cf1eb799367f2a31782c837c67345fbc + "timestamp": "2026-03-13T14:13:47.258652619", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 53557f314f15dab5e8879fd355081e688ce32843 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 14:37:07 +0100 Subject: [PATCH 460/872] add sort [skip ci] --- subworkflows/local/align/tests/main.nf.test | 9 ++++++--- .../local/align_bwa_bwamem2_bwameme/tests/main.nf.test | 6 ++++-- .../local/call_repeat_expansions/tests/main.nf.test | 3 ++- subworkflows/local/call_snv/tests/main.nf.test | 3 ++- .../local/call_structural_variants/tests/main.nf.test | 3 ++- subworkflows/local/qc_bam/tests/main.nf.test | 6 ++++-- 6 files changed, 20 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 6efa84853..410ea08d7 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -118,7 +118,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -221,7 +222,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -316,7 +318,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index b0cd92149..f45609486 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -57,7 +57,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -116,7 +117,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 049378ff5..c21805209 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -32,7 +32,8 @@ nextflow_workflow { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 87a4fca98..0d9fefce5 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -61,7 +61,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 614370b8c..94e520bcd 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -48,7 +48,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index edae66f98..79bbaaedc 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -56,7 +56,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.multiple_metrics .collect {it[1]} .flatten() @@ -137,7 +138,8 @@ nextflow_workflow { { assert snapshot( workflow.out.publish.flatten() .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name }, + .collect { new File(it).name } + .sort(), workflow.out.multiple_metrics .collect {it[1]} .flatten() From 221eee3669f49cc7ae5b6926e0587127b3924383 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 15:40:32 +0100 Subject: [PATCH 461/872] update sentieon snapshots [skip ci] --- .../align_sentieon/tests/main.nf.test.snap | 10 +-- .../local/qc_bam/tests/main.nf.test.snap | 64 +++++++++---------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b35de4106..acbf733be 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T14:06:49.285440618", + "timestamp": "2026-03-13T15:03:01.128235963", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index fd4bbf5e2..dcacf5eaf 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,12 +2,24 @@ "QC_BAM - test, bwamem2": { "content": [ [ - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.mosdepth.summary.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_qualimap", "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", "earlycasualcaiman_tidditcov_1.png", "earlycasualcaiman_tidditcov_10.png", "earlycasualcaiman_tidditcov_11.png", @@ -33,18 +45,6 @@ "earlycasualcaiman_tidditcov_M.png", "earlycasualcaiman_tidditcov_X.png", "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_qualimap", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ @@ -118,7 +118,7 @@ ] ] ], - "timestamp": "2026-03-13T14:12:57.09777024", + "timestamp": "2026-03-13T15:34:21.197802663", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -127,13 +127,24 @@ "QC_BAM - test, sentieon": { "content": [ [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", "earlycasualcaiman_mosdepth.mosdepth.summary.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_qualimap", "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_wgsmetrics.txt", + "earlycasualcaiman_tidditcov.wig", "earlycasualcaiman_tidditcov_1.png", "earlycasualcaiman_tidditcov_10.png", "earlycasualcaiman_tidditcov_11.png", @@ -159,18 +170,7 @@ "earlycasualcaiman_tidditcov_M.png", "earlycasualcaiman_tidditcov_X.png", "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_qualimap", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + "earlycasualcaiman_wgsmetrics.txt" ], [ "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", @@ -243,7 +243,7 @@ ] ] ], - "timestamp": "2026-03-13T14:13:47.258652619", + "timestamp": "2026-03-13T15:35:09.991615599", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 78bfd88df4d62d88800fd0af2f57e76e862a8c94 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 16:06:45 +0100 Subject: [PATCH 462/872] Update other snaps --- .../local/align/tests/main.nf.test.snap | 78 +++++++++---------- .../tests/main.nf.test.snap | 12 +-- .../tests/main.nf.test.snap | 6 +- .../local/call_snv/tests/main.nf.test.snap | 18 ++--- 4 files changed, 57 insertions(+), 57 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index db6a471d1..d1d0c7003 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,27 +2,27 @@ "align bwamem2 - wgs": { "content": [ [ - "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai", - "hugelymodelbat_sort_md.cram", - "hugelymodelbat_sort_md.cram.crai", + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", "earlycasualcaiman_sort_md.cram", "earlycasualcaiman_sort_md.cram.crai", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat.fastp.log", "hugelymodelbat.fastp.html", "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat_sort_md.cram", + "hugelymodelbat_sort_md.cram.crai", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "slowlycivilbuck.fastp.log", "slowlycivilbuck_R1.fastp.fastq.gz", "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.html", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.html" + "slowlycivilbuck_sort_md.cram", + "slowlycivilbuck_sort_md.cram.crai" ], [ [ @@ -261,7 +261,7 @@ ] ] ], - "timestamp": "2026-03-13T12:50:51.679790362", + "timestamp": "2026-03-13T14:53:02.154281647", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -270,12 +270,12 @@ "align bwameme - wgs": { "content": [ [ + "earlycasualcaiman_sort_md.cram", + "earlycasualcaiman_sort_md.cram.crai", "hugelymodelbat_sort_md.cram", "hugelymodelbat_sort_md.cram.crai", "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai", - "earlycasualcaiman_sort_md.cram", - "earlycasualcaiman_sort_md.cram.crai" + "slowlycivilbuck_sort_md.cram.crai" ], [ [ @@ -399,7 +399,7 @@ ] ], - "timestamp": "2026-03-13T12:57:17.001367202", + "timestamp": "2026-03-13T14:59:34.430725854", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -408,30 +408,30 @@ "align bwamem2 - wes": { "content": [ [ + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", "earlycasualcaiman_sorted_md.bam", + "earlycasualcaiman_sorted_md.bam.bai", "earlycasualcaiman_sorted_md.metrics.txt", + "hugelymodelbat.fastp.html", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", "hugelymodelbat_sorted_md.bam", - "hugelymodelbat_sorted_md.metrics.txt", - "slowlycivilbuck_sorted_md.bam", - "slowlycivilbuck_sorted_md.metrics.txt", - "earlycasualcaiman_sorted_md.bam.bai", "hugelymodelbat_sorted_md.bam.bai", - "slowlycivilbuck_sorted_md.bam.bai", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck.fastp.log", + "hugelymodelbat_sorted_md.metrics.txt", "slowlycivilbuck.fastp.html", "slowlycivilbuck.fastp.json", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat.fastp.log", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.html", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.html" + "slowlycivilbuck.fastp.log", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck_sorted_md.bam", + "slowlycivilbuck_sorted_md.bam.bai", + "slowlycivilbuck_sorted_md.metrics.txt" ], [ [ @@ -502,7 +502,7 @@ ] ], - "timestamp": "2026-03-13T12:51:28.25179825", + "timestamp": "2026-03-13T14:53:37.576915277", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 523ca0a8b..7632f79b8 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -3,8 +3,8 @@ "content": [ [ "test_sorted_md.bam", - "test_sorted_md.metrics.txt", - "test_sorted_md.bam.bai" + "test_sorted_md.bam.bai", + "test_sorted_md.metrics.txt" ], [ [ @@ -37,7 +37,7 @@ ] ] ], - "timestamp": "2026-03-13T13:02:30.573936764", + "timestamp": "2026-03-13T15:04:33.885203481", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -47,8 +47,8 @@ "content": [ [ "test_sorted_md.bam", - "test_sorted_md.metrics.txt", - "test_sorted_md.bam.bai" + "test_sorted_md.bam.bai", + "test_sorted_md.metrics.txt" ], [ [ @@ -81,7 +81,7 @@ ] ] ], - "timestamp": "2026-03-13T13:03:18.075557991", + "timestamp": "2026-03-13T15:05:20.75721248", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index ecfabe8f8..58e9e8bd7 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "CALL_REPEAT_EXPANSIONS": { "content": [ [ - "earlycasualcaiman_repeat_expansion.vcf", "earlycasualcaiman_exphunter_sorted.bam", - "earlycasualcaiman_exphunter_sorted.bam.bai" + "earlycasualcaiman_exphunter_sorted.bam.bai", + "earlycasualcaiman_repeat_expansion.vcf" ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-13T12:38:25.736225141", + "timestamp": "2026-03-13T15:42:01.510910485", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 6639eb9bb..da2926ecf 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -2,10 +2,10 @@ "CALL_SNV - deepvariant wgs": { "content": [ [ - "justhusky_snv.vcf.gz.tbi", - "justhusky_snv.vcf.gz", "justhusky_mitochondria.vcf.gz", - "justhusky_mitochondria.vcf.gz.tbi" + "justhusky_mitochondria.vcf.gz.tbi", + "justhusky_snv.vcf.gz", + "justhusky_snv.vcf.gz.tbi" ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", @@ -16,7 +16,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-13T13:11:10.952443789", + "timestamp": "2026-03-13T15:46:57.105465403", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -109,7 +109,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -118,7 +118,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -224,7 +224,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -233,7 +233,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -257,7 +257,7 @@ ] } ], - "timestamp": "2026-03-13T09:34:33.930010907", + "timestamp": "2026-03-13T15:48:00.031080535", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 736592df715f4515b6a1ada0583aad527fdfd60d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 17:20:29 +0100 Subject: [PATCH 463/872] update nxf version --- .github/workflows/nf-test.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index 6b7dade1f..a36628850 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -77,7 +77,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.04.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false diff --git a/nextflow.config b/nextflow.config index 4c212227e..47745af8d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -464,7 +464,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=25.04.0' + nextflowVersion = '!>=25.10.4' version = '2.7.0dev' doi = '10.5281/zenodo.7995798' } From 746ba255b735e460ab4a3b336bd7d1c7cdf1f5c2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:11:22 +0000 Subject: [PATCH 464/872] update snap for postprocess MT [skip ci] --- subworkflows/local/postprocess_MT_calls/main.nf | 6 +++--- .../local/postprocess_MT_calls/tests/main.nf.test.snap | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index ef10982ec..a9ecdf01b 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -125,7 +125,7 @@ workflow POSTPROCESS_MT_CALLS { .map { meta, value -> ['call_snv/mitochondria/', [meta, value]] } emit: - tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap index fa37649d4..6ddd843ef 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -38,7 +38,7 @@ ] ] ], - "ch_publish": [ + "publish": [ [ "call_snv/mitochondria/", [ @@ -76,7 +76,7 @@ ] } ], - "timestamp": "2026-03-12T23:41:04.472222425", + "timestamp": "2026-03-13T22:07:26.775535698", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 0b74fb3db869c878b79b98136752902e2f335c68 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 23:22:56 +0100 Subject: [PATCH 465/872] update sentieon snapshot --- .../local/align_sentieon/tests/main.nf.test.snap | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index acbf733be..2fcbd8e27 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -184,7 +184,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -200,7 +200,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -371,7 +371,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] ], [ @@ -387,7 +387,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" ] ] ], @@ -408,7 +408,7 @@ ] } ], - "timestamp": "2026-03-13T15:03:01.128235963", + "timestamp": "2026-03-13T23:08:12.022075352", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From ef5ec40cc6d6fb00038d1084690bb5370bfdeda8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:33:52 +0000 Subject: [PATCH 466/872] Update ro-crate-metadata.json --- ro-crate-metadata.json | 65 ++++++++++++++++++++++++------------------ 1 file changed, 37 insertions(+), 28 deletions(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d16ffbb32..d2187ded7 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T12:27:15+00:00", + "datePublished": "2026-03-13T22:32:54+00:00", "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067" + "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759" } ], "name": "nf-core/raredisease" @@ -134,26 +134,29 @@ ], "creator": [ { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0003-1316-2845" }, { - "@id": "https://orcid.org/0000-0002-4100-9963" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { "@id": "https://orcid.org/0000-0002-5044-7754" }, { - "@id": "https://orcid.org/0000-0003-1316-2845" + "@id": "https://orcid.org/0009-0005-4189-8704" }, { "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "https://orcid.org/0000-0002-2219-0197" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963" } ], "dateCreated": "", - "dateModified": "2025-07-08T14:27:15Z", + "dateModified": "2026-03-13T22:32:54Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +175,7 @@ ], "maintainer": [ { - "@id": "https://orcid.org/0000-0002-2219-0197" - }, - { - "@id": "https://orcid.org/0000-0002-4100-9963" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { "@id": "https://orcid.org/0000-0002-5044-7754" @@ -184,7 +184,10 @@ "@id": "#25568561+projectoriented@users.noreply.github.com" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "https://orcid.org/0000-0002-2219-0197" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963" } ], "name": [ @@ -214,14 +217,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.10.4" }, { - "@id": "#1b26a4ae-2b56-4c74-8235-6a6320ec1067", + "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759", "@type": "TestSuite", "instance": [ { - "@id": "#34b99e0d-03ba-4190-be8d-081702d44958" + "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636" } ], "mainEntity": { @@ -230,7 +233,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#34b99e0d-03ba-4190-be8d-081702d44958", + "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -369,16 +372,16 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0002-2219-0197", + "@id": "https://orcid.org/0000-0003-1316-2845", "@type": "Person", - "email": "jemten@users.noreply.github.com", - "name": "Anders Jemt" + "email": "raysloks@gmail.com", + "name": "Emil Bertilsson" }, { - "@id": "https://orcid.org/0000-0002-4100-9963", + "@id": "https://orcid.org/0000-0001-7313-3734", "@type": "Person", - "email": "Gwenna.breton@gu.se", - "name": "Gwenna Breton" + "email": "20065894+ramprasadn@users.noreply.github.com", + "name": "Ramprasad Neethiraj" }, { "@id": "https://orcid.org/0000-0002-5044-7754", @@ -387,10 +390,10 @@ "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" }, { - "@id": "https://orcid.org/0000-0003-1316-2845", + "@id": "https://orcid.org/0009-0005-4189-8704", "@type": "Person", - "email": "raysloks@gmail.com", - "name": "Emil Bertilsson" + "email": "75395041+ieduba@users.noreply.github.com", + "name": "Irene Duba" }, { "@id": "#25568561+projectoriented@users.noreply.github.com", @@ -399,10 +402,16 @@ "name": "Mei Wu" }, { - "@id": "https://orcid.org/0000-0001-7313-3734", + "@id": "https://orcid.org/0000-0002-2219-0197", "@type": "Person", - "email": "20065894+ramprasadn@users.noreply.github.com", - "name": "Ramprasad Neethiraj" + "email": "jemten@users.noreply.github.com", + "name": "Anders Jemt" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963", + "@type": "Person", + "email": "Gwenna.breton@gu.se", + "name": "Gwenna Breton" } ] } \ No newline at end of file From 21dc6957ab298eaad0116d37cb1efbfae905088c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:34:21 +0000 Subject: [PATCH 467/872] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ca86e4e5d..6a6abb6d0 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) From 4a3734c5718e45b075abfbcfcce2753f29bd9124 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 13 Mar 2026 22:41:37 +0000 Subject: [PATCH 468/872] Update nf-test.yml --- .github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index a36628850..1009d5eea 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -50,7 +50,7 @@ jobs: env: NFT_VER: ${{ env.NFT_VER }} with: - max_shards: 14 + max_shards: 20 - name: debug run: | From 6c7ba9b2805deb29d5f65ec536d62a24dacceeb4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 14 Mar 2026 00:04:03 +0100 Subject: [PATCH 469/872] update sentieon snapshot --- .../local/align_sentieon/tests/main.nf.test | 15 +- .../align_sentieon/tests/main.nf.test.snap | 533 +++++------------- 2 files changed, 141 insertions(+), 407 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 9c36901c8..4954858c8 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -49,7 +49,20 @@ nextflow_workflow { then { assert workflow.success - assert snapshot(workflow.out).match() + assert snapshot( + workflow.out.marked_bam, + workflow.out.marked_bai, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), + ).match() } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index 2fcbd8e27..b538612cb 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,414 +1,135 @@ { "align sentieon": { "content": [ - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" - ] - ], - "8": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" - ] - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" - ] + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" ] - } + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,e016dd74f156d0b31a787903b8fef29c" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,003ed2dae28d295e5005fc2be942fd24" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,c238cb8240e7145ea62fd7bc26787cf5" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,47dec263ece77d2f5816012a345e8531" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,a0ee4d2b9970df49fed3f262c10b5e16" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,8192ba26ccf5cea0778e9ed2cf187430" + ] + ], + [ + "test_dedup.bam", + "test_dedup.bam.bai", + "test_dedup.bam.metrics", + "test_dedup.bam.metrics.multiqc.tsv", + "test_dedup.score" + ] ], - "timestamp": "2026-03-13T23:08:12.022075352", + "timestamp": "2026-03-14T00:02:24.597092362", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 8096628179346e1ca183a51cba2bc0f78e5af1b0 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 08:29:12 +0100 Subject: [PATCH 470/872] update gens test --- subworkflows/local/gens/tests/main.nf.test | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index ca61de785..71a1dcc77 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -30,9 +30,13 @@ nextflow_workflow { [id:'earlycasualcaiman'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]) - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) - input[7] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) - input[8] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[6] = channel.of([ + [id:'earlycasualcaiman'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[9] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) """ } } @@ -65,9 +69,13 @@ nextflow_workflow { [id:'slowlycivilbuck'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]) - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) - input[7] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) - input[8] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[6] = channel.of([ + [id:'earlycasualcaiman'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([[id:'pon_female'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) + input[9] = channel.of([[id:'pon_male'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]) """ } } From cbf8643ca2079a4e9620d9921a006ebc11c6e87e Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 08:33:19 +0100 Subject: [PATCH 471/872] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02b3eedb3..bb03887ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed haplocheck [#778](https://github.com/nf-core/raredisease/pull/778) - Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) - Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) +- Replace local gens module with nf-core module [#785](https://github.com/nf-core/raredisease/pull/785) ### `Fixed` From dd12cd7f9798a2d2465ba7daefc88ccc68fbbc28 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 09:30:31 +0100 Subject: [PATCH 472/872] correct metadata for the test --- subworkflows/local/gens/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index 71a1dcc77..bdf25ae51 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -70,7 +70,7 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]) input[6] = channel.of([ - [id:'earlycasualcaiman'], + [id:'slowlycivilbuck'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) From 91a5479b3bd7f570140ee6001c339fb805213b8f Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 10:19:00 +0100 Subject: [PATCH 473/872] update gens snapshot --- .../local/gens/tests/main.nf.test.snap | 140 +++++------------- 1 file changed, 38 insertions(+), 102 deletions(-) diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap index 3fb7b91b6..6b9780bf1 100644 --- a/subworkflows/local/gens/tests/main.nf.test.snap +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -3,134 +3,70 @@ "content": [ { "0": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "2": [ + + ], + "3": [ + ], "gens_baf_bed_gz": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "gens_baf_bed_tbi": [ + ], "gens_cov_bed_gz": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "gens_cov_bed_tbi": [ + ] } ], - "timestamp": "2026-03-06T06:32:00.117867897", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-16T10:18:33.815461" }, "GENS - male sample, stub": { "content": [ { "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "2": [ + + ], + "3": [ + ], "gens_baf_bed_gz": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "gens_baf_bed_tbi": [ + ], "gens_cov_bed_gz": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + + ], + "gens_cov_bed_tbi": [ + ] } ], - "timestamp": "2026-03-06T06:31:24.998017159", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-16T10:17:56.295431" } } \ No newline at end of file From 233ab4d440fbfa35e5a4edd6ed4392212a78b008 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 10:34:44 +0100 Subject: [PATCH 474/872] add full meta --- subworkflows/local/gens/tests/main.nf.test | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index bdf25ae51..f0177721c 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -27,11 +27,11 @@ nextflow_workflow { input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz', checkIfExists: true)) input[5] = channel.of([ - [id:'earlycasualcaiman'], + [id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]) input[6] = channel.of([ - [id:'earlycasualcaiman'], + [id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) @@ -66,11 +66,11 @@ nextflow_workflow { input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[4] = channel.of(file(params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz', checkIfExists: true)) input[5] = channel.of([ - [id:'slowlycivilbuck'], + [id:'slowlycivilbuck', sample:'slowlycivilbuck', sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]) input[6] = channel.of([ - [id:'slowlycivilbuck'], + [id:'slowlycivilbuck', sample:'slowlycivilbuck', sex:2, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) From ac96e378f142fb9575cd70c1923c589cdaff3203 Mon Sep 17 00:00:00 2001 From: Peter Pruisscher Date: Mon, 16 Mar 2026 11:11:22 +0100 Subject: [PATCH 475/872] run tests in a unix env --- .../local/gens/tests/main.nf.test.snap | 224 ++++++++++++++++-- 1 file changed, 200 insertions(+), 24 deletions(-) diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap index 6b9780bf1..379966380 100644 --- a/subworkflows/local/gens/tests/main.nf.test.snap +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -3,70 +3,246 @@ "content": [ { "0": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "1": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "3": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "gens_baf_bed_gz": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "gens_baf_bed_tbi": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "gens_cov_bed_gz": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "gens_cov_bed_tbi": [ - + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] } ], + "timestamp": "2026-03-16T11:07:59.889224757", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-16T10:18:33.815461" + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } }, "GENS - male sample, stub": { "content": [ { "0": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "1": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "2": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "3": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "gens_baf_bed_gz": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "gens_baf_bed_tbi": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "gens_cov_bed_gz": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "gens_cov_bed_tbi": [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] } ], + "timestamp": "2026-03-16T11:07:05.988643484", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-16T10:17:56.295431" + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } } } \ No newline at end of file From fdd004010176631aaf2e1f196e13ad30b4f66c4c Mon Sep 17 00:00:00 2001 From: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Date: Mon, 16 Mar 2026 12:49:31 +0100 Subject: [PATCH 476/872] Update subworkflows/local/gens/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- subworkflows/local/gens/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/gens/main.nf b/subworkflows/local/gens/main.nf index dc8740193..9edb7a421 100644 --- a/subworkflows/local/gens/main.nf +++ b/subworkflows/local/gens/main.nf @@ -55,8 +55,7 @@ workflow GENS { GENS_GENERATE ( ch_denoisereadcounts_out .join(ch_gvcf) - .join(ch_gvcf_tbi) - .map { meta, counts, gvcf, gvcf_tbi -> tuple(meta, counts, gvcf, gvcf_tbi) }, + .join(ch_gvcf_tbi), ch_gnomad_pos ) From 0055bb5c07167940820285d19fe184574d45a70b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 16 Mar 2026 13:29:46 +0100 Subject: [PATCH 477/872] update SV caller priority with mitosalt --- main.nf | 6 +++++- subworkflows/local/annotate_mt_snvs/main.nf | 4 +--- subworkflows/local/call_structural_variants/main.nf | 5 +++++ subworkflows/local/call_sv_MT/main.nf | 5 ++--- tests/test_singleton.nf.test.snap | 5 +---- 5 files changed, 14 insertions(+), 11 deletions(-) diff --git a/main.nf b/main.nf index 5346dbd30..893e0e9df 100644 --- a/main.nf +++ b/main.nf @@ -312,13 +312,17 @@ workflow NFCORE_RAREDISEASE { // if (skip_germlinecnvcaller) { if (val_analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator", "mitosalt"]) + } else if (val_run_mt_for_wes) { + ch_svcaller_priority = channel.value(["mitosalt"]) } else { ch_svcaller_priority = channel.value([]) } } else { if (val_analysis_type.equals("wgs")) { ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) + } else if (val_run_mt_for_wes) { + ch_svcaller_priority = channel.value(["manta", "gcnvcaller", "mitosalt"]) } else { ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) } diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 0205ea285..154f687d3 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -10,7 +10,6 @@ include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../module include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../../modules/nf-core/haplogrep3/classify/main' include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' include { ANNOTATE_CADD } from '../annotate_cadd' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow ANNOTATE_MT_SNVS { take: @@ -45,9 +44,8 @@ workflow ANNOTATE_MT_SNVS { .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ZIP_TABIX_VCFANNO_MT(VCFANNO_MT.out.vcf) - ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_index.map{meta, vcf, _tbi -> return [meta, vcf]} + ch_vcfanno_vcf = VCFANNO_MT.out.vcf // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index e4d0b2ef2..72fda8525 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -176,8 +176,13 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index + } else { + TABIX_TABIX (mitosalt_vcf) + ch_merged_svs = mitosalt_vcf + ch_merged_tbi = TABIX_TABIX.out.index } + emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index bc2d90702..081f2041e 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -115,10 +115,9 @@ workflow CALL_SV_MT { val_saltshaker_multiple_threshold, val_saltshaker_noise_threshold ) - ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify SALTSHAKER_PLOT( - ch_mitosalt_vcf + SALTSHAKER_CLASSIFY.out.classify ) ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot } @@ -128,7 +127,7 @@ workflow CALL_SV_MT { emit: mitosalt_classify = SALTSHAKER_CLASSIFY.out.txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = ch_mitosalt_vcf // channel: [ val(meta), path(vcf) ] + mitosalt_vcf = SALTSHAKER_CLASSIFY.out.vcf // channel: [ val(meta), path(vcf) ] mitosalt_plot = ch_mitosalt_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] } diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 72f20808e..11e1825bb 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -732,14 +732,11 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], -<<<<<<< HEAD -======= "timestamp": "2026-03-10T15:15:02.654289867", ->>>>>>> e21520c9e47486b83bbbfd46e3bff18f6883013d "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" }, "timestamp": "2026-03-04T08:25:27.608017744" } -} \ No newline at end of file +} From 144bfa2d843662aab348fad8491828728e4fdbe0 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 16 Mar 2026 13:34:04 +0100 Subject: [PATCH 478/872] start updating tests and fixing chr name --- modules/local/saltshaker/classify/main.nf | 4 ++ .../local/call_structural_variants/main.nf | 4 +- .../tests/main.nf.test | 37 +++++++++++++++++++ subworkflows/local/call_sv_MT/main.nf | 3 +- workflows/raredisease.nf | 2 +- 5 files changed, 46 insertions(+), 4 deletions(-) diff --git a/modules/local/saltshaker/classify/main.nf b/modules/local/saltshaker/classify/main.nf index a473b5979..1b533570d 100644 --- a/modules/local/saltshaker/classify/main.nf +++ b/modules/local/saltshaker/classify/main.nf @@ -14,6 +14,7 @@ process SALTSHAKER_CLASSIFY { val high_het val mult_thresh val noise_thresh + val mito_name output: tuple val(meta), path("*_classify_metadata.tsv"), emit: classify @@ -36,6 +37,9 @@ process SALTSHAKER_CLASSIFY { --noise $noise_thresh \\ $args + cat ${prefix}.saltshaker.vcf | sed 's/chrM/${mito_name}/g' > ${prefix}.saltshaker.tmp.vcf + mv ${prefix}.saltshaker.tmp.vcf ${prefix}.saltshaker.vcf + """ stub: diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index e4d0b2ef2..6cf9795fb 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -28,7 +28,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] val_analysis_type // string: "wes", "wgs", or "mito" skip_germlinecnvcaller // boolean - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] @@ -96,7 +96,7 @@ workflow CALL_STRUCTURAL_VARIANTS { if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CALL_SV_MT( - ch_bam_bai, + ch_mt_bam_bai, ch_genome_chrsizes, ch_genome_fai, ch_genome_fasta, diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 139d26d58..30880c4b1 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -38,6 +38,43 @@ nextflow_workflow { input[12] = channel.of([[id:'gcnvcaller'], []]) input[13] = 'wgs' input[14] = true + inpul[15] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman +ch_genome_chrsizes +ch_genome_hisat2index +ch_mt_fai +ch_mt_fasta +ch_mt_lastdb +ch_reads +ch_subdepth +val_heavy_strand_origin_start +val_heavy_strand_origin_end +val_light_strand_origin_start +val_light_strand_origin_end +val_mito_length +val_mito_name +val_mitosalt_breakspan +val_mitosalt_breakthreshold +val_mitosalt_cluster_threshold +val_mitosalt_deletion_threshold_max +val_mitosalt_deletion_threshold_min +val_mitosalt_evalue_threshold +val_mitosalt_exclude +val_mitosalt_flank +val_mitosalt_heteroplasmy_limit +val_mitosalt_paired_distance +val_mitosalt_score_threshold +val_mitosalt_sizelimit +val_mitosalt_split_distance_threshold +val_mitosalt_split_length +val_saltshaker_dominant_fraction +val_saltshaker_group_radius +val_saltshaker_high_heteroplasmy +val_saltshaker_multiple_threshold +val_saltshaker_noise_threshold +val_run_mt_for_wes + """ } } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index bc2d90702..4d009a80e 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -106,7 +106,7 @@ workflow CALL_SV_MT { val_light_strand_origin_start, val_light_strand_origin_end ) - + SALTSHAKER_CLASSIFY( SALTSHAKER_CALL.out.call, val_saltshaker_dominant_fraction, @@ -114,6 +114,7 @@ workflow CALL_SV_MT { val_saltshaker_high_heteroplasmy, val_saltshaker_multiple_threshold, val_saltshaker_noise_threshold + val_mito_name ) ch_mitosalt_vcf = SALTSHAKER_CLASSIFY.out.classify diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index e431cab23..cef61a899 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -549,7 +549,7 @@ workflow RAREDISEASE { ch_gcnvcaller_model, val_analysis_type, skip_germlinecnvcaller, - ch_mapped.genome_marked_bam_bai, + ch_mapped.mt_bam_bai, ch_genome_chrsizes, ch_genome_hisat2index, ch_mt_fai, From 5dcbc151ebbb78428a8c0597ccab550f6600199b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 16 Mar 2026 14:19:58 +0100 Subject: [PATCH 479/872] finish tests and saltshaker mt name --- .../tests/main.nf.test | 76 ++++++++++--------- subworkflows/local/call_sv_MT/main.nf | 4 +- workflows/raredisease.nf | 1 - 3 files changed, 43 insertions(+), 38 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 30880c4b1..1212e4ec3 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -38,42 +38,48 @@ nextflow_workflow { input[12] = channel.of([[id:'gcnvcaller'], []]) input[13] = 'wgs' input[14] = true - inpul[15] = channel.of([ + input[15] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman -ch_genome_chrsizes -ch_genome_hisat2index -ch_mt_fai -ch_mt_fasta -ch_mt_lastdb -ch_reads -ch_subdepth -val_heavy_strand_origin_start -val_heavy_strand_origin_end -val_light_strand_origin_start -val_light_strand_origin_end -val_mito_length -val_mito_name -val_mitosalt_breakspan -val_mitosalt_breakthreshold -val_mitosalt_cluster_threshold -val_mitosalt_deletion_threshold_max -val_mitosalt_deletion_threshold_min -val_mitosalt_evalue_threshold -val_mitosalt_exclude -val_mitosalt_flank -val_mitosalt_heteroplasmy_limit -val_mitosalt_paired_distance -val_mitosalt_score_threshold -val_mitosalt_sizelimit -val_mitosalt_split_distance_threshold -val_mitosalt_split_length -val_saltshaker_dominant_fraction -val_saltshaker_group_radius -val_saltshaker_high_heteroplasmy -val_saltshaker_multiple_threshold -val_saltshaker_noise_threshold -val_run_mt_for_wes + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mtreverted.bam.bai', checkIfExists: true) + ]) + input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.chrsizes', checkIfExists: true)]).collect() + input[17] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/hisat2', checkIfExists: true)]).collect() + input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fai', checkIfExists: true)]).collect() + input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/lastdb', checkIfExists: true)]).collect() + input[21] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true)] + ]) + input[22] = 10000000 + input[23] = 16081 + input[24] = 407 + input[25] = 5730 + input[26] = 5763 + input[27] = 16569 + input[28] = 'MT' + input[29] = 15 + input[30] = 2 + input[31] = 5 + input[32] = 30000 + input[33] = 30 + input[34] = 0.00001 + input[35] = 5 + input[36] = 15 + input[37] = 0.01 + input[38] = 1000 + input[39] = 80 + input[40] = 10000 + input[41] = 5 + input[42] = 15 + input[43] = 0.5 + input[44] = 600 + input[45] = 10 + input[46] = 5 + input[47] = 0.3 + input[48] = true """ } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index af8f19008..440d77783 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -106,14 +106,14 @@ workflow CALL_SV_MT { val_light_strand_origin_start, val_light_strand_origin_end ) - + SALTSHAKER_CLASSIFY( SALTSHAKER_CALL.out.call, val_saltshaker_dominant_fraction, val_saltshaker_group_radius, val_saltshaker_high_heteroplasmy, val_saltshaker_multiple_threshold, - val_saltshaker_noise_threshold + val_saltshaker_noise_threshold, val_mito_name ) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index cef61a899..8200886b7 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -52,7 +52,6 @@ include { CALL_MOBILE_ELEMENTS } from '.. include { CALL_REPEAT_EXPANSIONS } from '../subworkflows/local/call_repeat_expansions' include { CALL_SNV } from '../subworkflows/local/call_snv' include { CALL_STRUCTURAL_VARIANTS } from '../subworkflows/local/call_structural_variants' -include { CALL_SV_MT } from '../subworkflows/local/call_sv_MT' include { GENERATE_CYTOSURE_FILES } from '../subworkflows/local/generate_cytosure_files' include { GENS } from '../subworkflows/local/gens' include { PREPARE_REFERENCES } from '../subworkflows/local/prepare_references' From 7dc333d112eb021080d3b3a8278fd409861fb0fc Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 16 Mar 2026 14:34:07 +0100 Subject: [PATCH 480/872] fix test data paths --- .../call_structural_variants/tests/main.nf.test | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 1212e4ec3..1c91e8691 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -44,16 +44,18 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mtreverted.bam.bai', checkIfExists: true) ]) input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.chrsizes', checkIfExists: true)]).collect() - input[17] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/hisat2', checkIfExists: true)]).collect() + input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fai', checkIfExists: true)]).collect() input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/lastdb', checkIfExists: true)]).collect() + input[20] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } input[21] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true)] + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] ]) - input[22] = 10000000 + input[22] = channel.value(10000000) input[23] = 16081 input[24] = 407 input[25] = 5730 @@ -79,7 +81,7 @@ nextflow_workflow { input[45] = 10 input[46] = 5 input[47] = 0.3 - input[48] = true + input[48] = true """ } From 1de736c2a57cc5c009bef039e1323b6610e0ba7a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 14:42:24 +0100 Subject: [PATCH 481/872] Migrate strange and subsampling workflows to output and update snapshot --- conf/modules/raredisease.config | 5 ----- conf/modules/subsample_mt_frac.config | 5 ----- conf/modules/subsample_mt_reads.config | 5 ----- subworkflows/local/subsample_mt_frac/main.nf | 6 ++++++ subworkflows/local/subsample_mt_reads/main.nf | 6 ++++++ tests/default.nf.test.snap | 12 +----------- tests/test_bam.nf.test.snap | 12 +----------- tests/test_singleton.nf.test.snap | 8 +------- workflows/raredisease.nf | 8 ++++++++ 9 files changed, 23 insertions(+), 44 deletions(-) diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index 0b01c4488..111949302 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -65,11 +65,6 @@ process { process { withName: '.*STRANGER' { ext.prefix = { "${meta.id}_repeat_expansion_stranger" } - publishDir = [ - path: { "${params.outdir}/repeat_expansions" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } diff --git a/conf/modules/subsample_mt_frac.config b/conf/modules/subsample_mt_frac.config index 5b3e6e17c..32ba66748 100644 --- a/conf/modules/subsample_mt_frac.config +++ b/conf/modules/subsample_mt_frac.config @@ -24,11 +24,6 @@ process { withName: '.*SUBSAMPLE_MT_FRAC:SAMTOOLS_VIEW' { ext.args = { "--output-fmt BAM -h -F 4 -s ${meta.seedfrac}" } ext.prefix = { "${meta.id}_mt_subsample" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config index 70f9a71ef..d8525b521 100644 --- a/conf/modules/subsample_mt_reads.config +++ b/conf/modules/subsample_mt_reads.config @@ -40,11 +40,6 @@ process { withName: '.*SUBSAMPLE_MT_READS:SAMTOOLS_SORT' { ext.prefix = { "${meta.id}_mt_subsample" } - publishDir = [ - path: { "${params.outdir}/alignment" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 6ac7c6c98..1ea24dac0 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -32,4 +32,10 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[],[]], [], 'bai') + ch_publish = SAMTOOLS_VIEW.out.bam + .mix(SAMTOOLS_VIEW.out.bai) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index e141eaea3..3f75a74d4 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -26,4 +26,10 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') + ch_publish = SAMTOOLS_SORT.out.bam + .mix(SAMTOOLS_SORT.out.bai) + .map { meta, value -> ['alignment/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 538aa9fcc..5652128ce 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -499,13 +499,6 @@ } }, [ - "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -703,9 +696,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -716,7 +706,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-12T22:37:05.921453831", + "timestamp": "2026-03-16T14:20:06.249313916", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9c508f269..07be8aab3 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -469,13 +469,6 @@ } }, [ - "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -663,9 +656,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -676,7 +666,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-12T22:43:18.380887473", + "timestamp": "2026-03-16T14:26:16.566396016", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f23ae4108..e970226a5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -482,9 +482,6 @@ } }, [ - "alignment", - "alignment/hugelymodelbat_mt_subsample.bam", - "alignment/hugelymodelbat_mt_subsample.bam.bai", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -568,9 +565,6 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", - "repeat_expansions", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", - "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -579,7 +573,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-12T22:47:05.119730547", + "timestamp": "2026-03-16T14:30:06.728297714", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8d78db201..0dc5c7385 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -213,6 +213,7 @@ workflow RAREDISEASE { ch_call_sv_mt_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() + ch_subsample_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -289,10 +290,12 @@ workflow RAREDISEASE { val_mt_subsample_rd, val_mt_subsample_seed ) + ch_subsample_publish = SUBSAMPLE_MT_FRAC.out.publish } else { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, ) + ch_subsample_publish = SUBSAMPLE_MT_READS.out.publish } } @@ -353,6 +356,10 @@ workflow RAREDISEASE { CALL_REPEAT_EXPANSIONS.out.vcf, ch_variant_catalog ) + ch_call_repeat_expansions_publish = ch_call_repeat_expansions_publish + .mix(STRANGER.out.vcf + .mix(STRANGER.out.tbi) + .map { meta, value -> ['repeat_expansions/', [meta, value]] }) } } @@ -910,6 +917,7 @@ workflow RAREDISEASE { versions = ch_versions // channel: [ path(versions.yml) ] publish = ch_align_publish .mix(ch_qc_bam_publish) + .mix(ch_subsample_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) .mix(ch_call_sv_mt_publish) From 2659d9797691124127b9120caa0324968c79cb1b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 14:43:33 +0100 Subject: [PATCH 482/872] Update nextflow.config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 4c212227e..4c6e7d0c0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -175,6 +175,7 @@ params { validate_params = true } +outputDir = params.outdir workflow.output.mode = 'copy' // Load base.config by default for all pipelines From 5890ec15f3d7d783b5416701f35942e42ac2e6f1 Mon Sep 17 00:00:00 2001 From: peterpru Date: Mon, 16 Mar 2026 14:47:51 +0100 Subject: [PATCH 483/872] delete old module and update changelog --- CHANGELOG.md | 63 +++++++++++++++++++------------------ modules/local/gens/main.nf | 39 ----------------------- modules/local/gens/meta.yml | 45 -------------------------- 3 files changed, 32 insertions(+), 115 deletions(-) delete mode 100644 modules/local/gens/main.nf delete mode 100644 modules/local/gens/meta.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index bb03887ab..8949b8594 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -57,37 +57,38 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| -------------------- | ----------- | ----------- | -| bcftools | 1.20 | 1.21 | -| bwa | 0.7.18 | 0.7.19 | -| deepvariant | 1.8.0 | 1.9.0 | -| eKLIPse | 1.8 | | -| ensemblvep/vep | 110 | 110.1 | -| ensemblvep/filtervep | 113 | 115.2 | -| fastp | 0.23.4 | 1.0.1 | -| gatk4 | 4.5.0.0 | 4.6.2.0 | -| gawk | 5.3.0 | 5.3.1 | -| genmod | 3.9 | 3.10.2 | -| gens-preproc | 1.0.11 | 1.1.2 | -| haplocheck | 1.3.3 | | -| hmtnote | 0.7.2 | | -| htslib | 1.20 | 1.21 | -| MitoSalt | | 1.1.1 | -| mosdepth | 0.3.8 | 0.3.11 | -| multiqc | 1.32 | 1.33 | -| ngsbits | 202411 | 202512 | -| picard | 3.3.0 | 3.4.0 | -| pigz | 2.3.4 | 2.8 | -| sambamba | | 1.0.1 | -| samtools | 1.21 | 1.22.1 | -| sentieon | 202503 | 202503.02 | -| stranger | 0.9.4 | 0.10.0 | -| svdb | 2.8.3 | 2.8.4 | -| tiddit | 3.6.1 | 3.9.4 | -| ucsc | 447 | 482 | -| vcfanno | 0.3.5 | 0.3.7 | -| vcf2cytosure | 0.9.1 | 0.9.3 | +| Tool | Old version | New version | +| --------------------- | ----------- | ----------- | +| bcftools | 1.20 | 1.21 | +| bwa | 0.7.18 | 0.7.19 | +| deepvariant | 1.8.0 | 1.9.0 | +| eKLIPse | 1.8 | | +| ensemblvep/vep | 110 | 110.1 | +| ensemblvep/filtervep | 113 | 115.2 | +| fastp | 0.23.4 | 1.0.1 | +| gatk4 | 4.5.0.0 | 4.6.2.0 | +| gawk | 5.3.0 | 5.3.1 | +| genmod | 3.9 | 3.10.2 | +| gens-preproc | 1.0.11 | | +| gens/preparecovandbaf | | 2.0.1 | +| haplocheck | 1.3.3 | | +| hmtnote | 0.7.2 | | +| htslib | 1.20 | 1.21 | +| MitoSalt | | 1.1.1 | +| mosdepth | 0.3.8 | 0.3.11 | +| multiqc | 1.32 | 1.33 | +| ngsbits | 202411 | 202512 | +| picard | 3.3.0 | 3.4.0 | +| pigz | 2.3.4 | 2.8 | +| sambamba | | 1.0.1 | +| samtools | 1.21 | 1.22.1 | +| sentieon | 202503 | 202503.02 | +| stranger | 0.9.4 | 0.10.0 | +| svdb | 2.8.3 | 2.8.4 | +| tiddit | 3.6.1 | 3.9.4 | +| ucsc | 447 | 482 | +| vcfanno | 0.3.5 | 0.3.7 | +| vcf2cytosure | 0.9.1 | 0.9.3 | ## 2.6.0 - Cacofonix [2025-06-25] diff --git a/modules/local/gens/main.nf b/modules/local/gens/main.nf deleted file mode 100644 index c7eb469a7..000000000 --- a/modules/local/gens/main.nf +++ /dev/null @@ -1,39 +0,0 @@ -process GENS { - tag "$meta.id" - label 'process_medium' - - container 'docker.io/clinicalgenomics/gens-preproc:1.1.2' - - input: - tuple val(meta), path(read_counts) - tuple val(meta2), path(gvcf) - path gnomad_positions - - output: - tuple val(meta), path('*.cov.bed') , emit: cov - tuple val(meta), path('*.baf.bed') , emit: baf - tuple val("${task.process}"), val('generate_gens_data'), eval("generate_gens_data.py --version"), topic: versions, emit: versions_generate_gens_data - tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions, emit: versions_python - - script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "The gens pre-processing module does not support Conda. Please use Docker / Singularity / Podman instead." - } - def prefix = task.ext.prefix ?: "${meta.id}" - """ - generate_gens_data.py \\ - --coverage $read_counts \\ - --gvcf $gvcf \\ - --label $prefix \\ - --baf_positions $gnomad_positions \\ - --outdir \$PWD - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.baf.bed - touch ${prefix}.cov.bed - """ -} diff --git a/modules/local/gens/meta.yml b/modules/local/gens/meta.yml deleted file mode 100644 index 44d0e7b75..000000000 --- a/modules/local/gens/meta.yml +++ /dev/null @@ -1,45 +0,0 @@ -name: gens -description: -keywords: - - bed - - vcf -tools: - - gens: - description: | - Gens is a web-based interactive tool to visualize genomic copy number profiles from WGS data (although it could theoretically be used for any type of data). - It plots the normalized read depth and alternative allele frequency. - homepage: https://github.com/Clinical-Genomics-Lund/gens - documentation: https://github.com/Clinical-Genomics-Lund/gens -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - read_counts: - type: file - description: Input standardized read counts file - pattern: "*.tsv" - - vcf: - type: file - description: Input vcf file - pattern: "*.vcf" - - gnomad_positions: - type: file - description: SNV filter file - pattern: "*.txt" -output: - - cov: - type: file - description: Gens preprocessed coverage file - pattern: "*.bed.gz" - - baf: - type: file - description: Gens preprocessed base allele frequency file - pattern: "*.bed.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@raysloks" From 96d7d64f61ad9bddecb4168a1916d70e18f8571b Mon Sep 17 00:00:00 2001 From: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Date: Mon, 16 Mar 2026 15:03:44 +0100 Subject: [PATCH 484/872] Update CHANGELOG.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8949b8594..322de52db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -70,7 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | gawk | 5.3.0 | 5.3.1 | | genmod | 3.9 | 3.10.2 | | gens-preproc | 1.0.11 | | -| gens/preparecovandbaf | | 2.0.1 | +| gens/preparecovandbaf | | 1.1.5 | | haplocheck | 1.3.3 | | | hmtnote | 0.7.2 | | | htslib | 1.20 | 1.21 | From 2f323543efe6c4eee961c3d715bf8d7ba4543b0a Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 16 Mar 2026 15:37:15 +0100 Subject: [PATCH 485/872] remove tabix double gzipping --- .../local/annotate_genome_snvs/main.nf | 5 +-- subworkflows/local/annotate_mt_snvs/main.nf | 4 +- .../local/call_sv_MT/tests/main.nf.test | 40 ++++++++++++------- 3 files changed, 28 insertions(+), 21 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 82535e9cb..db2325c81 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -13,7 +13,6 @@ include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../../modules/nf-core include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../../modules/nf-core/chromograph/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_BCFTOOLS_CONCAT } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_BCFTOOLS_VIEW } from '../../../modules/nf-core/tabix/tabix/main' @@ -101,9 +100,7 @@ workflow ANNOTATE_GENOME_SNVS { VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ZIP_TABIX_VCFANNO (VCFANNO.out.vcf) - - BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_index, [], [], []) // filter on frequencies + BCFTOOLS_VIEW(VCFANNO.out.tbi, [], [], []) // filter on frequencies // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 154f687d3..a0fe33a31 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -45,7 +45,7 @@ workflow ANNOTATE_MT_SNVS { VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ch_vcfanno_vcf = VCFANNO_MT.out.vcf + ch_vcfanno_vcf = VCFANNO_MT.out.vcf // Annotating with CADD if (!val_cadd_resources.equals(null)) { @@ -53,7 +53,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_resources, ch_fai, ch_cadd_header, - ZIP_TABIX_VCFANNO_MT.out.gz_index, + VCFANNO_MT.out.tbi, val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index feb8e8f0e..300e6cece 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -37,21 +37,31 @@ nextflow_workflow { ] ]) input[9] = channel.value(10000000) - input[10] = 15 - input[11] = 2 - input[12] = 2 - input[13] = 30000 - input[14] = 30 - input[15] = 0.00001 - input[16] = 5 - input[17] = 15 - input[18] = 0.01 - input[19] = 'chrM' - input[20] = 1000 - input[21] = 80 - input[22] = 10000 - input[23] = 5 - input[24] = 15 + input[10] = 16081 + input[11] = 407 + input[12] = 5730 + input[13] = 5763 + input[14] = 16569 + input[15] = 'chrM' + input[16] = 15 + input[17] = 2 + input[18] = 2 + input[19] = 30000 + input[20] = 30 + input[21] = 0.00001 + input[22] = 5 + input[23] = 15 + input[24] = 0.01 + input[25] = 1000 + input[26] = 80 + input[27] = 10000 + input[28] = 5 + input[29] = 15 + input[30] = 0.5 + input[31] = 600 + input[32] = 10 + input[33] = 5 + input[34] = 0.3 """ } } From 6b5625adba45341370e63bad3afbd0d8696a6726 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 18:28:04 +0100 Subject: [PATCH 486/872] update snapshot --- tests/default.nf.test.snap | 396 +++++++++++++++++++++++++++++- tests/test_bam.nf.test.snap | 365 ++++++++++++++++++++++++++- tests/test_singleton.nf.test.snap | 148 ++++++++++- 3 files changed, 906 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5652128ce..ddbbe0fb6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -499,6 +499,22 @@ } }, [ + "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", + "alignment/hugelymodelbat_mt_subsample.bam", + "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -653,6 +669,30 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/genome", + "call_sv/genome/justhusky_sv.vcf.gz", + "call_sv/genome/justhusky_sv.vcf.gz.tbi", + "call_sv/mitochondria", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", + "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", + "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", + "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -668,6 +708,10 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -683,6 +727,328 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", + "qc_bam", + "qc_bam/earlycasualcaiman", + "qc_bam/earlycasualcaiman/css", + "qc_bam/earlycasualcaiman/css/agogo.css", + "qc_bam/earlycasualcaiman/css/ajax-loader.gif", + "qc_bam/earlycasualcaiman/css/basic.css", + 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"repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", @@ -666,7 +1029,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-16T14:26:16.566396016", + "timestamp": "2026-03-16T18:18:03.478560166", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e970226a5..e597eca33 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -482,6 +482,12 @@ } }, [ + "alignment", + "alignment/hugelymodelbat_mt_subsample.bam", + "alignment/hugelymodelbat_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -528,6 +534,24 @@ "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", "annotate_sv/justhusky_svdbquery_vep_summary.html", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/genome", + "call_sv/genome/justhusky_sv.vcf.gz", + "call_sv/genome/justhusky_sv.vcf.gz.tbi", + "call_sv/mitochondria", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", + "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", + "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -537,6 +561,8 @@ "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -552,6 +578,114 @@ "pedigree/justhusky.ped", "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", + "qc_bam", + "qc_bam/hugelymodelbat", + "qc_bam/hugelymodelbat/css", + "qc_bam/hugelymodelbat/css/agogo.css", + "qc_bam/hugelymodelbat/css/ajax-loader.gif", + "qc_bam/hugelymodelbat/css/basic.css", + "qc_bam/hugelymodelbat/css/bgfooter.png", + "qc_bam/hugelymodelbat/css/bgtop.png", + "qc_bam/hugelymodelbat/css/comment-bright.png", + "qc_bam/hugelymodelbat/css/comment-close.png", + "qc_bam/hugelymodelbat/css/comment.png", + "qc_bam/hugelymodelbat/css/doctools.js", + "qc_bam/hugelymodelbat/css/down-pressed.png", + "qc_bam/hugelymodelbat/css/down.png", + "qc_bam/hugelymodelbat/css/file.png", + "qc_bam/hugelymodelbat/css/jquery.js", + "qc_bam/hugelymodelbat/css/minus.png", + "qc_bam/hugelymodelbat/css/plus.png", + "qc_bam/hugelymodelbat/css/pygments.css", + "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", + "qc_bam/hugelymodelbat/css/report.css", + "qc_bam/hugelymodelbat/css/searchtools.js", + "qc_bam/hugelymodelbat/css/underscore.js", + "qc_bam/hugelymodelbat/css/up-pressed.png", + "qc_bam/hugelymodelbat/css/up.png", + "qc_bam/hugelymodelbat/css/websupport.js", + "qc_bam/hugelymodelbat/genome_results.txt", + "qc_bam/hugelymodelbat/images_qualimapReport", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", + "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", + "qc_bam/hugelymodelbat/qualimapReport.html", + "qc_bam/hugelymodelbat/raw_data_qualimapReport", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", + "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", + "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.per-base.d4", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.summary.txt", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/hugelymodelbat_tidditcov.bed", + "qc_bam/hugelymodelbat_tidditcov.bw", + "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", + "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -565,15 +699,27 @@ "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", + "repeat_expansions", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-16T14:30:06.728297714", + "timestamp": "2026-03-16T18:21:47.347535507", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 88caf56cf0ca82e5a38cdb2b4cda48c5c6e79567 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 23:01:02 +0100 Subject: [PATCH 487/872] Migrate ann_csq_pli --- conf/modules/annotate_consequence_pli.config | 12 ----- .../local/annotate_consequence_pli/main.nf | 11 +++++ .../tests/main.nf.test | 7 +++ .../tests/main.nf.test.snap | 48 ++++++++++++++++++- workflows/raredisease.nf | 14 ++++-- 5 files changed, 74 insertions(+), 18 deletions(-) diff --git a/conf/modules/annotate_consequence_pli.config b/conf/modules/annotate_consequence_pli.config index 4175691d0..42b988256 100644 --- a/conf/modules/annotate_consequence_pli.config +++ b/conf/modules/annotate_consequence_pli.config @@ -56,17 +56,5 @@ process { withName: '.*ANN_CSQ_PLI_ME:CUSTOM_ADDMOSTSEVEREPLI' { ext.prefix = { "${meta.id}_me_pli_${meta.set}" } - publishDir = [ - path: { "${params.outdir}/annotate_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: '.*ANN_CSQ_PLI_ME:TABIX_TABIX' { - publishDir = [ - path: { "${params.outdir}/annotate_mobile_elements" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/annotate_consequence_pli/main.nf b/subworkflows/local/annotate_consequence_pli/main.nf index d1659cf21..111d49986 100644 --- a/subworkflows/local/annotate_consequence_pli/main.nf +++ b/subworkflows/local/annotate_consequence_pli/main.nf @@ -11,16 +11,27 @@ workflow ANNOTATE_CSQ_PLI { ch_variant_consequences // channel: [mandatory] [ path(consequences) ] ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] val_index // bool + val_publish_dir // val: destination string, or '' to skip publishing main: CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) CUSTOM_ADDMOSTSEVEREPLI (CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.vcf) + ch_tbi_publish = channel.empty() if (val_index) { TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) + ch_tbi_publish = TABIX_TABIX.out.index + } + + ch_publish = channel.empty() + if (val_publish_dir) { + ch_publish = CUSTOM_ADDMOSTSEVEREPLI.out.vcf + .mix(ch_tbi_publish) + .map { meta, value -> [val_publish_dir, [meta, value]] } } emit: vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test index 1c31b258b..da5fe378f 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -22,6 +22,7 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = false + input[3] = false """ } } @@ -51,6 +52,7 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = true + input[3] = "ann_csq" """ } } @@ -59,6 +61,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5, path(workflow.out.vcf_ann[0][1]).vcf.summary ).match() } @@ -81,6 +87,7 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = true + input[3] = "ann_csq" """ } } diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap index 8f9e23930..eb6659188 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap @@ -1,10 +1,14 @@ { "ANNOTATE_CSQ_PLI - with index": { "content": [ + [ + "severepli.vcf.gz", + "severepli.vcf.gz.tbi" + ], "58d9c7a329ee86094acc0826b671652c", "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-01T17:08:30.607457875", + "timestamp": "2026-03-16T22:58:51.504628424", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -32,6 +36,46 @@ "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "1": [ + [ + "ann_csq", + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "ann_csq", + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "ann_csq", + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "ann_csq", + [ + { + "id": "justhusky" + }, + "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "vcf_ann": [ [ { @@ -42,7 +86,7 @@ ] } ], - "timestamp": "2026-03-05T12:55:16.985254117", + "timestamp": "2026-03-16T22:56:18.385999497", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0dc5c7385..717c4b31e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -453,7 +453,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SNV ( ch_variant_consequences_snv, ch_ann_csq_snv_in, - false + false, + '' ) ANN_CSQ_PLI_SNV.out.vcf_ann @@ -522,7 +523,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_MT( ch_variant_consequences_snv, ch_ann_csq_mtsnv_in, - false + false, + '' ) ANN_CSQ_PLI_MT.out.vcf_ann @@ -612,7 +614,8 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SV ( ch_variant_consequences_sv, ch_ann_csq_sv_in, - false + false, + '' ) ANN_CSQ_PLI_SV.out.vcf_ann @@ -721,8 +724,11 @@ workflow RAREDISEASE { ANN_CSQ_PLI_ME( ch_variant_consequences_sv, ch_ann_csq_me_in, - true + true, + 'annotate_mobile_elements/' ) + ch_call_mobile_elements_publish = ch_call_mobile_elements_publish + .mix(ANN_CSQ_PLI_ME.out.publish) } } From 93ded3bf7ef0f23d04b313f34fe1c132cef956bd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 16 Mar 2026 23:57:27 +0100 Subject: [PATCH 488/872] Migrate annotate_genome_snvs and annotate_rhocallviz --- conf/modules/annotate_genome_snvs.config | 23 -- conf/modules/annotate_rhocallviz.config | 15 -- .../local/annotate_genome_snvs/main.nf | 8 + .../tests/main.nf.test.snap | 248 +++++++++++++++++- .../local/annotate_rhocallviz/main.nf | 9 + workflows/raredisease.nf | 5 +- 6 files changed, 268 insertions(+), 40 deletions(-) diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index 454690487..bdc33b5f1 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -54,11 +54,6 @@ process { ext.prefix = { "${meta7.upd_child}_chromograph_sites" } ext.args = { "--euploid" } tag = {"${meta7.upd_child}"} - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS' { @@ -66,11 +61,6 @@ process { ext.args = { '--euploid' } ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } tag = {"${meta6.upd_child}"} - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ANNOTATE_GENOME_SNVS:ZIP_TABIX_VCFANNO' { @@ -103,18 +93,5 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT' { ext.args = { "-Oz" } ext.prefix = { "${meta.prefix}_vep" } - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*ANNOTATE_GENOME_SNVS:TABIX_BCFTOOLS_CONCAT' { - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config index c88fa3a33..28296e484 100644 --- a/conf/modules/annotate_rhocallviz.config +++ b/conf/modules/annotate_rhocallviz.config @@ -35,31 +35,16 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:RHOCALL_VIZ' { ext.prefix = { "${meta.sample}_rhocallviz" } ext.args = { "--aftag GNOMADAF --wig" } - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG' { ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" } ext.args = { "--euploid" } ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_singleton', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:UCSC_WIGTOBIGWIG' { ext.prefix = { "${meta.sample}_rhocallviz" } ext.args = { "-clip" } - publishDir = [ - path: { "${params.outdir}/annotate_snv/genome/${meta.sample}_rhocallviz" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 82535e9cb..688986459 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -192,7 +192,15 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) + ch_publish = CHROMOGRAPH_SITES.out.plots + .mix(CHROMOGRAPH_REGIONS.out.plots) + .mix(BCFTOOLS_CONCAT.out.vcf) + .mix(TABIX_BCFTOOLS_CONCAT.out.index) + .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } + .mix(ANNOTATE_RHOCALLVIZ.out.publish) + emit: tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index 5c7ae9b36..e030f8a79 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -34,6 +34,252 @@ "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "2": [ + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "", + "prefix": "justhusky_rhocall_filter" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "annotate_snv/genome/earlycasualcaiman_rhocallviz/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "", + "prefix": "justhusky_rhocall_filter" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "annotate_snv/genome/earlycasualcaiman_rhocallviz/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -68,7 +314,7 @@ ] } ], - "timestamp": "2026-03-10T15:10:07.607984855", + "timestamp": "2026-03-16T23:12:33.480389323", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 5b24cc641..9431a4824 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -49,4 +49,13 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) + ch_publish = RHOCALL_VIZ.out.bed + .mix(RHOCALL_VIZ.out.wig) + .mix(CHROMOGRAPH_AUTOZYG.out.plots) + .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } + .mix(UCSC_WIGTOBIGWIG.out.bw + .map { meta, bw -> ["annotate_snv/genome/${meta.sample}_rhocallviz/", [meta, bw]] }) + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 717c4b31e..4388ea983 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -214,6 +214,7 @@ workflow RAREDISEASE { ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_subsample_publish = channel.empty() + ch_annotate_genome_snvs_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -428,6 +429,7 @@ workflow RAREDISEASE { val_genome, val_vep_cache_version ).set { ch_snv_annotate } + ch_annotate_genome_snvs_publish = ANNOTATE_GENOME_SNVS.out.publish ch_snv_annotate.vcf_ann .multiMap { meta, vcf -> @@ -928,7 +930,8 @@ workflow RAREDISEASE { .mix(ch_call_sv_publish) .mix(ch_call_sv_mt_publish) .mix(ch_call_repeat_expansions_publish) - .mix(ch_call_mobile_elements_publish) // channel: [ val(destination), val(value) ] + .mix(ch_call_mobile_elements_publish) + .mix(ch_annotate_genome_snvs_publish) // channel: [ val(destination), val(value) ] } From 7507ccecf9a2dcee1d5835a61a3ed7286f58f4b7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 00:06:46 +0100 Subject: [PATCH 489/872] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a0363cc0..fc2cc052b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Removed HmtNote [#779](https://github.com/nf-core/raredisease/pull/779) - Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#784](https://github.com/nf-core/raredisease/pull/784) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#786](https://github.com/nf-core/raredisease/pull/786) ### `Fixed` From e85d71e4364387c1d5b4647522b0424b65799100 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 00:23:26 +0100 Subject: [PATCH 490/872] Update generate_cytosure_files and scatter_genome --- conf/modules/generate_cytosure_files.config | 5 -- conf/modules/scatter_genome.config | 6 -- main.nf | 16 +++-- .../local/generate_cytosure_files/main.nf | 6 ++ subworkflows/local/scatter_genome/main.nf | 12 +++- .../local/scatter_genome/tests/main.nf.test | 1 + .../scatter_genome/tests/main.nf.test.snap | 70 ++++++++++++++++++- workflows/raredisease.nf | 5 +- 8 files changed, 98 insertions(+), 23 deletions(-) diff --git a/conf/modules/generate_cytosure_files.config b/conf/modules/generate_cytosure_files.config index 86e1fd01e..dd8f71ee1 100644 --- a/conf/modules/generate_cytosure_files.config +++ b/conf/modules/generate_cytosure_files.config @@ -45,10 +45,5 @@ process { '--maxbnd 5000' ].join(' ') } ext.prefix = { "${meta.custid}" ? "${meta.custid}" : "${meta.id}" } - publishDir = [ - path: { "${params.outdir}/vcf2cytosure" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } diff --git a/conf/modules/scatter_genome.config b/conf/modules/scatter_genome.config index 60730ea45..32ce0e700 100644 --- a/conf/modules/scatter_genome.config +++ b/conf/modules/scatter_genome.config @@ -25,11 +25,5 @@ process { withName: '.*SCATTER_GENOME:GATK4_SPLITINTERVALS' { ext.args = { "--scatter-count ${params.scatter_count}" } ext.prefix = { "${meta.id}_genome_intervals" } - publishDir = [ - enabled: params.save_reference, - path: { "${params.outdir}/processed_references" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/main.nf b/main.nf index f36c819a1..ccf71dd93 100644 --- a/main.nf +++ b/main.nf @@ -327,14 +327,17 @@ workflow NFCORE_RAREDISEASE { // // Create chromosome bed and intervals for splitting and gathering operations // - ch_scatter_split_intervals = channel.empty() + ch_scatter_split_intervals = channel.empty() + ch_scatter_genome_publish = channel.empty() if (!skip_snv_annotation) { SCATTER_GENOME ( ch_genome_dictionary, ch_genome_fai, - ch_genome_fasta - ).split_intervals - .set { ch_scatter_split_intervals } + ch_genome_fasta, + params.save_reference + ) + ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals + ch_scatter_genome_publish = SCATTER_GENOME.out.publish } RAREDISEASE ( @@ -465,8 +468,9 @@ workflow NFCORE_RAREDISEASE { val_vep_cache_version ) emit: - multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - publish = RAREDISEASE.out.publish // channel: [ val(destination), val(value) ] + multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + publish = RAREDISEASE.out.publish + .mix(ch_scatter_genome_publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/generate_cytosure_files/main.nf b/subworkflows/local/generate_cytosure_files/main.nf index 3c2444b9c..e9a67c6f9 100644 --- a/subworkflows/local/generate_cytosure_files/main.nf +++ b/subworkflows/local/generate_cytosure_files/main.nf @@ -86,4 +86,10 @@ workflow GENERATE_CYTOSURE_FILES { [[:], []], [[:], []], ch_blacklist ) + + ch_publish = VCF2CYTOSURE.out.cgh + .map { meta, value -> ['vcf2cytosure/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index 75f6da3d8..a93d8cfaa 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -9,8 +9,9 @@ workflow SCATTER_GENOME { take: ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + val_save_reference // bool main: @@ -18,7 +19,14 @@ workflow SCATTER_GENOME { GATK4_SPLITINTERVALS(GAWK.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) + ch_publish = channel.empty() + if (val_save_reference) { + ch_publish = GATK4_SPLITINTERVALS.out.split_intervals + .map { meta, value -> ['processed_references/', [meta, value]] } + } + emit: bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index c9e0bdbaf..4845e81c4 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -20,6 +20,7 @@ nextflow_workflow { input[0] = channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() input[1] = channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() input[2] = channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() + input[3] = "processed_references" """ } } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 0e41bad3f..095562f2d 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -72,6 +72,38 @@ "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] ], + "2": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ] + ] + ], "bed": [ [ { @@ -80,6 +112,38 @@ "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], + "publish": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ] + ] + ], "split_intervals": [ [ "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" @@ -144,10 +208,10 @@ ] } ], - "timestamp": "2026-02-09T10:18:23.261854", + "timestamp": "2026-03-17T00:19:06.789641139", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 4388ea983..847f1ac91 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -215,6 +215,7 @@ workflow RAREDISEASE { ch_call_mobile_elements_publish = channel.empty() ch_subsample_publish = channel.empty() ch_annotate_genome_snvs_publish = channel.empty() + ch_generate_cytosure_files_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -790,6 +791,7 @@ workflow RAREDISEASE { ch_sv_annotate.vcf_ann, val_sample_id_map ) + ch_generate_cytosure_files_publish = GENERATE_CYTOSURE_FILES.out.publish } /* @@ -931,7 +933,8 @@ workflow RAREDISEASE { .mix(ch_call_sv_mt_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) - .mix(ch_annotate_genome_snvs_publish) // channel: [ val(destination), val(value) ] + .mix(ch_annotate_genome_snvs_publish) + .mix(ch_generate_cytosure_files_publish) // channel: [ val(destination), val(value) ] } From 1ebf3ace5fce830edacd3693cd051dd0c2789f73 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 09:46:48 +0100 Subject: [PATCH 491/872] Update annotate_mt_snvs and annotate_structural_variants --- conf/modules/annotate_mt_snvs.config | 20 ----- .../annotate_structural_variants.config | 13 --- subworkflows/local/annotate_mt_snvs/main.nf | 10 ++- .../annotate_mt_snvs/tests/main.nf.test.snap | 76 +++++++++++++++- .../annotate_structural_variants/main.nf | 5 ++ .../tests/main.nf.test.snap | 88 ++++++++++++++++++- workflows/raredisease.nf | 6 ++ 7 files changed, 177 insertions(+), 41 deletions(-) diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config index afed4b153..d9b2844a0 100644 --- a/conf/modules/annotate_mt_snvs.config +++ b/conf/modules/annotate_mt_snvs.config @@ -37,21 +37,6 @@ process { '--uniprot' ].join(' ') } ext.prefix = { "${meta.prefix}" } - publishDir = [ - path: { "${params.outdir}/annotate_snv/mitochondria" }, - mode: params.publish_dir_mode, - pattern: "*{vcf.gz,vcf.gz.tbi}", - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*ANNOTATE_MT_SNVS:TABIX_TABIX_VEP_MT' { - publishDir = [ - path: { "${params.outdir}/annotate_snv/mitochondria" }, - mode: params.publish_dir_mode, - pattern: "*{vcf.gz,vcf.gz.tbi}", - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: '.*ANNOTATE_MT_SNVS:VCFANNO_MT' { @@ -71,10 +56,5 @@ process { withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' { ext.args = '--tree phylotree-rsrs@17.1' ext.prefix = { "${meta.prefix}_haplogrep" } - publishDir = [ - path: { "${params.outdir}/annotate_snv/mitochondria" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/annotate_structural_variants.config b/conf/modules/annotate_structural_variants.config index dd737e3bb..b9c98b920 100644 --- a/conf/modules/annotate_structural_variants.config +++ b/conf/modules/annotate_structural_variants.config @@ -47,18 +47,5 @@ process { '--symbol --tsl --uniprot --vcf' ].join(' ') } ext.prefix = { "${meta.id}_svdbquery_vep" } - publishDir = [ - path: { "${params.outdir}/annotate_sv" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: '.*ANNOTATE_STRUCTURAL_VARIANTS:TABIX_VEP' { - publishDir = [ - path: { "${params.outdir}/annotate_sv" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 0205ea285..d30efe460 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -95,9 +95,11 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = TABIX_TABIX_VEP_MT.out.index // Running haplogrep3 + ch_haplog_publish = channel.empty() if (!skip_haplogrep3) { HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in) - ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt + ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt + ch_haplog_publish = HAPLOGREP3_CLASSIFY_MT.out.txt } if (val_homoplasmy_af_threshold<1) { @@ -112,8 +114,14 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } + ch_publish = ENSEMBLVEP_MT.out.vcf + .mix(TABIX_TABIX_VEP_MT.out.index) + .mix(ch_haplog_publish) + .map { meta, value -> ['annotate_snv/mitochondria/', [meta, value]] } + emit: haplog = ch_haplog // channel: [ val(meta), path(txt) ] + publish = ch_publish // channel: [ val(destination), val(value) ] report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] tbi = ch_tbi // channel: [ val(meta), path(tbi) ] vcf_ann = ch_vcf // channel: [ val(meta), path(vcf) ] diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index 1b4910ca6..3a523ae7a 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -13,6 +13,41 @@ ] ], "1": [ + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ [ { "id": "justhusky", @@ -24,7 +59,7 @@ "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ + "3": [ [ { "id": "justhusky", @@ -34,7 +69,7 @@ "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "3": [ + "4": [ [ { "id": "justhusky", @@ -54,6 +89,41 @@ "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "publish": [ + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "report": [ [ { @@ -88,7 +158,7 @@ ] } ], - "timestamp": "2026-03-10T15:10:49.596531529", + "timestamp": "2026-03-17T09:41:21.295801257", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index d38a6c860..b8dc66d0d 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -96,7 +96,12 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) + ch_publish = ENSEMBLVEP_SV.out.vcf + .mix(TABIX_VEP.out.index) + .map { meta, value -> ['annotate_sv/', [meta, value]] } + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap index 038f2516c..f800fde6c 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap @@ -3,6 +3,26 @@ "content": [ { "0": [ + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ [ { "id": "test" @@ -10,7 +30,7 @@ "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "1": [ + "2": [ [ { "id": "test" @@ -18,6 +38,26 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "publish": [ + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -36,7 +76,7 @@ ] } ], - "timestamp": "2026-03-06T05:42:03.69156986", + "timestamp": "2026-03-17T09:42:05.850413808", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -46,6 +86,26 @@ "content": [ { "0": [ + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ [ { "id": "test" @@ -53,7 +113,7 @@ "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "1": [ + "2": [ [ { "id": "test" @@ -61,6 +121,26 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "publish": [ + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "tbi": [ [ { @@ -79,7 +159,7 @@ ] } ], - "timestamp": "2026-03-06T05:42:35.988656634", + "timestamp": "2026-03-17T09:42:34.500199452", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 847f1ac91..91c45962e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -215,6 +215,8 @@ workflow RAREDISEASE { ch_call_mobile_elements_publish = channel.empty() ch_subsample_publish = channel.empty() ch_annotate_genome_snvs_publish = channel.empty() + ch_annotate_mt_snvs_publish = channel.empty() + ch_annotate_sv_publish = channel.empty() ch_generate_cytosure_files_publish = channel.empty() // @@ -501,6 +503,7 @@ workflow RAREDISEASE { val_homoplasmy_af_threshold, val_vep_cache_version ).set { ch_mt_annotate } + ch_annotate_mt_snvs_publish = ch_mt_annotate.publish ch_mt_annotate.vcf_ann .multiMap { meta, vcf -> @@ -592,6 +595,7 @@ workflow RAREDISEASE { val_genome, val_vep_cache_version ).set { ch_sv_annotate } + ch_annotate_sv_publish = ch_sv_annotate.publish ch_sv_annotate.vcf_ann .multiMap { meta, vcf -> @@ -934,6 +938,8 @@ workflow RAREDISEASE { .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_genome_snvs_publish) + .mix(ch_annotate_mt_snvs_publish) + .mix(ch_annotate_sv_publish) .mix(ch_generate_cytosure_files_publish) // channel: [ val(destination), val(value) ] } From 3584dae0e5381b156234cb394a05321e1773ee5a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 10:24:23 +0100 Subject: [PATCH 492/872] Update gens --- conf/modules/gens.config | 5 - subworkflows/local/gens/main.nf | 7 + .../local/gens/tests/main.nf.test.snap | 256 +++++++++++++++++- workflows/raredisease.nf | 5 +- 4 files changed, 263 insertions(+), 10 deletions(-) diff --git a/conf/modules/gens.config b/conf/modules/gens.config index 691cacd74..683565ba8 100644 --- a/conf/modules/gens.config +++ b/conf/modules/gens.config @@ -26,10 +26,5 @@ process { withName: '.*GENS:GENS_GENERATE' { ext.prefix = { "${meta.id}_gens" } - publishDir = [ - path: { "${params.outdir}/gens" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/subworkflows/local/gens/main.nf b/subworkflows/local/gens/main.nf index 9edb7a421..22343f8d1 100644 --- a/subworkflows/local/gens/main.nf +++ b/subworkflows/local/gens/main.nf @@ -59,9 +59,16 @@ workflow GENS { ch_gnomad_pos ) + ch_publish = GENS_GENERATE.out.baf_gz + .mix(GENS_GENERATE.out.baf_tbi) + .mix(GENS_GENERATE.out.cov_gz) + .mix(GENS_GENERATE.out.cov_tbi) + .map { meta, value -> ['gens/', [meta, value]] } + emit: gens_baf_bed_gz = GENS_GENERATE.out.baf_gz // channel: [ val(meta), path(bed.gz) ] gens_baf_bed_tbi = GENS_GENERATE.out.baf_tbi // channel: [ val(meta), path(tbi) ] gens_cov_bed_gz = GENS_GENERATE.out.cov_gz // channel: [ val(meta), path(bed.gz) ] gens_cov_bed_tbi = GENS_GENERATE.out.cov_tbi // channel: [ val(meta), path(tbi) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap index 379966380..a260ae9c4 100644 --- a/subworkflows/local/gens/tests/main.nf.test.snap +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -58,6 +58,68 @@ "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "4": [ + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "gens_baf_bed_gz": [ [ { @@ -113,13 +175,75 @@ }, "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "publish": [ + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-16T11:07:59.889224757", + "timestamp": "2026-03-17T10:23:33.657234536", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } }, "GENS - male sample, stub": { @@ -181,6 +305,68 @@ "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "4": [ + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "gens_baf_bed_gz": [ [ { @@ -236,13 +422,75 @@ }, "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "publish": [ + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "gens/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-16T11:07:05.988643484", + "timestamp": "2026-03-17T10:22:58.267603177", "meta": { "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index c97a27700..7c13cf6ef 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -218,6 +218,7 @@ workflow RAREDISEASE { ch_annotate_mt_snvs_publish = channel.empty() ch_annotate_sv_publish = channel.empty() ch_generate_cytosure_files_publish = channel.empty() + ch_gens_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -816,6 +817,7 @@ workflow RAREDISEASE { ch_gens_pon_female, ch_gens_pon_male ) + ch_gens_publish = GENS.out.publish } /* @@ -941,7 +943,8 @@ workflow RAREDISEASE { .mix(ch_annotate_genome_snvs_publish) .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) - .mix(ch_generate_cytosure_files_publish) // channel: [ val(destination), val(value) ] + .mix(ch_generate_cytosure_files_publish) + .mix(ch_gens_publish) // channel: [ val(destination), val(value) ] } From 39d666d7deb0d183b5c4ef68c6175fff6c9b288f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 10:48:25 +0100 Subject: [PATCH 493/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bee56fdf7..5437f44df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,7 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated svbd module [#781](https://github.com/nf-core/raredisease/pull/781) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#784](https://github.com/nf-core/raredisease/pull/784) - Replace local gens module with nf-core module [#785](https://github.com/nf-core/raredisease/pull/785) -- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#786](https://github.com/nf-core/raredisease/pull/786) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#787](https://github.com/nf-core/raredisease/pull/787) ### `Fixed` From 0bd3ba3d1fe177924167ee7df10f42e5edff72ef Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 11:27:02 +0100 Subject: [PATCH 494/872] Update gens test and snapshot --- subworkflows/local/gens/tests/main.nf.test | 23 +- .../local/gens/tests/main.nf.test.snap | 600 ++++-------------- 2 files changed, 145 insertions(+), 478 deletions(-) diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index f0177721c..8184fd79e 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -44,7 +44,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.gens_baf_bed_gz, + workflow.out.gens_baf_bed_tbi, + workflow.out.gens_cov_bed_gz, + workflow.out.gens_cov_bed_tbi, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() } ) } } @@ -83,7 +92,17 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.gens_baf_bed_gz, + workflow.out.gens_baf_bed_tbi, + workflow.out.gens_cov_bed_gz, + workflow.out.gens_cov_bed_tbi, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() + } ) } } diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap index a260ae9c4..3cd91562a 100644 --- a/subworkflows/local/gens/tests/main.nf.test.snap +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -1,246 +1,70 @@ { "GENS - female sample, stub": { "content": [ - { - "0": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "3": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "gens_baf_bed_gz": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "gens_baf_bed_tbi": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gens_cov_bed_gz": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "gens_cov_bed_tbi": [ - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - } + ], + [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "slowlycivilbuck_gens.baf.bed.gz", + "slowlycivilbuck_gens.baf.bed.gz.tbi", + "slowlycivilbuck_gens.cov.bed.gz", + "slowlycivilbuck_gens.cov.bed.gz.tbi" + ] ], - "timestamp": "2026-03-17T10:23:33.657234536", + "timestamp": "2026-03-17T11:26:00.382738988", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -248,246 +72,70 @@ }, "GENS - male sample, stub": { "content": [ - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "3": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "gens_baf_bed_gz": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "gens_baf_bed_tbi": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gens_cov_bed_gz": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "gens_cov_bed_tbi": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "gens/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.baf.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ], + [ + "earlycasualcaiman_gens.baf.bed.gz", + "earlycasualcaiman_gens.baf.bed.gz.tbi", + "earlycasualcaiman_gens.cov.bed.gz", + "earlycasualcaiman_gens.cov.bed.gz.tbi" + ] ], - "timestamp": "2026-03-17T10:22:58.267603177", + "timestamp": "2026-03-17T11:25:27.677483077", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 409dcb16f0295a95ee72c8ae1d6f7ca1724d1aba Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 11:44:36 +0100 Subject: [PATCH 495/872] Mmigrate remaining subworkflows --- conf/modules/rank_variants.config | 15 ------- conf/modules/raredisease.config | 28 ------------ conf/modules/variant_evaluation.config | 5 --- main.nf | 7 ++- subworkflows/local/rank_variants/main.nf | 11 +++++ subworkflows/local/variant_evaluation/main.nf | 17 ++++++++ workflows/raredisease.nf | 43 ++++++++++++++++++- 7 files changed, 75 insertions(+), 51 deletions(-) diff --git a/conf/modules/rank_variants.config b/conf/modules/rank_variants.config index 878ebe6f9..0c31a1cd8 100644 --- a/conf/modules/rank_variants.config +++ b/conf/modules/rank_variants.config @@ -44,11 +44,6 @@ process { withName: '.*RANK_VARIANTS_SV:BCFTOOLS_SORT' { ext.args = "--output-type z --write-index=tbi" ext.prefix = { "${meta.id}_sv_ranked_${meta.set}" } - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } @@ -86,11 +81,6 @@ process { withName: '.*RANK_VARIANTS_SNV:TABIX_BGZIPTABIX' { ext.args2 = '-p vcf' ext.prefix = { "${meta.id}_snv_ranked_${meta.set}" } - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } @@ -128,11 +118,6 @@ process { withName: '.*RANK_VARIANTS_MT:TABIX_BGZIPTABIX' { ext.args2 = '-p vcf' ext.prefix = { "${meta.id}_mt_ranked_${meta.set}" } - publishDir = [ - path: { "${params.outdir}/rank_and_filter" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index 111949302..349c940a0 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -18,9 +18,6 @@ process { withName: '.*RAREDISEASE:SPRING_DECOMPRESS_.*' { ext.prefix = { "${spring.simpleName}" } - publishDir = [ - enabled: false - ] } } @@ -32,11 +29,6 @@ process { withName: '.*RAREDISEASE:FASTQC' { ext.args = '--quiet --dir ./' - publishDir = [ - path: { "${params.outdir}/fastqc/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } @@ -50,11 +42,6 @@ process { (params.genome == 'GRCh37') ? '--genome 37' : '--genome 38' } ext.prefix = { "${meta.id}_smncopynumbercaller" } - publishDir = [ - path: { "${params.outdir}/smncopynumbercaller" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } @@ -74,11 +61,6 @@ process { process { withName: '.*:PEDDY' { - publishDir = [ - path: { "${params.outdir}/peddy" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } @@ -89,11 +71,6 @@ process { process { withName: '.*RAREDISEASE:CREATE_PEDIGREE_FILE' { - publishDir = [ - path: { "${params.outdir}/pedigree" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] } } @@ -104,10 +81,5 @@ process { process { withName: '.*RAREDISEASE:MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } - publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/conf/modules/variant_evaluation.config b/conf/modules/variant_evaluation.config index 905a1d4d1..f140922a9 100644 --- a/conf/modules/variant_evaluation.config +++ b/conf/modules/variant_evaluation.config @@ -27,11 +27,6 @@ process { withName: '.*VARIANT_EVALUATION:RTGTOOLS_VCFEVAL' { ext.args = { "--sample ${meta.samplename} --output-mode=split" } ext.prefix = { "${meta.samplename}_vcfeval" } - publishDir = [ - path: { "${params.outdir}/rtgvcfeval" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } } diff --git a/main.nf b/main.nf index ccf71dd93..9c2f4c1da 100644 --- a/main.nf +++ b/main.nf @@ -280,7 +280,9 @@ workflow NFCORE_RAREDISEASE { // // Generate pedigree file // - ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped + ch_pedfile = CREATE_PEDIGREE_FILE(ch_samples.toList()).ped + ch_pedfile_publish = CREATE_PEDIGREE_FILE.out.ped + .map { ped -> ['pedigree/', [ped]] } // Tools skip_fastp = parseSkipList(val_skip_tools, 'fastp') @@ -470,7 +472,8 @@ workflow NFCORE_RAREDISEASE { emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html publish = RAREDISEASE.out.publish - .mix(ch_scatter_genome_publish) // channel: [ val(destination), val(value) ] + .mix(ch_scatter_genome_publish) + .mix(ch_pedfile_publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf index 820fdd01e..93b6093b3 100644 --- a/subworkflows/local/rank_variants/main.nf +++ b/subworkflows/local/rank_variants/main.nf @@ -31,12 +31,23 @@ workflow RANK_VARIANTS { GENMOD_COMPOUND(GENMOD_SCORE.out.vcf) + ch_sort_publish = channel.empty() + ch_tabix_publish = channel.empty() + if (process_with_sort) { ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf).vcf // SV file needs to be sorted before indexing + ch_sort_publish = BCFTOOLS_SORT.out.vcf + .mix(BCFTOOLS_SORT.out.tbi) + .map { meta, value -> ['rank_and_filter/', [meta, value]] } } else { ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_index.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs + ch_tabix_publish = TABIX_BGZIPTABIX.out.gz_index + .map { meta, gz, tbi -> ['rank_and_filter/', [meta, gz, tbi]] } } + ch_publish = ch_sort_publish.mix(ch_tabix_publish) + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] vcf = ch_vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/variant_evaluation/main.nf b/subworkflows/local/variant_evaluation/main.nf index 63ce6bfd9..e2df70802 100644 --- a/subworkflows/local/variant_evaluation/main.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -40,4 +40,21 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) + ch_publish = RTGTOOLS_VCFEVAL.out.tp_vcf + .mix(RTGTOOLS_VCFEVAL.out.tp_tbi) + .mix(RTGTOOLS_VCFEVAL.out.fn_vcf) + .mix(RTGTOOLS_VCFEVAL.out.fn_tbi) + .mix(RTGTOOLS_VCFEVAL.out.fp_vcf) + .mix(RTGTOOLS_VCFEVAL.out.fp_tbi) + .mix(RTGTOOLS_VCFEVAL.out.baseline_vcf) + .mix(RTGTOOLS_VCFEVAL.out.baseline_tbi) + .mix(RTGTOOLS_VCFEVAL.out.snp_roc) + .mix(RTGTOOLS_VCFEVAL.out.non_snp_roc) + .mix(RTGTOOLS_VCFEVAL.out.weighted_roc) + .mix(RTGTOOLS_VCFEVAL.out.summary) + .mix(RTGTOOLS_VCFEVAL.out.phasing) + .map { meta, value -> ['rtgvcfeval/', [meta, value]] } + + emit: + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 7c13cf6ef..0f6443be4 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -219,6 +219,14 @@ workflow RAREDISEASE { ch_annotate_sv_publish = channel.empty() ch_generate_cytosure_files_publish = channel.empty() ch_gens_publish = channel.empty() + ch_fastqc_publish = channel.empty() + ch_smncopynumbercaller_publish = channel.empty() + ch_peddy_publish = channel.empty() + ch_multiqc_publish = channel.empty() + ch_rank_snv_publish = channel.empty() + ch_rank_mt_publish = channel.empty() + ch_rank_sv_publish = channel.empty() + ch_variant_evaluation_publish = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -247,6 +255,9 @@ workflow RAREDISEASE { if (!skip_fastqc) { FASTQC (ch_input_fastqs) fastqc_report = FASTQC.out.zip + ch_fastqc_publish = FASTQC.out.html + .mix(FASTQC.out.zip) + .map { meta, value -> ["fastqc/${meta.id}/", [meta, value]] } } /* @@ -479,6 +490,7 @@ workflow RAREDISEASE { ch_ranksnv_nuclear_in, false ) + ch_rank_snv_publish = RANK_VARIANTS_SNV.out.publish } // @@ -550,6 +562,7 @@ workflow RAREDISEASE { ch_ranksnv_mt_in, false ) + ch_rank_mt_publish = RANK_VARIANTS_MT.out.publish } } @@ -642,6 +655,7 @@ workflow RAREDISEASE { ch_ranksnv_sv_in, true ) + ch_rank_sv_publish = RANK_VARIANTS_SV.out.publish } } /* @@ -767,6 +781,9 @@ workflow RAREDISEASE { SMNCOPYNUMBERCALLER ( ch_bams_bais ) + ch_smncopynumbercaller_publish = SMNCOPYNUMBERCALLER.out.smncopynumber + .mix(SMNCOPYNUMBERCALLER.out.run_metrics) + .map { meta, value -> ['smncopynumbercaller/', [meta, value]] } } /* @@ -780,6 +797,17 @@ workflow RAREDISEASE { ch_pedfile.map{ped -> return[[id:"pedigree"], ped]}, [[:],[]] ) + ch_peddy_publish = PEDDY.out.vs_html + .mix(PEDDY.out.html) + .mix(PEDDY.out.ped) + .mix(PEDDY.out.het_check_png) + .mix(PEDDY.out.ped_check_png) + .mix(PEDDY.out.sex_check_png) + .mix(PEDDY.out.het_check_csv) + .mix(PEDDY.out.ped_check_csv) + .mix(PEDDY.out.sex_check_csv) + .mix(PEDDY.out.ped_check_rel_difference_csv) + .map { meta, value -> ['peddy/', [meta, value]] } } /* @@ -832,6 +860,7 @@ workflow RAREDISEASE { ch_sdf, CALL_SNV.out.genome_vcf_tabix ) + ch_variant_evaluation_publish = VARIANT_EVALUATION.out.publish } /* @@ -929,6 +958,10 @@ workflow RAREDISEASE { [], ch_multiqc_samples ) + ch_multiqc_publish = MULTIQC.out.report + .mix(MULTIQC.out.data) + .mix(MULTIQC.out.plots) + .map { value -> ['multiqc/', [value]] } emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] @@ -944,7 +977,15 @@ workflow RAREDISEASE { .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) .mix(ch_generate_cytosure_files_publish) - .mix(ch_gens_publish) // channel: [ val(destination), val(value) ] + .mix(ch_gens_publish) + .mix(ch_fastqc_publish) + .mix(ch_smncopynumbercaller_publish) + .mix(ch_peddy_publish) + .mix(ch_multiqc_publish) + .mix(ch_rank_snv_publish) + .mix(ch_rank_mt_publish) + .mix(ch_rank_sv_publish) + .mix(ch_variant_evaluation_publish) // channel: [ val(destination), val(value) ] } From 9460b5679693c9872f8d7247cda2c615c35fe17c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 11:51:48 +0100 Subject: [PATCH 496/872] Add vep report to publish channel --- subworkflows/local/annotate_structural_variants/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index b8dc66d0d..93dee9517 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -97,6 +97,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) ch_publish = ENSEMBLVEP_SV.out.vcf + .mix(ENSEMBLVEP_SV.out.report) .mix(TABIX_VEP.out.index) .map { meta, value -> ['annotate_sv/', [meta, value]] } From 728e1c9b9b6cf57dfae7ee284cb13b44d22837ba Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 12:00:46 +0100 Subject: [PATCH 497/872] update annotate_sv_variants --- .../annotate_structural_variants/main.nf | 2 +- .../tests/main.nf.test.snap | 40 ++++++++++++++++++- 2 files changed, 39 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index 93dee9517..7aa9c63fa 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -97,7 +97,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { TABIX_VEP (ENSEMBLVEP_SV.out.vcf) ch_publish = ENSEMBLVEP_SV.out.vcf - .mix(ENSEMBLVEP_SV.out.report) + .mix(ENSEMBLVEP_SV.out.report.map{ meta, process, vep, html -> return [meta, html] }) .mix(TABIX_VEP.out.index) .map { meta, value -> ['annotate_sv/', [meta, value]] } diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap index f800fde6c..043a9a3dd 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap @@ -12,6 +12,15 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "annotate_sv/", [ @@ -48,6 +57,15 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "annotate_sv/", [ @@ -76,7 +94,7 @@ ] } ], - "timestamp": "2026-03-17T09:42:05.850413808", + "timestamp": "2026-03-17T11:59:48.286796435", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -95,6 +113,15 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "annotate_sv/", [ @@ -131,6 +158,15 @@ "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "annotate_sv/", [ @@ -159,7 +195,7 @@ ] } ], - "timestamp": "2026-03-17T09:42:34.500199452", + "timestamp": "2026-03-17T12:00:18.702004904", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 7c5ed4faa1cf079d4c3ba2cc7f7a024917e25ee4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 17 Mar 2026 12:02:26 +0100 Subject: [PATCH 498/872] fix bcftools input and test path --- subworkflows/local/annotate_genome_snvs/main.nf | 6 ++++-- .../local/call_structural_variants/tests/main.nf.test | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index db2325c81..a605437d4 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -98,9 +98,11 @@ workflow ANNOTATE_GENOME_SNVS { .combine(ch_vcfanno_extra) .set { ch_vcfanno_in } - VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) + VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources).out.vcf + .join(VCFANNO.out.tbi) + .set { ch_vcfanno_out } - BCFTOOLS_VIEW(VCFANNO.out.tbi, [], [], []) // filter on frequencies + BCFTOOLS_VIEW(ch_vcfanno_out, [], [], []) // filter on frequencies // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 1c91e8691..8ebc85534 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -40,8 +40,8 @@ nextflow_workflow { input[14] = true input[15] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mtreverted.bam.bai', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.chrsizes', checkIfExists: true)]).collect() input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } From ed64d2b91834bde02886447c82b6ea066c97d236 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 17 Mar 2026 12:08:06 +0100 Subject: [PATCH 499/872] fix bcftools input --- subworkflows/local/annotate_genome_snvs/main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index a605437d4..d407351db 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -98,7 +98,9 @@ workflow ANNOTATE_GENOME_SNVS { .combine(ch_vcfanno_extra) .set { ch_vcfanno_in } - VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources).out.vcf + VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) + + VCFANNO.out.vcf .join(VCFANNO.out.tbi) .set { ch_vcfanno_out } From 0f1d170b2b0849d9b8e294bced399eaf8ce950ff Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 13:11:51 +0100 Subject: [PATCH 500/872] Update snapshot and changelog --- CHANGELOG.md | 1 + conf/modules/raredisease.config | 19 ------- .../rank_variants/tests/main.nf.test.snap | 54 ++++++++++++++++++- 3 files changed, 53 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index edb1be6d7..72eab2ab8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Replace local gens module with nf-core module [#785](https://github.com/nf-core/raredisease/pull/785) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#787](https://github.com/nf-core/raredisease/pull/787) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#788](https://github.com/nf-core/raredisease/pull/788) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) ### `Fixed` diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index 349c940a0..b6890afcd 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -55,25 +55,6 @@ process { } } -// -// Peddy options -// - -process { - withName: '.*:PEDDY' { - } -} - -// -// Generate Pedigree File -// - -process { - - withName: '.*RAREDISEASE:CREATE_PEDIGREE_FILE' { - } -} - // // Multiqc options // diff --git a/subworkflows/local/rank_variants/tests/main.nf.test.snap b/subworkflows/local/rank_variants/tests/main.nf.test.snap index 77b6eb7ef..d1cc348be 100644 --- a/subworkflows/local/rank_variants/tests/main.nf.test.snap +++ b/subworkflows/local/rank_variants/tests/main.nf.test.snap @@ -3,6 +3,18 @@ "content": [ { "0": [ + [ + "rank_and_filter/", + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ [ { "id": "justhusky", @@ -11,6 +23,18 @@ "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "publish": [ + [ + "rank_and_filter/", + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], "vcf": [ [ { @@ -22,7 +46,7 @@ ] } ], - "timestamp": "2026-03-04T13:56:59.686533478", + "timestamp": "2026-03-17T13:09:47.357626106", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -32,6 +56,19 @@ "content": [ { "0": [ + [ + "rank_and_filter/", + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ [ { "id": "justhusky", @@ -40,6 +77,19 @@ "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "publish": [ + [ + "rank_and_filter/", + [ + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], "vcf": [ [ { @@ -51,7 +101,7 @@ ] } ], - "timestamp": "2026-03-04T13:57:53.225169802", + "timestamp": "2026-03-17T13:09:21.870979671", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From a954a9d016912e8e89b3d8443c9ab5fd67f67bd8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 13:46:09 +0100 Subject: [PATCH 501/872] Update nextflow.config --- tests/nextflow.config | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 3e0bd54b4..22dff14f7 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -20,13 +20,9 @@ params { aws.client.anonymous = true // fixes S3 access issues on self-hosted runners -env { - // NOTE This is how pipeline users will use Sentieon in real world use - SENTIEON_LICENSE = System.getenv('SENTIEON_LICSRVR_IP') +// NOTE This is how pipeline users will use Sentieon in real world use +env.SENTIEON_LICENSE = env('SENTIEON_LICSRVR_IP') - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how pipeline users will test out Sentieon with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) -} +// NOTE This should only happen in GitHub actions or nf-core MegaTests +env.SENTIEON_AUTH_MECH = env('SENTIEON_AUTH_MECH') +env.SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA From 2b0384c6e4892ab2a4c4171adf542fa6c550019c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 19:12:37 +0100 Subject: [PATCH 502/872] refactor and tiddit fix --- conf/modules/annotate_genome_snvs.config | 4 +-- modules.json | 2 +- modules/nf-core/tiddit/sv/main.nf | 2 +- modules/nf-core/tiddit/sv/meta.yml | 5 +++ modules/nf-core/tiddit/sv/tests/main.nf.test | 18 ++++++---- .../local/annotate_genome_snvs/main.nf | 35 +++++++++---------- .../annotate_genome_snvs/tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 24 ++++++------- subworkflows/local/annotate_mt_snvs/main.nf | 13 ++----- .../local/annotate_mt_snvs/tests/main.nf.test | 3 +- .../annotate_structural_variants/main.nf | 5 +-- subworkflows/local/call_snv/main.nf | 1 + .../local/call_snv/tests/main.nf.test.snap | 28 ++++++++++++--- .../local/call_structural_variants/main.nf | 2 +- subworkflows/local/call_sv_tiddit/main.nf | 3 +- .../local/call_sv_tiddit/tests/main.nf.test | 14 ++++---- tests/default.nf.test.snap | 11 +----- tests/test_bam.nf.test.snap | 13 ++----- tests/test_singleton.nf.test.snap | 13 ++----- workflows/raredisease.nf | 2 +- 20 files changed, 96 insertions(+), 104 deletions(-) diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index bdc33b5f1..5d448dd31 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -69,7 +69,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_VIEW' { ext.prefix = { "${meta.prefix}_filter_${meta.scatterid}" } - ext.args = { '--output-type z --exclude "INFO/GNOMADAF > 0.70 | INFO/GNOMADAF_popmax > 0.70" ' } + ext.args = { '--output-type z --write-index=tbi --exclude "INFO/GNOMADAF > 0.70 | INFO/GNOMADAF_popmax > 0.70" ' } } withName: '.*ANNOTATE_GENOME_SNVS:ENSEMBLVEP_SNV' { @@ -91,7 +91,7 @@ process { } withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT' { - ext.args = { "-Oz" } + ext.args = { "-Oz --write-index=tbi" } ext.prefix = { "${meta.prefix}_vep" } } } diff --git a/modules.json b/modules.json index 568e1cbf5..52b5ec8b0 100644 --- a/modules.json +++ b/modules.json @@ -528,7 +528,7 @@ }, "tiddit/sv": { "branch": "master", - "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", + "git_sha": "7d7b05291926e7bce86096a0ed49499c200924a5", "installed_by": ["modules"] }, "ucsc/wigtobigwig": { diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index c3808ed3d..429695e21 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -9,7 +9,7 @@ process TIDDIT_SV { input: tuple val(meta), path(input), path(input_index) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta), path(fai) tuple val(meta3), path(bwa_index) output: diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index b27987926..78232760c 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -39,6 +39,11 @@ input: description: Input FASTA file pattern: "*.{fasta,fa}" ontologies: [] + - fai: + type: file + description: Input FASTA index file + pattern: "*.{fai}" + ontologies: [] - - meta3: type: map description: | diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test b/modules/nf-core/tiddit/sv/tests/main.nf.test index 090175ee4..3b136b3f5 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test @@ -35,7 +35,8 @@ nextflow_process { ] // fasta input[1] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] // bwa_index input[2] = BWA_INDEX.out.index @@ -66,7 +67,8 @@ nextflow_process { ] // fasta input[1] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] // bwa_index input[2] = [ [], [] ] @@ -93,7 +95,8 @@ nextflow_process { process { """ input[0] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -109,7 +112,8 @@ nextflow_process { ] // fasta input[1] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] // bwa_index input[2] = BWA_INDEX.out.index @@ -139,7 +143,8 @@ nextflow_process { ] // fasta input[1] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] // bwa_index input[2] = [ [], [] ] @@ -169,7 +174,8 @@ nextflow_process { ] // fasta input[1] = [ [id: 'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] // bwa_index input[2] = [ [], [] ] diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 688986459..3f9f7e37f 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -14,9 +14,6 @@ include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../../modules/nf-core include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_BCFTOOLS_CONCAT } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_BCFTOOLS_VIEW } from '../../../modules/nf-core/tabix/tabix/main' include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' include { ANNOTATE_CADD } from '../annotate_cadd' include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' @@ -107,10 +104,9 @@ workflow ANNOTATE_GENOME_SNVS { // Annotating with CADD if (!val_cadd_resources.equals(null)) { - TABIX_BCFTOOLS_VIEW (BCFTOOLS_VIEW.out.vcf) BCFTOOLS_VIEW.out.vcf - .join(TABIX_BCFTOOLS_VIEW.out.index, failOnMismatch:true, failOnDuplicate:true) + .join(BCFTOOLS_VIEW.out.tbi, failOnMismatch:true, failOnDuplicate:true) .set { ch_cadd_in } ANNOTATE_CADD ( @@ -150,12 +146,13 @@ workflow ANNOTATE_GENOME_SNVS { ENSEMBLVEP_SNV.out.vcf .map { meta, vcf -> [meta - meta.subMap('scatterid'), vcf] } - .set { ch_vep_out } + .set { ch_vep_vcf_out } + ENSEMBLVEP_SNV.out.tbi + .map { meta, tbi -> [meta - meta.subMap('scatterid'), tbi] } + .set { ch_vep_tbi_out } - TABIX_VEP (ch_vep_out) - - ch_vep_out - .join(TABIX_VEP.out.index, failOnMismatch:true) + ch_vep_vcf_out + .join(ch_vep_tbi_out, failOnMismatch:true) .groupTuple() .map { meta, vcfs, tbis -> def sortedvcfs = vcfs.sort { vcf -> vcf.baseName } @@ -182,25 +179,25 @@ workflow ANNOTATE_GENOME_SNVS { BCFTOOLS_CONCAT.out.vcf .map { meta, vcf -> [meta - meta.subMap('prefix'), vcf] } - .set { ch_concat_out } + .set { ch_concat_vcf_out } - TABIX_BCFTOOLS_CONCAT (ch_concat_out) + BCFTOOLS_CONCAT.out.tbi + .map { meta, tbi -> [meta - meta.subMap('prefix'), tbi] } + .set { ch_concat_tbi_out } - ch_vep_ann = ch_concat_out - ch_vep_index = TABIX_BCFTOOLS_CONCAT.out.index - ch_vep_ann_index = ch_concat_out.join(TABIX_BCFTOOLS_CONCAT.out.index) + ch_vep_ann_index = ch_concat_vcf_out.join(ch_concat_tbi_out, failOnMismatch:true, failOnDuplicate:true) //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) ch_publish = CHROMOGRAPH_SITES.out.plots .mix(CHROMOGRAPH_REGIONS.out.plots) - .mix(BCFTOOLS_CONCAT.out.vcf) - .mix(TABIX_BCFTOOLS_CONCAT.out.index) + .mix(ch_concat_vcf_out) + .mix(ch_concat_tbi_out) .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } .mix(ANNOTATE_RHOCALLVIZ.out.publish) emit: - tbi = ch_vep_index // channel: [ val(meta), path(tbi) ] - vcf_ann = ch_vep_ann // channel: [ val(meta), path(vcf) ] + tbi = ch_concat_tbi_out // channel: [ val(meta), path(tbi) ] + vcf_ann = ch_concat_vcf_out // channel: [ val(meta), path(vcf) ] publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 81134bdf0..d885c2c63 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[1] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index e030f8a79..a72ddc9ce 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -47,10 +47,9 @@ ], "mother": "", - "father": "", - "prefix": "justhusky_rhocall_filter" + "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -67,7 +66,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -82,7 +81,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -97,7 +96,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -170,10 +169,9 @@ ], "mother": "", - "father": "", - "prefix": "justhusky_rhocall_filter" + "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -190,7 +188,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -205,7 +203,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -220,7 +218,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -314,7 +312,7 @@ ] } ], - "timestamp": "2026-03-16T23:12:33.480389323", + "timestamp": "2026-03-17T17:25:23.200645941", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 0205ea285..12af61d60 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -4,7 +4,6 @@ include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt' -include { TABIX_TABIX as TABIX_TABIX_MT } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../../modules/nf-core/tabix/tabix/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../modules/nf-core/ensemblvep/vep/main' include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../../modules/nf-core/haplogrep3/classify/main' @@ -18,7 +17,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_resources // channel: [mandatory] [ path(annotation) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_fai // channel: [mandatory] [ path(fai) ] - ch_mt_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_mt_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] @@ -34,12 +33,8 @@ workflow ANNOTATE_MT_SNVS { main: ch_haplog = channel.empty() - // Index vcf - TABIX_TABIX_MT(ch_mt_vcf) - ch_mt_vcf_index = ch_mt_vcf.join(TABIX_TABIX_MT.out.index) - // Vcfanno - ch_mt_vcf_index + ch_mt_vcf_tbi .combine(ch_vcfanno_extra) .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } @@ -89,10 +84,8 @@ workflow ANNOTATE_MT_SNVS { ch_vep_extra_files ) - TABIX_TABIX_VEP_MT(ENSEMBLVEP_MT.out.vcf) - ch_vcf = ENSEMBLVEP_MT.out.vcf - ch_tbi = TABIX_TABIX_VEP_MT.out.index + ch_tbi = ENSEMBLVEP_MT.out.tbi // Running haplogrep3 if (!skip_haplogrep3) { diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 82626ffff..6fa7ba1e5 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -20,7 +20,8 @@ nextflow_workflow { input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[4] = channel.of([ [id:'justhusky', case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz.tbi', checkIfExists: true), ]) input[5] = channel.value([[]]) input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index d38a6c860..755d87199 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -7,7 +7,6 @@ include { SVDB_QUERY as SVDB_QUERY_BEDPE } from '../../../modules/nf-core/svdb/ include { PICARD_SORTVCF } from '../../../modules/nf-core/picard/sortvcf/main' include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_TABIX as TABIX_VEP } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_STRUCTURAL_VARIANTS { @@ -94,9 +93,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_vep_extra_files ) - TABIX_VEP (ENSEMBLVEP_SV.out.vcf) - emit: - tbi = TABIX_VEP.out.index // channel: [ val(meta), path(tbi) ] + tbi = ENSEMBLVEP_SV.out.tbi // channel: [ val(meta), path(tbi) ] vcf_ann = ENSEMBLVEP_SV.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 266ec9881..543e259a1 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -166,5 +166,6 @@ workflow CALL_SNV { genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] + mt_vcf_tbi = ch_mt_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi)] publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index da2926ecf..03e1d2ca2 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -103,13 +103,22 @@ ] ], "7": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ [ "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -118,7 +127,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -217,6 +226,15 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "mt_vcf_tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], "publish": [ [ "call_snv/genome/", @@ -224,7 +242,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -233,7 +251,7 @@ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -257,7 +275,7 @@ ] } ], - "timestamp": "2026-03-13T15:48:00.031080535", + "timestamp": "2026-03-17T17:37:11.970412775", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index c6588e55e..f9ef01c2a 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -40,7 +40,7 @@ workflow CALL_STRUCTURAL_VARIANTS { } if (val_analysis_type.equals("wgs")) { - CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fasta, ch_bwa_index, ch_case_info) + CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } .set { tiddit_vcf } diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index ac3d457fd..0d7d512d0 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -10,12 +10,13 @@ include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_TIDDIT } from '../../../modules/nf-core workflow CALL_SV_TIDDIT { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] ch_case_info // channel: [mandatory] [ val(case_info) ] main: - TIDDIT_SV ( ch_bam_bai, ch_genome_fasta, ch_bwa_index ) + TIDDIT_SV ( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai), ch_bwa_index ) INDEX_TIDDIT (TIDDIT_SV.out.vcf) BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_index, [], [], []).vcf diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index 6d4bc7f3a..7059a1be7 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -34,9 +34,10 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] ) - input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[2] = BWA_INDEX.out.index.collect() - input[3] = channel.of([id:'justhusky']) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = BWA_INDEX.out.index.collect() + input[4] = channel.of([id:'justhusky']) """ } } @@ -79,9 +80,10 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/slowlycivilbuck_sorted_md.bam.bai', checkIfExists: true)] ) - input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[2] = BWA_INDEX.out.index.collect() - input[3] = channel.of([id:'justhusky']) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[3] = BWA_INDEX.out.index.collect() + input[4] = channel.of([id:'justhusky']) """ } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ddbbe0fb6..dcae17c82 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -408,9 +408,6 @@ "TABIX_ANNOTATE": { "tabix": 1.21 }, - "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.21 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "bgzip": 1.21, "tabix": 1.21 @@ -446,12 +443,6 @@ "TABIX_TABIX_MT": { "tabix": 1.21 }, - "TABIX_TABIX_VEP_MT": { - "tabix": 1.21 - }, - "TABIX_VEP": { - "tabix": 1.21 - }, "TIDDIT_COV": { "tiddit": "3.9.4" }, @@ -1100,7 +1091,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-16T18:11:52.56937148", + "timestamp": "2026-03-17T16:52:17.64647915", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9dc8f8ef8..9d91e0519 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 785, + 773, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -378,9 +378,6 @@ "TABIX_ANNOTATE": { "tabix": 1.21 }, - "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.21 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "bgzip": 1.21, "tabix": 1.21 @@ -416,12 +413,6 @@ "TABIX_TABIX_MT": { "tabix": 1.21 }, - "TABIX_TABIX_VEP_MT": { - "tabix": 1.21 - }, - "TABIX_VEP": { - "tabix": 1.21 - }, "TIDDIT_COV": { "tiddit": "3.9.4" }, @@ -1029,7 +1020,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-16T18:18:03.478560166", + "timestamp": "2026-03-17T16:58:22.361988613", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e597eca33..c86d7ea91 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 359, + 353, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -397,9 +397,6 @@ "TABIX_ANNOTATE": { "tabix": 1.21 }, - "TABIX_BCFTOOLS_CONCAT": { - "tabix": 1.21 - }, "TABIX_BGZIPINDEX_PADDED_BED": { "bgzip": 1.21, "tabix": 1.21 @@ -435,12 +432,6 @@ "TABIX_TABIX_MT": { "tabix": 1.21 }, - "TABIX_TABIX_VEP_MT": { - "tabix": 1.21 - }, - "TABIX_VEP": { - "tabix": 1.21 - }, "TIDDIT_COV": { "tiddit": "3.9.4" }, @@ -719,7 +710,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-16T18:21:47.347535507", + "timestamp": "2026-03-17T17:02:07.664289531", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2cd462457..c4df3e7bd 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -488,7 +488,7 @@ workflow RAREDISEASE { ch_cadd_resources, ch_genome_fasta, ch_genome_fai, - CALL_SNV.out.mt_vcf, + CALL_SNV.out.mt_vcf_tbi, ch_vcfanno_extra, ch_vcfanno_lua, ch_vcfanno_resources, From e6732c90e794efa06dbe74be2d37bf8501e9549c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 19:28:57 +0100 Subject: [PATCH 503/872] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 72eab2ab8..ec02ff25b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#787](https://github.com/nf-core/raredisease/pull/787) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#788](https://github.com/nf-core/raredisease/pull/788) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) +- Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) ### `Fixed` From 600da332c621168734b950801437d851b842ca1d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 19:36:57 +0100 Subject: [PATCH 504/872] Update main.nf --- subworkflows/local/annotate_mt_snvs/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 1d8496540..82972aa71 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -108,7 +108,7 @@ workflow ANNOTATE_MT_SNVS { } ch_publish = ENSEMBLVEP_MT.out.vcf - .mix(TABIX_TABIX_VEP_MT.out.index) + .mix(ENSEMBLVEP_MT.out.tbi) .mix(ch_haplog_publish) .map { meta, value -> ['annotate_snv/mitochondria/', [meta, value]] } From 4a97deeac0d2f0ceb35a06551cf3d49c6da17d4d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 21:19:35 +0100 Subject: [PATCH 505/872] Update snapshots --- .../local/annotate_mt_snvs/tests/main.nf.test | 11 +- .../annotate_mt_snvs/tests/main.nf.test.snap | 218 +++++----- .../local/call_snv/tests/main.nf.test | 11 +- .../local/call_snv/tests/main.nf.test.snap | 386 ++++++++++-------- .../call_snv_deepvariant/tests/main.nf.test | 11 +- .../tests/main.nf.test.snap | 190 +++++---- 6 files changed, 481 insertions(+), 346 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 6fa7ba1e5..8d9331dff 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -41,7 +41,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index 3a523ae7a..d743c345b 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -1,20 +1,10 @@ { "ANNOTATE_MT_SNVS - GRCh37, stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", @@ -23,20 +13,64 @@ }, "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "1", + [ + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + [ + "2", [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "3", [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", @@ -47,118 +81,114 @@ ] ] ], - "2": [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", - "ensemblvep", - "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ + [ + "4", [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ], - "4": [ + [ + "haplog", [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], - "haplog": [ + [ + "publish", [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/mitochondria/", + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ], - "publish": [ + [ + "report", [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "tbi", [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "vcf_ann", [ - "annotate_snv/mitochondria/", [ { "id": "justhusky", "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] - ], - "report": [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", - "ensemblvep", - "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tbi": [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf_ann": [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] ] - } + ] ], - "timestamp": "2026-03-17T09:41:21.295801257", + "timestamp": "2026-03-17T21:00:26.870834221", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 0d9fefce5..e0441ce9b 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -126,7 +126,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 03e1d2ca2..18448fdee 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -24,123 +24,86 @@ }, "CALL_SNV - deepvariant wgs, stub": { "content": [ - { - "0": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" - ] - ], - "2": [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "4": [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ + [ + [ + "0", [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] ] ], - "7": [ + [ + "1", [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] ] ], - "8": [ + [ + "2", [ - "call_snv/genome/", [ { "id": "justhusky" }, "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "3", [ - "call_snv/genome/", [ { "id": "justhusky" }, "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], + ] + ], + [ + "4", [ - "call_snv/mitochondria/", [ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "5", [ - "call_snv/mitochondria/", [ { "id": "justhusky" @@ -149,133 +112,224 @@ ] ] ], - "genome_gtabix": [ + [ + "6", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" - ] - ], - "genome_gvcf": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ], - "genome_tabix": [ + [ + "7", [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], - "genome_vcf": [ + [ + "8", [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ], - "genome_vcf_tabix": [ + [ + "genome_gtabix", [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] ] ], - "mt_tabix": [ + [ + "genome_gvcf", [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] ] ], - "mt_vcf": [ + [ + "genome_tabix", [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], - "mt_vcf_tbi": [ + [ + "genome_vcf", [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ], - "publish": [ + [ + "genome_vcf_tabix", [ - "call_snv/genome/", [ { "id": "justhusky" }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "mt_tabix", [ - "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "mt_vcf", [ - "call_snv/mitochondria/", [ { "id": "justhusky" }, "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], + ] + ], + [ + "mt_vcf_tbi", [ - "call_snv/mitochondria/", [ { "id": "justhusky" }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] + ], + [ + "publish", + [ + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_snv/genome/", + [ + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "call_snv/mitochondria/", + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] ] - } + ] ], - "timestamp": "2026-03-17T17:37:11.970412775", + "timestamp": "2026-03-17T21:09:07.488338837", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 74f3c814a..9400b109f 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -72,7 +72,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index ded5b9a08..f0200a39c 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -1,114 +1,138 @@ { "CALL_SNV_DEEPVARIANT - wgs, stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] ] ], - "1": [ + [ + "1", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] ] ], - "2": [ + [ + "2", [ - { - "id": "justhusky" - }, - "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], - "3": [ + [ + "3", [ - { - "id": "justhusky" - }, - "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ], - "gvcf": [ + [ + "gvcf", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] ] ], - "gvcf_tabix": [ + [ + "gvcf_tabix", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" + ] ] ], - "tabix": [ + [ + "tabix", [ - { - "id": "justhusky" - }, - "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], - "vcf": [ + [ + "vcf", [ - { - "id": "justhusky" - }, - "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "justhusky" + }, + "justhusky_split_rmdup_info.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ] - } + ] ], - "timestamp": "2026-03-04T21:10:26.381980616", + "timestamp": "2026-03-17T21:18:23.06423637", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From d4db45e3d8553a05a70069682e2d44e896e0cbf5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 21:35:11 +0100 Subject: [PATCH 506/872] Update snapshot --- .../local/annotate_mt_snvs/tests/main.nf.test | 2 +- .../local/annotate_mt_snvs/tests/main.nf.test.snap | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 8d9331dff..a3edaccf6 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[1] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } input[2] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[4] = channel.of([ diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index d743c345b..e9250771b 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -37,7 +37,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -48,7 +48,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ] @@ -118,7 +118,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -129,7 +129,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -140,7 +140,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ] @@ -188,7 +188,7 @@ ] ] ], - "timestamp": "2026-03-17T21:00:26.870834221", + "timestamp": "2026-03-17T21:33:10.709529628", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 51460f423261f9d8a78690269ac73a7051da68e0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 22:00:26 +0100 Subject: [PATCH 507/872] update snapshots --- .../annotate_genome_snvs/tests/main.nf.test | 11 +- .../tests/main.nf.test.snap | 492 +++++++++--------- .../tests/main.nf.test | 22 +- .../tests/main.nf.test.snap | 268 +++++----- .../local/call_sv_MT/tests/main.nf.test | 11 +- .../local/call_sv_MT/tests/main.nf.test.snap | 276 +++++----- 6 files changed, 597 insertions(+), 483 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index d885c2c63..33e8e50a1 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -43,7 +43,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index a72ddc9ce..8282d96de 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -1,42 +1,10 @@ { "ANNOTATE_GENOME_SNVS - GRCh37, stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - { - "id": "justhusky", - "probands": [ - "earlycasualcaiman" - ], - "upd_children": [ - - ], - "mother": "", - "father": "" - }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "justhusky", - "probands": [ - "earlycasualcaiman" - ], - "upd_children": [ - - ], - "mother": "", - "father": "" - }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "2": [ - [ - "annotate_snv/genome/", [ { "id": "justhusky", @@ -51,9 +19,11 @@ }, "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "1", [ - "annotate_snv/genome/", [ { "id": "justhusky", @@ -68,97 +38,261 @@ }, "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], + ] + ], + [ + "2", [ - "annotate_snv/genome/", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "annotate_snv/genome/", + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "annotate_snv/genome/", + "annotate_snv/genome/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, + "annotate_snv/genome/earlycasualcaiman_rhocallviz/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", [ - "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", - 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"justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ] ], - "publish": [ + [ + "tbi", [ - "annotate_snv/genome/", [ { "id": "justhusky", @@ -173,9 +307,11 @@ }, "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "vcf_ann", [ - "annotate_snv/genome/", [ { "id": "justhusky", @@ -190,129 +326,11 @@ }, "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], - [ - "annotate_snv/genome/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - 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[ - [ - { - "id": "justhusky", - "probands": [ - "earlycasualcaiman" - ], - "upd_children": [ - - ], - "mother": "", - "father": "" - }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf_ann": [ - [ - { - "id": "justhusky", - "probands": [ - "earlycasualcaiman" - ], - "upd_children": [ - - ], - "mother": "", - "father": "" - }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] - } + ] ], - "timestamp": "2026-03-17T17:25:23.200645941", + "timestamp": "2026-03-17T21:53:44.635464033", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test b/subworkflows/local/annotate_structural_variants/tests/main.nf.test index d51227ffc..f5c55436c 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test @@ -39,7 +39,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } @@ -78,7 +87,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap index 043a9a3dd..83f90b36f 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap @@ -1,28 +1,42 @@ { "ANNOTATE_STRUCTURAL_VARIANTS - no SVDB queries, stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - "annotate_sv/", [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "annotate_sv/", + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ - { - "id": "test" - }, - "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ], + ] + ], + [ + "1", [ - "annotate_sv/", [ { "id": "test" @@ -31,43 +45,52 @@ ] ] ], - "1": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "publish": [ + [ + "2", [ - "annotate_sv/", [ { "id": "test" }, "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], + ] + ], + [ + "publish", [ - "annotate_sv/", [ - { - "id": "test" - }, - "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ], + ] + ], + [ + "tbi", [ - "annotate_sv/", [ { "id": "test" @@ -76,25 +99,20 @@ ] ] ], - "tbi": [ + [ + "vcf_ann", [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf_ann": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ] - } + ] ], - "timestamp": "2026-03-17T11:59:48.286796435", + "timestamp": "2026-03-17T21:58:02.743192536", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -102,28 +120,42 @@ }, "ANNOTATE_STRUCTURAL_VARIANTS - with SVDB_QUERY_DB, stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - "annotate_sv/", [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "annotate_sv/", + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ - { - "id": "test" - }, - "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ], + ] + ], + [ + "1", [ - "annotate_sv/", [ { "id": "test" @@ -132,43 +164,52 @@ ] ] ], - "1": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "publish": [ + [ + "2", [ - "annotate_sv/", [ { "id": "test" }, "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] - ], + ] + ], + [ + "publish", [ - "annotate_sv/", [ - { - "id": "test" - }, - "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_sv/", + [ + { + "id": "test" + }, + "test_svdbquery_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ], + ] + ], + [ + "tbi", [ - "annotate_sv/", [ { "id": "test" @@ -177,25 +218,20 @@ ] ] ], - "tbi": [ + [ + "vcf_ann", [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "vcf_ann": [ - [ - { - "id": "test" - }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + [ + { + "id": "test" + }, + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ] - } + ] ], - "timestamp": "2026-03-17T12:00:18.702004904", + "timestamp": "2026-03-17T21:58:31.731044029", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index feb8e8f0e..7098599df 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -59,7 +59,16 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { a, b -> + def a_file = a instanceof List ? a[-1].toString() : a.toString() + def b_file = b instanceof List ? b[-1].toString() : b.toString() + a_file <=> b_file + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } ) } } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index dc0f6c7af..92678b80e 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,64 +1,10 @@ { "CALL_SV_MT - stub": { "content": [ - { - "0": [ + [ + [ + "0", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -73,11 +19,13 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "1", [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -92,11 +40,13 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "2", [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -111,67 +61,75 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], - "mitosalt_breakpoint": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "mitosalt_cluster": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "mt_del_result": [ + [ + "3", [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ], - "publish": [ + [ + "mitosalt_breakpoint", [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -186,11 +144,13 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "mitosalt_cluster", [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -205,11 +165,13 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], + ] + ], + [ + "mt_del_result", [ - "call_sv/mitochondria/", [ { "id": "earlycasualcaiman", @@ -224,13 +186,75 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/mitochondria/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ] ] - } + ] ], - "timestamp": "2026-03-13T09:44:41.052362674", + "timestamp": "2026-03-17T21:45:09.657781226", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 5f2b40981172ded0150d2cb4385922972485c960 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 17 Mar 2026 23:51:49 +0100 Subject: [PATCH 508/872] Update test and snapshots --- .../annotate_genome_snvs/tests/main.nf.test | 15 ++- .../tests/main.nf.test.snap | 122 +++++++++--------- .../local/annotate_mt_snvs/tests/main.nf.test | 10 +- .../annotate_mt_snvs/tests/main.nf.test.snap | 10 +- .../tests/main.nf.test | 20 +-- .../tests/main.nf.test.snap | 20 +-- .../local/call_snv/tests/main.nf.test | 10 +- .../local/call_snv/tests/main.nf.test.snap | 36 +++--- .../call_snv_deepvariant/tests/main.nf.test | 10 +- .../tests/main.nf.test.snap | 4 +- .../local/call_sv_MT/tests/main.nf.test | 10 +- .../local/call_sv_MT/tests/main.nf.test.snap | 2 +- 12 files changed, 143 insertions(+), 126 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 33e8e50a1..a3119827a 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -45,13 +45,18 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + // Unwrap nested lists to get the filename + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + // Extract filename: strip :md5, suffix then take basename only + // (sortKey may be a raw Path with an absolute work-dir prefix) + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + }.sort { it[0] } ).match() } ) } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index 8282d96de..a5435526a 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -70,7 +70,33 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], [ @@ -100,33 +126,7 @@ "maternal": 0, "case_id": "justhusky" }, - [ - "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -143,7 +143,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -160,7 +160,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -195,7 +195,33 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], [ @@ -225,33 +251,7 @@ "maternal": 0, "case_id": "justhusky" }, - [ - "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -268,7 +268,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -285,7 +285,7 @@ "mother": "", "father": "" }, - "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -330,7 +330,7 @@ ] ] ], - "timestamp": "2026-03-17T21:53:44.635464033", + "timestamp": "2026-03-17T22:35:10.37613529", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index a3edaccf6..8bf721bf9 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -43,10 +43,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index e9250771b..ad603f11d 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -26,7 +26,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -48,7 +48,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -118,7 +118,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -140,7 +140,7 @@ "case_id": "justhusky", "prefix": "vcfanno_gnomad_mt_vcfanno_vep" }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -188,7 +188,7 @@ ] ] ], - "timestamp": "2026-03-17T21:33:10.709529628", + "timestamp": "2026-03-17T22:54:47.201373396", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test b/subworkflows/local/annotate_structural_variants/tests/main.nf.test index f5c55436c..190b2f6cb 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test @@ -41,10 +41,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name @@ -89,10 +91,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap index 83f90b36f..3915529a0 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test.snap @@ -11,7 +11,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -20,7 +20,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -65,7 +65,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -74,7 +74,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -112,7 +112,7 @@ ] ] ], - "timestamp": "2026-03-17T21:58:02.743192536", + "timestamp": "2026-03-17T22:56:56.445250387", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -130,7 +130,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -139,7 +139,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -184,7 +184,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -193,7 +193,7 @@ { "id": "test" }, - "test_svdbquery_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test_svdbquery_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -231,7 +231,7 @@ ] ] ], - "timestamp": "2026-03-17T21:58:31.731044029", + "timestamp": "2026-03-17T22:57:23.293047427", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index e0441ce9b..279c35119 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -128,10 +128,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 18448fdee..ebe790f53 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -16,7 +16,7 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-13T15:46:57.105465403", + "timestamp": "2026-03-17T23:03:58.765265498", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -139,39 +139,39 @@ "8", [ [ - "call_snv/genome/", + "call_snv/mitochondria/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ - "call_snv/genome/", + "call_snv/mitochondria/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_snv/mitochondria/", + "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ - "call_snv/mitochondria/", + "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] @@ -290,46 +290,46 @@ "publish", [ [ - "call_snv/genome/", + "call_snv/mitochondria/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ - "call_snv/genome/", + "call_snv/mitochondria/", [ { "id": "justhusky" }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_snv/mitochondria/", + "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ - "call_snv/mitochondria/", + "call_snv/genome/", [ { "id": "justhusky" }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ] ] ] ], - "timestamp": "2026-03-17T21:09:07.488338837", + "timestamp": "2026-03-17T23:05:05.226361531", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 9400b109f..64bc5a53b 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -74,10 +74,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index f0200a39c..e7c2ff4fd 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -132,7 +132,7 @@ ] ] ], - "timestamp": "2026-03-17T21:18:23.06423637", + "timestamp": "2026-03-17T23:21:43.293315837", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -148,7 +148,7 @@ "earlycasualcaiman_deepvar.g.vcf.gz" ] ], - "timestamp": "2026-03-01T18:14:03.103819136", + "timestamp": "2026-03-17T23:21:13.603834111", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 7098599df..002a4ccdc 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -61,10 +61,12 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { a, b -> - def a_file = a instanceof List ? a[-1].toString() : a.toString() - def b_file = b instanceof List ? b[-1].toString() : b.toString() - a_file <=> b_file + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] } [name, sorted_channel] }.sort { it[0] } // Sort by channel name diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 92678b80e..8efaafae7 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -254,7 +254,7 @@ ] ] ], - "timestamp": "2026-03-17T21:45:09.657781226", + "timestamp": "2026-03-17T23:49:47.786799067", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 37a053ff516754a37bcecc823078bd4af20b2619 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 18 Mar 2026 08:50:10 +0100 Subject: [PATCH 509/872] update sv merge logic --- main.nf | 2 +- subworkflows/local/call_structural_variants/main.nf | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 893e0e9df..0facf585c 100644 --- a/main.nf +++ b/main.nf @@ -320,7 +320,7 @@ workflow NFCORE_RAREDISEASE { } } else { if (val_analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator", "mitosalt"]) } else if (val_run_mt_for_wes) { ch_svcaller_priority = channel.value(["manta", "gcnvcaller", "mitosalt"]) } else { diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 21008b478..e8d27899e 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -136,7 +136,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .set { mitosalt_vcf } } - //merge if (skip_germlinecnvcaller) { if (val_analysis_type.equals("wgs")) { @@ -167,6 +166,9 @@ workflow CALL_STRUCTURAL_VARIANTS { } if (!val_analysis_type.equals("mito")) { + ch_case_info.view() + ch_svcaller_priority.view() + vcf_list.view() ch_case_info .combine(vcf_list) .set { merge_input_vcfs } From c9ebe12dd99b6dcdb70e56b6f998adf591a29cc8 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 18 Mar 2026 11:52:12 +0100 Subject: [PATCH 510/872] replace local saltshaker with nf-core --- modules.json | 15 ++ .../saltshaker/call/environment.yml} | 2 +- .../saltshaker/call/main.nf | 19 +- modules/nf-core/saltshaker/call/meta.yml | 99 +++++++++++ .../saltshaker/call/tests/main.nf.test | 94 ++++++++++ .../saltshaker/call/tests/main.nf.test.snap | 54 ++++++ .../saltshaker/call/tests/nextflow.config | 5 + .../saltshaker/classify/environment.yml} | 2 +- .../saltshaker/classify/main.nf | 39 +++-- modules/nf-core/saltshaker/classify/meta.yml | 106 +++++++++++ .../saltshaker/classify/tests/main.nf.test | 164 ++++++++++++++++++ .../classify/tests/main.nf.test.snap | 160 +++++++++++++++++ .../saltshaker/classify/tests/nextflow.config | 5 + .../saltshaker/plot/environment.yml} | 2 +- .../saltshaker/plot/main.nf | 13 +- modules/nf-core/saltshaker/plot/meta.yml | 67 +++++++ .../saltshaker/plot/tests/main.nf.test | 108 ++++++++++++ .../saltshaker/plot/tests/main.nf.test.snap | 54 ++++++ .../saltshaker/plot/tests/nextflow.config | 5 + subworkflows/local/call_sv_MT/main.nf | 16 +- 20 files changed, 989 insertions(+), 40 deletions(-) rename modules/{local/saltshaker/call/environment.yaml => nf-core/saltshaker/call/environment.yml} (84%) rename modules/{local => nf-core}/saltshaker/call/main.nf (85%) create mode 100644 modules/nf-core/saltshaker/call/meta.yml create mode 100644 modules/nf-core/saltshaker/call/tests/main.nf.test create mode 100644 modules/nf-core/saltshaker/call/tests/main.nf.test.snap create mode 100644 modules/nf-core/saltshaker/call/tests/nextflow.config rename modules/{local/saltshaker/plot/environment.yaml => nf-core/saltshaker/classify/environment.yml} (84%) rename modules/{local => nf-core}/saltshaker/classify/main.nf (64%) create mode 100644 modules/nf-core/saltshaker/classify/meta.yml create mode 100644 modules/nf-core/saltshaker/classify/tests/main.nf.test create mode 100644 modules/nf-core/saltshaker/classify/tests/main.nf.test.snap create mode 100644 modules/nf-core/saltshaker/classify/tests/nextflow.config rename modules/{local/saltshaker/classify/environment.yaml => nf-core/saltshaker/plot/environment.yml} (84%) rename modules/{local => nf-core}/saltshaker/plot/main.nf (84%) create mode 100644 modules/nf-core/saltshaker/plot/meta.yml create mode 100644 modules/nf-core/saltshaker/plot/tests/main.nf.test create mode 100644 modules/nf-core/saltshaker/plot/tests/main.nf.test.snap create mode 100644 modules/nf-core/saltshaker/plot/tests/nextflow.config diff --git a/modules.json b/modules.json index b20d83981..945e77402 100644 --- a/modules.json +++ b/modules.json @@ -391,6 +391,21 @@ "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", "installed_by": ["modules"] }, + "saltshaker/call": { + "branch": "master", + "git_sha": "9d051963759dda1a424374e23f4f22aaa2b0bd60", + "installed_by": ["modules"] + }, + "saltshaker/classify": { + "branch": "master", + "git_sha": "659c65b93278533f1a29c4d4235851b4f29242da", + "installed_by": ["modules"] + }, + "saltshaker/plot": { + "branch": "master", + "git_sha": "95fc5183fd3a798ea4ff0978bc10c526e87a49cc", + "installed_by": ["modules"] + }, "sambamba/depth": { "branch": "master", "git_sha": "ca6da11b05740de461b1e2714037345c0f856201", diff --git a/modules/local/saltshaker/call/environment.yaml b/modules/nf-core/saltshaker/call/environment.yml similarity index 84% rename from modules/local/saltshaker/call/environment.yaml rename to modules/nf-core/saltshaker/call/environment.yml index 57b633f58..f76c4bf5a 100644 --- a/modules/local/saltshaker/call/environment.yaml +++ b/modules/nf-core/saltshaker/call/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - pip + - pip==26.0.1 - pip: - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/call/main.nf b/modules/nf-core/saltshaker/call/main.nf similarity index 85% rename from modules/local/saltshaker/call/main.nf rename to modules/nf-core/saltshaker/call/main.nf index c3b8c8b09..7565ce603 100644 --- a/modules/local/saltshaker/call/main.nf +++ b/modules/nf-core/saltshaker/call/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_CALL { tag "$meta.id" - label "process_single" + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -8,9 +8,8 @@ process SALTSHAKER_CALL { 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" input: - tuple val(meta), path(breakpoint) - tuple val(meta2), path(cluster) - tuple val(meta3), path(mtfasta) + tuple val(meta), path(breakpoint), path(cluster) + tuple val(meta2), path(mtfasta) val flank val heteroplasmy_limit val mito_length @@ -23,9 +22,13 @@ process SALTSHAKER_CALL { tuple val(meta), path("*_call_metadata.tsv"), emit: call tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + when: + task.ext.when == null || task.ext.when + script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + """ saltshaker call \\ --prefix $prefix \\ @@ -41,15 +44,15 @@ process SALTSHAKER_CALL { --ori-l-start $light_strand_origin_start \\ --ori-l-end $light_strand_origin_end \\ $args - """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.saltshaker_call_metadata.tsv + echo $args + touch ${prefix}.saltshaker_call_metadata.tsv """ - } diff --git a/modules/nf-core/saltshaker/call/meta.yml b/modules/nf-core/saltshaker/call/meta.yml new file mode 100644 index 000000000..51be6c452 --- /dev/null +++ b/modules/nf-core/saltshaker/call/meta.yml @@ -0,0 +1,99 @@ +name: "saltshaker_call" +description: mtDNA deletion and duplication calling downstream of mitosalt +keywords: + - saltshaker + - mitosalt + - mtDNA + - structural-variant calling +tools: + - "saltshaker": + description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." + homepage: "https://github.com/aksenia/saltshaker" + documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - breakpoint: + type: file + description: breakpoint file from mitosalt + pattern: "*.{breakpoint}" + ontologies: [] + - cluster: + type: file + description: cluster file from mitosalt + pattern: "*.{cluster}" + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - mtfasta: + type: file + description: Reference mitochondrial genome in FASTA format + pattern: "*.{fasta,fa}" + ontologies: [] + - flank: + type: integer + description: Basepairs flanking a deletion + - heteroplasmy_limit: + type: float + description: Minimum heteroplasmy level to report a deletion/duplication + - mito_length: + type: integer + description: Length of the mitochondrial genome + - heavy_strand_origin_start: + type: integer + description: Start position of the heavy strand origin of replication + - heavy_strand_origin_end: + type: integer + description: End position of the heavy strand origin of replication + - light_strand_origin_start: + type: integer + description: Start position of the light strand origin of replication + - light_strand_origin_end: + type: integer + description: End position of the light strand origin of replication + +output: + call: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_call_metadata.tsv": + type: file + description: tsv with variant call metadata to be used in saltshaker_classify + pattern: "*_call_metadata.tsv" + ontologies: [] + versions_saltshaker: + - - "${task.process}": + type: string + description: The name of the process + - "saltshaker": + type: string + description: The name of the tool + - "1.0.0": + type: string + description: Hardcoded version of saltshaker used in the module + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - saltshaker: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: Hardcoded version of saltshaker used in the module +authors: + - "@ieduba" +maintainers: + - "@ieduba" diff --git a/modules/nf-core/saltshaker/call/tests/main.nf.test b/modules/nf-core/saltshaker/call/tests/main.nf.test new file mode 100644 index 000000000..8bb37c3b9 --- /dev/null +++ b/modules/nf-core/saltshaker/call/tests/main.nf.test @@ -0,0 +1,94 @@ +nextflow_process { + + name "Test Process SALTSHAKER_CALL" + script "../main.nf" + process "SALTSHAKER_CALL" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "saltshaker" + tag "saltshaker/call" + + test("call - tsv") { + + when { + process { + """ + + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.breakpoint', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.cluster', checkIfExists: true), + ] + + input[1] = [ + [ id:'hg38' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/human_mt_rCRS.fasta', checkIfExists: true), + ] + + input[2] = 15 + input[3] = 0.01 + input[4] = 16569 + input[5] = 16081 + input[6] = 407 + input[7] = 5730 + input[8] = 5763 + + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out) + ).match() } + ) + } + + } + + test("call - tsv - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.breakpoint', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.cluster', checkIfExists: true), + ] + + input[1] = [ + [ id:'hg38' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/human_mt_rCRS.fasta', checkIfExists: true), + ] + + input[2] = 15 + input[3] = 0.01 + input[4] = 16569 + input[5] = 16081 + input[6] = 407 + input[7] = 5730 + input[8] = 5763 + + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out) + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/saltshaker/call/tests/main.nf.test.snap b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap new file mode 100644 index 000000000..d377c6626 --- /dev/null +++ b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap @@ -0,0 +1,54 @@ +{ + "call - tsv": { + "content": [ + { + "call": [ + [ + { + "id": "test" + }, + "test.saltshaker_call_metadata.tsv:md5,f0e21ea8c12afecbae37cd9b55f8f8c2" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CALL", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-06T15:18:19.555305", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + }, + "call - tsv - stub": { + "content": [ + { + "call": [ + [ + { + "id": "test" + }, + "test.saltshaker_call_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CALL", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-05T09:54:13.739643", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/saltshaker/call/tests/nextflow.config b/modules/nf-core/saltshaker/call/tests/nextflow.config new file mode 100644 index 000000000..ba448353c --- /dev/null +++ b/modules/nf-core/saltshaker/call/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'SALTSHAKER_CALL' { + ext.args = '--blacklist' + } +} diff --git a/modules/local/saltshaker/plot/environment.yaml b/modules/nf-core/saltshaker/classify/environment.yml similarity index 84% rename from modules/local/saltshaker/plot/environment.yaml rename to modules/nf-core/saltshaker/classify/environment.yml index 57b633f58..f76c4bf5a 100644 --- a/modules/local/saltshaker/plot/environment.yaml +++ b/modules/nf-core/saltshaker/classify/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - pip + - pip==26.0.1 - pip: - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/classify/main.nf b/modules/nf-core/saltshaker/classify/main.nf similarity index 64% rename from modules/local/saltshaker/classify/main.nf rename to modules/nf-core/saltshaker/classify/main.nf index 1b533570d..209312974 100644 --- a/modules/local/saltshaker/classify/main.nf +++ b/modules/nf-core/saltshaker/classify/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_CLASSIFY { tag "$meta.id" - label "process_single" + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -9,47 +9,48 @@ process SALTSHAKER_CLASSIFY { input: tuple val(meta), path(call) - val dom_frac + val dominant_fraction val group_radius - val high_het - val mult_thresh - val noise_thresh - val mito_name + val high_heteroplasmy + val multiple_threshold + val noise_threshold output: tuple val(meta), path("*_classify_metadata.tsv"), emit: classify tuple val(meta), path("*_classify.txt") , emit: txt - tuple val(meta), path("*saltshaker.vcf") , emit: vcf + tuple val(meta), path("*saltshaker.vcf") , emit: vcf, optional: true tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + when: + task.ext.when == null || task.ext.when + script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + """ saltshaker classify \\ --prefix $prefix \\ --input-dir . \\ - --vcf \\ - --dominant-fraction $dom_frac \\ + --dominant-fraction $dominant_fraction \\ --radius $group_radius \\ - --high-het $high_het \\ - --multiple-threshold $mult_thresh \\ - --noise $noise_thresh \\ + --high-het $high_heteroplasmy \\ + --multiple-threshold $multiple_threshold \\ + --noise $noise_threshold \\ $args - cat ${prefix}.saltshaker.vcf | sed 's/chrM/${mito_name}/g' > ${prefix}.saltshaker.tmp.vcf - mv ${prefix}.saltshaker.tmp.vcf ${prefix}.saltshaker.vcf - """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def touch_vcf = args.contains('--vcf') ? "touch ${prefix}.saltshaker.vcf" : '' """ - touch ${prefix}.saltshaker.vcf + echo $args + + $touch_vcf touch ${prefix}.saltshaker_classify.txt touch ${prefix}.saltshaker_classify_metadata.tsv - """ - } diff --git a/modules/nf-core/saltshaker/classify/meta.yml b/modules/nf-core/saltshaker/classify/meta.yml new file mode 100644 index 000000000..182df6566 --- /dev/null +++ b/modules/nf-core/saltshaker/classify/meta.yml @@ -0,0 +1,106 @@ +name: "saltshaker_classify" +description: mtDNA deletion and duplication classification downstream of mitosalt +keywords: + - saltshaker + - mitosalt + - mtDNA + - structural-variant calling +tools: + - "saltshaker": + description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." + homepage: "https://github.com/aksenia/saltshaker" + documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - call: + type: file + description: call metadata file from saltshaker_call + pattern: "*_call_metadata.tsv" + ontologies: + - edam: http://edamontology.org/operation_3227 #variant calling + - edam: http://edamontology.org/format_3475 #tsv + - dominant_fraction: + type: float + description: Minimum heteroplasmy fraction to classify as dominant in saltshaker + - group_radius: + type: integer + description: Spatial clustering radius for saltshaker grouping + - high_heteroplasmy: + type: float + description: High heteroplasmy threshold for saltshaker classification + - multiple_threshold: + type: float + description: Heteroplasmy threshold for multiple classification in saltshaker + - noise_threshold: + type: float + description: Heteroplasmy threshold for noise in saltshaker classification +output: + classify: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_classify_metadata.tsv": + type: file + description: tsv with classified call metadata to be used in saltshaker_plot + pattern: "*_classify_metadata.tsv" + ontologies: + - edam: http://edamontology.org/operation_3225 #classification + - edam: http://edamontology.org/format_3475 #tsv + txt: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_classify.txt": + type: file + description: txt file with case classification + pattern: "*_classify.txt" + ontologies: + - edam: http://edamontology.org/operation_3225 #classification + - edam: http://edamontology.org/format_2330 #txt + vcf: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*saltshaker.vcf": + type: file + description: vcf file with classified calls + pattern: "*saltshaker.vcf" + ontologies: + - edam: http://edamontology.org/operation_3225 #classification + - edam: http://edamontology.org/format_3016 #vcf + versions_saltshaker: + - - ${task.process}: + type: string + description: The name of the process + - saltshaker: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: Hardcoded version of saltshaker used in the module +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - saltshaker: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: Hardcoded version of saltshaker used in the module +authors: + - "@ieduba" +maintainers: + - "@ieduba" diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test b/modules/nf-core/saltshaker/classify/tests/main.nf.test new file mode 100644 index 000000000..12cc1ec94 --- /dev/null +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test @@ -0,0 +1,164 @@ +nextflow_process { + + name "Test Process SALTSHAKER_CLASSIFY" + script "../main.nf" + process "SALTSHAKER_CLASSIFY" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "saltshaker" + tag "saltshaker/call" + tag "saltshaker/classify" + + setup { + run("SALTSHAKER_CALL") { + script "../../call/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.breakpoint', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.cluster', checkIfExists: true), + ] + + input[1] = [ + [ id:'hg38' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/human_mt_rCRS.fasta', checkIfExists: true), + ] + + input[2] = 15 + input[3] = 0.01 + input[4] = 16569 + input[5] = 16081 + input[6] = 407 + input[7] = 5730 + input[8] = 5763 + """ + } + } + } + + test("classify - vcf") { + + when { + params { + module_args = '--blacklist --vcf' + } + process { + """ + input[0] = SALTSHAKER_CALL.out.call + input[1] = 0.5 + input[2] = 600 + input[3] = 10 + input[4] = 5 + input[5] = 0.3 + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + + ) + } + + } + + test("classify - vcf - stub") { + + options "-stub" + + when { + params { + module_args = '--blacklist --vcf' + } + process { + """ + input[0] = SALTSHAKER_CALL.out.call + input[1] = 0.5 + input[2] = 600 + input[3] = 10 + input[4] = 5 + input[5] = 0.3 + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + ) + } + + } + + test("classify - no-vcf") { + + when { + params { + module_args = '--blacklist' + } + process { + """ + input[0] = SALTSHAKER_CALL.out.call + input[1] = 0.5 + input[2] = 600 + input[3] = 10 + input[4] = 5 + input[5] = 0.3 + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + + ) + } + + } + + test("classify - no-vcf - stub") { + + options "-stub" + + when { + params { + module_args = '--blacklist' + } + process { + """ + input[0] = SALTSHAKER_CALL.out.call + input[1] = 0.5 + input[2] = 600 + input[3] = 10 + input[4] = 5 + input[5] = 0.3 + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap new file mode 100644 index 000000000..ff226554f --- /dev/null +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap @@ -0,0 +1,160 @@ +{ + "classify - no-vcf": { + "content": [ + { + "classify": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + ] + ], + "vcf": [ + + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CLASSIFY", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-17T11:02:38.830976", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + }, + "classify - vcf - stub": { + "content": [ + { + "classify": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.saltshaker.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CLASSIFY", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-16T10:53:38.916497", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + }, + "classify - vcf": { + "content": [ + { + "classify": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.saltshaker.vcf:md5,6669688cfb486e6c98f0aadb8e41ed88" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CLASSIFY", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-17T10:17:34.236265", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + }, + "classify - no-vcf - stub": { + "content": [ + { + "classify": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_CLASSIFY", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-17T11:02:43.86661", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/saltshaker/classify/tests/nextflow.config b/modules/nf-core/saltshaker/classify/tests/nextflow.config new file mode 100644 index 000000000..97d25b454 --- /dev/null +++ b/modules/nf-core/saltshaker/classify/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'SALTSHAKER_CLASSIFY' { + ext.args = params.module_args + } +} diff --git a/modules/local/saltshaker/classify/environment.yaml b/modules/nf-core/saltshaker/plot/environment.yml similarity index 84% rename from modules/local/saltshaker/classify/environment.yaml rename to modules/nf-core/saltshaker/plot/environment.yml index 57b633f58..f76c4bf5a 100644 --- a/modules/local/saltshaker/classify/environment.yaml +++ b/modules/nf-core/saltshaker/plot/environment.yml @@ -2,6 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - pip + - pip==26.0.1 - pip: - saltshaker==1.0.0 diff --git a/modules/local/saltshaker/plot/main.nf b/modules/nf-core/saltshaker/plot/main.nf similarity index 84% rename from modules/local/saltshaker/plot/main.nf rename to modules/nf-core/saltshaker/plot/main.nf index fcfd9455f..56e7b9a3e 100644 --- a/modules/local/saltshaker/plot/main.nf +++ b/modules/nf-core/saltshaker/plot/main.nf @@ -1,6 +1,6 @@ process SALTSHAKER_PLOT { tag "$meta.id" - label "process_single" + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -14,9 +14,13 @@ process SALTSHAKER_PLOT { tuple val(meta), path("*saltshaker.png"), emit: plot tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + when: + task.ext.when == null || task.ext.when + script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + """ saltshaker plot \\ --prefix $prefix \\ @@ -26,11 +30,12 @@ process SALTSHAKER_PLOT { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.saltshaker.png + echo $args + touch ${prefix}.saltshaker.png """ - } diff --git a/modules/nf-core/saltshaker/plot/meta.yml b/modules/nf-core/saltshaker/plot/meta.yml new file mode 100644 index 000000000..b95deb3f5 --- /dev/null +++ b/modules/nf-core/saltshaker/plot/meta.yml @@ -0,0 +1,67 @@ +name: "saltshaker_plot" +description: mtDNA deletion and duplication plotting downstream of mitosalt +keywords: + - saltshaker + - mitosalt + - mtDNA + - structural-variant calling +tools: + - "saltshaker": + description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." + homepage: "https://github.com/aksenia/saltshaker" + documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - classify: + type: file + description: classify metadata file from saltshaker_classify + pattern: "*_classify_metadata.tsv" + ontologies: + - edam: http://edamontology.org/operation_3225 #classification + - edam: http://edamontology.org/format_3475 #tsv + +output: + plot: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*saltshaker.png": + type: file + description: png file with saltshaker plot + pattern: "*saltshaker.png" + ontologies: + - edam: http://edamontology.org/operation_0337 #visualization + - edam: http://edamontology.org/format_3603 #png + versions_saltshaker: + - - "${task.process}": + type: string + description: The name of the process + - "saltshaker": + type: string + description: The name of the tool + - "1.0.0": + type: string + description: Hardcoded version of saltshaker used in the module + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - saltshaker: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: Hardcoded version of saltshaker used in the module +authors: + - "@ieduba" +maintainers: + - "@ieduba" diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test b/modules/nf-core/saltshaker/plot/tests/main.nf.test new file mode 100644 index 000000000..3aa867a9e --- /dev/null +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process SALTSHAKER_PLOT" + script "../main.nf" + process "SALTSHAKER_PLOT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "saltshaker" + tag "saltshaker/call" + tag "saltshaker/classify" + tag "saltshaker/plot" + + setup { + run("SALTSHAKER_CALL") { + script "../../call/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.breakpoint', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/mitosalt/test_mitosalt.cluster', checkIfExists: true), + ] + + input[1] = [ + [ id:'hg38' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/human_mt_rCRS.fasta', checkIfExists: true), + ] + + input[2] = 15 + input[3] = 0.01 + input[4] = 16569 + input[5] = 16081 + input[6] = 407 + input[7] = 5730 + input[8] = 5763 + """ + } + } + + run("SALTSHAKER_CLASSIFY") { + script "../../classify/main.nf" + process { + """ + input[0] = SALTSHAKER_CALL.out.call + input[1] = 0.5 + input[2] = 600 + input[3] = 10 + input[4] = 5 + input[5] = 0.3 + """ + } + } + } + + + test("plot - png") { + + when { + params { + module_args = '--blacklist' + } + process { + """ + input[0] = SALTSHAKER_CLASSIFY.out.classify + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + ) + } + + } + + test("plot - png - stub") { + + options "-stub" + + when { + params { + module_args = '--blacklist' + } + process { + """ + input[0] = SALTSHAKER_CLASSIFY.out.classify + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + sanitizeOutput(process.out), + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap new file mode 100644 index 000000000..ea7f4d94c --- /dev/null +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap @@ -0,0 +1,54 @@ +{ + "plot - png - stub": { + "content": [ + { + "plot": [ + [ + { + "id": "test" + }, + "test.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_PLOT", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-17T14:57:52.937691", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + }, + "plot - png": { + "content": [ + { + "plot": [ + [ + { + "id": "test" + }, + "test.saltshaker.png:md5,c5c8f7b96daab112b53dfe42194855af" + ] + ], + "versions_saltshaker": [ + [ + "SALTSHAKER_PLOT", + "saltshaker", + "1.0.0" + ] + ] + } + ], + "timestamp": "2026-03-17T14:57:46.77575", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.0" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/saltshaker/plot/tests/nextflow.config b/modules/nf-core/saltshaker/plot/tests/nextflow.config new file mode 100644 index 000000000..51393788b --- /dev/null +++ b/modules/nf-core/saltshaker/plot/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'SALTSHAKER_PLOT' { + ext.args = params.module_args + } +} diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 440d77783..ade224a3a 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -6,9 +6,9 @@ include { MT_DELETION } from '../../../modules/local/mt_deletion_script' include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' include { MITOSALT } from '../../../modules/local/mitosalt/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' -include { SALTSHAKER_CALL } from '../../../modules/local/saltshaker/call/main' -include { SALTSHAKER_CLASSIFY } from '../../../modules/local/saltshaker/classify/main' -include { SALTSHAKER_PLOT } from '../../../modules/local/saltshaker/plot/main' +include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' +include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' +include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' workflow CALL_SV_MT { take: @@ -90,10 +90,14 @@ workflow CALL_SV_MT { ch_mt_lastdb ) MITOSALT.out.cluster - .filter{ meta, out -> out.countLines() > 0 } - .set{ch_saltshaker_in} + .filter{ _meta, out -> out.countLines() > 0 } + .set{ch_cluster} + + if (ch_cluster) { + MITOSALT.out.breakpoint + .join(ch_cluster) + .set{ch_saltshaker_in} - if (ch_saltshaker_in) { SALTSHAKER_CALL( MITOSALT.out.breakpoint, ch_saltshaker_in, From 33cc1e42715be3abd3095562e4fd7e8ec2e2cc52 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:10:15 +0100 Subject: [PATCH 511/872] Migrate publishDir to output block --- conf/modules/prepare_references.config | 9 ---- main.nf | 8 +++- subworkflows/local/prepare_references/main.nf | 44 +++++++++++++++++++ 3 files changed, 50 insertions(+), 11 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index e433191ad..846f03d2e 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -16,15 +16,6 @@ // process { - withName: '.*PREPARE_REFERENCES:.*' { - publishDir = [ - path: { "${params.outdir}/references" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference, - ] - } - withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { ext.args = '-a meme' } diff --git a/main.nf b/main.nf index 9c2f4c1da..44e5463ef 100644 --- a/main.nf +++ b/main.nf @@ -90,6 +90,7 @@ workflow NFCORE_RAREDISEASE { val_sample_id_map val_samtools_sort_threads val_save_mapped_as_cram + val_save_reference val_score_config_mt val_score_config_snv val_score_config_sv @@ -148,7 +149,8 @@ workflow NFCORE_RAREDISEASE { val_sequence_dictionary, val_target_bed, val_vcfanno_extra_resources, - val_vep_cache + val_vep_cache, + val_save_reference ) .set { ch_references } @@ -473,7 +475,8 @@ workflow NFCORE_RAREDISEASE { multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html publish = RAREDISEASE.out.publish .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) // channel: [ val(destination), val(value) ] + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -552,6 +555,7 @@ workflow { params.sample_id_map, params.samtools_sort_threads, params.save_mapped_as_cram, + params.save_reference, params.score_config_mt, params.score_config_snv, params.score_config_sv, diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 096e644d9..462eec4b9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -56,6 +56,7 @@ workflow PREPARE_REFERENCES { val_target_bed // String: path to target bed file val_vcfanno_extra // String: path to additional annotation files used by vcfanno val_vep_cache // String: path to vep cache folder + val_save_reference // Boolean: whether to save generated reference files main: @@ -266,6 +267,48 @@ workflow PREPARE_REFERENCES { ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf } + ch_publish = channel.empty() + if (val_save_reference) { + ch_publish = ch_dbsnp + .mix(ch_dbsnp_tbi) + .mix(ch_bwa) + .mix(ch_genome_bwamem2_index) + .mix(ch_genome_bwameme_index) + .mix(ch_genome_fai) + .mix(ch_genome_fasta) + .mix(ch_genome_hisat2_index) + .mix(ch_genome_dict) + .mix(ch_mt_bwa_index) + .mix(ch_mt_bwamem2_index) + .mix(ch_mt_dict) + .mix(ch_mt_fai) + .mix(ch_mt_fasta) + .mix(ch_mt_last_index) + .mix(ch_mtshift_backchain) + .mix(ch_mtshift_bwa_index) + .mix(ch_mtshift_bwamem2_index) + .mix(ch_mtshift_dict) + .mix(ch_mtshift_fai) + .mix(ch_mtshift_fasta) + .mix(ch_sdf) + .map { meta, value -> ['references/', [meta, value]] } + .mix( + ch_target_bed_gz_tbi + .map { meta, gz, index -> ['references/', [meta, gz, index]] } + ) + .mix( + ch_bait_intervals + .mix(ch_chrom_sizes) + .mix(ch_shiftfasta_mtintervals.intervals) + .mix(ch_shiftfasta_mtintervals.shift_intervals) + .mix(ch_target_intervals) + .mix(ch_gnomad_af_idx) + .mix(ch_vcfanno_extra) + .mix(ch_vep_resources) + .map { value -> ['references/', [value]] } + ) + } + emit: bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] @@ -298,4 +341,5 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From 0e18fb83bc154f2f79efbd1af7ff0ee4f1d770f4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:12:00 +0100 Subject: [PATCH 512/872] Migrate publishDir to output block --- conf/modules/prepare_references.config | 9 ++++ main.nf | 8 +--- subworkflows/local/prepare_references/main.nf | 44 ------------------- 3 files changed, 11 insertions(+), 50 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index 846f03d2e..e433191ad 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -16,6 +16,15 @@ // process { + withName: '.*PREPARE_REFERENCES:.*' { + publishDir = [ + path: { "${params.outdir}/references" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_reference, + ] + } + withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { ext.args = '-a meme' } diff --git a/main.nf b/main.nf index 44e5463ef..9c2f4c1da 100644 --- a/main.nf +++ b/main.nf @@ -90,7 +90,6 @@ workflow NFCORE_RAREDISEASE { val_sample_id_map val_samtools_sort_threads val_save_mapped_as_cram - val_save_reference val_score_config_mt val_score_config_snv val_score_config_sv @@ -149,8 +148,7 @@ workflow NFCORE_RAREDISEASE { val_sequence_dictionary, val_target_bed, val_vcfanno_extra_resources, - val_vep_cache, - val_save_reference + val_vep_cache ) .set { ch_references } @@ -475,8 +473,7 @@ workflow NFCORE_RAREDISEASE { multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html publish = RAREDISEASE.out.publish .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + .mix(ch_pedfile_publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -555,7 +552,6 @@ workflow { params.sample_id_map, params.samtools_sort_threads, params.save_mapped_as_cram, - params.save_reference, params.score_config_mt, params.score_config_snv, params.score_config_sv, diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 462eec4b9..096e644d9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -56,7 +56,6 @@ workflow PREPARE_REFERENCES { val_target_bed // String: path to target bed file val_vcfanno_extra // String: path to additional annotation files used by vcfanno val_vep_cache // String: path to vep cache folder - val_save_reference // Boolean: whether to save generated reference files main: @@ -267,48 +266,6 @@ workflow PREPARE_REFERENCES { ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf } - ch_publish = channel.empty() - if (val_save_reference) { - ch_publish = ch_dbsnp - .mix(ch_dbsnp_tbi) - .mix(ch_bwa) - .mix(ch_genome_bwamem2_index) - .mix(ch_genome_bwameme_index) - .mix(ch_genome_fai) - .mix(ch_genome_fasta) - .mix(ch_genome_hisat2_index) - .mix(ch_genome_dict) - .mix(ch_mt_bwa_index) - .mix(ch_mt_bwamem2_index) - .mix(ch_mt_dict) - .mix(ch_mt_fai) - .mix(ch_mt_fasta) - .mix(ch_mt_last_index) - .mix(ch_mtshift_backchain) - .mix(ch_mtshift_bwa_index) - .mix(ch_mtshift_bwamem2_index) - .mix(ch_mtshift_dict) - .mix(ch_mtshift_fai) - .mix(ch_mtshift_fasta) - .mix(ch_sdf) - .map { meta, value -> ['references/', [meta, value]] } - .mix( - ch_target_bed_gz_tbi - .map { meta, gz, index -> ['references/', [meta, gz, index]] } - ) - .mix( - ch_bait_intervals - .mix(ch_chrom_sizes) - .mix(ch_shiftfasta_mtintervals.intervals) - .mix(ch_shiftfasta_mtintervals.shift_intervals) - .mix(ch_target_intervals) - .mix(ch_gnomad_af_idx) - .mix(ch_vcfanno_extra) - .mix(ch_vep_resources) - .map { value -> ['references/', [value]] } - ) - } - emit: bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] @@ -341,5 +298,4 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] - publish = ch_publish // channel: [ val(destination), val(value) ] } From 7a33c7631933b445b087908874eaa79cf03235e9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:13:35 +0100 Subject: [PATCH 513/872] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ec02ff25b..0d4b03041 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#788](https://github.com/nf-core/raredisease/pull/788) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) +- Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791) ### `Fixed` From 31c139b4e103e7d21b65b6d341506a77df46131e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:15:51 +0100 Subject: [PATCH 514/872] Revert "Migrate publishDir to output block" This reverts commit 0e18fb83bc154f2f79efbd1af7ff0ee4f1d770f4. --- conf/modules/prepare_references.config | 9 ---- main.nf | 8 +++- subworkflows/local/prepare_references/main.nf | 44 +++++++++++++++++++ 3 files changed, 50 insertions(+), 11 deletions(-) diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config index e433191ad..846f03d2e 100644 --- a/conf/modules/prepare_references.config +++ b/conf/modules/prepare_references.config @@ -16,15 +16,6 @@ // process { - withName: '.*PREPARE_REFERENCES:.*' { - publishDir = [ - path: { "${params.outdir}/references" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference, - ] - } - withName: '.*PREPARE_REFERENCES:BWAMEME_INDEX_GENOME' { ext.args = '-a meme' } diff --git a/main.nf b/main.nf index 9c2f4c1da..44e5463ef 100644 --- a/main.nf +++ b/main.nf @@ -90,6 +90,7 @@ workflow NFCORE_RAREDISEASE { val_sample_id_map val_samtools_sort_threads val_save_mapped_as_cram + val_save_reference val_score_config_mt val_score_config_snv val_score_config_sv @@ -148,7 +149,8 @@ workflow NFCORE_RAREDISEASE { val_sequence_dictionary, val_target_bed, val_vcfanno_extra_resources, - val_vep_cache + val_vep_cache, + val_save_reference ) .set { ch_references } @@ -473,7 +475,8 @@ workflow NFCORE_RAREDISEASE { multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html publish = RAREDISEASE.out.publish .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) // channel: [ val(destination), val(value) ] + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -552,6 +555,7 @@ workflow { params.sample_id_map, params.samtools_sort_threads, params.save_mapped_as_cram, + params.save_reference, params.score_config_mt, params.score_config_snv, params.score_config_sv, diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 096e644d9..462eec4b9 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -56,6 +56,7 @@ workflow PREPARE_REFERENCES { val_target_bed // String: path to target bed file val_vcfanno_extra // String: path to additional annotation files used by vcfanno val_vep_cache // String: path to vep cache folder + val_save_reference // Boolean: whether to save generated reference files main: @@ -266,6 +267,48 @@ workflow PREPARE_REFERENCES { ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf } + ch_publish = channel.empty() + if (val_save_reference) { + ch_publish = ch_dbsnp + .mix(ch_dbsnp_tbi) + .mix(ch_bwa) + .mix(ch_genome_bwamem2_index) + .mix(ch_genome_bwameme_index) + .mix(ch_genome_fai) + .mix(ch_genome_fasta) + .mix(ch_genome_hisat2_index) + .mix(ch_genome_dict) + .mix(ch_mt_bwa_index) + .mix(ch_mt_bwamem2_index) + .mix(ch_mt_dict) + .mix(ch_mt_fai) + .mix(ch_mt_fasta) + .mix(ch_mt_last_index) + .mix(ch_mtshift_backchain) + .mix(ch_mtshift_bwa_index) + .mix(ch_mtshift_bwamem2_index) + .mix(ch_mtshift_dict) + .mix(ch_mtshift_fai) + .mix(ch_mtshift_fasta) + .mix(ch_sdf) + .map { meta, value -> ['references/', [meta, value]] } + .mix( + ch_target_bed_gz_tbi + .map { meta, gz, index -> ['references/', [meta, gz, index]] } + ) + .mix( + ch_bait_intervals + .mix(ch_chrom_sizes) + .mix(ch_shiftfasta_mtintervals.intervals) + .mix(ch_shiftfasta_mtintervals.shift_intervals) + .mix(ch_target_intervals) + .mix(ch_gnomad_af_idx) + .mix(ch_vcfanno_extra) + .mix(ch_vep_resources) + .map { value -> ['references/', [value]] } + ) + } + emit: bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] @@ -298,4 +341,5 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From 1f7fbb872d6c23a580c052c00db5f35bb0dbff85 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:41:01 +0100 Subject: [PATCH 515/872] Update test and snapshot --- .../prepare_references/tests/main.nf.test | 22 +- .../tests/main.nf.test.snap | 2674 ++++++++++++----- 2 files changed, 1961 insertions(+), 735 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 85d94b7e8..1e9c6e312 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -35,13 +35,31 @@ nextflow_workflow { input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' input[18] = null input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' + input[20] = true """ } } then { - assert workflow.success - assert snapshot(workflow.out).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + // Unwrap nested lists to get the filename + def sortKey = item + while (sortKey instanceof List && !sortKey.isEmpty()) { + sortKey = sortKey[-1] + } + // Extract filename: strip :md5, suffix then take basename only + // (sortKey may be a raw Path with an absolute work-dir prefix) + def parts = sortKey.toString().split(':md5,')[0].tokenize('/') + parts ? parts[-1] : '' + } + [name, sorted_channel] + }.sort { it[0] } + ).match() } + ) } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index ccd669709..7cd790736 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -1,960 +1,2168 @@ { "Should run without failures": { "content": [ - { - "0": [ + [ + [ + "0", [ - "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" + [ + "target_bait.intervals_list:md5,84cbdac15bdfcd14b8a810e35f7ccc54" + ] ] ], - "1": [ + [ + "1", [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] ] ], - "10": [ + [ + "10", [ - { - "id": "reference" - }, - "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + [ + { + "id": "reference" + }, + "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + ] ] ], - "11": [ + [ + "11", [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" + ] ] ], - "12": [ + [ + "12", [ - { - "id": "reference" - }, [ - "reference_mt.amb:md5,6749f645487281112c254ab829ea048c", - "reference_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "reference_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", - "reference_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", - "reference_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" + { + "id": "reference" + }, + [ + "reference_mt.amb:md5,6749f645487281112c254ab829ea048c", + "reference_mt.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_mt.bwt:md5,96337a6d9dc0d7afc562fee8b1afb673", + "reference_mt.pac:md5,ecbea80d481b6e8e70da3f464b977d91", + "reference_mt.sa:md5,7c06a2c0b4f23e785e2f85383b9d1317" + ] ] ] ], - "13": [ - - ], - "14": [ + [ + "13", [ - { - "id": "reference" - }, - "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" + ] ], - "15": [ + [ + "14", [ - { - "id": "reference" - }, - "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + [ + { + "id": "reference" + }, + "reference_mt.dict:md5,9b0db3306084213d47d83aa994b219f6" + ] ] ], - "16": [ + [ + "15", [ - { - "id": "reference" - }, - "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + [ + { + "id": "reference" + }, + "reference_mt.fa.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + ] ] ], - "17": [ + [ + "16", [ - "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" + [ + { + "id": "reference" + }, + "reference_mt.fa:md5,dcff3c6dd92e01b11edf7586ca4f5a78" + ] ] ], - "18": [ + [ + "17", [ - { - "id": "reference" - }, [ - "reference.bck:md5,cb2ea69e38f2f48b0e9fd86511f00efa", - "reference.des:md5,d9189e49407ad59a8d15e527a5262d88", - "reference.prj:md5,afb6ee4759a4ccd9edb52fdb8e5a3a26", - "reference.sds:md5,503e83c0d24f5ea38d9d6c013d9777d1", - "reference.ssp:md5,5c62ddb0bd75481784efb7120045bf42", - "reference.suf:md5,b2180a9a2d85be97f896808c05b0e38c", - "reference.tis:md5,c4167c6aebb2139c3dc9b07a65830c3d" + "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" ] ] ], - "19": [ + [ + "18", [ - { - "id": "reference" - }, - "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + [ + { + "id": "reference" + }, + [ + "reference.bck:md5,cb2ea69e38f2f48b0e9fd86511f00efa", + "reference.des:md5,d9189e49407ad59a8d15e527a5262d88", + "reference.prj:md5,afb6ee4759a4ccd9edb52fdb8e5a3a26", + "reference.sds:md5,503e83c0d24f5ea38d9d6c013d9777d1", + "reference.ssp:md5,5c62ddb0bd75481784efb7120045bf42", + "reference.suf:md5,b2180a9a2d85be97f896808c05b0e38c", + "reference.tis:md5,c4167c6aebb2139c3dc9b07a65830c3d" + ] + ] ] ], - "2": [ + [ + "19", [ - { - "id": "dbsnp_-138-" - }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + [ + { + "id": "reference" + }, + "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + ] ] ], - "20": [ + [ + "2", [ - { - "id": "reference" - }, [ - "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", - "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", - "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", - "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", - "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + { + "id": "dbsnp_-138-" + }, + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" ] ] ], - "21": [ - + [ + "20", + [ + [ + { + "id": "reference" + }, + [ + "reference_shift.amb:md5,ad1d6545efc080e69ad54ecdbcd0720c", + "reference_shift.ann:md5,4111990d7eae543ed95cb82a5e32b04a", + "reference_shift.bwt:md5,c13d3e8c5ac29b56b31e1882e2111491", + "reference_shift.pac:md5,0ead764b2f8fa112e3351ca517d2e125", + "reference_shift.sa:md5,9ef1b52de302c6957f4dc82ed2f21bd1" + ] + ] + ] ], - "22": [ + [ + "21", [ - { - "id": "reference" - }, - "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" + ] ], - "23": [ + [ + "22", [ - { - "id": "reference" - }, - "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + [ + { + "id": "reference" + }, + "reference_shift.dict:md5,a714408661d0f6403f417304342574fc" + ] ] ], - "24": [ + [ + "23", [ - { - "id": "reference" - }, - "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + [ + { + "id": "reference" + }, + "reference_shift.fasta.fai:md5,fa8117aab64eeceb3f0800d473bd2a2b" + ] ] ], - "25": [ + [ + "24", [ - "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + [ + { + "id": "reference" + }, + "reference_shift.fasta:md5,3bb4de5911acad2dd87e8a183251d0dc" + ] ] ], - "26": [ - + [ + "25", + [ + [ + "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" + ] + ] ], - "27": [ + [ + "26", [ - { - "id": "target" - }, - "target_pad100.bed.gz:md5,7122d49f10e69c54d429a95cf4cf8fc9", - 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"timestamp": "2026-03-18T16:38:00.703982992", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 73ca8042ee264b5b5629d574ac37366d4811443c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 16:58:02 +0100 Subject: [PATCH 516/872] Update test --- .../local/prepare_references/tests/main.nf.test | 15 +++++++++++---- .../prepare_references/tests/main.nf.test.snap | 2 +- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 1e9c6e312..2102c3bb6 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -46,13 +46,20 @@ nextflow_workflow { { assert snapshot( workflow.out.collect { name, channel -> def sorted_channel = channel.toList().sort { item -> - // Unwrap nested lists to get the filename def sortKey = item while (sortKey instanceof List && !sortKey.isEmpty()) { - sortKey = sortKey[-1] + def next = sortKey[-1] + if (next instanceof List && next.every { !(it instanceof List) }) { + // Leaf file list (e.g. BWA index [amb,ann,bwt,pac,sa]). + // File order inside this list is non-deterministic, so sort + // basenames and join to produce a stable, environment-independent key. + return next.findAll { !(it instanceof Map) } + .collect { it.toString().split(':md5,')[0].tokenize('/').last() ?: '' } + .sort() + .join(',') + } + sortKey = next } - // Extract filename: strip :md5, suffix then take basename only - // (sortKey may be a raw Path with an absolute work-dir prefix) def parts = sortKey.toString().split(':md5,')[0].tokenize('/') parts ? parts[-1] : '' } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 7cd790736..b2d739fe1 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -2162,7 +2162,7 @@ ] ] ], - "timestamp": "2026-03-18T16:38:00.703982992", + "timestamp": "2026-03-18T16:49:39.590122429", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 982da9d97f15d1fdbd6ba12d2fa6d2808c871eaa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 22:04:02 +0100 Subject: [PATCH 517/872] Update snapshot --- .../prepare_references/tests/main.nf.test | 22 +- .../tests/main.nf.test.snap | 1116 ++++++++--------- 2 files changed, 576 insertions(+), 562 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 2102c3bb6..3dceb0611 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -50,11 +50,25 @@ nextflow_workflow { while (sortKey instanceof List && !sortKey.isEmpty()) { def next = sortKey[-1] if (next instanceof List && next.every { !(it instanceof List) }) { - // Leaf file list (e.g. BWA index [amb,ann,bwt,pac,sa]). - // File order inside this list is non-deterministic, so sort - // basenames and join to produce a stable, environment-independent key. + // Leaf list: could be [meta, path] or [file1, file2, ...]. + // For directory outputs (e.g. BWA/BWAMEM2/HISAT2 index folders), + // nf-test represents the value as a Path at sort time rather than + // expanding it to a file list. List the directory contents to + // produce a stable, unique sort key across same-named directories. return next.findAll { !(it instanceof Map) } - .collect { it.toString().split(':md5,')[0].tokenize('/').last() ?: '' } + .collect { v -> + def s = v.toString() + if (s.contains(':md5,')) { + return s.split(':md5,')[0].tokenize('/').last() ?: '' + } + try { + def f = new File(s) + if (f.isDirectory()) { + return f.listFiles()?.collect { it.name }?.sort()?.join(',') ?: s.tokenize('/').last() ?: '' + } + } catch (e) {} + return s.tokenize('/').last() ?: '' + } .sort() .join(',') } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index b2d739fe1..ee140eaa3 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -510,268 +510,6 @@ ] ] ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - 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<20065894+ramprasadn@users.noreply.github.com> Date: Wed, 18 Mar 2026 23:00:01 +0100 Subject: [PATCH 518/872] Update usage.md --- docs/usage.md | 29 +++++++++++++++++++++-------- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a406550ff..8f2c5cd37 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -50,7 +50,7 @@ nf-core/raredisease is a bioinformatics best-practice analysis pipeline to call, ## Prerequisites -1. Install Nextflow (>=24.04.2) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation) +1. Install Nextflow (>=25.10.4) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation) 2. Install one of the following technologies for full pipeline reproducibility: Docker, Singularity, Podman, Shifter or Charliecloud. > Almost all nf-core pipelines give you the option to use conda as well. However, some tools used in the raredisease pipeline do not have a conda package so we do not support conda at the moment. @@ -136,8 +136,8 @@ The nf-core/raredisease pipeline can handle duplicate-marked BAM files as input. | Fields | Description | | ------------- | ------------------------------------------------------------------------------------------------------------------------------ | | `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | -| `bam` | Absolute path to FASTQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `bai` | Absolute path to FASTQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `bam` | Absolute path to a duplicate-marked BAM file. | +| `bai` | Absolute path to the BAM index file (.bai). | | `sex` | Sex (1=male; 2=female; for unknown sex use 0 or 'other'). | | `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | | `paternal_id` | Sample ID of the father, can be blank if the father isn't part of the analysis or for samples other than the proband. | @@ -169,6 +169,16 @@ genome: "GRCh37" Note that the pipeline is modular in architecture. It offers you the flexibility to choose between different tools. For example, you can align with bwamem2 or bwa or Sentieon BWA mem and call SNVs with either DeepVariant or Sentieon DNAscope. You also have the option to turn off sections of the pipeline if you do not want to run the. For example, snv annotation can be turned off by adding `--skip_subworkflows snv_annotation` flag in the command line, or by setting it to true in a parameter file. This flexibility means that in any given analysis run, a combination of tools included in the pipeline will not be executed. So the pipeline is written in a way that can account for these differences while working with reference parameters. If a tool is not going to be executed during the course of a run, parameters used only by that tool need not be provided. For example, for SNV calling if you use DeepVariant as your variant caller, you need not provide the parameter `--ml_model`, which is only used by Sentieon DNAscope. +The pipeline is modular — individual tools and subworkflows can be skipped using `--skip_tools` and `--skip_subworkflows` (comma-separated). The valid values are: + +| `--skip_tools` | +| ----------------------------------------------------------------------------------------------- | +| `fastp`, `fastqc`, `gens`, `germlinecnvcaller`, `haplogrep3`, `ngsbits`, `peddy`, `qualimap`, `smncopynumbercaller`, `vcf2cytosure` | + +| `--skip_subworkflows` | +| ------------------------------------------------------------------------------------------------------------------------------------------- | +| `generate_clinical_set`, `me_annotation`, `me_calling`, `mt_annotation`, `mt_subsample`, `repeat_annotation`, `repeat_calling`, `snv_annotation`, `snv_calling`, `sv_annotation`, `sv_calling` | + nf-core/raredisease consists of several tools used for various purposes. For convenience, we have grouped those tools under the following categories: 1. Alignment (bwamem2/bwa/bwameme/Sentieon BWA mem) @@ -293,7 +303,7 @@ no header and the following columns: `CHROM POS REF_ALLELE,ALT_ALLELE AF`. Sampl 7File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html). 8A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv).
    9Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
    -10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into canditate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set.
    +10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into candidate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set. To skip this splitting entirely, add `generate_clinical_set` to `--skip_subworkflows`.
    11Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
    :::note @@ -316,17 +326,21 @@ We use CADD only to annotate small indels. To annotate SNVs with precomputed CAD ##### 9. Mitochondrial annotation +Mitochondrial analysis runs automatically for `wgs` and `mito` analysis types. For WES runs, set `--run_mt_for_wes true` to enable it. + | Mandatory | Optional | | ------------------------ | --------------------------------- | -| genome | vep_filters/vep_filters_scout_fmt | -| mito_name | vep_plugin_files | -| vcfanno_resources | | +| genome | run_mt_for_wes1 | +| mito_name | vep_filters/vep_filters_scout_fmt | +| vcfanno_resources | vep_plugin_files | | vcfanno_toml | | | vep_cache_version | | | vep_cache | | | score_config_mt | | | variant_consequences_snv | | +1Set to `true` to enable mitochondrial analysis for WES runs. Default is `false`.
    + ##### 10. Mobile element calling | Mandatory | Optional | @@ -443,7 +457,6 @@ with: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` From 2c39e60dccfccadefe57af309411c4963edf7b63 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Mar 2026 10:18:47 +0100 Subject: [PATCH 519/872] Update citations --- CITATIONS.md | 24 ++++++++------ README.md | 32 ++++++++++++------- .../utils_nfcore_raredisease_pipeline/main.nf | 20 +++++++----- 3 files changed, 47 insertions(+), 29 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 7c25c42cf..02b84e877 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -42,9 +42,7 @@ > Poplin R, Chang PC, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol. 2018;36(10):983-987. doi:10.1038/nbt.4235 -- [eKLIPse](https://www.nature.com/articles/s41436-018-0350-8) - - > Goudenège D, Bris C, Hoffmann V, et al. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 21, 1407–1416 (2019). doi:10.1038/s41436-018-0350-8 +- [Chromograph](https://github.com/Clinical-Genomics/chromograph) - [Ensembl VEP](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4) @@ -76,13 +74,9 @@ > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081 -- [HaploGrep 2](https://academic.oup.com/nar/article/44/W1/W58/2499296) - - > Weissensteiner H, Pacher D, Kloss-Brandstätter A, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58-W63. doi:10.1093/nar/gkw233 +- [HaploGrep 3](https://academic.oup.com/nar/article/51/W1/W263/7177898) -- [Hmtnote](https://doi.org/10.1101/600619) - - > Preste R, Clima R, Attimonelli M. Human mitochondrial variant annotation with HmtNote. bioRxiv 600619; doi:10.1101/600619 + > Schönherr S, Weissensteiner H, Kronenberg F, Forer L. Haplogrep 3 an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 2023;51(W1):W263-W268. doi:10.1093/nar/gkad284 - [Manta](https://academic.oup.com/bioinformatics/article/32/8/1220/1743909?login=true) @@ -118,6 +112,10 @@ > John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, and Francisco M. De La Vega. "Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines." bioRxiv, 2015. doi:10.1101/023754. +- [Sambamba](https://academic.oup.com/bioinformatics/article/31/12/2032/213831) + + > Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics. 2015;31(12):2032-2034. doi:10.1093/bioinformatics/btv098 + - [Sentieon DNAscope](https://www.biorxiv.org/content/10.1101/2022.05.20.492556v1.abstract) > Freed D, Pan R, Chen H, Li Z, Hu J, Aldana R. DNAscope: High Accuracy Small Variant Calling Using Machine Learning. Bioinformatics; 2022. doi:10.1101/2022.05.20.492556 @@ -130,6 +128,10 @@ > Chen X, Sanchis-Juan A, French CE, Connel AJ, Delon I, Kingsbury Z, Chawla A, Halpern AL, Taft RJ, NIHR BioResource, Bentley DR, Butchbach MER, Raymond FL, Eberle MA. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med. February 2020:1-9. doi:10.1038/s41436-020-0754-0 +- [Spring](https://academic.oup.com/bioinformatics/article/35/15/2674/5232998) + + > Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T. SPRING: a next-generation compressor for FASTQ data. Bioinformatics. 2019;35(15):2674-2676. doi:10.1093/bioinformatics/bty1015 + - [stranger](https://github.com/Clinical-Genomics/stranger) > Nilsson D, Magnusson M. moonso/stranger v0.7.1. Published online February 18, 2021. doi:10.5281/ZENODO.4548873 @@ -146,6 +148,8 @@ > Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017;6:664. doi:10.12688/f1000research.11168.2 +- [UPD](https://github.com/bjhall/upd) + - [UCSC Bigwig and Bigbed](https://academic.oup.com/bioinformatics/article/26/17/2204/199001?login=true) > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010;26(17):2204-2207. doi:10.1093/bioinformatics/btq351 @@ -156,7 +160,7 @@ > Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016;17(1):118. doi:10.1186/s13059-016-0973-5 -- [VerifyBamID2]() +- [VerifyBamID2](https://genome.cshlp.org/content/30/2/185) > Zhang F, Flickinger M, Taliun SAG, Consortium IPG, Abecasis GR, Scott LJ, McCaroll SA, Pato CN, Boehnke M, & Kang HM. (2020). Ancestry-agnostic estimation of DNA sample contamination from sequence reads. Genome Research, 30(2), 185–194. https://doi.org/10.1101/gr.246934.118 diff --git a/README.md b/README.md index 6a6abb6d0..28d82f736 100644 --- a/README.md +++ b/README.md @@ -48,25 +48,36 @@ On release, automated continuous integration tests run the pipeline on a full-si nf-core/raredisease workflow -**1. Metrics:** +**1. Preprocessing:** + +- [fastp](https://github.com/OpenGene/fastp) +- [Spring](https://github.com/shubhamchandak94/Spring) + +**2. Alignment:** + +- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) +- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME) +- [BWA](https://github.com/lh3/bwa) +- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/) + +**3. Metrics:** - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - [Mosdepth](https://github.com/brentp/mosdepth) - [MultiQC](http://multiqc.info/) -- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/) +- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/) - [Qualimap](http://qualimap.conesalab.org/) +- [Sambamba](https://github.com/biod/sambamba) - [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/) - [TIDDIT's cov](https://github.com/J35P312/) - [VerifyBamID2](https://github.com/Griffan/VerifyBamID) -**2. Alignment:** +**4. Sex check:** -- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) -- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME) -- [BWA](https://github.com/lh3/bwa) -- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/) +- [NGSbits SampleGender](https://github.com/imgag/ngs-bits) +- [Peddy](https://github.com/brentp/peddy) -**3. Variant calling - SNV:** +**5. Variant calling - SNV:** - [DeepVariant](https://github.com/google/deepvariant) - [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/) @@ -78,6 +89,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - Copy number variant calling: - [CNVnator](https://github.com/abyzovlab/CNVnator) - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) + - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller) **5. Annotation - SNV:** @@ -96,10 +108,8 @@ On release, automated continuous integration tests run the pipeline on a full-si **7. Mitochondrial analysis:** - [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-) -- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master) - Annotation: - - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd) - - [Hmtnote](https://github.com/robertopreste/HmtNote) + - [HaploGrep3](https://github.com/genepi/haplogrep3) - [vcfanno](https://github.com/brentp/vcfanno) - [CADD](https://cadd.gs.washington.edu/) - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index a933ee921..4b9472567 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -263,6 +263,10 @@ def channelFromSamplesheet(samplesheetPath, schemaPath, collect = true) { return collect ? ch_out.collect() : ch_out } +def boolean hasSpringInput() { + return file(params.input).readLines().any { line -> line.contains('.spring') } +} + def generateReadGroupLine(file, meta, params) { return "\'@RG\\tID:" + file.simpleName + "_" + meta.lane + "\\tPL:" + params.platform.toUpperCase() + "\\tSM:" + meta.id + "\'" } @@ -497,8 +501,7 @@ def toolCitationText() { sv_calls_text = [ params.analysis_type.equals("wgs") ? "CNVnator (Abyzov et al., 2011)," : "", params.analysis_type.equals("wgs") ? "TIDDIT (Eisfeldt et al., 2017)," : "", - "Manta (Chen et al., 2016),", - params.analysis_type.equals("wgs") ? "eKLIPse (Goudenge et al., 2019)," : "" + "Manta (Chen et al., 2016)," ] } if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('mt_annotation')) && (params.analysis_type.equals("wgs") || params.run_mt_for_wes)) { @@ -506,7 +509,6 @@ def toolCitationText() { "CADD (Rentzsch et al., 2019, 2021),", "VEP (McLaren et al., 2016),", "Vcfanno (Pedersen et al., 2016),", - "Hmtnote (Preste et al., 2019),", "Genmod (Magnusson et al., 2018)," ] if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) { @@ -531,6 +533,7 @@ def toolCitationText() { qc_bam_text = [ "Picard (Broad Institute, 2023)", "Qualimap (Okonechnikov et al., 2016),", + "Sambamba (Tarasov et al., 2015),", "TIDDIT (Eisfeldt et al., 2017),", "UCSC Bigwig and Bigbed (Kent et al., 2010),", (params.verifybamid_svd_bed && params.verifybamid_svd_mu && params.verifybamid_svd_ud) ? "VerifyBamID2 (Zhang et al., 2020)," : "", @@ -538,7 +541,8 @@ def toolCitationText() { ] preprocessing_text = [ "FastQC (Andrews 2010),", - (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "Fastp (Chen, 2023)," + (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "Fastp (Chen, 2023),", + hasSpringInput() ? "Spring (Chandak et al., 2019)," : "" ] other_citation_text = [ "BCFtools (Danecek et al., 2021),", @@ -625,8 +629,7 @@ def toolBibliographyText() { sv_calls_text = [ params.analysis_type.equals("wgs") ? "
  • Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011). CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research, 21(6), 974–984. https://doi.org/10.1101/gr.114876.110
    • " : "", params.analysis_type.equals("wgs") ? "
  • Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6, 664. https://doi.org/10.12688/f1000research.11168.2
    • " : "", - "
  • Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A. J., Kruglyak, S., & Saunders, C. T. (2016). Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32(8), 1220–1222. https://doi.org/10.1093/bioinformatics/btv710
    • ", - "
  • Goudenège, D., Bris, C., Hoffmann, V., Desquiret-Dumas, V., Jardel, C., Rucheton, B., Bannwarth, S., Paquis-Flucklinger, V., Lebre, A. S., Colin, E., Amati-Bonneau, P., Bonneau, D., Reynier, P., Lenaers, G., & Procaccio, V. (2019). eKLIPse: A sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genetics in Medicine, 21(6), 1407–1416. https://doi.org/10.1038/s41436-018-0350-8
    • " + "
  • Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A. J., Kruglyak, S., & Saunders, C. T. (2016). Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32(8), 1220–1222. https://doi.org/10.1093/bioinformatics/btv710
    • " ] } @@ -636,7 +639,6 @@ def toolBibliographyText() { "
  • Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019). CADD: Predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research, 47(D1), D886–D894. https://doi.org/10.1093/nar/gky1016
    • ", "
  • Pedersen, B. S., Layer, R. M., & Quinlan, A. R. (2016). Vcfanno: Fast, flexible annotation of genetic variants. Genome Biology, 17(1), 118. https://doi.org/10.1186/s13059-016-0973-5
    • ", "
  • McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016). The Ensembl Variant Effect Predictor. Genome Biology, 17(1), 122. https://doi.org/10.1186/s13059-016-0974-4
    • ", - "
  • Preste, R., Clima, R., & Attimonelli, M. (2019). Human mitochondrial variant annotation with HmtNote [Preprint]. Bioinformatics. https://doi.org/10.1101/600619
    • ", "
  • Magnusson, M., Hughes, T., Glabilloy, & Bitdeli Chef. (2018). genmod: Version 3.7.3 (3.7.3) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3841142
    • " ] if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) { @@ -660,6 +662,7 @@ def toolBibliographyText() { qc_bam_text = [ "
  • Broad Institute. (2023). Picard Tools. In Broad Institute, GitHub repository. http://broadinstitute.github.io/picard/
    • ", "
  • Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics, 32(2), 292–294. https://doi.org/10.1093/bioinformatics/btv566
    • ", + "
  • Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: Fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032–2034. https://doi.org/10.1093/bioinformatics/btv098
    • ", "
  • Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6, 664. https://doi.org/10.12688/f1000research.11168.2
    • ", "
  • Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S., & Karolchik, D. (2010). BigWig and BigBed: Enabling browsing of large distributed datasets. Bioinformatics, 26(17), 2204–2207. https://doi.org/10.1093/bioinformatics/btq351
    • ", (params.verifybamid_svd_bed && params.verifybamid_svd_mu && params.verifybamid_svd_ud) ? "
  • Zhang, F., Flickinger, M., Taliun, S. A. G., Consortium, I. P. G., Abecasis, G. R., Scott, L. J., McCaroll, S. A., Pato, C. N., Boehnke, M., & Kang, H. M. (2020). Ancestry-agnostic estimation of DNA sample contamination from sequence reads. Genome Research, 30(2), 185–194. https://doi.org/10.1101/gr.246934.118
    • " : "", @@ -667,7 +670,8 @@ def toolBibliographyText() { ] preprocessing_text = [ "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    • ", - (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "
  • Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107
    • " + (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "
  • Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107
    • ", + hasSpringInput() ? "
  • Chandak, S., Tatwawadi, K., Ochoa, I., Hernaez, M., & Weissman, T. (2019). SPRING: A next-generation compressor for FASTQ data. Bioinformatics, 35(15), 2674–2676. https://doi.org/10.1093/bioinformatics/bty1015
    • " : "" ] other_citation_text = [ From 64e9e0aead3c0929ef52d9f34dba4da9531daed6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Mar 2026 10:24:00 +0100 Subject: [PATCH 520/872] Create CONTRIBUTING_GUIDELINES.md --- CONTRIBUTING_GUIDELINES.md | 109 +++++++++++++++++++++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 CONTRIBUTING_GUIDELINES.md diff --git a/CONTRIBUTING_GUIDELINES.md b/CONTRIBUTING_GUIDELINES.md new file mode 100644 index 000000000..26fdc19e5 --- /dev/null +++ b/CONTRIBUTING_GUIDELINES.md @@ -0,0 +1,109 @@ +# Contributing Guidelines + +## Table of contents + +- [Contribution workflow](#contribution-workflow) +- [Architecture & structure](#architecture--structure) +- [Adding a new step](#adding-a-new-step) +- [Channel conventions](#channel-conventions) +- [Params & analysis types](#params--analysis-types) +- [Publishing](#publishing) +- [Configuration](#configuration) +- [Testing](#testing) +- [Style](#style) +- [Nextflow version bumping](#nextflow-version-bumping) +- [Images and figures](#images-and-figures) + +## Contribution workflow + +1. Check that there isn't already an issue about your idea in the [nf-core/raredisease issues](https://github.com/nf-core/raredisease/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this. +2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/raredisease repository](https://github.com/nf-core/raredisease) to your GitHub account. +3. Make the necessary changes / additions within your forked repository following the conventions below. +4. Use `nf-core pipelines schema build` to add any new parameters to `nextflow_schema.json`. +5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged. + +## Architecture & structure + +- **One subworkflow per biological task** — alignment, QC, variant calling, annotation, and ranking are each their own subworkflow under `subworkflows/local/`. Don't add logic to `workflows/raredisease.nf` that belongs in a subworkflow. +- **Reuse over duplication** — `RANK_VARIANTS`, `ANNOTATE_CSQ_PLI`, and `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` are intentionally included multiple times under different aliases. Follow this pattern before creating a near-identical subworkflow. +- **nf-core modules first** — prefer a module from `modules/nf-core/` over writing a local one. Only add to `modules/local/` when no nf-core module exists or the use case is too pipeline-specific. + +## Adding a new step + +1. Define the corresponding input channel into your new process from the expected previous process channel. +2. Write the process block. +3. Define the output channel if needed. +4. Add any new parameters to `nextflow.config` with a default. +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). +6. Add sanity checks and validation for all relevant parameters. +7. Perform local tests to validate that the new code works as expected. +8. If applicable, add a new test in the `tests` directory. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://multiqc.info/) module. +10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. + +## Channel conventions + +- **Skip lists**: use `parseSkipList()` and the `skip_tools` / `skip_subworkflows` params. Don't gate logic with raw string comparisons against params directly. +- **Conditional channels**: always initialize to `channel.empty()` before any `if` block that may or may not assign them. Never leave a channel potentially undefined. +- **Channel helpers**: use `channelFromPath`, `channelFromPathWithMeta`, and `channelFromSamplesheet` from `utils_nfcore_raredisease_pipeline` rather than rolling your own `channel.fromPath` calls. + +## Params & analysis types + +- `params` must only be accessed in the main unnamed workflow (`workflow` in `main.nf`). Subworkflows and named workflows receive all values as explicit `val_*` arguments. Never reference `params` directly inside a subworkflow. +- New tools that only apply to `wgs`, `wes`, or `mito` must be gated on `val_analysis_type`. +- Skippable tools must be added to the `--skip_tools` or `--skip_subworkflows` param and handled via `parseSkipList()`. +- Default params go in `nextflow.config`. Don't hardcode values that a user might reasonably want to change. Once added, run `nf-core pipelines schema build` to register them in `nextflow_schema.json`. + +## Publishing + +- Build a single `ch_publish` channel inside each subworkflow by mixing all publishable outputs into `[destination, value]` tuples. +- The emit name must always be `publish = ch_publish` — never the bare shorthand. +- Group channels that share a destination with `mix` first, then apply **one** `.map` per destination group — never one map per channel. +- If your subworkflow calls inner subworkflows, always mix their `.out.publish` into the outer `ch_publish`. Never discard it. +- Remove the corresponding `publishDir` entry from `conf/modules/` when adding a process to `ch_publish`. + +## Configuration + +- Process-level options go in `conf/modules/.config`, not inline in the subworkflow `.nf` file. +- Only `ext.args`, `ext.args2`, and `ext.prefix` belong in module configs. Don't add business logic there. +- Conditional behavior (e.g. save as CRAM vs BAM) is handled in the subworkflow via `channel.empty()` gating — not via config-level flags. +- Process resource requirements (CPUs / memory / time) go in `conf/base.config` using `withLabel:` selectors so they can be shared across processes. Use `${task.cpus}` and `${task.memory}` in `script:` blocks to apply them dynamically. + +## Testing + +- Every subworkflow should have a test at `subworkflows/local//tests/main.nf.test`. +- Use `-stub` in the `when:` block only when real test data is difficult to generate. Prefer running with real data where it is reasonably available. +- Snapshot files (`*.nf.test.snap`) are committed alongside tests — update them when outputs change. +- Pipeline-level tests live in `tests/` and cover `default`, `test_bam`, and `test_singleton` profiles. +- Run `nf-test test ` for a single test, `nf-test test` for all. + +## Style + +- Both `take:` and `emit:` block entries require an inline type comment. Use `name // type: [mandatory|optional] description` for `take:` and `name = value // channel: [type description]` for `emit:`. Always include the comment — never leave an entry uncommented. + + ```groovy + take: + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_reduced_penetrance // channel: [optional] [ path(penetrance) ] + val_aligner // string: [mandatory] aligner name (bwa/bwamem2/bwameme) + process_with_sort // Boolean + + emit: + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] + ``` + +- Intermediate publish channels in `workflows/raredisease.nf` follow the `ch__publish` naming convention and are assigned immediately after the subworkflow call, not inline in the emit block. +- Initialize all `ch_*_publish` variables at the top of the `main:` block alongside `ch_multiqc_files`. + +## Nextflow version bumping + +If you are using a new feature from core Nextflow, bump the minimum required version with: + +```bash +nf-core pipelines bump-version --nextflow . [min-nf-version] +``` + +## Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). From 06bb07474179757fff9f427891acf8e34e2cc627 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Mar 2026 10:26:41 +0100 Subject: [PATCH 521/872] Update usage.md --- docs/usage.md | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 8f2c5cd37..f605967ad 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -133,16 +133,16 @@ If you would like to see more examples of what a typical samplesheet looks like The nf-core/raredisease pipeline can handle duplicate-marked BAM files as input. In such cases, samplesheet should contain the following columns: -| Fields | Description | -| ------------- | ------------------------------------------------------------------------------------------------------------------------------ | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | -| `bam` | Absolute path to a duplicate-marked BAM file. | -| `bai` | Absolute path to the BAM index file (.bai). | -| `sex` | Sex (1=male; 2=female; for unknown sex use 0 or 'other'). | -| `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | -| `paternal_id` | Sample ID of the father, can be blank if the father isn't part of the analysis or for samples other than the proband. | -| `maternal_id` | Sample ID of the mother, can be blank if the mother isn't part of the analysis or for samples other than the proband. | -| `case_id` | Case ID, for the analysis used when generating a family VCF. | +| Fields | Description | +| ------------- | --------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | +| `bam` | Absolute path to a duplicate-marked BAM file. | +| `bai` | Absolute path to the BAM index file (.bai). | +| `sex` | Sex (1=male; 2=female; for unknown sex use 0 or 'other'). | +| `phenotype` | Affected status of patient (0 = missing; 1=unaffected; 2=affected). | +| `paternal_id` | Sample ID of the father, can be blank if the father isn't part of the analysis or for samples other than the proband. | +| `maternal_id` | Sample ID of the mother, can be blank if the mother isn't part of the analysis or for samples other than the proband. | +| `case_id` | Case ID, for the analysis used when generating a family VCF. | If you would like to see an example of what a typical samplesheet looks like in this case, follow this [link.](https://github.com/nf-core/test-datasets/blob/raredisease/testdata/samplesheet_bam.csv) @@ -171,12 +171,12 @@ Note that the pipeline is modular in architecture. It offers you the flexibility The pipeline is modular — individual tools and subworkflows can be skipped using `--skip_tools` and `--skip_subworkflows` (comma-separated). The valid values are: -| `--skip_tools` | -| ----------------------------------------------------------------------------------------------- | +| `--skip_tools` | +| ----------------------------------------------------------------------------------------------------------------------------------- | | `fastp`, `fastqc`, `gens`, `germlinecnvcaller`, `haplogrep3`, `ngsbits`, `peddy`, `qualimap`, `smncopynumbercaller`, `vcf2cytosure` | -| `--skip_subworkflows` | -| ------------------------------------------------------------------------------------------------------------------------------------------- | +| `--skip_subworkflows` | +| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `generate_clinical_set`, `me_annotation`, `me_calling`, `mt_annotation`, `mt_subsample`, `repeat_annotation`, `repeat_calling`, `snv_annotation`, `snv_calling`, `sv_annotation`, `sv_calling` | nf-core/raredisease consists of several tools used for various purposes. For convenience, we have grouped those tools under the following categories: From cd88d5402e224f9bad9d600ed7be0d9981ff2d2c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Mar 2026 10:31:34 +0100 Subject: [PATCH 522/872] Update CONTRIBUTING_GUIDELINES.md --- CONTRIBUTING_GUIDELINES.md | 45 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/CONTRIBUTING_GUIDELINES.md b/CONTRIBUTING_GUIDELINES.md index 26fdc19e5..57f774a98 100644 --- a/CONTRIBUTING_GUIDELINES.md +++ b/CONTRIBUTING_GUIDELINES.md @@ -12,6 +12,7 @@ - [Testing](#testing) - [Style](#style) - [Nextflow version bumping](#nextflow-version-bumping) +- [Adding citations](#adding-citations) - [Images and figures](#images-and-figures) ## Contribution workflow @@ -104,6 +105,50 @@ If you are using a new feature from core Nextflow, bump the minimum required ver nf-core pipelines bump-version --nextflow . [min-nf-version] ``` +## Adding citations + +When adding a new tool to the pipeline, update the following three locations: + +### 1. `CITATIONS.md` + +Add an entry for the tool in alphabetical order under `## Pipeline tools`. If the tool has a publication, include a `>` citation block: + +```markdown +- [ToolName](https://link-to-paper-or-repo) + + > Author A, Author B. Title. Journal. Year;vol(issue):pages. doi:... +``` + +If the tool has no publication, list only the link: + +```markdown +- [ToolName](https://github.com/org/toolname) +``` + +### 2. `subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf` + +Add citation text and bibliography entries inside `toolCitationText()` and `toolBibliographyText()`. Both functions are structured identically — group the tool's entry under the relevant category variable (e.g. `align_text`, `qc_bam_text`, `preprocessing_text`, `snv_annotation_text`). Mirror any conditional logic that gates the tool's execution (e.g. skip params, analysis type, or input content) so the citation only appears when the tool actually runs: + +```groovy +// toolCitationText() +qc_bam_text = [ + ..., + (condition) ? "ToolName (Author et al., Year)," : "" +] + +// toolBibliographyText() +qc_bam_text = [ + ..., + (condition) ? "
  • Author A, Author B. Title. Journal. Year. doi:...
    • " : "" +] +``` + +For tools that run only when the input samplesheet contains a particular file type, use a helper function rather than a param check — see `hasSpringInput()` as an example. + +### 3. `README.md` + +Add the tool to the relevant numbered section in the **Pipeline summary**. If the tool belongs to a new category not yet represented, add a new numbered section in the appropriate position. + ## Images and figures For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). From 26e1f00f5733ba8a198c9fe08734d293bb5893f7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 19 Mar 2026 15:23:14 +0100 Subject: [PATCH 523/872] Merge contributing docs --- .github/CONTRIBUTING.md | 197 ++++++++++++++++++++++++++++--------- CONTRIBUTING_GUIDELINES.md | 154 ----------------------------- 2 files changed, 152 insertions(+), 199 deletions(-) delete mode 100644 CONTRIBUTING_GUIDELINES.md diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 4be355edd..aa03cdafc 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -12,19 +12,40 @@ Contributions to the code are even more welcome ;) > [!NOTE] > If you need help using or modifying nf-core/raredisease then the best place to ask is on the nf-core Slack [#raredisease](https://nfcore.slack.com/channels/raredisease) channel ([join our Slack here](https://nf-co.re/join/slack)). -## Contribution workflow - -If you'd like to write some code for nf-core/raredisease, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/raredisease issues](https://github.com/nf-core/raredisease/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/raredisease repository](https://github.com/nf-core/raredisease) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged +## Table of contents + +- [General](#general) + - [Contribution workflow](#contribution-workflow) + - [Running tests](#running-tests) + - [Patch](#patch) + - [Getting help](#getting-help) + - [Nextflow version bumping](#nextflow-version-bumping) + - [Images and figures](#images-and-figures) + - [GitHub Codespaces](#github-codespaces) +- [Pipeline-specific conventions](#pipeline-specific-conventions) + - [Architecture & structure](#architecture--structure) + - [Adding a new step](#adding-a-new-step) + - [Channel conventions](#channel-conventions) + - [Params & analysis types](#params--analysis-types) + - [Publishing](#publishing) + - [Configuration](#configuration) + - [Writing tests](#writing-tests) + - [Style](#style) + - [Adding citations](#adding-citations) + +## General + +### Contribution workflow + +1. Check that there isn't already an issue about your idea in the [nf-core/raredisease issues](https://github.com/nf-core/raredisease/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this. +2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/raredisease repository](https://github.com/nf-core/raredisease) to your GitHub account. +3. Make the necessary changes / additions within your forked repository following the conventions below. +4. Use `nf-core pipelines schema build` to add any new parameters to `nextflow_schema.json`. +5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged. If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). -## Tests +### Running tests You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: @@ -37,21 +58,21 @@ Typically, pull-requests are only fully reviewed when these tests are passing, t There are typically two types of tests that run: -### Lint tests +#### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. -### Pipeline tests +#### Pipeline tests Each `nf-core` pipeline should be set up with a minimal set of test-data. `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. If there are any failures then the automated tests fail. These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. -## Patch +### Patch :warning: Only in the unlikely and regretful event of a release happening with a bug. @@ -59,67 +80,153 @@ These tests are run both with the latest available version of `Nextflow` and als - Fix the bug, and bump version (X.Y.Z+1). - Open a pull-request from `patch` to `main`/`master` with the changes. -## Getting help +### Getting help For further information/help, please consult the [nf-core/raredisease documentation](https://nf-co.re/raredisease/usage) and don't hesitate to get in touch on the nf-core Slack [#raredisease](https://nfcore.slack.com/channels/raredisease) channel ([join our Slack here](https://nf-co.re/join/slack)). -## Pipeline contribution conventions +### Nextflow version bumping -To make the `nf-core/raredisease` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +If you are using a new feature from core Nextflow, bump the minimum required version with: -### Adding a new step +```bash +nf-core pipelines bump-version --nextflow . [min-nf-version] +``` + +### Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). + +### GitHub Codespaces -If you wish to contribute a new step, please use the following coding standards: +This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. + +To get started: + +- Open the repo in [Codespaces](https://github.com/nf-core/raredisease/codespaces) +- Tools installed + - nf-core + - Nextflow + +Devcontainer specs: + +- [DevContainer config](.devcontainer/devcontainer.json) + +## Pipeline-specific conventions + +### Architecture & structure + +- **One subworkflow per biological task** — alignment, QC, variant calling, annotation, and ranking are each their own subworkflow under `subworkflows/local/`. Don't add logic to `workflows/raredisease.nf` that belongs in a subworkflow. +- **Reuse over duplication** — `RANK_VARIANTS`, `ANNOTATE_CSQ_PLI`, and `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` are intentionally included multiple times under different aliases. Follow this pattern before creating a near-identical subworkflow. +- **nf-core modules first** — prefer a module from `modules/nf-core/` over writing a local one. Only add to `modules/local/` when no nf-core module exists or the use case is too pipeline-specific. + +### Adding a new step 1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). +2. Write the process block. +3. Define the output channel if needed. +4. Add any new parameters to `nextflow.config` with a default. 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. +9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. -### Default values +### Channel conventions -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. +- **Skip lists**: use `parseSkipList()` and the `skip_tools` / `skip_subworkflows` params. Don't gate logic with raw string comparisons against params directly. +- **Conditional channels**: always initialize to `channel.empty()` before any `if` block that may or may not assign them. Never leave a channel potentially undefined. +- **Channel helpers**: use `channelFromPath`, `channelFromPathWithMeta`, and `channelFromSamplesheet` from `utils_nfcore_raredisease_pipeline` rather than rolling your own `channel.fromPath` calls. -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. +### Params & analysis types -### Default processes resource requirements +- `params` must only be accessed in the main unnamed workflow (`workflow` in `main.nf`). Subworkflows and named workflows receive all values as explicit `val_*` arguments. Never reference `params` directly inside a subworkflow. +- New tools that only apply to `wgs`, `wes`, or `mito` must be gated on `val_analysis_type`. +- Skippable tools must be added to the `--skip_tools` or `--skip_subworkflows` param and handled via `parseSkipList()`. +- Default params go in `nextflow.config`. Don't hardcode values that a user might reasonably want to change. Once added, run `nf-core pipelines schema build` to register them in `nextflow_schema.json`. -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +### Publishing -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. +- Build a single `ch_publish` channel inside each subworkflow by mixing all publishable outputs into `[destination, value]` tuples. +- The emit name must always be `publish = ch_publish` — never the bare shorthand. +- Group channels that share a destination with `mix` first, then apply **one** `.map` per destination group — never one map per channel. +- If your subworkflow calls inner subworkflows, always mix their `.out.publish` into the outer `ch_publish`. Never discard it. +- Remove the corresponding `publishDir` entry from `conf/modules/` when adding a process to `ch_publish`. -### Naming schemes +### Configuration -Please use the following naming schemes, to make it easy to understand what is going where. +- Process-level options go in `conf/modules/.config`, not inline in the subworkflow `.nf` file. +- Only `ext.args`, `ext.args2`, and `ext.prefix` belong in module configs. Don't add business logic there. +- Conditional behavior (e.g. save as CRAM vs BAM) is handled in the subworkflow via `channel.empty()` gating — not via config-level flags. +- Process resource requirements (CPUs / memory / time) go in `conf/base.config` using `withLabel:` selectors so they can be shared across processes. Use `${task.cpus}` and `${task.memory}` in `script:` blocks to apply them dynamically. -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` +### Writing tests -### Nextflow version bumping +- Every subworkflow should have a test at `subworkflows/local//tests/main.nf.test`. +- Use `-stub` in the `when:` block only when real test data is difficult to generate. Prefer running with real data where it is reasonably available. +- Snapshot files (`*.nf.test.snap`) are committed alongside tests — update them when outputs change. +- Pipeline-level tests live in `tests/` and cover `default`, `test_bam`, and `test_singleton` profiles. +- Run `nf-test test ` for a single test, `nf-test test` for all. -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` +### Style -### Images and figures +- Both `take:` and `emit:` block entries require an inline type comment. Use `name // type: [mandatory|optional] description` for `take:` and `name = value // channel: [type description]` for `emit:`. Always include the comment — never leave an entry uncommented. -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). + ```groovy + take: + ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] + ch_reduced_penetrance // channel: [optional] [ path(penetrance) ] + val_aligner // string: [mandatory] aligner name (bwa/bwamem2/bwameme) + process_with_sort // Boolean -## GitHub Codespaces + emit: + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + publish = ch_publish // channel: [ val(destination), val(value) ] + ``` -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. +- Intermediate publish channels in `workflows/raredisease.nf` follow the `ch__publish` naming convention and are assigned immediately after the subworkflow call, not inline in the emit block. +- Initialize all `ch_*_publish` variables at the top of the `main:` block alongside `ch_multiqc_files`. -To get started: +### Adding citations -- Open the repo in [Codespaces](https://github.com/nf-core/raredisease/codespaces) -- Tools installed - - nf-core - - Nextflow +When adding a new tool to the pipeline, update the following three locations: -Devcontainer specs: +#### 1. `CITATIONS.md` -- [DevContainer config](.devcontainer/devcontainer.json) +Add an entry for the tool in alphabetical order under `## Pipeline tools`. If the tool has a publication, include a `>` citation block: + +```markdown +- [ToolName](https://link-to-paper-or-repo) + + > Author A, Author B. Title. Journal. Year;vol(issue):pages. doi:... +``` + +If the tool has no publication, list only the link: + +```markdown +- [ToolName](https://github.com/org/toolname) +``` + +#### 2. `subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf` + +Add citation text and bibliography entries inside `toolCitationText()` and `toolBibliographyText()`. Both functions are structured identically — group the tool's entry under the relevant category variable (e.g. `align_text`, `qc_bam_text`, `preprocessing_text`, `snv_annotation_text`). Mirror any conditional logic that gates the tool's execution (e.g. skip params, analysis type, or input content) so the citation only appears when the tool actually runs: + +```groovy +// toolCitationText() +qc_bam_text = [ + ..., + (condition) ? "ToolName (Author et al., Year)," : "" +] + +// toolBibliographyText() +qc_bam_text = [ + ..., + (condition) ? "
  • Author A, Author B. Title. Journal. Year. doi:...
    • " : "" +] +``` + +For tools that run only when the input samplesheet contains a particular file type, use a helper function rather than a param check — see `hasSpringInput()` as an example. + +#### 3. `README.md` + +Add the tool to the relevant numbered section in the **Pipeline summary**. If the tool belongs to a new category not yet represented, add a new numbered section in the appropriate position. diff --git a/CONTRIBUTING_GUIDELINES.md b/CONTRIBUTING_GUIDELINES.md deleted file mode 100644 index 57f774a98..000000000 --- a/CONTRIBUTING_GUIDELINES.md +++ /dev/null @@ -1,154 +0,0 @@ -# Contributing Guidelines - -## Table of contents - -- [Contribution workflow](#contribution-workflow) -- [Architecture & structure](#architecture--structure) -- [Adding a new step](#adding-a-new-step) -- [Channel conventions](#channel-conventions) -- [Params & analysis types](#params--analysis-types) -- [Publishing](#publishing) -- [Configuration](#configuration) -- [Testing](#testing) -- [Style](#style) -- [Nextflow version bumping](#nextflow-version-bumping) -- [Adding citations](#adding-citations) -- [Images and figures](#images-and-figures) - -## Contribution workflow - -1. Check that there isn't already an issue about your idea in the [nf-core/raredisease issues](https://github.com/nf-core/raredisease/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this. -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/raredisease repository](https://github.com/nf-core/raredisease) to your GitHub account. -3. Make the necessary changes / additions within your forked repository following the conventions below. -4. Use `nf-core pipelines schema build` to add any new parameters to `nextflow_schema.json`. -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged. - -## Architecture & structure - -- **One subworkflow per biological task** — alignment, QC, variant calling, annotation, and ranking are each their own subworkflow under `subworkflows/local/`. Don't add logic to `workflows/raredisease.nf` that belongs in a subworkflow. -- **Reuse over duplication** — `RANK_VARIANTS`, `ANNOTATE_CSQ_PLI`, and `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` are intentionally included multiple times under different aliases. Follow this pattern before creating a near-identical subworkflow. -- **nf-core modules first** — prefer a module from `modules/nf-core/` over writing a local one. Only add to `modules/local/` when no nf-core module exists or the use case is too pipeline-specific. - -## Adding a new step - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block. -3. Define the output channel if needed. -4. Add any new parameters to `nextflow.config` with a default. -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -## Channel conventions - -- **Skip lists**: use `parseSkipList()` and the `skip_tools` / `skip_subworkflows` params. Don't gate logic with raw string comparisons against params directly. -- **Conditional channels**: always initialize to `channel.empty()` before any `if` block that may or may not assign them. Never leave a channel potentially undefined. -- **Channel helpers**: use `channelFromPath`, `channelFromPathWithMeta`, and `channelFromSamplesheet` from `utils_nfcore_raredisease_pipeline` rather than rolling your own `channel.fromPath` calls. - -## Params & analysis types - -- `params` must only be accessed in the main unnamed workflow (`workflow` in `main.nf`). Subworkflows and named workflows receive all values as explicit `val_*` arguments. Never reference `params` directly inside a subworkflow. -- New tools that only apply to `wgs`, `wes`, or `mito` must be gated on `val_analysis_type`. -- Skippable tools must be added to the `--skip_tools` or `--skip_subworkflows` param and handled via `parseSkipList()`. -- Default params go in `nextflow.config`. Don't hardcode values that a user might reasonably want to change. Once added, run `nf-core pipelines schema build` to register them in `nextflow_schema.json`. - -## Publishing - -- Build a single `ch_publish` channel inside each subworkflow by mixing all publishable outputs into `[destination, value]` tuples. -- The emit name must always be `publish = ch_publish` — never the bare shorthand. -- Group channels that share a destination with `mix` first, then apply **one** `.map` per destination group — never one map per channel. -- If your subworkflow calls inner subworkflows, always mix their `.out.publish` into the outer `ch_publish`. Never discard it. -- Remove the corresponding `publishDir` entry from `conf/modules/` when adding a process to `ch_publish`. - -## Configuration - -- Process-level options go in `conf/modules/.config`, not inline in the subworkflow `.nf` file. -- Only `ext.args`, `ext.args2`, and `ext.prefix` belong in module configs. Don't add business logic there. -- Conditional behavior (e.g. save as CRAM vs BAM) is handled in the subworkflow via `channel.empty()` gating — not via config-level flags. -- Process resource requirements (CPUs / memory / time) go in `conf/base.config` using `withLabel:` selectors so they can be shared across processes. Use `${task.cpus}` and `${task.memory}` in `script:` blocks to apply them dynamically. - -## Testing - -- Every subworkflow should have a test at `subworkflows/local//tests/main.nf.test`. -- Use `-stub` in the `when:` block only when real test data is difficult to generate. Prefer running with real data where it is reasonably available. -- Snapshot files (`*.nf.test.snap`) are committed alongside tests — update them when outputs change. -- Pipeline-level tests live in `tests/` and cover `default`, `test_bam`, and `test_singleton` profiles. -- Run `nf-test test ` for a single test, `nf-test test` for all. - -## Style - -- Both `take:` and `emit:` block entries require an inline type comment. Use `name // type: [mandatory|optional] description` for `take:` and `name = value // channel: [type description]` for `emit:`. Always include the comment — never leave an entry uncommented. - - ```groovy - take: - ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] - ch_reduced_penetrance // channel: [optional] [ path(penetrance) ] - val_aligner // string: [mandatory] aligner name (bwa/bwamem2/bwameme) - process_with_sort // Boolean - - emit: - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] - ``` - -- Intermediate publish channels in `workflows/raredisease.nf` follow the `ch__publish` naming convention and are assigned immediately after the subworkflow call, not inline in the emit block. -- Initialize all `ch_*_publish` variables at the top of the `main:` block alongside `ch_multiqc_files`. - -## Nextflow version bumping - -If you are using a new feature from core Nextflow, bump the minimum required version with: - -```bash -nf-core pipelines bump-version --nextflow . [min-nf-version] -``` - -## Adding citations - -When adding a new tool to the pipeline, update the following three locations: - -### 1. `CITATIONS.md` - -Add an entry for the tool in alphabetical order under `## Pipeline tools`. If the tool has a publication, include a `>` citation block: - -```markdown -- [ToolName](https://link-to-paper-or-repo) - - > Author A, Author B. Title. Journal. Year;vol(issue):pages. doi:... -``` - -If the tool has no publication, list only the link: - -```markdown -- [ToolName](https://github.com/org/toolname) -``` - -### 2. `subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf` - -Add citation text and bibliography entries inside `toolCitationText()` and `toolBibliographyText()`. Both functions are structured identically — group the tool's entry under the relevant category variable (e.g. `align_text`, `qc_bam_text`, `preprocessing_text`, `snv_annotation_text`). Mirror any conditional logic that gates the tool's execution (e.g. skip params, analysis type, or input content) so the citation only appears when the tool actually runs: - -```groovy -// toolCitationText() -qc_bam_text = [ - ..., - (condition) ? "ToolName (Author et al., Year)," : "" -] - -// toolBibliographyText() -qc_bam_text = [ - ..., - (condition) ? "
  • Author A, Author B. Title. Journal. Year. doi:...
    • " : "" -] -``` - -For tools that run only when the input samplesheet contains a particular file type, use a helper function rather than a param check — see `hasSpringInput()` as an example. - -### 3. `README.md` - -Add the tool to the relevant numbered section in the **Pipeline summary**. If the tool belongs to a new category not yet represented, add a new numbered section in the appropriate position. - -## Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). From 180bdf3d40de1418595d9f28a5d5bd9ee8ad3e2d Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 20 Mar 2026 10:32:56 +0100 Subject: [PATCH 524/872] add PLI line to config for hisat2 bug --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 477d58e02..b4d6e049f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -341,6 +341,7 @@ env { R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" + NXF_SINGULARITY_NEW_PID_NAMESPACE = false } // Set bash options From 5df75fc881f503886bae169fdb65be3fa8fe9d4e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 20 Mar 2026 12:34:11 +0100 Subject: [PATCH 525/872] move optional saltshaker inputs --- conf/modules/call_sv_MT.config | 6 +++++- subworkflows/local/call_structural_variants/main.nf | 12 +----------- subworkflows/local/call_sv_MT/main.nf | 13 +------------ workflows/raredisease.nf | 5 ----- 4 files changed, 7 insertions(+), 29 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index c2ace0c04..321f23add 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -20,13 +20,17 @@ process { withName: '.*CALL_SV_MT:MT_DELETION' { ext.args = '-s --insert-size 16000' ext.prefix = { "${meta.id}_mitochondria_deletions" } + } withName: '.*CALL_SV_MT:SALTSHAKER_CALL' { ext.args = '--blacklist' } withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' { - ext.args = '--blacklist --vcf' + ext.args = { "--blacklist --vcf --dominant-fraction ${params.saltshaker_dominant_fraction} \ + --radius ${params.saltshaker_group_radius} --high-het ${params.saltshaker_high_heteroplasmy} \ + --multiple-threshold ${params.saltshaker_multiple_threshold} --noise ${params.saltshaker_noise_threshold}" + } } withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index a3174e134..abcb82218 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -56,11 +56,6 @@ workflow CALL_STRUCTURAL_VARIANTS { val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold val_mitosalt_split_length // string: [mandatory] mitosalt_split_length - val_saltshaker_dominant_fraction // string: [mandatory] saltshaker_dominant_fraction - val_saltshaker_group_radius // string: [mandatory] saltshaker_group_radius - val_saltshaker_high_heteroplasmy // string: [mandatory] saltshaker_high_heteroplasmy - val_saltshaker_multiple_threshold // string: [mandatory] saltshaker_multiple_threshold - val_saltshaker_noise_threshold // string: [mandatory] saltshaker_noise_threshold val_run_mt_for_wes // boolean: [mandatory] run_mt_for_wes main: @@ -125,12 +120,7 @@ workflow CALL_STRUCTURAL_VARIANTS { val_mitosalt_score_threshold, val_mitosalt_sizelimit, val_mitosalt_split_distance_threshold, - val_mitosalt_split_length, - val_saltshaker_dominant_fraction, - val_saltshaker_group_radius, - val_saltshaker_high_heteroplasmy, - val_saltshaker_multiple_threshold, - val_saltshaker_noise_threshold) + val_mitosalt_split_length) .mitosalt_vcf .collect{ _meta, vcf -> vcf } .set { mitosalt_vcf } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index c983e5b28..a428dd7d1 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -42,11 +42,6 @@ workflow CALL_SV_MT { val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold val_mitosalt_split_length // string: [mandatory] mitosalt_split_length - val_saltshaker_dominant_fraction // string: [mandatory] saltshaker_dominant_fraction - val_saltshaker_group_radius // string: [mandatory] saltshaker_group_radius - val_saltshaker_high_heteroplasmy // string: [mandatory] saltshaker_high_heteroplasmy - val_saltshaker_multiple_threshold // string: [mandatory] saltshaker_multiple_threshold - val_saltshaker_noise_threshold // string: [mandatory] saltshaker_noise_threshold main: ch_mitosalt_publish = channel.empty() @@ -114,22 +109,16 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY( SALTSHAKER_CALL.out.call, - val_saltshaker_dominant_fraction, - val_saltshaker_group_radius, - val_saltshaker_high_heteroplasmy, - val_saltshaker_multiple_threshold, - val_saltshaker_noise_threshold, val_mito_name ) SALTSHAKER_PLOT( SALTSHAKER_CLASSIFY.out.classify ) - ch_mitosalt_plot = SALTSHAKER_PLOT.out.plot } ch_mitosalt_publish = SALTSHAKER_CLASSIFY.out.txt .mix(SALTSHAKER_CLASSIFY.out.vcf) - .mix(SALTSHAKER_PLOT.out.plot + .mix(SALTSHAKER_PLOT.out.plot) } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 5f95b5963..a87baf1c0 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -616,11 +616,6 @@ workflow RAREDISEASE { params.mitosalt_sizelimit, params.mitosalt_split_distance_threshold, params.mitosalt_split_length, - params.saltshaker_dominant_fraction, - params.saltshaker_group_radius, - params.saltshaker_high_heteroplasmy, - params.saltshaker_multiple_threshold, - params.saltshaker_noise_threshold, val_run_mt_for_wes ) ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish From af418591a841a04edbdb3251ed8b0eeb40d53179 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 20 Mar 2026 13:08:23 +0100 Subject: [PATCH 526/872] update saltshaker modules --- modules.json | 4 +- .../saltshaker/classify/environment.yml | 2 +- modules/nf-core/saltshaker/classify/main.nf | 18 ++---- modules/nf-core/saltshaker/classify/meta.yml | 22 ++------ .../saltshaker/classify/tests/main.nf.test | 36 ++++-------- .../classify/tests/main.nf.test.snap | 56 +++++++++---------- .../saltshaker/plot/tests/main.nf.test | 6 +- 7 files changed, 52 insertions(+), 92 deletions(-) diff --git a/modules.json b/modules.json index 870531678..26986ceb5 100644 --- a/modules.json +++ b/modules.json @@ -403,12 +403,12 @@ }, "saltshaker/classify": { "branch": "master", - "git_sha": "659c65b93278533f1a29c4d4235851b4f29242da", + "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", "installed_by": ["modules"] }, "saltshaker/plot": { "branch": "master", - "git_sha": "95fc5183fd3a798ea4ff0978bc10c526e87a49cc", + "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", "installed_by": ["modules"] }, "sambamba/depth": { diff --git a/modules/nf-core/saltshaker/classify/environment.yml b/modules/nf-core/saltshaker/classify/environment.yml index f76c4bf5a..3672c7873 100644 --- a/modules/nf-core/saltshaker/classify/environment.yml +++ b/modules/nf-core/saltshaker/classify/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.0 + - saltshaker==1.0.1 diff --git a/modules/nf-core/saltshaker/classify/main.nf b/modules/nf-core/saltshaker/classify/main.nf index 209312974..72fa27c16 100644 --- a/modules/nf-core/saltshaker/classify/main.nf +++ b/modules/nf-core/saltshaker/classify/main.nf @@ -4,22 +4,18 @@ process SALTSHAKER_CLASSIFY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': - 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0c/0c955cc086622ef50876a10e58a1e6711e42b70a0e4cbbc377142b62b0ad4f47/data': + 'community.wave.seqera.io/library/pip_saltshaker:ef543ea5ca09afbe' }" input: tuple val(meta), path(call) - val dominant_fraction - val group_radius - val high_heteroplasmy - val multiple_threshold - val noise_threshold + val mito_name output: tuple val(meta), path("*_classify_metadata.tsv"), emit: classify tuple val(meta), path("*_classify.txt") , emit: txt tuple val(meta), path("*saltshaker.vcf") , emit: vcf, optional: true - tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.0.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when @@ -32,11 +28,7 @@ process SALTSHAKER_CLASSIFY { saltshaker classify \\ --prefix $prefix \\ --input-dir . \\ - --dominant-fraction $dominant_fraction \\ - --radius $group_radius \\ - --high-het $high_heteroplasmy \\ - --multiple-threshold $multiple_threshold \\ - --noise $noise_threshold \\ + --chr-format $mito_name \\ $args """ diff --git a/modules/nf-core/saltshaker/classify/meta.yml b/modules/nf-core/saltshaker/classify/meta.yml index 182df6566..be07a8946 100644 --- a/modules/nf-core/saltshaker/classify/meta.yml +++ b/modules/nf-core/saltshaker/classify/meta.yml @@ -24,21 +24,9 @@ input: ontologies: - edam: http://edamontology.org/operation_3227 #variant calling - edam: http://edamontology.org/format_3475 #tsv - - dominant_fraction: - type: float - description: Minimum heteroplasmy fraction to classify as dominant in saltshaker - - group_radius: - type: integer - description: Spatial clustering radius for saltshaker grouping - - high_heteroplasmy: - type: float - description: High heteroplasmy threshold for saltshaker classification - - multiple_threshold: - type: float - description: Heteroplasmy threshold for multiple classification in saltshaker - - noise_threshold: - type: float - description: Heteroplasmy threshold for noise in saltshaker classification + - mito_name: + type: string + description: Name of the mitochondrial chromosome output: classify: - - meta: @@ -86,7 +74,7 @@ output: - saltshaker: type: string description: The name of the tool - - 1.0.0: + - 1.0.1: type: string description: Hardcoded version of saltshaker used in the module topics: @@ -97,7 +85,7 @@ topics: - saltshaker: type: string description: The name of the tool - - 1.0.0: + - 1.0.1: type: string description: Hardcoded version of saltshaker used in the module authors: diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test b/modules/nf-core/saltshaker/classify/tests/main.nf.test index 12cc1ec94..3830b1832 100644 --- a/modules/nf-core/saltshaker/classify/tests/main.nf.test +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test @@ -43,16 +43,12 @@ nextflow_process { when { params { - module_args = '--blacklist --vcf' + module_args = '--blacklist --vcf --dominant-fraction 0.5 --radius 600 --high-het 10 --multiple-threshold 5 --noise 0.3' } process { """ input[0] = SALTSHAKER_CALL.out.call - input[1] = 0.5 - input[2] = 600 - input[3] = 10 - input[4] = 5 - input[5] = 0.3 + input[1] = "MT" """ } } @@ -75,16 +71,12 @@ nextflow_process { when { params { - module_args = '--blacklist --vcf' + module_args = '--blacklist --vcf --dominant-fraction 0.5 --radius 600 --high-het 10 --multiple-threshold 5 --noise 0.3' } process { """ input[0] = SALTSHAKER_CALL.out.call - input[1] = 0.5 - input[2] = 600 - input[3] = 10 - input[4] = 5 - input[5] = 0.3 + input[1] = "MT" """ } } @@ -100,20 +92,16 @@ nextflow_process { } - test("classify - no-vcf") { + test("classify - defaults") { when { params { - module_args = '--blacklist' + module_args = '' } process { """ input[0] = SALTSHAKER_CALL.out.call - input[1] = 0.5 - input[2] = 600 - input[3] = 10 - input[4] = 5 - input[5] = 0.3 + input[1] = "MT" """ } } @@ -130,22 +118,18 @@ nextflow_process { } - test("classify - no-vcf - stub") { + test("classify - defaults - stub") { options "-stub" when { params { - module_args = '--blacklist' + module_args = '' } process { """ input[0] = SALTSHAKER_CALL.out.call - input[1] = 0.5 - input[2] = 600 - input[3] = 10 - input[4] = 5 - input[5] = 0.3 + input[1] = "MT" """ } } diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap index ff226554f..507105e8c 100644 --- a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "classify - no-vcf": { + "classify - defaults - stub": { "content": [ { "classify": [ @@ -7,7 +7,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "txt": [ @@ -15,7 +15,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -25,18 +25,18 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.0" + "1.0.1" ] ] } ], - "timestamp": "2026-03-17T11:02:38.830976", + "timestamp": "2026-03-20T12:29:31.591954", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.0" } }, - "classify - vcf - stub": { + "classify - defaults": { "content": [ { "classify": [ @@ -44,7 +44,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" ] ], "txt": [ @@ -52,33 +52,28 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" ] ], "vcf": [ - [ - { - "id": "test" - }, - "test.saltshaker.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions_saltshaker": [ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.0" + "1.0.1" ] ] } ], - "timestamp": "2026-03-16T10:53:38.916497", + "timestamp": "2026-03-20T12:29:26.57794", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.0" } }, - "classify - vcf": { + "classify - vcf - stub": { "content": [ { "classify": [ @@ -86,7 +81,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "txt": [ @@ -94,7 +89,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -102,25 +97,25 @@ { "id": "test" }, - "test.saltshaker.vcf:md5,6669688cfb486e6c98f0aadb8e41ed88" + "test.saltshaker.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions_saltshaker": [ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.0" + "1.0.1" ] ] } ], - "timestamp": "2026-03-17T10:17:34.236265", + "timestamp": "2026-03-20T11:05:52.842015", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.0" } }, - "classify - no-vcf - stub": { + "classify - vcf": { "content": [ { "classify": [ @@ -128,7 +123,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" ] ], "txt": [ @@ -136,22 +131,27 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" ] ], "vcf": [ - + [ + { + "id": "test" + }, + "test.saltshaker.vcf:md5,0c59728289ee8bcb19d44aea4d3155ab" + ] ], "versions_saltshaker": [ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.0" + "1.0.1" ] ] } ], - "timestamp": "2026-03-17T11:02:43.86661", + "timestamp": "2026-03-20T11:05:45.058275", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.0" diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test b/modules/nf-core/saltshaker/plot/tests/main.nf.test index 3aa867a9e..ec18cc241 100644 --- a/modules/nf-core/saltshaker/plot/tests/main.nf.test +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test @@ -44,11 +44,7 @@ nextflow_process { process { """ input[0] = SALTSHAKER_CALL.out.call - input[1] = 0.5 - input[2] = 600 - input[3] = 10 - input[4] = 5 - input[5] = 0.3 + input[1] = "MT" """ } } From 493a43a8435644f10c82acc4cc22cdc818fc8427 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 20 Mar 2026 14:42:56 +0100 Subject: [PATCH 527/872] empty saltshaker output channels for if it does not run --- subworkflows/local/call_sv_MT/main.nf | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index a428dd7d1..e920521c7 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -89,6 +89,11 @@ workflow CALL_SV_MT { .filter{ _meta, out -> out.countLines() > 0 } .set{ch_cluster} + ch_saltshaker_txt = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_saltshaker_plot = channel.empty() + ch_mitosalt_publish = channel.empty() + if (ch_cluster) { MITOSALT.out.breakpoint .join(ch_cluster) @@ -111,15 +116,18 @@ workflow CALL_SV_MT { SALTSHAKER_CALL.out.call, val_mito_name ) + ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt + ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf SALTSHAKER_PLOT( SALTSHAKER_CLASSIFY.out.classify ) - } - ch_mitosalt_publish = SALTSHAKER_CLASSIFY.out.txt - .mix(SALTSHAKER_CLASSIFY.out.vcf) - .mix(SALTSHAKER_PLOT.out.plot) + ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot + ch_mitosalt_publish = ch_saltshaker_txt + .mix(ch_saltshaker_vcf) + .mix(ch_saltshaker_plot) + } } MT_DELETION(ch_bam_bai, ch_genome_fasta) @@ -128,9 +136,9 @@ workflow CALL_SV_MT { .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } emit: - mitosalt_classify = SALTSHAKER_CLASSIFY.out.txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = SALTSHAKER_CLASSIFY.out.vcf // channel: [ val(meta), path(vcf) ] - mitosalt_plot = SALTSHAKER_PLOT.out.plot // channel: [ val(meta), path(png) ] + mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + mitosalt_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] publish = ch_publish // channel: [ val(destination), val(value) ] } From 7ad1d26e3ab943f4eb48d4a50ebb52355cf5cdcc Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 23 Mar 2026 09:57:44 +0100 Subject: [PATCH 528/872] fix MT sv inputs --- subworkflows/local/call_sv_MT/.main.nf.swp | Bin 0 -> 16384 bytes subworkflows/local/call_sv_MT/main.nf | 1 - .../local/call_sv_MT/tests/main.nf.test | 5 ----- 3 files changed, 6 deletions(-) create mode 100644 subworkflows/local/call_sv_MT/.main.nf.swp diff --git a/subworkflows/local/call_sv_MT/.main.nf.swp b/subworkflows/local/call_sv_MT/.main.nf.swp new file mode 100644 index 0000000000000000000000000000000000000000..40dddbc060b90b6ff9eaf18b41b5246d4b160e95 GIT binary patch literal 16384 zcmeHOUx*|}8LuRI$(h76e+VcFeL2a@guR~g3`Pzwu$~*U+-z=>T`z=VX=`R`b}HNd z(p|H+o8>Mjg7_dJD1tBI|HI@_$a&(U2^!GXJS7+e9~8tq+*6M-fIO$3?k5^@jxIx08(IRDrC|C`4M`8)78;IF{P~3;6Zz zgt)-{z$-@xc?NjrgM@q&uz@!|K*-mC6TokgjMxT_0oRbYSOa>%=Yjiy`+ys$&t+g2 zSOuN{P6D!?cL0UU%3Xu8v(5a#W6oe4#ry>pFOjUs`qL}x&f4ncg^lIjW}6sg8!Jz3 zo_98u*VcP0RvSzaqr=$2dk#YuigCx3E|gEroV9d;JqWx$_nBl$IkYo;WVMgCLmE*p zw&NWhIwA<%*m~$8tMH>8hb|ZG)>5kjQeWWJin!hKxCmnEidLu7u?|w_U``h~;iT{K zcx*|psP8k^W?m@v+Z|PL`Hse!RB@NOsirdNxXj-cW9_rLce_?BBJOXWu`YSkA5sxS z`&-t`WL8mGky<6xc#T9*f503uj#xYn+@ZA?by0DS8MMC3;g@tEd)1oJibQLf?hk?} z>$MiDci&VjXAdb}w;4LRk~8vJ_MBol`YP{PQjusi zJqS2H^-4NpB38kx6pM5vW2`n=8G~eSHV9q5Jr)keXAI0v5b+3Y7R@SrNh^%%#vBF%#t9}Hu;Z;U@~o+ zbL}Ph0JUc`?sRoxZOv+;S0H&l^Lq_D6ST8rT?(lfx79+Zvt^p_goAlR4ErW+_S-@x zlm*Ge{UO`y6pW1Id#YL1+~>uOctUZNncz86^XuVE@SK5UK|1C!6{l4tO?G@++(3q< z+)P!t7B^ECsH7evIzL#88<>)TtGpI^^Uon{u0J{{*NR=aypP8)5OqU05bCAsRypap-txxA>f_H^hanx{v5Wa=zmgag zI<&X)MerhNc7LTPtp&Vg&x;)d!V6tiVALDAgsj@l=_~4b)GTlrJHtBfrd(mf!r6|g zK)AN)d|{=xvblQU$(et18z*s2IJ4znJcxKGT7-1F__NL-qSnSmYi(2hAou@&z<&8* z?5pMeU!U*)348q;zz=}00z=?)z%k%0?EQZMOn}D$3wRIv{?~z*fvdneAaeo#Kn~zF z;8(zPnGXP70GW3_J+j0ubPBCGay~415N-9XJBKhdjjV z!0&+{0?z}V1Wo`S1+F7E@eJ@T;`d!(36Qbu0L|4z;QuEASBM^bvbmsHVn`Rxxf}Dj zT6GSYT&PjGwZ-yK&Wpf=>Df^7U}1<+4B4}I;_B_dSqxmW;m{5y!ZxLfhP=#lEB1t8 zAjy0=a#Bn@KbxOnm624S+Cb=Umm1g|jC5oS1A4YqMy5j51|U;vK+nLiGT#8IkMe2* znGi9|ahbH9tbpy&&^oYWOjV;zn04|o>rzY3)A$ctT{$bNO#53r}nWQtB(IuCydC+kSJalGQ@@}SOls-$_`^@)TKto2krEs{HRMfWWADpm&vOQcF{GdDpkt%>f#0WRl@77D7c3sjV-0R+8b!9(HIE?Nef>=#4$%F0z;hmNOmN zFa^mWP|ieyVB(7&PHN(I$9l{CJD1atkV7&kp8$)4qu9wf;C z%Bw_DADN_yYSW9Nnm*^LlQYk4YNT`LF!QC=z&pQK#bA*!!U)Bj@xhQujzwxrGw5W` tM{2}p`_@?|U!Hfo4<))+qm(>?3pcZQOi)8UOZyk)vJdsV(*M*`{V%I7Ows@V literal 0 HcmV?d00001 diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index a428dd7d1..87fd6118f 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -95,7 +95,6 @@ workflow CALL_SV_MT { .set{ch_saltshaker_in} SALTSHAKER_CALL( - MITOSALT.out.breakpoint, ch_saltshaker_in, ch_mt_fasta, val_mitosalt_flank, diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 7743e79ec..bf9930146 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -57,11 +57,6 @@ nextflow_workflow { input[27] = 10000 input[28] = 5 input[29] = 15 - input[30] = 0.5 - input[31] = 600 - input[32] = 10 - input[33] = 5 - input[34] = 0.3 """ } } From b2964c5d55dfb0b843155438a161217ae09b915c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 23 Mar 2026 09:58:32 +0100 Subject: [PATCH 529/872] fix MT sv inputs --- subworkflows/local/call_sv_MT/.main.nf.swp | Bin 16384 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 subworkflows/local/call_sv_MT/.main.nf.swp diff --git a/subworkflows/local/call_sv_MT/.main.nf.swp b/subworkflows/local/call_sv_MT/.main.nf.swp deleted file mode 100644 index 40dddbc060b90b6ff9eaf18b41b5246d4b160e95..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16384 zcmeHOUx*|}8LuRI$(h76e+VcFeL2a@guR~g3`Pzwu$~*U+-z=>T`z=VX=`R`b}HNd z(p|H+o8>Mjg7_dJD1tBI|HI@_$a&(U2^!GXJS7+e9~8tq+*6M-fIO$3?k5^@jxIx08(IRDrC|C`4M`8)78;IF{P~3;6Zz zgt)-{z$-@xc?NjrgM@q&uz@!|K*-mC6TokgjMxT_0oRbYSOa>%=Yjiy`+ys$&t+g2 zSOuN{P6D!?cL0UU%3Xu8v(5a#W6oe4#ry>pFOjUs`qL}x&f4ncg^lIjW}6sg8!Jz3 zo_98u*VcP0RvSzaqr=$2dk#YuigCx3E|gEroV9d;JqWx$_nBl$IkYo;WVMgCLmE*p zw&NWhIwA<%*m~$8tMH>8hb|ZG)>5kjQeWWJin!hKxCmnEidLu7u?|w_U``h~;iT{K zcx*|psP8k^W?m@v+Z|PL`Hse!RB@NOsirdNxXj-cW9_rLce_?BBJOXWu`YSkA5sxS z`&-t`WL8mGky<6xc#T9*f503uj#xYn+@ZA?by0DS8MMC3;g@tEd)1oJibQLf?hk?} z>$MiDci&VjXAdb}w;4LRk~8vJ_MBol`YP{PQjusi zJqS2H^-4NpB38kx6pM5vW2`n=8G~eSHV9q5Jr)keXAI0v5b+3Y7R@SrNh^%%#vBF%#t9}Hu;Z;U@~o+ zbL}Ph0JUc`?sRoxZOv+;S0H&l^Lq_D6ST8rT?(lfx79+Zvt^p_goAlR4ErW+_S-@x zlm*Ge{UO`y6pW1Id#YL1+~>uOctUZNncz86^XuVE@SK5UK|1C!6{l4tO?G@++(3q< z+)P!t7B^ECsH7evIzL#88<>)TtGpI^^Uon{u0J{{*NR=aypP8)5OqU05bCAsRypap-txxA>f_H^hanx{v5Wa=zmgag zI<&X)MerhNc7LTPtp&Vg&x;)d!V6tiVALDAgsj@l=_~4b)GTlrJHtBfrd(mf!r6|g zK)AN)d|{=xvblQU$(et18z*s2IJ4znJcxKGT7-1F__NL-qSnSmYi(2hAou@&z<&8* z?5pMeU!U*)348q;zz=}00z=?)z%k%0?EQZMOn}D$3wRIv{?~z*fvdneAaeo#Kn~zF z;8(zPnGXP70GW3_J+j0ubPBCGay~415N-9XJBKhdjjV z!0&+{0?z}V1Wo`S1+F7E@eJ@T;`d!(36Qbu0L|4z;QuEASBM^bvbmsHVn`Rxxf}Dj zT6GSYT&PjGwZ-yK&Wpf=>Df^7U}1<+4B4}I;_B_dSqxmW;m{5y!ZxLfhP=#lEB1t8 zAjy0=a#Bn@KbxOnm624S+Cb=Umm1g|jC5oS1A4YqMy5j51|U;vK+nLiGT#8IkMe2* znGi9|ahbH9tbpy&&^oYWOjV;zn04|o>rzY3)A$ctT{$bNO#53r}nWQtB(IuCydC+kSJalGQ@@}SOls-$_`^@)TKto2krEs{HRMfWWADpm&vOQcF{GdDpkt%>f#0WRl@77D7c3sjV-0R+8b!9(HIE?Nef>=#4$%F0z;hmNOmN zFa^mWP|ieyVB(7&PHN(I$9l{CJD1atkV7&kp8$)4qu9wf;C z%Bw_DADN_yYSW9Nnm*^LlQYk4YNT`LF!QC=z&pQK#bA*!!U)Bj@xhQujzwxrGw5W` tM{2}p`_@?|U!Hfo4<))+qm(>?3pcZQOi)8UOZyk)vJdsV(*M*`{V%I7Ows@V From 9a43f04aaffb9674eb36b3ea4d0f381c1f253233 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 23 Mar 2026 11:38:11 +0100 Subject: [PATCH 530/872] update logic for sv merging --- main.nf | 8 ++------ .../local/call_structural_variants/main.nf | 19 +++++++++++++------ subworkflows/local/call_sv_MT/main.nf | 10 +++++----- 3 files changed, 20 insertions(+), 17 deletions(-) diff --git a/main.nf b/main.nf index 12b6af1e1..44e5463ef 100644 --- a/main.nf +++ b/main.nf @@ -316,17 +316,13 @@ workflow NFCORE_RAREDISEASE { // if (skip_germlinecnvcaller) { if (val_analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator", "mitosalt"]) - } else if (val_run_mt_for_wes) { - ch_svcaller_priority = channel.value(["mitosalt"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "cnvnator"]) } else { ch_svcaller_priority = channel.value([]) } } else { if (val_analysis_type.equals("wgs")) { - ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator", "mitosalt"]) - } else if (val_run_mt_for_wes) { - ch_svcaller_priority = channel.value(["manta", "gcnvcaller", "mitosalt"]) + ch_svcaller_priority = channel.value(["tiddit", "manta", "gcnvcaller", "cnvnator"]) } else { ch_svcaller_priority = channel.value(["manta", "gcnvcaller"]) } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index abcb82218..bb5de98a0 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -132,7 +132,6 @@ workflow CALL_STRUCTURAL_VARIANTS { tiddit_vcf .combine(manta_vcf) .combine(cnvnator_vcf) - .combine(mitosalt_vcf) .toList() .set { vcf_list } } else if (!val_analysis_type.equals("mito")) { @@ -145,7 +144,6 @@ workflow CALL_STRUCTURAL_VARIANTS { .combine(manta_vcf) .combine(gcnvcaller_vcf) .combine(cnvnator_vcf) - .combine(mitosalt_vcf) .toList() .set { vcf_list } } else if (!val_analysis_type.equals("mito")) { @@ -156,19 +154,28 @@ workflow CALL_STRUCTURAL_VARIANTS { } if (!val_analysis_type.equals("mito")) { - ch_case_info.view() - ch_svcaller_priority.view() - vcf_list.view() + if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { + channel.of(ch_svcaller_priority, "mitosalt") + .collect() + .set { ch_svcaller_priority } + channel.of(vcf_list, mitosalt_vcf) + .collect() + .set { vcf_list } + } + ch_case_info .combine(vcf_list) .set { merge_input_vcfs } + ch_case_info.view() + ch_svcaller_priority.view() + vcf_list.view() SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - } else { + } else if (!mitosalt_vcf.equals(null)) { TABIX_TABIX (mitosalt_vcf) ch_merged_svs = mitosalt_vcf ch_merged_tbi = TABIX_TABIX.out.index diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 5a5b57e25..292739fbd 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -135,9 +135,9 @@ workflow CALL_SV_MT { .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } emit: - mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] - mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(null) // channel: [ val(meta), path(vcf) ] + mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From d99b63bc496ff49911bba2cab26644a60915ffdc Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Mon, 23 Mar 2026 14:33:38 +0100 Subject: [PATCH 531/872] Address PR review: refactor parse_contamination, fix changelog, add nf-tests - Convert parse_contamination inline Python to module binary (bin/) - Add stub section to parse_contamination module - Move CHANGELOG entries into 2.7.0dev section with PR links and tables - Revert unrelated publishDir changes in align config - Add nf-test subworkflow tests for contamination_check (WGS + WES) --- CHANGELOG.md | 25 ++-- conf/modules/align_bwa_bwamem2_bwameme.config | 4 +- .../bin/parse_contamination.py | 40 +++++++ modules/local/parse_contamination/main.nf | 57 ++++----- .../contamination_check/tests/main.nf.test | 112 ++++++++++++++++++ .../tests/main.nf.test.snap | 40 +++++++ .../contamination_check/tests/nextflow.config | 12 ++ 7 files changed, 236 insertions(+), 54 deletions(-) create mode 100755 modules/local/parse_contamination/bin/parse_contamination.py create mode 100644 subworkflows/local/contamination_check/tests/main.nf.test create mode 100644 subworkflows/local/contamination_check/tests/main.nf.test.snap create mode 100644 subworkflows/local/contamination_check/tests/nextflow.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 722db653d..0add9b2cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,19 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] -### Added - -- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2 -- New parameters: `run_contamination`, `contamination_sites`, `contamination_sites_tbi` -- CONTAMINATION_CHECK subworkflow using GATK4 GetPileupSummaries and CalculateContamination -- PARSE_CONTAMINATION module for MultiQC integration -- Contamination results displayed in MultiQC with color-coded thresholds - -### Changed - -- Updated MultiQC configuration to include GATK contamination metrics ## 2.7.0dev - Semiautomatix [xxxx-xx-xx] ### `Added` @@ -24,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for call_repeat_expansions and qc_bam subworkflows [#713](https://github.com/nf-core/raredisease/pull/713) - Feature to subsample mitochondrial alignments based on number of reads [#748](https://github.com/nf-core/raredisease/pull/748) - Functionality to generate coverage information using Sambamba depth [#752](https://github.com/nf-core/raredisease/pull/752) +- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2 [#758](https://github.com/nf-core/raredisease/pull/758) +- GATK Contamination results displayed in MultiQC with color-coded thresholds [#758](https://github.com/nf-core/raredisease/pull/758) ### `Changed` @@ -44,9 +34,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------- | ---------------- | -| | sambamba_regions | +| Old parameter | New parameter | +| ------------- | ----------------------- | +| | sambamba_regions | +| | run_contamination | +| | contamination_sites | +| | contamination_sites_tbi | ### Tool updates @@ -61,6 +54,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | gens-preproc | 1.0.11 | 1.1.2 | | samtools (sort & view) | 1.21 | 1.22.1 | | sambamba | | 1.0.1 | +| gatk4/calculatecontamination | | 4.6.2.0 | +| gatk4/getpileupsummaries | | 4.6.2.0 | ## 2.6.0 - Cacofonix [2025-06-25] diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index 5d7708c6f..d3dab330f 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -58,7 +58,7 @@ process { ext.args = "--TMP_DIR ." ext.prefix = { "${meta.id}_sorted_md" } publishDir = [ - enabled: true, + enabled: !params.save_mapped_as_cram, path: { "${params.outdir}/alignment" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } @@ -67,7 +67,7 @@ process { withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' { publishDir = [ - enabled: true, + enabled: !params.save_mapped_as_cram, path: { "${params.outdir}/alignment" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } diff --git a/modules/local/parse_contamination/bin/parse_contamination.py b/modules/local/parse_contamination/bin/parse_contamination.py new file mode 100755 index 000000000..dcde01e06 --- /dev/null +++ b/modules/local/parse_contamination/bin/parse_contamination.py @@ -0,0 +1,40 @@ +#!/usr/bin/env python3 +"""Parse GATK CalculateContamination output for MultiQC.""" + +import argparse + + +def parse_contamination(contamination_table, sample_id, prefix): + """Parse contamination table and write MultiQC output.""" + with open(contamination_table, 'r') as f: + lines = f.readlines() + data_line = lines[1].strip().split('\t') + contamination = float(data_line[1]) + contamination_pct = contamination * 100 + + with open(f"{prefix}_contamination_mqc.tsv", 'w') as out: + out.write("# id: 'gatk_contamination'\n") + out.write("# section_name: 'GATK Contamination'\n") + out.write("# description: 'Sample contamination estimates from GATK CalculateContamination'\n") + out.write("# plot_type: 'generalstats'\n") + out.write("# pconfig:\n") + out.write("# contamination_pct:\n") + out.write("# title: 'Contamination'\n") + out.write("# description: 'Estimated sample contamination percentage'\n") + out.write("# max: 10\n") + out.write("# min: 0\n") + out.write("# scale: 'RdYlGn-rev'\n") + out.write("# suffix: '%'\n") + out.write("# format: '{:,.2f}'\n") + out.write("Sample\tcontamination_pct\n") + out.write(f"{sample_id}\t{contamination_pct:.4f}\n") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Parse GATK contamination output for MultiQC") + parser.add_argument("--input", required=True, help="GATK contamination table") + parser.add_argument("--sample_id", required=True, help="Sample ID") + parser.add_argument("--prefix", required=True, help="Output prefix") + args = parser.parse_args() + + parse_contamination(args.input, args.sample_id, args.prefix) \ No newline at end of file diff --git a/modules/local/parse_contamination/main.nf b/modules/local/parse_contamination/main.nf index ad957390b..d8be68d13 100644 --- a/modules/local/parse_contamination/main.nf +++ b/modules/local/parse_contamination/main.nf @@ -20,42 +20,25 @@ process PARSE_CONTAMINATION { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - #!/usr/bin/env python3 - - import csv - - # Read GATK contamination table - with open("${contamination_table}", 'r') as f: - lines = f.readlines() - # Skip header, get contamination value - data_line = lines[1].strip().split('\\t') - sample = data_line[0] - contamination = float(data_line[1]) - contamination_pct = contamination * 100 - - # Write MultiQC custom content file - with open("${prefix}_contamination_mqc.tsv", 'w') as out: - # Header with MultiQC configuration - out.write("# id: 'gatk_contamination'\\n") - out.write("# section_name: 'GATK Contamination'\\n") - out.write("# description: 'Sample contamination estimates from GATK CalculateContamination'\\n") - out.write("# plot_type: 'generalstats'\\n") - out.write("# pconfig:\\n") - out.write("# contamination_pct:\\n") - out.write("# title: 'Contamination'\\n") - out.write("# description: 'Estimated sample contamination percentage'\\n") - out.write("# max: 10\\n") - out.write("# min: 0\\n") - out.write("# scale: 'RdYlGn-rev'\\n") - out.write("# suffix: '%'\\n") - out.write("# format: '{:,.2f}'\\n") - # Data - out.write("Sample\\tcontamination_pct\\n") - out.write(f"${meta.id}\\t{contamination_pct:.4f}\\n") - - # Create versions file - with open("versions.yml", 'w') as v: - v.write('"${task.process}":\\n') - v.write(' python: "3.11"\\n') + python3 ${moduleDir}/bin/parse_contamination.py \\ + --input ${contamination_table} \\ + --sample_id ${meta.id} \\ + --prefix ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_contamination_mqc.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //') + END_VERSIONS """ } diff --git a/subworkflows/local/contamination_check/tests/main.nf.test b/subworkflows/local/contamination_check/tests/main.nf.test new file mode 100644 index 000000000..2909dccd7 --- /dev/null +++ b/subworkflows/local/contamination_check/tests/main.nf.test @@ -0,0 +1,112 @@ +nextflow_workflow { + + name "Test Workflow CONTAMINATION_CHECK" + script "subworkflows/local/contamination_check/main.nf" + workflow "CONTAMINATION_CHECK" + tag "subworkflows" + tag "contamination_check" + config "./nextflow.config" + + test("CONTAMINATION_CHECK - WGS, no intervals") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, sex:1, phenotype:1, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[4] = channel.of( + [ + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz.tbi', checkIfExists: true) + ] + ).collect() + input[5] = Channel.empty() + """ + } + } + + then { + assertAll ( + { assert workflow.success }, + { assert snapshot( + workflow.out.contamination_table + .collect { it[1] } + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.pileup_table + .collect { it[1] } + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.versions + ).match() + } + ) + } + + } + + test("CONTAMINATION_CHECK - WES, with intervals") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, sex:1, phenotype:1, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[4] = channel.of( + [ + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz.tbi', checkIfExists: true) + ] + ).collect() + input[5] = Channel.fromPath(params.pipelines_testdata_base_path + 'reference/target.bed', checkIfExists: true).collect() + """ + } + } + + then { + assertAll ( + { assert workflow.success }, + { assert snapshot( + workflow.out.contamination_table + .collect { it[1] } + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.pileup_table + .collect { it[1] } + .flatten() + .collect { file(it).name } + .toSorted(), + workflow.out.versions + ).match() + } + ) + } + + } + +} diff --git a/subworkflows/local/contamination_check/tests/main.nf.test.snap b/subworkflows/local/contamination_check/tests/main.nf.test.snap new file mode 100644 index 000000000..c9b91a552 --- /dev/null +++ b/subworkflows/local/contamination_check/tests/main.nf.test.snap @@ -0,0 +1,40 @@ +{ + "CONTAMINATION_CHECK - WGS, no intervals": { + "content": [ + [ + "earlycasualcaiman_contamination.contamination.table" + ], + [ + "earlycasualcaiman_pileups.pileups.table" + ], + [ + "versions.yml:md5,46fc6219f36f2e8e436a824f3c0f9a4a", + "versions.yml:md5,dd08885235dcc7e9f408eba91ef7303e" + ] + ], + "timestamp": "2026-03-23T14:29:41.579345381", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "CONTAMINATION_CHECK - WES, with intervals": { + "content": [ + [ + "earlycasualcaiman_contamination.contamination.table" + ], + [ + "earlycasualcaiman_pileups.pileups.table" + ], + [ + "versions.yml:md5,46fc6219f36f2e8e436a824f3c0f9a4a", + "versions.yml:md5,dd08885235dcc7e9f408eba91ef7303e" + ] + ], + "timestamp": "2026-03-23T14:31:02.497064504", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/contamination_check/tests/nextflow.config b/subworkflows/local/contamination_check/tests/nextflow.config new file mode 100644 index 000000000..3a5a56e5c --- /dev/null +++ b/subworkflows/local/contamination_check/tests/nextflow.config @@ -0,0 +1,12 @@ +process { + + withName: '.*CONTAMINATION_CHECK:GATK4_GETPILEUPSUMMARIES' { + ext.args = '--disable-sequence-dictionary-validation' + ext.prefix = { "${meta.id}_pileups" } + } + + withName: '.*CONTAMINATION_CHECK:GATK4_CALCULATECONTAMINATION' { + ext.args = '' + ext.prefix = { "${meta.id}_contamination" } + } +} From 297e9478a7319cd324ba33c083480cb2a72a19f7 Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Tue, 24 Mar 2026 08:45:00 +0100 Subject: [PATCH 532/872] Fix missing EOF newline and extra blank line in CHANGELOG --- CHANGELOG.md | 1 - modules/local/parse_contamination/bin/parse_contamination.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0add9b2cc..6d9c6e2ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - ## 2.7.0dev - Semiautomatix [xxxx-xx-xx] ### `Added` diff --git a/modules/local/parse_contamination/bin/parse_contamination.py b/modules/local/parse_contamination/bin/parse_contamination.py index dcde01e06..5f5b3f1e0 100755 --- a/modules/local/parse_contamination/bin/parse_contamination.py +++ b/modules/local/parse_contamination/bin/parse_contamination.py @@ -37,4 +37,4 @@ def parse_contamination(contamination_table, sample_id, prefix): parser.add_argument("--prefix", required=True, help="Output prefix") args = parser.parse_args() - parse_contamination(args.input, args.sample_id, args.prefix) \ No newline at end of file + parse_contamination(args.input, args.sample_id, args.prefix) From a6142d3f896b78895ffcfd28fca5c89315aefc55 Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Tue, 24 Mar 2026 09:07:22 +0100 Subject: [PATCH 533/872] Fix malformed modules.json entry for gatk4/getpileupsummaries Missing closing brace and installed_by field caused nf-core lint to crash with TypeError during dependency recreation. --- modules.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules.json b/modules.json index cbd844c1c..eec4c6203 100644 --- a/modules.json +++ b/modules.json @@ -265,6 +265,8 @@ "gatk4/getpileupsummaries": { "branch": "master", "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "installed_by": ["modules"] + }, "gawk": { "branch": "master", "git_sha": "5ee4d69ed992c3ce81cfbbdd0bef932fcb81c75a", From 4f054cd097df2a00d753b579598a2d57d0d6b5f6 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 24 Mar 2026 09:08:26 +0100 Subject: [PATCH 534/872] fix sv merge logic for mitosalt --- .../local/call_structural_variants/main.nf | 35 ++++++++----------- workflows/raredisease.nf | 1 + 2 files changed, 16 insertions(+), 20 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index bb5de98a0..5eb8bc9f6 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -132,45 +132,38 @@ workflow CALL_STRUCTURAL_VARIANTS { tiddit_vcf .combine(manta_vcf) .combine(cnvnator_vcf) - .toList() - .set { vcf_list } + .set { vcf_paths } } else if (!val_analysis_type.equals("mito")) { manta_vcf - .toList() - .set { vcf_list } + .set { vcf_paths } } } else if (val_analysis_type.equals("wgs")) { tiddit_vcf .combine(manta_vcf) .combine(gcnvcaller_vcf) .combine(cnvnator_vcf) - .toList() - .set { vcf_list } + .set { vcf_paths } } else if (!val_analysis_type.equals("mito")) { manta_vcf .combine(gcnvcaller_vcf) - .toList() - .set { vcf_list } + .set { vcf_paths } } if (!val_analysis_type.equals("mito")) { if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { - channel.of(ch_svcaller_priority, "mitosalt") + ch_svcaller_priority.combine(["mitosalt"]) .collect() .set { ch_svcaller_priority } - channel.of(vcf_list, mitosalt_vcf) - .collect() - .set { vcf_list } + vcf_paths.combine(mitosalt_vcf) + .set { vcf_paths } } + vcf_list = vcf_paths.toList() ch_case_info .combine(vcf_list) - .set { merge_input_vcfs } + .set { merge_vcfs_in } - ch_case_info.view() - ch_svcaller_priority.view() - vcf_list.view() - SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority, true) + SVDB_MERGE (merge_vcfs_in, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf @@ -184,9 +177,11 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_publish = ch_merged_svs .mix(ch_merged_tbi) .map { meta, value -> ['call_sv/genome/', [meta, value]] } + ch_publish_mt = CALL_SV_MT.out.publish emit: - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] - tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + publish = ch_publish // channel: [ val(destination), val(value) ] + publish_mt = ch_publish_mt // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a87baf1c0..0d05274c0 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -619,6 +619,7 @@ workflow RAREDISEASE { val_run_mt_for_wes ) ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish + ch_call_sv_mt_publish = CALL_STRUCTURAL_VARIANTS.out.publish_mt // // ANNOTATE STRUCTURAL VARIANTS From 5a89e52c1633c44b5f69ad0e855367de332c4444 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 24 Mar 2026 09:24:36 +0100 Subject: [PATCH 535/872] change nulls to none string --- subworkflows/local/call_structural_variants/main.nf | 4 ++-- .../local/call_structural_variants/tests/main.nf.test | 2 +- subworkflows/local/call_sv_MT/main.nf | 10 +++++----- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 5eb8bc9f6..1e1b4c7c0 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -150,7 +150,7 @@ workflow CALL_STRUCTURAL_VARIANTS { } if (!val_analysis_type.equals("mito")) { - if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { + if (!mitosalt_vcf.equals('none') && val_analysis_type.equals("wgs")) { ch_svcaller_priority.combine(["mitosalt"]) .collect() .set { ch_svcaller_priority } @@ -168,7 +168,7 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - } else if (!mitosalt_vcf.equals(null)) { + } else if (!mitosalt_vcf.equals('none')) { TABIX_TABIX (mitosalt_vcf) ch_merged_svs = mitosalt_vcf ch_merged_tbi = TABIX_TABIX.out.index diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 8847320d4..831e421e7 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -43,7 +43,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.chrsizes', checkIfExists: true)]).collect() + input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)]).collect() input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fai', checkIfExists: true)]).collect() input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 292739fbd..fe708d149 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -135,9 +135,9 @@ workflow CALL_SV_MT { .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } emit: - mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(null) // channel: [ val(meta), path(vcf) ] - mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(['meta','none']) // channel: [ val(meta), path(vcf) ] + mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From 09b9d853aada77d1b985a48c82f11a0e3dd57d6b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 24 Mar 2026 09:31:52 +0100 Subject: [PATCH 536/872] fix test data path --- subworkflows/local/call_structural_variants/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 831e421e7..f3dde334c 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -45,7 +45,7 @@ nextflow_workflow { ]) input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)]).collect() input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fai', checkIfExists: true)]).collect() + input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[20] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } input[21] = channel.of([ From 8d30a6018b4c0ceeb529118cd35d3ec8844c99dd Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Tue, 24 Mar 2026 09:38:52 +0100 Subject: [PATCH 537/872] Fix modules.json SHA for gatk4 contamination modules Update git_sha to ae8cd884f895 which matches the actual installed module versions (GATK 4.6.2.0 with nf-core code style updates). --- modules.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index eec4c6203..be7408569 100644 --- a/modules.json +++ b/modules.json @@ -259,12 +259,12 @@ }, "gatk4/calculatecontamination": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", "installed_by": ["modules"] }, "gatk4/getpileupsummaries": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", "installed_by": ["modules"] }, "gawk": { From 7e928edb0a0b1237890bee403828e4a76f89c359 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 24 Mar 2026 10:13:02 +0100 Subject: [PATCH 538/872] change back to null and fix more test paths --- subworkflows/local/call_structural_variants/main.nf | 4 ++-- .../local/call_structural_variants/tests/main.nf.test | 9 ++------- .../call_structural_variants/tests/main.nf.test.snap | 2 +- subworkflows/local/call_sv_MT/main.nf | 10 +++++----- 4 files changed, 10 insertions(+), 15 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 1e1b4c7c0..5eb8bc9f6 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -150,7 +150,7 @@ workflow CALL_STRUCTURAL_VARIANTS { } if (!val_analysis_type.equals("mito")) { - if (!mitosalt_vcf.equals('none') && val_analysis_type.equals("wgs")) { + if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { ch_svcaller_priority.combine(["mitosalt"]) .collect() .set { ch_svcaller_priority } @@ -168,7 +168,7 @@ workflow CALL_STRUCTURAL_VARIANTS { TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - } else if (!mitosalt_vcf.equals('none')) { + } else if (!mitosalt_vcf.equals(null)) { TABIX_TABIX (mitosalt_vcf) ch_merged_svs = mitosalt_vcf ch_merged_tbi = TABIX_TABIX.out.index diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index f3dde334c..16f7b8845 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -43,7 +43,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[16] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)]).collect() + input[16] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)) input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() @@ -76,12 +76,7 @@ nextflow_workflow { input[40] = 10000 input[41] = 5 input[42] = 15 - input[43] = 0.5 - input[44] = 600 - input[45] = 10 - input[46] = 5 - input[47] = 0.3 - input[48] = true + input[43] = true """ } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index f73f465ab..50456cee3 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -12,7 +12,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-13T13:21:51.525587168", + "timestamp": "2026-03-24T09:56:24.619874", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index fe708d149..404636ef0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -135,9 +135,9 @@ workflow CALL_SV_MT { .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } emit: - mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(['meta','none']) // channel: [ val(meta), path(vcf) ] - mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(['meta', null]) // channel: [ val(meta), path(vcf) ] + mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From dc5ce8ce677f60639455a3815fcbb58894af3ac9 Mon Sep 17 00:00:00 2001 From: Doroteja Vujinovic <56053vujinovic@slurm.lan.kclj.si> Date: Tue, 24 Mar 2026 10:20:31 +0100 Subject: [PATCH 539/872] Fix trailing whitespace in raredisease.nf --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 460a10366..42fd8be16 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -897,7 +897,7 @@ workflow RAREDISEASE { ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) - + // Add contamination results to MultiQC ch_multiqc_files = ch_multiqc_files.mix(ch_contamination_mqc.map { _meta, file -> file }) From 3cb6da3d92580d405454a9c646cb9672a69fed60 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Mar 2026 09:50:50 +0100 Subject: [PATCH 540/872] Update --- conf/modules/call_sv_MT.config | 22 +++ .../local/call_structural_variants/main.nf | 119 ++++++++++----- subworkflows/local/call_sv_MT/main.nf | 141 +++++++++++++----- workflows/raredisease.nf | 1 - 4 files changed, 205 insertions(+), 78 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index be140cabe..601e43bf6 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -22,4 +22,26 @@ process { ext.prefix = { "${meta.id}_mitochondria_deletions" } } +<<<<<<< Updated upstream +======= + withName: '.*CALL_SV_MT:SALTSHAKER_CALL' { + ext.args = '--blacklist' + } + + withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' { + ext.args = { "--blacklist --vcf --dominant-fraction ${params.saltshaker_dominant_fraction} \ + --radius ${params.saltshaker_group_radius} --high-het ${params.saltshaker_high_heteroplasmy} \ + --multiple-threshold ${params.saltshaker_multiple_threshold} --noise ${params.saltshaker_noise_threshold}" + } + } + + withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { + ext.args = '--blacklist --genes' + } + + withName: '.*CALL_SV_MT:SVDB_MERGE' { + ext.prefix = { "${meta.id}_saltshaker" } + } + +>>>>>>> Stashed changes } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index f9ef01c2a..7a40cdcf7 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -29,81 +29,124 @@ workflow CALL_STRUCTURAL_VARIANTS { skip_germlinecnvcaller // boolean main: - ch_merged_svs = channel.empty() - ch_merged_tbi = channel.empty() + ch_cnvnator_vcf = channel.empty() + ch_gcnvcaller_vcf = channel.empty() + ch_manta_vcf = channel.empty() + ch_merged_svs = channel.empty() + ch_merged_tbi = channel.empty() + ch_publish_mt = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_tiddit_vcf = channel.empty() if (!val_analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } - .set{ manta_vcf } + .set{ ch_manta_vcf } } if (val_analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { tiddit_vcf } + .set { ch_tiddit_vcf } CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { cnvnator_vcf } + .set { ch_cnvnator_vcf } } if (!skip_germlinecnvcaller) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf .collect{ _meta, vcf -> vcf } - .set { gcnvcaller_vcf } + .set { ch_gcnvcaller_vcf } } - //merge - if (skip_germlinecnvcaller) { - if (val_analysis_type.equals("wgs")) { - tiddit_vcf - .combine(manta_vcf) - .combine(cnvnator_vcf) - .toList() - .set { vcf_list } - } else if (!val_analysis_type.equals("mito")) { - manta_vcf - .toList() - .set { vcf_list } - } - } else if (val_analysis_type.equals("wgs")) { - tiddit_vcf - .combine(manta_vcf) - .combine(gcnvcaller_vcf) - .combine(cnvnator_vcf) - .toList() - .set { vcf_list } - } else if (!val_analysis_type.equals("mito")) { - manta_vcf - .combine(gcnvcaller_vcf) - .toList() - .set { vcf_list } + if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { + CALL_SV_MT( + ch_mt_bam_bai, + ch_case_info, + ch_genome_chrsizes, + ch_genome_fai, + ch_genome_fasta, + ch_genome_hisat2index, + ch_mt_fai, + ch_mt_fasta, + ch_mt_lastdb, + ch_reads, + ch_subdepth, + ch_svcaller_priority, + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end, + val_mito_length, + val_mito_name, + val_mitosalt_breakspan, + val_mitosalt_breakthreshold, + val_mitosalt_cluster_threshold, + val_mitosalt_deletion_threshold_max, + val_mitosalt_deletion_threshold_min, + val_mitosalt_evalue_threshold, + val_mitosalt_exclude, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, + val_mitosalt_paired_distance, + val_mitosalt_score_threshold, + val_mitosalt_sizelimit, + val_mitosalt_split_distance_threshold, + val_mitosalt_split_length + ) + .set {ch_sv_mt_out} + + ch_sv_mt_out.saltshaker_vcf + .collect{ _meta, vcf -> vcf } + .set { ch_saltshaker_vcf } + + ch_publish_mt = ch_sv_mt_out.publish + ch_svcaller_priority = ch_sv_mt_out.updated_priority } + // Merge - with consistent ordering using concat if (!val_analysis_type.equals("mito")) { + // Concatenate in specific order: tiddit -> manta -> gcnvcaller -> cnvnator -> mitosalt + // Empty channels won't contribute any items + ch_tiddit_vcf + .concat(ch_manta_vcf) + .concat(ch_gcnvcaller_vcf) + .concat(ch_cnvnator_vcf) + .concat(ch_saltshaker_vcf) + .collect() + .map { vcf_list -> [vcf_list] } // + .set { ch_vcf_paths } + ch_case_info - .combine(vcf_list) - .set { merge_input_vcfs } + .combine(ch_vcf_paths) + .set { ch_merge_vcfs_in } - SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority, true) + SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index + + } else { + // For mito-only analysis, use mitosalt_vcf directly + TABIX_TABIX (ch_saltshaker_vcf) + ch_merged_svs = ch_saltshaker_vcf + ch_merged_tbi = TABIX_TABIX.out.index } ch_publish = ch_merged_svs .mix(ch_merged_tbi) - .map { meta, value -> ['call_sv/genome/', [meta, value]] } + .map { meta, value -> ['call_sv/', [meta, value]] } + .mix(ch_publish_mt) emit: - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] - tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 5b74b7ba2..6b0459904 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -2,41 +2,54 @@ // Call SV MT // -include { MT_DELETION } from '../../../modules/local/mt_deletion_script' -include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { MT_DELETION } from '../../../modules/local/mt_deletion_script' +include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' +include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' +include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' +include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' +include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' workflow CALL_SV_MT { take: - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] - ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] - ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - val_breakspan // string: [mandatory] mitosalt_break_span - val_breakthreshold // string: [mandatory] mitosalt_break_threshold - val_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold - val_deletion_threshold_max // string: [mandatory] mitosalt_del_threshold_max - val_deletion_threshold_min // string: [mandatory] mitosalt_del_threshold_min - val_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold - val_exclude // string: [mandatory] mitosalt_exclude - val_flank // string: [mandatory] mitosalt_flank - val_hplimit // string: [mandatory] mitosalt_hp_limit - val_mito_name // string: [mandatory] mito_name - val_paired_distance // string: [mandatory] mitosalt_paired_distance - val_score_threshold // string: [mandatory] mitosalt_score_threshold - val_sizelimit // string: [mandatory] mitosalt_size_limit - val_split_distance_threshold // string: [mandatory] mitosalt_split_dist_threshold - val_split_length // string: [mandatory] mitosalt_split_length + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] + val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start + val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end + val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start + val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end + val_mito_length // string: [mandatory] mito_length + val_mito_name // string: [mandatory] mito_name + val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan + val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold + val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold + val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max + val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min + val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold + val_mitosalt_exclude // string: [mandatory] mitosalt_exclude + val_mitosalt_flank // string: [mandatory] mitosalt_flank + val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit + val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance + val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold + val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit + val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold + val_mitosalt_split_length // string: [mandatory] mitosalt_split_length main: - ch_mitosalt_publish = channel.empty() + ch_saltshaker_txt = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_saltshaker_plot = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -77,19 +90,69 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) - ch_mitosalt_publish = MITOSALT.out.breakpoint - .mix(MITOSALT.out.cluster) + + MITOSALT.out.cluster + .filter{ _meta, out -> out.countLines() > 0 } + .set{ch_cluster} + + MITOSALT.out.breakpoint + .join(ch_cluster) + .set{ch_saltshaker_in} + + SALTSHAKER_CALL( + ch_saltshaker_in, + ch_mt_fasta, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, + val_mito_length, + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end + ) + + SALTSHAKER_CLASSIFY( + SALTSHAKER_CALL.out.call, + val_mito_name + ) + ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt + ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + + SALTSHAKER_PLOT( + SALTSHAKER_CLASSIFY.out.classify + ) + ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot + + SALTSHAKER_CLASSIFY.out.vcf + .collect{_meta, vcf -> vcf} + .toList() + .set { ch_vcf_file_list } + + ch_case_info + .combine(ch_vcf_file_list) + .set { ch_merge_input_vcfs } + + SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf + .set {ch_saltshaker_vcf} + // Update priority list when we know saltshaker will run + ch_svcaller_priority = ch_svcaller_priority + .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) + .collect() } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_mitosalt_publish - .mix(MT_DELETION.out.mt_del_result) - .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } + ch_publish = ch_saltshaker_txt + .mix(ch_saltshaker_vcf) + .mix(ch_saltshaker_plot) + .mix(MT_DELETION.out.mt_del_result) + .map { meta, value -> ['call_sv/', [meta, value]] } emit: - mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] - mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + saltshaker_txt = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + updated_priority = ch_svcaller_priority // channel: [ val(["caller1", "caller2", ...]) ] - includes "mitosalt" if it ran + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 93220ee89..0e5a1e2dd 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -970,7 +970,6 @@ workflow RAREDISEASE { .mix(ch_subsample_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) - .mix(ch_call_sv_mt_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_genome_snvs_publish) From ec00e295989e02266cfbbe8eb6d89e2afd549c10 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Mar 2026 09:57:32 +0100 Subject: [PATCH 541/872] Update logic --- conf/modules/call_sv_MT.config | 4 + .../local/call_structural_variants/main.nf | 93 +++++++-------- subworkflows/local/call_sv_MT/main.nf | 110 ++++++++++-------- workflows/raredisease.nf | 2 - 4 files changed, 111 insertions(+), 98 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 321f23add..c9535499b 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -37,4 +37,8 @@ process { ext.args = '--blacklist --genes' } + withName: '.*CALL_SV_MT:SVDB_MERGE' { + ext.prefix = { "${meta.id}_saltshaker" } + } + } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 5eb8bc9f6..bdfb02dc4 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -59,39 +59,46 @@ workflow CALL_STRUCTURAL_VARIANTS { val_run_mt_for_wes // boolean: [mandatory] run_mt_for_wes main: - ch_merged_svs = channel.empty() - ch_merged_tbi = channel.empty() + ch_cnvnator_vcf = channel.empty() + ch_gcnvcaller_vcf = channel.empty() + ch_manta_vcf = channel.empty() + ch_merged_svs = channel.empty() + ch_merged_tbi = channel.empty() + ch_publish_mt = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_tiddit_vcf = channel.empty() if (!val_analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } - .set{ manta_vcf } + .set{ ch_manta_vcf } } if (val_analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { tiddit_vcf } + .set { ch_tiddit_vcf } CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { cnvnator_vcf } + .set { ch_cnvnator_vcf } } if (!skip_germlinecnvcaller) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf .collect{ _meta, vcf -> vcf } - .set { gcnvcaller_vcf } + .set { ch_gcnvcaller_vcf } } if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { CALL_SV_MT( ch_mt_bam_bai, + ch_case_info, ch_genome_chrsizes, ch_genome_fai, ch_genome_fasta, @@ -101,6 +108,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_mt_lastdb, ch_reads, ch_subdepth, + ch_svcaller_priority, val_heavy_strand_origin_start, val_heavy_strand_origin_end, val_light_strand_origin_start, @@ -120,68 +128,55 @@ workflow CALL_STRUCTURAL_VARIANTS { val_mitosalt_score_threshold, val_mitosalt_sizelimit, val_mitosalt_split_distance_threshold, - val_mitosalt_split_length) - .mitosalt_vcf + val_mitosalt_split_length + ) + .set {ch_sv_mt_out} + + ch_sv_mt_out.saltshaker_vcf .collect{ _meta, vcf -> vcf } - .set { mitosalt_vcf } - } + .set { ch_saltshaker_vcf } - //merge - if (skip_germlinecnvcaller) { - if (val_analysis_type.equals("wgs")) { - tiddit_vcf - .combine(manta_vcf) - .combine(cnvnator_vcf) - .set { vcf_paths } - } else if (!val_analysis_type.equals("mito")) { - manta_vcf - .set { vcf_paths } - } - } else if (val_analysis_type.equals("wgs")) { - tiddit_vcf - .combine(manta_vcf) - .combine(gcnvcaller_vcf) - .combine(cnvnator_vcf) - .set { vcf_paths } - } else if (!val_analysis_type.equals("mito")) { - manta_vcf - .combine(gcnvcaller_vcf) - .set { vcf_paths } + ch_publish_mt = ch_sv_mt_out.publish + ch_svcaller_priority = ch_sv_mt_out.updated_priority } + // Merge - with consistent ordering using concat if (!val_analysis_type.equals("mito")) { - if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { - ch_svcaller_priority.combine(["mitosalt"]) - .collect() - .set { ch_svcaller_priority } - vcf_paths.combine(mitosalt_vcf) - .set { vcf_paths } - } - - vcf_list = vcf_paths.toList() + // Concatenate in specific order: tiddit -> manta -> gcnvcaller -> cnvnator -> mitosalt + // Empty channels won't contribute any items + ch_tiddit_vcf + .concat(ch_manta_vcf) + .concat(ch_gcnvcaller_vcf) + .concat(ch_cnvnator_vcf) + .concat(ch_saltshaker_vcf) + .collect() + .map { vcf_list -> [vcf_list] } // + .set { ch_vcf_paths } + ch_case_info - .combine(vcf_list) - .set { merge_vcfs_in } + .combine(ch_vcf_paths) + .set { ch_merge_vcfs_in } - SVDB_MERGE (merge_vcfs_in, ch_svcaller_priority, true) + SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - } else if (!mitosalt_vcf.equals(null)) { - TABIX_TABIX (mitosalt_vcf) - ch_merged_svs = mitosalt_vcf + + } else { + // For mito-only analysis, use mitosalt_vcf directly + TABIX_TABIX (ch_saltshaker_vcf) + ch_merged_svs = ch_saltshaker_vcf ch_merged_tbi = TABIX_TABIX.out.index } ch_publish = ch_merged_svs .mix(ch_merged_tbi) - .map { meta, value -> ['call_sv/genome/', [meta, value]] } - ch_publish_mt = CALL_SV_MT.out.publish + .mix(ch_publish_mt) + .map { meta, value -> ['call_sv/', [meta, value]] } emit: vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] publish = ch_publish // channel: [ val(destination), val(value) ] - publish_mt = ch_publish_mt // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 404636ef0..439fb9077 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -9,10 +9,12 @@ include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' +include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' workflow CALL_SV_MT { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] @@ -22,6 +24,7 @@ workflow CALL_SV_MT { ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start @@ -44,7 +47,9 @@ workflow CALL_SV_MT { val_mitosalt_split_length // string: [mandatory] mitosalt_split_length main: - ch_mitosalt_publish = channel.empty() + ch_saltshaker_txt = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_saltshaker_plot = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -85,59 +90,70 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) + MITOSALT.out.cluster .filter{ _meta, out -> out.countLines() > 0 } .set{ch_cluster} - ch_saltshaker_txt = channel.empty() - ch_saltshaker_vcf = channel.empty() - ch_saltshaker_plot = channel.empty() - ch_mitosalt_publish = channel.empty() - - if (ch_cluster) { - MITOSALT.out.breakpoint - .join(ch_cluster) - .set{ch_saltshaker_in} - - SALTSHAKER_CALL( - ch_saltshaker_in, - ch_mt_fasta, - val_mitosalt_flank, - val_mitosalt_heteroplasmy_limit, - val_mito_length, - val_heavy_strand_origin_start, - val_heavy_strand_origin_end, - val_light_strand_origin_start, - val_light_strand_origin_end - ) - - SALTSHAKER_CLASSIFY( - SALTSHAKER_CALL.out.call, - val_mito_name - ) - ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt - ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf - - SALTSHAKER_PLOT( - SALTSHAKER_CLASSIFY.out.classify - ) - ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot - - ch_mitosalt_publish = ch_saltshaker_txt - .mix(ch_saltshaker_vcf) - .mix(ch_saltshaker_plot) - } + MITOSALT.out.breakpoint + .join(ch_cluster) + .set{ch_saltshaker_in} + + SALTSHAKER_CALL( + ch_saltshaker_in, + ch_mt_fasta, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, + val_mito_length, + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end + ) + + SALTSHAKER_CLASSIFY( + SALTSHAKER_CALL.out.call, + val_mito_name + ) + ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt + ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + + SALTSHAKER_PLOT( + SALTSHAKER_CLASSIFY.out.classify + ) + ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot + + SALTSHAKER_CLASSIFY.out.vcf + .collect{_meta, vcf -> vcf} + .toList() + .set { ch_vcf_file_list } + + ch_case_info + .combine(ch_vcf_file_list) + .set { ch_merge_input_vcfs } + + SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf + .set {ch_saltshaker_vcf} + // Update priority list when we know saltshaker will run + ch_svcaller_priority = ch_svcaller_priority + .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) + .collect() + .dump(tag:'updatedprio') + } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_mitosalt_publish - .mix(MT_DELETION.out.mt_del_result) - .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } + ch_publish = ch_saltshaker_txt + .mix(ch_saltshaker_vcf) + .mix(ch_saltshaker_plot) + .mix(MT_DELETION.out.mt_del_result) + .map { meta, value -> ['call_sv/', [meta, value]] } emit: - mitosalt_classify = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] - mitosalt_vcf = ch_saltshaker_vcf.ifEmpty(['meta', null]) // channel: [ val(meta), path(vcf) ] - mitosalt_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + saltshaker_txt = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] + saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + updated_priority = ch_svcaller_priority // channel: [ val(["caller1", "caller2", ...]) ] - includes "mitosalt" if it ran + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0d05274c0..0f600b2fa 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -619,7 +619,6 @@ workflow RAREDISEASE { val_run_mt_for_wes ) ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish - ch_call_sv_mt_publish = CALL_STRUCTURAL_VARIANTS.out.publish_mt // // ANNOTATE STRUCTURAL VARIANTS @@ -964,7 +963,6 @@ workflow RAREDISEASE { .mix(ch_subsample_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) - .mix(ch_call_sv_mt_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_genome_snvs_publish) From 5acf08c9967d02cbb7f55f9239905f57e6404ede Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 25 Mar 2026 10:02:38 +0100 Subject: [PATCH 542/872] test --- subworkflows/local/call_structural_variants/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 5eb8bc9f6..843473585 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -125,7 +125,7 @@ workflow CALL_STRUCTURAL_VARIANTS { .collect{ _meta, vcf -> vcf } .set { mitosalt_vcf } } - + mitosalt_vcf.view() //merge if (skip_germlinecnvcaller) { if (val_analysis_type.equals("wgs")) { @@ -151,6 +151,7 @@ workflow CALL_STRUCTURAL_VARIANTS { if (!val_analysis_type.equals("mito")) { if (!mitosalt_vcf.equals(null) && val_analysis_type.equals("wgs")) { + mitosalt_vcf.view() ch_svcaller_priority.combine(["mitosalt"]) .collect() .set { ch_svcaller_priority } From bf25713006b417b77a588e8013f6894aebfa5003 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Mar 2026 10:05:37 +0100 Subject: [PATCH 543/872] Revert "Update" This reverts commit 3cb6da3d92580d405454a9c646cb9672a69fed60. --- conf/modules/call_sv_MT.config | 22 --- .../local/call_structural_variants/main.nf | 119 +++++---------- subworkflows/local/call_sv_MT/main.nf | 141 +++++------------- workflows/raredisease.nf | 1 + 4 files changed, 78 insertions(+), 205 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 601e43bf6..be140cabe 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -22,26 +22,4 @@ process { ext.prefix = { "${meta.id}_mitochondria_deletions" } } -<<<<<<< Updated upstream -======= - withName: '.*CALL_SV_MT:SALTSHAKER_CALL' { - ext.args = '--blacklist' - } - - withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' { - ext.args = { "--blacklist --vcf --dominant-fraction ${params.saltshaker_dominant_fraction} \ - --radius ${params.saltshaker_group_radius} --high-het ${params.saltshaker_high_heteroplasmy} \ - --multiple-threshold ${params.saltshaker_multiple_threshold} --noise ${params.saltshaker_noise_threshold}" - } - } - - withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { - ext.args = '--blacklist --genes' - } - - withName: '.*CALL_SV_MT:SVDB_MERGE' { - ext.prefix = { "${meta.id}_saltshaker" } - } - ->>>>>>> Stashed changes } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 7a40cdcf7..f9ef01c2a 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -29,124 +29,81 @@ workflow CALL_STRUCTURAL_VARIANTS { skip_germlinecnvcaller // boolean main: - ch_cnvnator_vcf = channel.empty() - ch_gcnvcaller_vcf = channel.empty() - ch_manta_vcf = channel.empty() - ch_merged_svs = channel.empty() - ch_merged_tbi = channel.empty() - ch_publish_mt = channel.empty() - ch_saltshaker_vcf = channel.empty() - ch_tiddit_vcf = channel.empty() + ch_merged_svs = channel.empty() + ch_merged_tbi = channel.empty() if (!val_analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } - .set{ ch_manta_vcf } + .set{ manta_vcf } } if (val_analysis_type.equals("wgs")) { CALL_SV_TIDDIT (ch_genome_bam_bai, ch_genome_fai, ch_genome_fasta, ch_bwa_index, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { ch_tiddit_vcf } + .set { tiddit_vcf } CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } - .set { ch_cnvnator_vcf } + .set { cnvnator_vcf } } if (!skip_germlinecnvcaller) { CALL_SV_GERMLINECNVCALLER (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_readcount_intervals, ch_genome_dictionary, ch_ploidy_model, ch_gcnvcaller_model, ch_case_info) .genotyped_filtered_segments_vcf .collect{ _meta, vcf -> vcf } - .set { ch_gcnvcaller_vcf } + .set { gcnvcaller_vcf } } - if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { - CALL_SV_MT( - ch_mt_bam_bai, - ch_case_info, - ch_genome_chrsizes, - ch_genome_fai, - ch_genome_fasta, - ch_genome_hisat2index, - ch_mt_fai, - ch_mt_fasta, - ch_mt_lastdb, - ch_reads, - ch_subdepth, - ch_svcaller_priority, - val_heavy_strand_origin_start, - val_heavy_strand_origin_end, - val_light_strand_origin_start, - val_light_strand_origin_end, - val_mito_length, - val_mito_name, - val_mitosalt_breakspan, - val_mitosalt_breakthreshold, - val_mitosalt_cluster_threshold, - val_mitosalt_deletion_threshold_max, - val_mitosalt_deletion_threshold_min, - val_mitosalt_evalue_threshold, - val_mitosalt_exclude, - val_mitosalt_flank, - val_mitosalt_heteroplasmy_limit, - val_mitosalt_paired_distance, - val_mitosalt_score_threshold, - val_mitosalt_sizelimit, - val_mitosalt_split_distance_threshold, - val_mitosalt_split_length - ) - .set {ch_sv_mt_out} - - ch_sv_mt_out.saltshaker_vcf - .collect{ _meta, vcf -> vcf } - .set { ch_saltshaker_vcf } - - ch_publish_mt = ch_sv_mt_out.publish - ch_svcaller_priority = ch_sv_mt_out.updated_priority + //merge + if (skip_germlinecnvcaller) { + if (val_analysis_type.equals("wgs")) { + tiddit_vcf + .combine(manta_vcf) + .combine(cnvnator_vcf) + .toList() + .set { vcf_list } + } else if (!val_analysis_type.equals("mito")) { + manta_vcf + .toList() + .set { vcf_list } + } + } else if (val_analysis_type.equals("wgs")) { + tiddit_vcf + .combine(manta_vcf) + .combine(gcnvcaller_vcf) + .combine(cnvnator_vcf) + .toList() + .set { vcf_list } + } else if (!val_analysis_type.equals("mito")) { + manta_vcf + .combine(gcnvcaller_vcf) + .toList() + .set { vcf_list } } - // Merge - with consistent ordering using concat if (!val_analysis_type.equals("mito")) { - // Concatenate in specific order: tiddit -> manta -> gcnvcaller -> cnvnator -> mitosalt - // Empty channels won't contribute any items - ch_tiddit_vcf - .concat(ch_manta_vcf) - .concat(ch_gcnvcaller_vcf) - .concat(ch_cnvnator_vcf) - .concat(ch_saltshaker_vcf) - .collect() - .map { vcf_list -> [vcf_list] } // - .set { ch_vcf_paths } - ch_case_info - .combine(ch_vcf_paths) - .set { ch_merge_vcfs_in } + .combine(vcf_list) + .set { merge_input_vcfs } - SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, true) + SVDB_MERGE (merge_input_vcfs, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) ch_merged_svs = SVDB_MERGE.out.vcf ch_merged_tbi = TABIX_TABIX.out.index - - } else { - // For mito-only analysis, use mitosalt_vcf directly - TABIX_TABIX (ch_saltshaker_vcf) - ch_merged_svs = ch_saltshaker_vcf - ch_merged_tbi = TABIX_TABIX.out.index } ch_publish = ch_merged_svs .mix(ch_merged_tbi) - .map { meta, value -> ['call_sv/', [meta, value]] } - .mix(ch_publish_mt) + .map { meta, value -> ['call_sv/genome/', [meta, value]] } emit: - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] - tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6b0459904..5b74b7ba2 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -2,54 +2,41 @@ // Call SV MT // -include { MT_DELETION } from '../../../modules/local/mt_deletion_script' -include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' -include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' -include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' -include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' -include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' +include { MT_DELETION } from '../../../modules/local/mt_deletion_script' +include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' +include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' workflow CALL_SV_MT { take: - ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] - ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] - ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] - val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start - val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end - val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start - val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end - val_mito_length // string: [mandatory] mito_length - val_mito_name // string: [mandatory] mito_name - val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan - val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold - val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold - val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max - val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min - val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold - val_mitosalt_exclude // string: [mandatory] mitosalt_exclude - val_mitosalt_flank // string: [mandatory] mitosalt_flank - val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit - val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance - val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold - val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit - val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold - val_mitosalt_split_length // string: [mandatory] mitosalt_split_length + ch_bam_bai // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(genomefai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] + ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + val_breakspan // string: [mandatory] mitosalt_break_span + val_breakthreshold // string: [mandatory] mitosalt_break_threshold + val_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold + val_deletion_threshold_max // string: [mandatory] mitosalt_del_threshold_max + val_deletion_threshold_min // string: [mandatory] mitosalt_del_threshold_min + val_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold + val_exclude // string: [mandatory] mitosalt_exclude + val_flank // string: [mandatory] mitosalt_flank + val_hplimit // string: [mandatory] mitosalt_hp_limit + val_mito_name // string: [mandatory] mito_name + val_paired_distance // string: [mandatory] mitosalt_paired_distance + val_score_threshold // string: [mandatory] mitosalt_score_threshold + val_sizelimit // string: [mandatory] mitosalt_size_limit + val_split_distance_threshold // string: [mandatory] mitosalt_split_dist_threshold + val_split_length // string: [mandatory] mitosalt_split_length main: - ch_saltshaker_txt = channel.empty() - ch_saltshaker_vcf = channel.empty() - ch_saltshaker_plot = channel.empty() + ch_mitosalt_publish = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) @@ -90,69 +77,19 @@ workflow CALL_SV_MT { ch_mt_fasta, ch_mt_lastdb ) - - MITOSALT.out.cluster - .filter{ _meta, out -> out.countLines() > 0 } - .set{ch_cluster} - - MITOSALT.out.breakpoint - .join(ch_cluster) - .set{ch_saltshaker_in} - - SALTSHAKER_CALL( - ch_saltshaker_in, - ch_mt_fasta, - val_mitosalt_flank, - val_mitosalt_heteroplasmy_limit, - val_mito_length, - val_heavy_strand_origin_start, - val_heavy_strand_origin_end, - val_light_strand_origin_start, - val_light_strand_origin_end - ) - - SALTSHAKER_CLASSIFY( - SALTSHAKER_CALL.out.call, - val_mito_name - ) - ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt - ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf - - SALTSHAKER_PLOT( - SALTSHAKER_CLASSIFY.out.classify - ) - ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot - - SALTSHAKER_CLASSIFY.out.vcf - .collect{_meta, vcf -> vcf} - .toList() - .set { ch_vcf_file_list } - - ch_case_info - .combine(ch_vcf_file_list) - .set { ch_merge_input_vcfs } - - SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf - .set {ch_saltshaker_vcf} - // Update priority list when we know saltshaker will run - ch_svcaller_priority = ch_svcaller_priority - .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) - .collect() + ch_mitosalt_publish = MITOSALT.out.breakpoint + .mix(MITOSALT.out.cluster) } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_saltshaker_txt - .mix(ch_saltshaker_vcf) - .mix(ch_saltshaker_plot) - .mix(MT_DELETION.out.mt_del_result) - .map { meta, value -> ['call_sv/', [meta, value]] } + ch_publish = ch_mitosalt_publish + .mix(MT_DELETION.out.mt_del_result) + .map { meta, value -> ['call_sv/mitochondria/', [meta, value]] } emit: - saltshaker_txt = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] - saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] - saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] - updated_priority = ch_svcaller_priority // channel: [ val(["caller1", "caller2", ...]) ] - includes "mitosalt" if it ran - publish = ch_publish // channel: [ val(destination), val(value) ] + mitosalt_breakpoint = MITOSALT.out.breakpoint // channel: [ val(meta), path(breakpoint) ] + mitosalt_cluster = MITOSALT.out.cluster // channel: [ val(meta), path(cluster) ] + mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0e5a1e2dd..93220ee89 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -970,6 +970,7 @@ workflow RAREDISEASE { .mix(ch_subsample_publish) .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) + .mix(ch_call_sv_mt_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_genome_snvs_publish) From b1d6581e94862045375920213fceaec1412eb70f Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 25 Mar 2026 13:39:00 +0100 Subject: [PATCH 544/872] fixed logic and new snaps --- .../local/call_structural_variants/main.nf | 4 +- subworkflows/local/call_sv_MT/main.nf | 2 +- tests/default.nf.test.snap | 52 ++++++------------- tests/test_bam.nf.test.snap | 27 +++------- tests/test_singleton.nf.test.snap | 36 ++++--------- 5 files changed, 36 insertions(+), 85 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index bdfb02dc4..a546736a8 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -135,7 +135,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_sv_mt_out.saltshaker_vcf .collect{ _meta, vcf -> vcf } .set { ch_saltshaker_vcf } - + ch_saltshaker_vcf.view() ch_publish_mt = ch_sv_mt_out.publish ch_svcaller_priority = ch_sv_mt_out.updated_priority } @@ -152,11 +152,9 @@ workflow CALL_STRUCTURAL_VARIANTS { .collect() .map { vcf_list -> [vcf_list] } // .set { ch_vcf_paths } - ch_case_info .combine(ch_vcf_paths) .set { ch_merge_vcfs_in } - SVDB_MERGE (ch_merge_vcfs_in, ch_svcaller_priority, true) TABIX_TABIX (SVDB_MERGE.out.vcf) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 439fb9077..1c8ec1e1c 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -130,6 +130,7 @@ workflow CALL_SV_MT { ch_case_info .combine(ch_vcf_file_list) + .filter{ it -> it.size() == 2} .set { ch_merge_input_vcfs } SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf @@ -138,7 +139,6 @@ workflow CALL_SV_MT { ch_svcaller_priority = ch_svcaller_priority .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) .collect() - .dump(tag:'updatedprio') } MT_DELETION(ch_bam_bai, ch_genome_fasta) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 11cdd475c..13065ec14 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -328,7 +328,7 @@ "saltshaker": "1.0.0" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.0" + "saltshaker": "1.0.1" }, "SALTSHAKER_PLOT": { "saltshaker": "1.0.0" @@ -488,14 +488,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -680,31 +672,18 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker.png", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker.vcf", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker_classify.txt", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.saltshaker_classify_metadata.tsv", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker.png", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker.vcf", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker_classify.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.saltshaker_classify_metadata.tsv", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker.png", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker.vcf", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker_classify.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.saltshaker_classify_metadata.tsv", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "call_sv/earlycasualcaiman_LNUMBER1.saltshaker.png", + "call_sv/earlycasualcaiman_LNUMBER1.saltshaker_classify.txt", + "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat_LNUMBER3.saltshaker.png", + "call_sv/hugelymodelbat_LNUMBER3.saltshaker_classify.txt", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_saltshaker.vcf.gz", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck_LNUMBER2.saltshaker.png", + "call_sv/slowlycivilbuck_LNUMBER2.saltshaker_classify.txt", + "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -1112,11 +1091,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:52:17.64647915", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.4" }, - "timestamp": "2026-03-03T15:58:44.610805525" + "timestamp": "2026-03-25T12:44:18.757225141" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 312c4c3e4..b95de6087 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 773, + 770, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -449,14 +449,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -632,13 +624,11 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", + "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -1020,11 +1010,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:58:22.361988613", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.4" }, - "timestamp": "2026-02-27T09:07:42.308738867" + "timestamp": "2026-03-25T13:30:33.907974648" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 58d706c23..413bcd76d 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 353, + 354, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -320,7 +320,7 @@ "saltshaker": "1.0.0" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.0" + "saltshaker": "1.0.1" }, "SALTSHAKER_PLOT": { "saltshaker": "1.0.0" @@ -471,14 +471,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -545,17 +537,12 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/genome", - "call_sv/genome/justhusky_sv.vcf.gz", - "call_sv/genome/justhusky_sv.vcf.gz.tbi", - "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker.png", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker.vcf", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker_classify.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.saltshaker_classify_metadata.tsv", - "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/hugelymodelbat_LNUMBER1.saltshaker.png", + "call_sv/hugelymodelbat_LNUMBER1.saltshaker_classify.txt", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_saltshaker.vcf.gz", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -723,11 +710,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-17T17:02:07.664289531", "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.2" + "nextflow": "25.10.4" }, - "timestamp": "2026-03-04T08:25:27.608017744" + "timestamp": "2026-03-25T12:48:18.971209768" } -} +} \ No newline at end of file From 31b0964a4f83858a8f7610108e8aaf7f68dddeb6 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 25 Mar 2026 14:59:33 +0100 Subject: [PATCH 545/872] update test inputs --- .../local/call_sv_MT/tests/main.nf.test | 60 ++++++++++--------- 1 file changed, 31 insertions(+), 29 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index bf9930146..abfb895d9 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -22,41 +22,43 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[4] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[5] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[7] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[8] = channel.of([ + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[9] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[9] = channel.value(10000000) - input[10] = 16081 - input[11] = 407 - input[12] = 5730 - input[13] = 5763 - input[14] = 16569 - input[15] = 'chrM' - input[16] = 15 - input[17] = 2 - input[18] = 2 - input[19] = 30000 - input[20] = 30 - input[21] = 0.00001 - input[22] = 5 - input[23] = 15 - input[24] = 0.01 - input[25] = 1000 - input[26] = 80 - input[27] = 10000 - input[28] = 5 - input[29] = 15 + input[10] = channel.value(10000000) + input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[12] = 16081 + input[13] = 407 + input[14] = 5730 + input[15] = 5763 + input[16] = 16569 + input[17] = 'chrM' + input[18] = 15 + input[19] = 2 + input[20] = 2 + input[21] = 30000 + input[22] = 30 + input[23] = 0.00001 + input[24] = 5 + input[25] = 15 + input[26] = 0.01 + input[27] = 1000 + input[28] = 80 + input[29] = 10000 + input[30] = 5 + input[31] = 15 """ } } From 75cd6f803afed6dab9e7fc07ee272c63c65dd644 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 25 Mar 2026 16:04:32 +0100 Subject: [PATCH 546/872] update snaps --- .../tests/main.nf.test.snap | 10 +- .../local/call_sv_MT/tests/main.nf.test.snap | 178 ++++++++++++------ 2 files changed, 127 insertions(+), 61 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 50456cee3..120b54b2c 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -2,6 +2,10 @@ "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ [ + "earlycasualcaiman.saltshaker.png", + "earlycasualcaiman.saltshaker_classify.txt", + "earlycasualcaiman_mitochondria_deletions.txt", + "justhusky_saltshaker.vcf.gz", "justhusky_sv.vcf.gz", "justhusky_sv.vcf.gz.tbi" ], @@ -12,10 +16,10 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-24T09:56:24.619874", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-25T16:02:32.429241176" } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 8efaafae7..ffff40473 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -19,12 +19,23 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], [ "1", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "2", [ [ { @@ -40,12 +51,12 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], [ - "2", + "3", [ [ { @@ -66,10 +77,21 @@ ] ], [ - "3", + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", [ [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -84,11 +106,11 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -103,11 +125,11 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -124,48 +146,15 @@ }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ] - ] - ], - [ - "mitosalt_breakpoint", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "mitosalt_cluster", - [ + ], [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] ] ], @@ -194,7 +183,7 @@ "publish", [ [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -209,11 +198,11 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.breakpoint:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -228,11 +217,11 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.cluster:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - "call_sv/mitochondria/", + "call_sv/", [ { "id": "earlycasualcaiman", @@ -249,15 +238,88 @@ }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_txt", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" ] ] ] ] ], - "timestamp": "2026-03-17T23:49:47.786799067", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-25T15:53:51.569932008" } } \ No newline at end of file From b30d641edb7b68874cf162c3733fc5b4d00f06d0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:38:27 +0100 Subject: [PATCH 547/872] module fixes and updates --- modules/local/split_chr/main.nf | 32 + modules/nf-core/cat/fastq/environment.yml | 12 + modules/nf-core/cat/fastq/main.nf | 69 ++ modules/nf-core/cat/fastq/meta.yml | 67 ++ modules/nf-core/cat/fastq/tests/main.nf.test | 405 ++++++++++++ .../nf-core/cat/fastq/tests/main.nf.test.snap | 588 ++++++++++++++++++ .../custom/addmostsevereconsequence/main.nf | 2 +- .../custom/addmostsevereconsequence/meta.yml | 4 +- .../tests/main.nf.test.snap | 20 +- .../nf-core/custom/addmostseverepli/main.nf | 2 +- .../nf-core/custom/addmostseverepli/meta.yml | 4 +- .../addmostseverepli/tests/main.nf.test.snap | 20 +- .../ensemblvep/vep/ensemblvep-vep.diff | 29 +- .../nf-core/ensemblvep/vep/environment.yml | 1 + modules/nf-core/ensemblvep/vep/main.nf | 4 +- 15 files changed, 1217 insertions(+), 42 deletions(-) create mode 100644 modules/local/split_chr/main.nf create mode 100644 modules/nf-core/cat/fastq/environment.yml create mode 100644 modules/nf-core/cat/fastq/main.nf create mode 100644 modules/nf-core/cat/fastq/meta.yml create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test.snap diff --git a/modules/local/split_chr/main.nf b/modules/local/split_chr/main.nf new file mode 100644 index 000000000..c41580530 --- /dev/null +++ b/modules/local/split_chr/main.nf @@ -0,0 +1,32 @@ +process SPLIT_CHR { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioawk:1.0--h5bf99c6_6': + 'biocontainers/bioawk:1.0--h5bf99c6_6' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("chr_split"), emit: output + tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + """ + mkdir -p chr_split + bioawk -v outdir="chr_split" 'BEGIN{RS=">"; FS="\\n"} NR>1 {fnme=outdir "/" \$1 ".fa"; print ">" \$0 > fnme; close(fnme); if (NR==25) exit;}' ${input} + """ + + stub: + """ + mkdir -p chr_split + touch chr_split/test1.fa + touch chr_split/test2.fa + """ +} diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 000000000..9b926b1ff --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,12 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::coreutils=9.5 + - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf new file mode 100644 index 000000000..e70af3d11 --- /dev/null +++ b/modules/nf-core/cat/fastq/main.nf @@ -0,0 +1,69 @@ +process CAT_FASTQ { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + + output: + tuple val(meta), path("*.merged.fastq.gz"), emit: reads + tuple val("${task.process}"), val("cat"), eval("cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//'"), emit: versions_cat, topic: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect { item -> item.toString() } : [reads.toString()] + def compress = readList[0]?.endsWith('.gz') ? '' : '| gzip' + if (meta.single_end) { + if (readList.size >= 1) { + """ + cat ${readList.join(' ')} ${compress} > ${prefix}.merged.fastq.gz + """ + } else { + error("Could not find any FASTQ files to concatenate in the process input") + } + } + else { + if (readList.size >= 2) { + def read1 = [] + def read2 = [] + readList.eachWithIndex { v, ix -> (ix & 1 ? read2 : read1) << v } + """ + cat ${read1.join(' ')} ${compress} > ${prefix}_1.merged.fastq.gz + cat ${read2.join(' ')} ${compress} > ${prefix}_2.merged.fastq.gz + """ + } else { + error("Could not find any FASTQ file pairs to concatenate in the process input") + } + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect { item -> item.toString() } : [reads.toString()] + if (meta.single_end) { + if (readList.size >= 1) { + """ + echo '' | gzip > ${prefix}.merged.fastq.gz + """ + } else { + error("Could not find any FASTQ files to concatenate in the process input") + } + } + else { + if (readList.size >= 2) { + """ + echo '' | gzip > ${prefix}_1.merged.fastq.gz + echo '' | gzip > ${prefix}_2.merged.fastq.gz + """ + } else { + error("Could not find any FASTQ file pairs to concatenate in the process input") + } + } +} diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml new file mode 100644 index 000000000..6fefd6e0e --- /dev/null +++ b/modules/nf-core/cat/fastq/meta.yml @@ -0,0 +1,67 @@ +name: cat_fastq +description: Concatenates fastq files. Supports both compressed (.gz) and uncompressed inputs; uncompressed files are automatically gzip-compressed during concatenation. +keywords: + - cat + - fastq + - concatenate + - compress +tools: + - cat: + description: | + The cat utility reads files sequentially, writing them to the standard output. + documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. + Accepts both gzip-compressed (.fastq.gz) and uncompressed (.fastq) files. + ontologies: [] +output: + reads: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" + ontologies: [] + versions_cat: + - - ${task.process}: + type: string + description: The process the versions were collected from + - cat: + type: string + description: The tool name + - cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//': + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - cat: + type: string + description: The tool name + - cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//': + type: eval + description: The expression to obtain the version of the tool + +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 000000000..21052d90f --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,405 @@ +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + tag "gunzip" + + test("test_cat_fastq_single_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_uncompressed") { + + setup { + run("GUNZIP") { + script "../../../gunzip/main.nf" + process { + """ + input[0] = Channel.of( + [[ id:'r1' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)], + [[ id:'r2' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ) + """ + } + } + } + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + .toSortedList { a, b -> a[0].id <=> b[0].id } + .map { items -> [[ id: 'test', single_end: true ], items.collect { it[1] }] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_uncompressed") { + + setup { + run("GUNZIP") { + script "../../../gunzip/main.nf" + process { + """ + input[0] = Channel.of( + [[ id:'a' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)], + [[ id:'b' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)], + [[ id:'c' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true)], + [[ id:'d' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ) + """ + } + } + } + + when { + process { + """ + input[0] = GUNZIP.out.gunzip + .toSortedList { a, b -> a[0].id <=> b[0].id } + .map { items -> [[ id: 'test', single_end: false ], items.collect { it[1] }] } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_no_files") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_paired_end_no_files") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_single_end_no_files - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_paired_end_no_files - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 000000000..6375b2ab2 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,588 @@ +{ + "test_cat_fastq_paired_end_no_files - stub": { + "content": [ + " Could not find any FASTQ file pairs to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:51.248685461" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:42.84401526" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:36.820489323" + }, + "test_cat_fastq_paired_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:32:06.262192935" + }, + "test_cat_fastq_single_end_uncompressed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-09T10:03:24.344628" + }, + "test_cat_fastq_paired_end_uncompressed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-02-09T10:03:37.568053" + }, + "test_cat_fastq_single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:18.859169785" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:30.942615287" + }, + "test_cat_fastq_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:48.827990633" + }, + "test_cat_fastq_paired_end_no_files": { + "content": [ + " Could not find any FASTQ file pairs to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:40.806088747" + }, + "test_cat_fastq_single_end_no_files - stub": { + "content": [ + " Could not find any FASTQ files to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:45.852365218" + }, + "test_cat_fastq_single_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:32:00.586584379" + }, + "test_cat_fastq_paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:25.159365603" + }, + "test_cat_fastq_single_end_no_files": { + "content": [ + " Could not find any FASTQ files to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:35.695192409" + }, + "test_cat_fastq_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:31:54.850702874" + }, + "test_cat_fastq_single_end_single_file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions_cat": [ + [ + "CAT_FASTQ", + "cat", + "9.5" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2025-12-10T14:32:11.746498148" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/addmostsevereconsequence/main.nf b/modules/nf-core/custom/addmostsevereconsequence/main.nf index 5dfbd8798..c165cea0a 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/main.nf +++ b/modules/nf-core/custom/addmostsevereconsequence/main.nf @@ -14,7 +14,7 @@ process CUSTOM_ADDMOSTSEVERECONSEQUENCE { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('addmostsevereconsequence'), val("1.1"), topic: versions, emit: versions_addmostsevereconsequence + tuple val("${task.process}"), val('addmostsevereconsequence'), val("1.2.0"), topic: versions, emit: versions_addmostsevereconsequence tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: diff --git a/modules/nf-core/custom/addmostsevereconsequence/meta.yml b/modules/nf-core/custom/addmostsevereconsequence/meta.yml index 3f4e97af1..496063ee8 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/meta.yml +++ b/modules/nf-core/custom/addmostsevereconsequence/meta.yml @@ -54,7 +54,7 @@ output: - addmostsevereconsequence: type: string description: The name of the tool - - "1.1": + - 1.2.0: type: string description: The expression to obtain the version of the tool versions_bgzip: @@ -75,7 +75,7 @@ topics: - addmostsevereconsequence: type: string description: The name of the tool - - "1.1": + - 1.2.0: type: string description: The expression to obtain the version of the tool - - ${task.process}: diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap index 5fad697fd..9d5640c13 100644 --- a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap +++ b/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "CUSTOM_ADDMOSTSEVERECONSEQUENCE", "addmostsevereconsequence", - "1.1" + "1.2.0" ] ], "2": [ @@ -36,7 +36,7 @@ [ "CUSTOM_ADDMOSTSEVERECONSEQUENCE", "addmostsevereconsequence", - "1.1" + "1.2.0" ] ], "versions_bgzip": [ @@ -48,11 +48,11 @@ ] } ], - "timestamp": "2026-02-16T10:54:09.581706", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-20T13:39:46.791679914" }, "vcf - stub": { "content": [ @@ -69,7 +69,7 @@ [ "CUSTOM_ADDMOSTSEVERECONSEQUENCE", "addmostsevereconsequence", - "1.1" + "1.2.0" ] ], "2": [ @@ -91,7 +91,7 @@ [ "CUSTOM_ADDMOSTSEVERECONSEQUENCE", "addmostsevereconsequence", - "1.1" + "1.2.0" ] ], "versions_bgzip": [ @@ -103,10 +103,10 @@ ] } ], - "timestamp": "2026-02-16T10:54:14.314711", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-20T13:39:51.821372334" } } \ No newline at end of file diff --git a/modules/nf-core/custom/addmostseverepli/main.nf b/modules/nf-core/custom/addmostseverepli/main.nf index f3fd3122c..078dd2cb7 100644 --- a/modules/nf-core/custom/addmostseverepli/main.nf +++ b/modules/nf-core/custom/addmostseverepli/main.nf @@ -12,7 +12,7 @@ process CUSTOM_ADDMOSTSEVEREPLI { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - tuple val("${task.process}"), val('addmostseverepli'), val("1.1"), topic: versions, emit: versions_addmostseverepli + tuple val("${task.process}"), val('addmostseverepli'), val("1.2.0"), topic: versions, emit: versions_addmostseverepli tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip when: diff --git a/modules/nf-core/custom/addmostseverepli/meta.yml b/modules/nf-core/custom/addmostseverepli/meta.yml index e17225229..1c02be4f5 100644 --- a/modules/nf-core/custom/addmostseverepli/meta.yml +++ b/modules/nf-core/custom/addmostseverepli/meta.yml @@ -44,7 +44,7 @@ output: - addmostseverepli: type: string description: The name of the tool - - "1.1": + - 1.2.0: type: string description: The expression to obtain the version of the tool versions_bgzip: @@ -65,7 +65,7 @@ topics: - addmostseverepli: type: string description: The name of the tool - - "1.1": + - 1.2.0: type: string description: The expression to obtain the version of the tool - - ${task.process}: diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap index d492bb3ce..6b3da9e0e 100644 --- a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap +++ b/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap @@ -14,7 +14,7 @@ [ "CUSTOM_ADDMOSTSEVEREPLI", "addmostseverepli", - "1.1" + "1.2.0" ] ], "2": [ @@ -36,7 +36,7 @@ [ "CUSTOM_ADDMOSTSEVEREPLI", "addmostseverepli", - "1.1" + "1.2.0" ] ], "versions_bgzip": [ @@ -48,11 +48,11 @@ ] } ], - "timestamp": "2026-02-16T10:53:27.215565", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-20T13:39:23.157595356" }, "vcf - stub": { "content": [ @@ -69,7 +69,7 @@ [ "CUSTOM_ADDMOSTSEVEREPLI", "addmostseverepli", - "1.1" + "1.2.0" ] ], "2": [ @@ -91,7 +91,7 @@ [ "CUSTOM_ADDMOSTSEVEREPLI", "addmostseverepli", - "1.1" + "1.2.0" ] ], "versions_bgzip": [ @@ -103,10 +103,10 @@ ] } ], - "timestamp": "2026-02-16T10:53:31.072965", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-20T13:39:28.679239093" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index b94671e36..017250d91 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -1,15 +1,4 @@ Changes in component 'nf-core/ensemblvep/vep' -Changes in 'ensemblvep/vep/environment.yml': ---- modules/nf-core/ensemblvep/vep/environment.yml -+++ modules/nf-core/ensemblvep/vep/environment.yml -@@ -4,5 +4,5 @@ - - conda-forge - - bioconda - dependencies: -- - bioconda::ensembl-vep=115.2 -+ - bioconda::ensembl-vep=110.1 - - bioconda::perl-math-cdf=0.1 - 'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged Changes in 'ensemblvep/vep/main.nf': --- modules/nf-core/ensemblvep/vep/main.nf @@ -20,15 +9,27 @@ Changes in 'ensemblvep/vep/main.nf': container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" -+ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' -+ : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" ++ ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/da/da2ef7e58823df3fc9d6c0a9927e219435329a52173f871a6fa2b5302679f7b2/data' ++ : 'community.wave.seqera.io/library/ensembl-vep_perl-list-moreutils_perl-math-cdf:3c62f15be110ccc2'}" input: tuple val(meta), path(vcf), path(custom_extra_files) -'modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap' is unchanged +Changes in 'ensemblvep/vep/environment.yml': +--- modules/nf-core/ensemblvep/vep/environment.yml ++++ modules/nf-core/ensemblvep/vep/environment.yml +@@ -4,5 +4,6 @@ + - conda-forge + - bioconda + dependencies: +- - bioconda::ensembl-vep=115.2 ++ - bioconda::ensembl-vep=110.1 ++ - bioconda::perl-list-moreutils=0.430 + - bioconda::perl-math-cdf=0.1 + 'modules/nf-core/ensemblvep/vep/tests/tab.gz.config' is unchanged 'modules/nf-core/ensemblvep/vep/tests/vcf.config' is unchanged +'modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap' is unchanged 'modules/nf-core/ensemblvep/vep/tests/nextflow.config' is unchanged 'modules/nf-core/ensemblvep/vep/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 744ccc71c..3662a9ac5 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -5,4 +5,5 @@ channels: - bioconda dependencies: - bioconda::ensembl-vep=110.1 + - bioconda::perl-list-moreutils=0.430 - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 2e79210f3..4ec78eab4 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/486485f638979d64bfff7634647833ecfd9fff050c1c2ed17cb65174d7f94c53/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:3ebe91ef7d23400f'}" + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/da/da2ef7e58823df3fc9d6c0a9927e219435329a52173f871a6fa2b5302679f7b2/data' + : 'community.wave.seqera.io/library/ensembl-vep_perl-list-moreutils_perl-math-cdf:3c62f15be110ccc2'}" input: tuple val(meta), path(vcf), path(custom_extra_files) From 06ee964b2d969f45dd0aaf28a3a976049cf95baf Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:52:49 +0100 Subject: [PATCH 548/872] Update subworkflow configs --- conf/modules/annotate_cadd.config | 6 +++++- conf/modules/call_snv.config | 2 +- conf/modules/call_sv_cnvnator.config | 11 +++++------ 3 files changed, 11 insertions(+), 8 deletions(-) diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index 8d47b5543..7cce27e23 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -21,7 +21,7 @@ process { } withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' { - ext.args = { "--output-type z --types indels,other" } + ext.args = { "--output-type z --write-index=tbi --types indels,other" } ext.prefix = { "${vcf.simpleName}_indels" } } @@ -50,4 +50,8 @@ process { ext.prefix = "reference_to_cadd" ext.suffix = "txt" } + + withName: '.*:ANNOTATE_CADD:RENAME_CHRNAMES' { + ext.args = { "--output-type z" } + } } diff --git a/conf/modules/call_snv.config b/conf/modules/call_snv.config index 2648a2d75..f5184c021 100644 --- a/conf/modules/call_snv.config +++ b/conf/modules/call_snv.config @@ -19,7 +19,7 @@ process { } withName: '.*CALL_SNV:BCFTOOLS_CONCAT' { - ext.args = { "--write-index=tbi" } + ext.args = { "--write-index=tbi --output-type z" } ext.prefix = { "${meta.id}_mt_and_nuclear_snvs" } } } diff --git a/conf/modules/call_sv_cnvnator.config b/conf/modules/call_sv_cnvnator.config index fcd9e88ff..8ba66dac8 100644 --- a/conf/modules/call_sv_cnvnator.config +++ b/conf/modules/call_sv_cnvnator.config @@ -16,30 +16,29 @@ // process { - withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_HIST" { tag = { "$meta2.id" } - ext.args = { "-his ${params.cnvnator_binsize}" } + ext.args = { "-genome ${params.genome} -his ${params.cnvnator_binsize}" } } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_STAT" { tag = { "$meta2.id" } - ext.args = { "-stat ${params.cnvnator_binsize}" } + ext.args = { "-genome ${params.genome} -stat ${params.cnvnator_binsize}" } } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_PARTITION" { tag = { "$meta2.id" } - ext.args = { "-partition ${params.cnvnator_binsize}" } + ext.args = { "-genome ${params.genome} -partition ${params.cnvnator_binsize}" } } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CALL" { tag = { "$meta2.id" } - ext.args = { "-call ${params.cnvnator_binsize}" } + ext.args = { "-genome ${params.genome} -call ${params.cnvnator_binsize}" } } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF" { ext.prefix = { "${meta.id}_cnvnator" } - ext.args = { "-call ${params.cnvnator_binsize}" } + ext.args = { "-reference ${params.genome}" } } withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR" { From 93a0487dee44d68de083c600e40af3781cf93d2e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:53:20 +0100 Subject: [PATCH 549/872] refactor channel creation --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 44e5463ef..51c7742ff 100644 --- a/main.nf +++ b/main.nf @@ -187,7 +187,6 @@ workflow NFCORE_RAREDISEASE { ch_vep_cache = ch_references.vep_resources // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) - ch_cadd_resources = channelFromPath(val_cadd_resources, true) ch_multiqc_samples = channelFromPath(val_multiqc_samples, true) ch_reduced_penetrance = channelFromPath(val_reduced_penetrance, true) ch_rtg_truthvcfs = channelFromPath(val_rtg_truthvcfs, true) @@ -210,6 +209,7 @@ workflow NFCORE_RAREDISEASE { ch_svd_ud = channelFromPath(val_verifybamid_svd_ud) // Using channelFromPathWithMeta helper (with simpleName). If filepath is null, returns, [[:],[]] + ch_cadd_resources = channelFromPathWithMeta(val_cadd_resources, true) ch_call_interval = channelFromPathWithMeta(val_call_interval, true) ch_ml_model = channelFromPathWithMeta(val_ml_model, true) ch_variant_catalog = channelFromPathWithMeta(val_variant_catalog, true) @@ -229,10 +229,10 @@ workflow NFCORE_RAREDISEASE { // Using channelFromSamplesheet helper. Returns either an empty channel or validated channel. ch_me_references = channelFromSamplesheet(val_mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json", false) - ch_me_svdb_resources = channelFromSamplesheet(val_mobile_element_svdb_annotations, "${projectDir}/assets/svdb_query_vcf_schema.json") + ch_me_svdb_resources = channelFromSamplesheet(val_mobile_element_svdb_annotations, "${projectDir}/assets/svdb_query_vcf_schema.json", false) ch_sample_id_map = channelFromSamplesheet(val_sample_id_map, "${projectDir}/assets/sample_id_map.json") - ch_svdb_bedpedbs = channelFromSamplesheet(val_svdb_query_bedpedbs, "${projectDir}/assets/svdb_query_bedpe_schema.json") - ch_svdb_dbs = channelFromSamplesheet(val_svdb_query_dbs, "${projectDir}/assets/svdb_query_vcf_schema.json") + ch_svdb_bedpedbs = channelFromSamplesheet(val_svdb_query_bedpedbs, "${projectDir}/assets/svdb_query_bedpe_schema.json", false) + ch_svdb_dbs = channelFromSamplesheet(val_svdb_query_dbs, "${projectDir}/assets/svdb_query_vcf_schema.json", false) ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() From 9995a816347d800d998fb57687e272470ed35898 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 26 Mar 2026 15:56:32 +0100 Subject: [PATCH 550/872] subworkflow updates --- modules.json | 9 +++++-- subworkflows/local/annotate_cadd/main.nf | 2 +- .../local/annotate_genome_snvs/main.nf | 9 ++++--- subworkflows/local/annotate_mt_snvs/main.nf | 6 ++--- subworkflows/local/call_sv_MT/main.nf | 24 ++++++++++++++++++- subworkflows/local/call_sv_cnvnator/main.nf | 4 +++- subworkflows/local/call_sv_tiddit/main.nf | 3 ++- subworkflows/local/prepare_references/main.nf | 2 +- 8 files changed, 45 insertions(+), 14 deletions(-) diff --git a/modules.json b/modules.json index 52b5ec8b0..150f303ef 100644 --- a/modules.json +++ b/modules.json @@ -105,6 +105,11 @@ "git_sha": "7ed72ef972290b93d0bdd7c60ff00a693250f77a", "installed_by": ["modules"] }, + "cat/fastq": { + "branch": "master", + "git_sha": "5d28ea7cfaebcfae6f74d1067ea766d8ff19dff3", + "installed_by": ["modules"] + }, "chromograph": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", @@ -122,12 +127,12 @@ }, "custom/addmostsevereconsequence": { "branch": "master", - "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", + "git_sha": "0e225fbda197093af4d54a88b9a2908c14ce660b", "installed_by": ["modules"] }, "custom/addmostseverepli": { "branch": "master", - "git_sha": "0f04646a9282049b16b3eb35b042e94dfb3340a0", + "git_sha": "0e225fbda197093af4d54a88b9a2908c14ce660b", "installed_by": ["modules"] }, "deepvariant/rundeepvariant": { diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 03a31d925..a6052fdff 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -53,7 +53,7 @@ workflow ANNOTATE_CADD { .join(CADD.out.tsv) .join(TABIX_CADD.out.index) .map { meta, vcf, tbi, ann, ann_tbi -> [ meta, vcf, tbi, ann, ann_tbi, [] ] } - .combine(ch_header.map { _meta, header -> header }) + .combine(ch_header) .combine(ch_rename_chrs) .set { ch_annotate_in } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 3f9f7e37f..61e5c2263 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -13,7 +13,6 @@ include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../../modules/nf-core include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../../modules/nf-core/chromograph/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' include { ANNOTATE_CADD } from '../annotate_cadd' include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' @@ -98,9 +97,13 @@ workflow ANNOTATE_GENOME_SNVS { VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ZIP_TABIX_VCFANNO (VCFANNO.out.vcf) + VCFANNO.out.vcf + .join(VCFANNO.out.tbi, failOnMismatch:true, failOnDuplicate:true) + .set { ch_bcftools_view_in } - BCFTOOLS_VIEW(ZIP_TABIX_VCFANNO.out.gz_index, [], [], []) // filter on frequencies + BCFTOOLS_VIEW( + ch_bcftools_view_in, + [], [], []) // filter on frequencies // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 82972aa71..a0a4ba373 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -9,7 +9,6 @@ include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../module include { HAPLOGREP3_CLASSIFY as HAPLOGREP3_CLASSIFY_MT } from '../../../modules/nf-core/haplogrep3/classify/main' include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' include { ANNOTATE_CADD } from '../annotate_cadd' -include { TABIX_BGZIPTABIX as ZIP_TABIX_VCFANNO_MT } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow ANNOTATE_MT_SNVS { take: @@ -40,9 +39,8 @@ workflow ANNOTATE_MT_SNVS { .set { ch_in_vcfanno } VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ZIP_TABIX_VCFANNO_MT(VCFANNO_MT.out.vcf) - ch_vcfanno_vcf = ZIP_TABIX_VCFANNO_MT.out.gz_index.map{meta, vcf, _tbi -> return [meta, vcf]} + ch_vcfanno_vcf = VCFANNO_MT.out.vcf // Annotating with CADD if (!val_cadd_resources.equals(null)) { @@ -50,7 +48,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_resources, ch_fai, ch_cadd_header, - ZIP_TABIX_VCFANNO_MT.out.gz_index, + VCFANNO_MT.out.vcf.join(VCFANNO_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true), val_genome ) ch_cadd_vcf = ANNOTATE_CADD.out.vcf diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 5b74b7ba2..aa5210788 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -6,6 +6,7 @@ include { MT_DELETION } from '../../../modules/local/mt_deletion_script' include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' include { MITOSALT } from '../../../modules/local/mitosalt/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' workflow CALL_SV_MT { take: @@ -39,7 +40,28 @@ workflow CALL_SV_MT { ch_mitosalt_publish = channel.empty() if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { - ch_reads_subdepth = ch_reads.combine(ch_subdepth) + + ch_reads + .map { meta, reads -> + def groupKey = meta.sample + return [groupKey, meta, reads] + } + .groupTuple(by: 0) + .map { sample_id, meta_list, reads_list -> + def combined_meta = meta_list[0].clone() + combined_meta.id = sample_id + combined_meta.remove('lane') + combined_meta.remove('read_group') + + def all_reads = reads_list.flatten() + + [combined_meta, all_reads] + } + .set {ch_cat_fastq} + + CAT_FASTQ(ch_cat_fastq) + + ch_reads_subdepth = CAT_FASTQ.out.reads.combine(ch_subdepth) SEQTK_SAMPLE (ch_reads_subdepth) diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 36756a898..0516419b4 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -2,6 +2,7 @@ // A subworkflow to call CNVs using cnvnator // +include { SPLIT_CHR } from '../../../modules/local/split_chr/main.nf' include { CNVNATOR_CNVNATOR as CNVNATOR_RD } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' include { CNVNATOR_CNVNATOR as CNVNATOR_HIST } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' include { CNVNATOR_CNVNATOR as CNVNATOR_STAT } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' @@ -21,8 +22,9 @@ workflow CALL_SV_CNVNATOR { main: + SPLIT_CHR (ch_fasta) CNVNATOR_RD ( ch_bam_bai, [[:],[]], [[:],[]], [[:],[]], "rd" ) - CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, ch_fasta, ch_fai, "his" ) + CNVNATOR_HIST ( [[:],[],[]], CNVNATOR_RD.out.root, SPLIT_CHR.out.output, [[:],[]], "his" ) CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]], "stat" ) CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]], "partition" ) CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]], "call" ) diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index 0d7d512d0..f3f7386da 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -16,7 +16,8 @@ workflow CALL_SV_TIDDIT { ch_case_info // channel: [mandatory] [ val(case_info) ] main: - TIDDIT_SV ( ch_bam_bai, ch_genome_fasta.join(ch_genome_fai), ch_bwa_index ) + ch_genome_fa_fai = ch_genome_fasta.join(ch_genome_fai).collect() + TIDDIT_SV ( ch_bam_bai, ch_genome_fa_fai, ch_bwa_index ) INDEX_TIDDIT (TIDDIT_SV.out.vcf) BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_index, [], [], []).vcf diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 462eec4b9..5eb8bfbbf 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -243,7 +243,7 @@ workflow PREPARE_REFERENCES { } else { TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in) channel.empty() - .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_index, TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_csi) + .mix(TABIX_BGZIPINDEX_VCFANNOEXTRA.out.gz_index) .map { _meta, vcf, index -> return [[vcf,index]] } .set {ch_vcfanno_extra} } From c86e3a6763c768084c852c05f01510b55f4a436c Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Thu, 26 Mar 2026 17:18:03 +0100 Subject: [PATCH 551/872] Added tags in subworkflow tests --- subworkflows/local/align/tests/main.nf.test | 9 +++++++++ subworkflows/local/align_MT/tests/main.nf.test | 10 ++++++++++ .../align_bwa_bwamem2_bwameme/tests/main.nf.test | 11 +++++++++++ .../local/align_sentieon/tests/main.nf.test | 8 ++++++++ .../local/annotate_cadd/tests/main.nf.test | 8 ++++++++ .../annotate_consequence_pli/tests/main.nf.test | 5 +++++ .../local/annotate_genome_snvs/tests/main.nf.test | 15 +++++++++++++++ .../annotate_mobile_elements/tests/main.nf.test | 7 +++++++ .../local/annotate_mt_snvs/tests/main.nf.test | 10 ++++++++++ .../local/annotate_rhocallviz/tests/main.nf.test | 8 ++++++++ .../tests/main.nf.test | 7 +++++++ .../local/call_mobile_elements/tests/main.nf.test | 10 ++++++++++ .../call_repeat_expansions/tests/main.nf.test | 10 ++++++++++ subworkflows/local/call_snv/tests/main.nf.test | 9 +++++++++ subworkflows/local/call_snv_MT/tests/main.nf.test | 4 ++++ .../local/call_snv_deepvariant/tests/main.nf.test | 8 ++++++++ .../local/call_snv_sentieon/tests/main.nf.test | 10 ++++++++++ .../call_structural_variants/tests/main.nf.test | 8 ++++++++ .../local/call_sv_cnvnator/tests/main.nf.test | 7 +++++++ 19 files changed, 164 insertions(+) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 410ea08d7..afb6b485d 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -3,8 +3,17 @@ nextflow_workflow { name "Test Workflow ALIGN" script "subworkflows/local/align/main.nf" workflow "ALIGN" + tag "subworkflows" tag "align" + tag "align_bwa_bwamem2_bwameme" + tag "align_sentieon" + tag "align_MT" + tag "convert_mt_bam_to_fastq" + + tag "fastp" + tag "samtools/view" + config "./nextflow.config" setup { diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 6deaaba85..c44453a09 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -3,8 +3,18 @@ nextflow_workflow { name "Test Workflow ALIGN_MT" script "subworkflows/local/align_MT/main.nf" workflow "ALIGN_MT" + tag "subworkflows" tag "align_mt" + + tag "bwa/mem" + tag "bwamem2/mem" + tag "sentieon/bwamem" + tag "gatk4/mergebamalignment" + tag "picard/addorreplacereadgroups" + tag "picard/markduplicates" + tag "samtools/sort" + config "./nextflow.config" test("align mt - bwamem2") { diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index f45609486..7e64d0355 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -3,8 +3,19 @@ nextflow_workflow { name "Test Workflow ALIGN_BWA_BWAMEM2_BWAMEME" script "subworkflows/local/align_bwa_bwamem2_bwameme/main.nf" workflow "ALIGN_BWA_BWAMEM2_BWAMEME" + tag "subworkflows" tag "align_bwa_bwamem2_bwameme" + + tag "bwa/mem" + tag "bwamem2/mem" + tag "bwameme/mem" + tag "samtools/index" + tag "samtools/stats" + tag "samtools/merge" + tag "samtools/view" + tag "picard/markduplicates" + config "./nextflow.config" test("align bwamem2") { diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 4954858c8..efd9ac4a2 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -3,8 +3,16 @@ nextflow_workflow { name "Test Workflow ALIGN_SENTIEON" script "subworkflows/local/align_sentieon/main.nf" workflow "ALIGN_SENTIEON" + tag "subworkflows" tag "align_sentieon" + + tag "sentieon/bwamem" + tag "sentieon/datametrics" + tag "sentieon/dedup" + tag "sentieon/readwriter" + tag "samtools/view" + config "./nextflow.config" test("align sentieon") { diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test index 3dfdf1f18..fe87a881e 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -3,8 +3,16 @@ nextflow_workflow { name "Test Workflow ANNOTATE_CADD" script "subworkflows/local/annotate_cadd/main.nf" workflow "ANNOTATE_CADD" + tag "subworkflows" tag "annotate_cadd" + + tag "bcftools/annotate" + tag "bcftools/view" + tag "cadd" + tag "gawk" + tag "tabix/tabix" + config "./nextflow.config" test("ANNOTATE_CADD - GRCh37, stub") { diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test index da5fe378f..f25124a68 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -3,6 +3,11 @@ nextflow_workflow { name "Test Workflow ANNOTATE_CSQ_PLI" script "subworkflows/local/annotate_consequence_pli/main.nf" workflow "ANNOTATE_CSQ_PLI" + + tag "custom/addmostsevereconsequence" + tag "custom/addmostseverepli" + tag "tabix/tabix" + tag "subworkflows" tag "annotate_consequence_pli" diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index a3119827a..cb11eff34 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -3,8 +3,23 @@ nextflow_workflow { name "Test Workflow ANNOTATE_GENOME_SNVS" script "subworkflows/local/annotate_genome_snvs/main.nf" workflow "ANNOTATE_GENOME_SNVS" + tag "subworkflows" tag "annotate_genome_snvs" + tag"annotate_cadd" + tag "annotate_rhocallviz" + + tag "vcfanno" + tag "bcftools/concat" + tag "bcftools/roh" + tag "bcftools/view" + tag "rhocall/annotate" + tag "upd" + tag "chromograph" + tag "ensemblvep/vep" + tag "tabix/bgziptabix" + tag "gatk4/selectvariants" + config "./nextflow.config" test("ANNOTATE_GENOME_SNVS - GRCh37, stub") { diff --git a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test index 819d2ea98..fb46452da 100644 --- a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test +++ b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test @@ -3,8 +3,15 @@ nextflow_workflow { name "Test Workflow ANNOTATE_MOBILE_ELEMENTS" script "subworkflows/local/annotate_mobile_elements/main.nf" workflow "ANNOTATE_MOBILE_ELEMENTS" + tag "subworkflows" tag "annotate_mobile_elements" + + tag"bcftools/view" + tag "ensemblvep/vep" + tag "picard/sortvcf" + tag "svdb/query" + config "./nextflow.config" test("ANNOTATE_MOBILE_ELEMENTS - GRCh37, stub") { diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 8bf721bf9..dc40257e8 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -3,8 +3,18 @@ nextflow_workflow { name "Test Workflow ANNOTATE_MT_SNVS" script "subworkflows/local/annotate_mt_snvs/main.nf" workflow "ANNOTATE_MT_SNVS" + tag "subworkflows" tag "annotate_mt_snvs" + tag "annotate_cadd" + + tag "bcftools/pluginsetgt" + tag "tabix/tabix" + tag "ensemblvep/vep" + tag "haplogrep3/classify" + tag "vcfanno" + tag "tabix/bgziptabix" + config "./nextflow.config" test("ANNOTATE_MT_SNVS - GRCh37, stub") { diff --git a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test index 683898fbd..291fba0ab 100644 --- a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test +++ b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test @@ -3,8 +3,16 @@ nextflow_workflow { name "Test Workflow ANNOTATE_RHOCALLVIZ" script "subworkflows/local/annotate_rhocallviz/main.nf" workflow "ANNOTATE_RHOCALLVIZ" + tag "subworkflows" tag "annotate_rhocallviz" + + tag "bcftools/view" + tag "bcftools/roh" + tag "rhocall/viz" + tag "ucsc/wigtobigwig" + tag "chromograph" + config "./nextflow.config" test("ANNOTATE_RHOCALLVIZ - stub") { diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test b/subworkflows/local/annotate_structural_variants/tests/main.nf.test index 190b2f6cb..978c80c32 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test @@ -3,8 +3,15 @@ nextflow_workflow { name "Test Workflow ANNOTATE_STRUCTURAL_VARIANTS" script "subworkflows/local/annotate_structural_variants/main.nf" workflow "ANNOTATE_STRUCTURAL_VARIANTS" + tag "subworkflows" tag "annotate_structural_variants" + + tag "svdb/query" + tag "picard/sortvcf" + tag "bcftools/view" + tag "ensemblvep/vep" + config "./nextflow.config" test("ANNOTATE_STRUCTURAL_VARIANTS - no SVDB queries, stub") { diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test b/subworkflows/local/call_mobile_elements/tests/main.nf.test index 5655d906b..c25f9457a 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test @@ -3,9 +3,19 @@ nextflow_workflow { name "Test Workflow CALL_MOBILE_ELEMENTS" script "subworkflows/local/call_mobile_elements/main.nf" workflow "CALL_MOBILE_ELEMENTS" + tag "subworkflows" tag "call_mobile_elements" + tag "bcftools/reheader" + tag "bcftools/concat" + tag "bcftools/sort" + tag "retroseq/discover" + tag "retroseq/call" + tag "samtools/view" + tag "tabix/tabix" + tag "svdb/merge" + test("CALL_MOBILE_ELEMENTS - stub") { options "-stub" diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index c21805209..298e271e3 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -3,8 +3,18 @@ nextflow_workflow { name "Test Workflow CALL_REPEAT_EXPANSIONS" script "subworkflows/local/call_repeat_expansions/main.nf" workflow "CALL_REPEAT_EXPANSIONS" + tag "subworkflows" tag "call_repeat_expansions" + + tag "bcftools/norm" + tag "bcftools/reheader" + tag "expansionhunter" + tag "picard/renamesampleinvcf" + tag "samtools/sort" + tag "svdb/merge" + tag "tabix/tabix" + config "./nextflow.config" test("CALL_REPEAT_EXPANSIONS") { diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 279c35119..9ec028ea8 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -3,8 +3,17 @@ nextflow_workflow { name "Test Workflow CALL_SNV" script "subworkflows/local/call_snv/main.nf" workflow "CALL_SNV" + tag "subworkflows" tag "call_snv" + tag "call_snv_deepvariant" + tag "call_snv_sentieon" + tag "call_snv_MT" + tag "postprocess_MT_calls" + + tag "gatk4_selectvariants" + tag "bcftools_concat" + test("CALL_SNV - deepvariant wgs") { diff --git a/subworkflows/local/call_snv_MT/tests/main.nf.test b/subworkflows/local/call_snv_MT/tests/main.nf.test index 558a81d49..bc4dee845 100644 --- a/subworkflows/local/call_snv_MT/tests/main.nf.test +++ b/subworkflows/local/call_snv_MT/tests/main.nf.test @@ -3,9 +3,13 @@ nextflow_workflow { name "Test Workflow CALL_SNV_MT" script "subworkflows/local/call_snv_MT/main.nf" workflow "CALL_SNV_MT" + tag "subworkflows" tag "call_snv_MT" + tag "gatk4/mutect2" + tag "gatk4/filtermutectcalls" + test("CALL_SNV_MT") { when { diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 64bc5a53b..799a20c43 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -3,9 +3,17 @@ nextflow_workflow { name "Test Workflow CALL_SNV_DEEPVARIANT" script "subworkflows/local/call_snv_deepvariant/main.nf" workflow "CALL_SNV_DEEPVARIANT" + tag "subworkflows" tag "call_snv_deepvariant" + tag "bcftools/annotate" + tag "bcftools/norm" + tag "deepvariant/rundeepvariant" + tag "glnexus" + tag "tabix/bgzip" + tag "local/add_varcallername_to_bed" + config "./nextflow.config" test("CALL_SNV_DEEPVARIANT - wgs") { diff --git a/subworkflows/local/call_snv_sentieon/tests/main.nf.test b/subworkflows/local/call_snv_sentieon/tests/main.nf.test index 4b9ced510..b80e0d774 100644 --- a/subworkflows/local/call_snv_sentieon/tests/main.nf.test +++ b/subworkflows/local/call_snv_sentieon/tests/main.nf.test @@ -3,8 +3,18 @@ nextflow_workflow { name "Test Workflow CALL_SNV_SENTIEON" script "subworkflows/local/call_snv_sentieon/main.nf" workflow "CALL_SNV_SENTIEON" + tag "subworkflows" tag "call_snv_sentieon" + + tag "sentieon/dnascope" + tag "sentieon/dnamodelapply" + tag "bcftools/merge" + tag "bcftools/norm" + tag "bcftools/filter" + tag "bcftools/annotate" + tag "add_varcallername_to_bed" + config "./nextflow.config" test("CALL_SNV_SENTIEON - single sample, stub") { diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 94e520bcd..e196d2de2 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -3,8 +3,16 @@ nextflow_workflow { name "Test Workflow CALL_STRUCTURAL_VARIANTS" script "subworkflows/local/call_structural_variants/main.nf" workflow "CALL_STRUCTURAL_VARIANTS" + tag "subworkflows" tag "call_structural_variants" + tag "call_sv_manta" + tag "call_sv_tiddit" + tag "call_sv_germlinecnvcaller" + tag "call_sv_cnvnator" + + tag "svdb/merge" + tag "tabix/tabix" test("CALL_STRUCTURAL_VARIANTS - wgs, stub") { diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test index ce9b011e3..e83917364 100644 --- a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test @@ -3,9 +3,16 @@ nextflow_workflow { name "Test Workflow CALL_SV_CNVNATOR" script "subworkflows/local/call_sv_cnvnator/main.nf" workflow "CALL_SV_CNVNATOR" + tag "subworkflows" tag "call_sv_cnvnator" + tag "cnvnator/cnvnator" + tag "cnvnator/convert2vcf" + tag "tabix/bgziptabix" + tag "bcftools/view" + tag "svdb/merge" + config "./nextflow.config" test("CALL_SV_CNVNATOR") { From b0b7567dcdac69ac9e9f4070174e43e9e6bfa34d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 10:09:54 +0100 Subject: [PATCH 552/872] Update peddy container --- modules.json | 2 +- modules/nf-core/peddy/environment.yml | 1 + modules/nf-core/peddy/main.nf | 4 ++-- modules/nf-core/peddy/tests/main.nf.test.snap | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/modules.json b/modules.json index 150f303ef..987c2d9e8 100644 --- a/modules.json +++ b/modules.json @@ -333,7 +333,7 @@ }, "peddy": { "branch": "master", - "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", + "git_sha": "7773ae1c42342cacb0b99794aa3827af0d523678", "installed_by": ["modules"] }, "picard/addorreplacereadgroups": { diff --git a/modules/nf-core/peddy/environment.yml b/modules/nf-core/peddy/environment.yml index 2bb1deb8e..6deea82ac 100644 --- a/modules/nf-core/peddy/environment.yml +++ b/modules/nf-core/peddy/environment.yml @@ -5,3 +5,4 @@ channels: - bioconda dependencies: - bioconda::peddy=0.4.8 + - conda-forge::numpy=1.26.4 diff --git a/modules/nf-core/peddy/main.nf b/modules/nf-core/peddy/main.nf index 0090f4e28..ba91db235 100644 --- a/modules/nf-core/peddy/main.nf +++ b/modules/nf-core/peddy/main.nf @@ -4,8 +4,8 @@ process PEDDY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a1f7f39ed4c0e429d5a5805cdfa5251cbe56d4f2cf9cf4257172db1a56ab6bf/data' : - 'community.wave.seqera.io/library/peddy:0.4.8--e3cef30bae621593' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4db23bec88305fd6ded604f143d6292303a9822677e007fbdc14f9a763e097ec/data' : + 'community.wave.seqera.io/library/peddy_numpy:a2456db0b53651ad' }" input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/nf-core/peddy/tests/main.nf.test.snap b/modules/nf-core/peddy/tests/main.nf.test.snap index c122208ad..60551fd04 100644 --- a/modules/nf-core/peddy/tests/main.nf.test.snap +++ b/modules/nf-core/peddy/tests/main.nf.test.snap @@ -198,7 +198,7 @@ ] } ], - "timestamp": "2026-02-18T10:39:07.038845862", + "timestamp": "2026-03-24T11:53:32.465432", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -403,7 +403,7 @@ ] } ], - "timestamp": "2026-02-18T10:44:20.669530641", + "timestamp": "2026-03-24T11:53:24.822041", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 9c383a26e6179cd88adb3e0d0f462f4f8e28b83f Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 27 Mar 2026 10:19:46 +0100 Subject: [PATCH 553/872] Addded tags in subworkflow tests pt2 --- .../local/call_sv_MT/tests/main.nf.test | 7 ++++++ .../tests/main.nf.test | 9 ++++++++ .../local/call_sv_manta/tests/main.nf.test | 5 ++++ .../local/call_sv_tiddit/tests/main.nf.test | 7 ++++++ .../tests/main.nf.test | 6 +++++ .../tests/main.nf.test | 7 ++++++ subworkflows/local/gens/tests/main.nf.test | 6 +++++ .../postprocess_MT_calls/tests/main.nf.test | 10 ++++++++ .../prepare_references/tests/main.nf.test | 23 +++++++++++++++++++ subworkflows/local/qc_bam/tests/main.nf.test | 15 ++++++++++++ .../local/rank_variants/tests/main.nf.test | 8 +++++++ .../local/scatter_genome/tests/main.nf.test | 7 ++++++ .../subsample_mt_frac/tests/main.nf.test | 5 ++++ .../subsample_mt_reads/tests/main.nf.test | 6 +++++ .../variant_evaluation/tests/main.nf.test | 6 +++++ 15 files changed, 127 insertions(+) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 002a4ccdc..853ae705d 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -3,8 +3,15 @@ nextflow_workflow { name "Test Workflow CALL_SV_MT" script "subworkflows/local/call_sv_MT/main.nf" workflow "CALL_SV_MT" + tag "subworkflows" tag "call_sv_mt" + + tag "mt_deletion_script" + tag "prep_mitosalt" + tag "mitosalt" + tag "seqtk/sample" + config "./nextflow.config" test("CALL_SV_MT - stub") { diff --git a/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test index eb8ca9888..6a37ee5d3 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test +++ b/subworkflows/local/call_sv_germlinecnvcaller/tests/main.nf.test @@ -3,9 +3,18 @@ nextflow_workflow { name "Test Workflow CALL_SV_GERMLINECNVCALLER" script "subworkflows/local/call_sv_germlinecnvcaller/main.nf" workflow "CALL_SV_GERMLINECNVCALLER" + tag "subworkflows" tag "call_sv_germlinecnvcaller" + tag "gatk4/collectreadcounts" + tag "gatk4/determinegermlinecontigploidy" + tag "gatk4/germlinecnvcaller" + tag "gatk4/postprocessgermlinecnvcalls" + tag "bcftools/view" + tag "tabix/tabix" + tag "svdb/merge" + config "./nextflow.config" test("CALL_SV_GERMLINECNVCALLER - stub") { diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test index 44124b955..fd43a3cda 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -3,8 +3,13 @@ nextflow_workflow { name "Test Workflow CALL_SV_MANTA" script "subworkflows/local/call_sv_manta/main.nf" workflow "CALL_SV_MANTA" + tag "subworkflows" tag "call_sv_manta" + + tag "manta/germline" + tag "bcftools/view" + config "./nextflow.config" test("CALL_SV_MANTA - wgs") { diff --git a/subworkflows/local/call_sv_tiddit/tests/main.nf.test b/subworkflows/local/call_sv_tiddit/tests/main.nf.test index 7059a1be7..c3ad01291 100644 --- a/subworkflows/local/call_sv_tiddit/tests/main.nf.test +++ b/subworkflows/local/call_sv_tiddit/tests/main.nf.test @@ -3,8 +3,15 @@ nextflow_workflow { name "Test Workflow CALL_SV_TIDDIT" script "subworkflows/local/call_sv_tiddit/main.nf" workflow "CALL_SV_TIDDIT" + tag "subworkflows" tag "call_sv_tiddit" + + tag "tiddit/sv" + tag "svdb/merge" + tag "tabix/bgziptabix" + tag "bcftools/view" + config "./nextflow.config" test("CALL_SV_TIDDIT") { diff --git a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test index b7f335fc3..f3451fd0f 100644 --- a/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test +++ b/subworkflows/local/convert_mt_bam_to_fastq/tests/main.nf.test @@ -3,9 +3,15 @@ nextflow_workflow { name "Test Workflow CONVERT_MT_BAM_TO_FASTQ" script "subworkflows/local/convert_mt_bam_to_fastq/main.nf" workflow "CONVERT_MT_BAM_TO_FASTQ" + tag "subworkflows" tag "convert_mt_bam_to_fastq" + tag "gatk4/printreads" + tag "gatk4/revertsam" + tag "gatk4/samtofastq" + tag "samtools/index" + test("CONVERT_MT_BAM_TO_FASTQ") { when { diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test b/subworkflows/local/generate_cytosure_files/tests/main.nf.test index 7934620de..fa7d9442d 100644 --- a/subworkflows/local/generate_cytosure_files/tests/main.nf.test +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test @@ -3,8 +3,15 @@ nextflow_workflow { name "Test Workflow GENERATE_CYTOSURE_FILES" script "subworkflows/local/generate_cytosure_files/main.nf" workflow "GENERATE_CYTOSURE_FILES" + tag "subworkflows" tag "generate_cytosure_files" + + tag "bcftools/view" + tag "bcftools/reheader" + tag "tiddit/cov" + tag "vcf2cytosure" + config "./nextflow.config" test("GENERATE_CYTOSURE_FILES - no sample_id_map, stub") { diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index 8184fd79e..de8af8f40 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -3,8 +3,14 @@ nextflow_workflow { name "Test Workflow GENS" script "subworkflows/local/gens/main.nf" workflow "GENS" + tag "subworkflows" tag "gens" + + tag "gatk4/collectreadcounts" + tag "gatk4/denoisereadcounts" + tag "gens/preparecovandbaf" + config "./nextflow.config" test("GENS - male sample, stub") { diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test index 116242b76..bcdc5217e 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test @@ -3,9 +3,19 @@ nextflow_workflow { name "Test Workflow POSTPROCESS_MT_CALLS" script "subworkflows/local/postprocess_MT_calls/main.nf" workflow "POSTPROCESS_MT_CALLS" + tag "subworkflows" tag "postprocess_MT_calls" + tag "gatk4/mergevcfs" + tag "gatk4/variantfiltration" + tag "bcftools/norm" + tag "tabix/tabix" + tag "bcftools/merge" + tag "picard/liftovervcf" + tag "bcftools/annotate" + tag "local/add_varcallername_to_bed" + test("POSTPROCESS_MT_CALLS - stub") { options "-stub" diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 3dceb0611..56e9d6831 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -3,6 +3,29 @@ nextflow_workflow { name "Test Workflow PREPARE_REFERENCES" script "subworkflows/local/prepare_references/main.nf" workflow "PREPARE_REFERENCES" + + tag "subworkflows" + tag "prepare_references" + + tag "bedtools/slop" + tag "bwa/index" + tag "bwamem2/index" + tag "bwameme/index" + tag "cat/cat" + tag "gatk4/bedtointervallist" + tag "gatk4/createsequencedictionary" + tag "gatk4/intervallisttools" + tag "gatk4/shiftfasta" + tag "get_chrom_sizes" + tag "hisat2/build" + tag "last/lastdb" + tag "rtgtools/format" + tag "samtools/faidx" + tag "sentieon/bwaindex" + tag "tabix/bgziptabix" + tag "tabix/tabix" + tag "untar" + config "./nextflow.config" test("Should run without failures") { diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 79bbaaedc..f205534f5 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -3,8 +3,23 @@ nextflow_workflow { name "Test Workflow QC_BAM" script "subworkflows/local/qc_bam/main.nf" workflow "QC_BAM" + tag "subworkflows" tag "qc_bam" + + tag "picard/collectmultiplemetrics" + tag "picard/collecthsmetrics" + tag "chromograph" + tag "qualimap/bamqc" + tag "tiddit/cov" + tag "mosdepth" + tag "sambamba/depth" + tag "ucsc/wigtobigwig" + tag "picard/collectwgsmetrics" + tag "sentieon/wgsmetrics" + tag "ngsbits/samplegender" + tag "verifybamid/verifybamid2" + config "./nextflow.config" test("QC_BAM - test, bwamem2") { diff --git a/subworkflows/local/rank_variants/tests/main.nf.test b/subworkflows/local/rank_variants/tests/main.nf.test index 0525da75e..28c9e510f 100644 --- a/subworkflows/local/rank_variants/tests/main.nf.test +++ b/subworkflows/local/rank_variants/tests/main.nf.test @@ -3,9 +3,17 @@ nextflow_workflow { name "Test Workflow RANK_VARIANTS" script "subworkflows/local/rank_variants/main.nf" workflow "RANK_VARIANTS" + tag "subworkflows" tag "rank_variants" + tag "genmod/annotate" + tag "genmod/models" + tag "genmod/score" + tag "genmod/compound" + tag "bcftools/sort" + tag "tabix/bgziptabix" + test("RANK_VARIANTS - SNV (process_with_sort = false), stub") { options "-stub" diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 4845e81c4..8ea9a772c 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -3,6 +3,13 @@ nextflow_workflow { name "Test Workflow SCATTER_GENOME" script "subworkflows/local/scatter_genome/main.nf" workflow "SCATTER_GENOME" + + tag "subworkflows" + tag "scatter_genome" + + tag "gawk" + tag "gatk4_splitintervals" + config "./nextflow.config" test("Should run without failures") { diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test b/subworkflows/local/subsample_mt_frac/tests/main.nf.test index 24c5982d2..9f2ddf63f 100644 --- a/subworkflows/local/subsample_mt_frac/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test @@ -5,6 +5,11 @@ nextflow_workflow { workflow "SUBSAMPLE_MT_FRAC" tag "subworkflows" tag "subsample_mt_frac" + + tag "bedtools/genomecov" + tag "calculate_seed_fraction" + tag "samtools/view" + config "./nextflow.config" test("SUBSAMPLE_MT_FRAC") { diff --git a/subworkflows/local/subsample_mt_reads/tests/main.nf.test b/subworkflows/local/subsample_mt_reads/tests/main.nf.test index 07d84f05c..21b924311 100644 --- a/subworkflows/local/subsample_mt_reads/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_reads/tests/main.nf.test @@ -5,6 +5,12 @@ nextflow_workflow { workflow "SUBSAMPLE_MT_READS" tag "subworkflows" tag "subsample_mt_reads" + + tag "samtools/view" + tag "samtools/collate" + tag "samtools/sort" + tag "gawk" + config "./nextflow.config" test("SUBSAMPLE_MT_READS") { diff --git a/subworkflows/local/variant_evaluation/tests/main.nf.test b/subworkflows/local/variant_evaluation/tests/main.nf.test index f08aef3fd..76ab3e7d3 100644 --- a/subworkflows/local/variant_evaluation/tests/main.nf.test +++ b/subworkflows/local/variant_evaluation/tests/main.nf.test @@ -3,9 +3,15 @@ nextflow_workflow { name "Test Workflow VARIANT_EVALUATION" script "subworkflows/local/variant_evaluation/main.nf" workflow "VARIANT_EVALUATION" + tag "subworkflows" tag "variant_evaluation" + tag "rtgtools/vcfeval" + tag "bcftools/reheader" + tag "tabix/tabix" + + test("VARIANT_EVALUATION - stub") { options "-stub" From e7babddecb336ede950e2e8643797ddf87d332f4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 27 Mar 2026 09:22:38 +0000 Subject: [PATCH 554/872] [automated] Fix code linting --- subworkflows/local/align_MT/tests/main.nf.test | 4 ++-- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- .../local/annotate_structural_variants/tests/main.nf.test | 2 +- subworkflows/local/call_mobile_elements/tests/main.nf.test | 2 +- subworkflows/local/call_repeat_expansions/tests/main.nf.test | 2 +- subworkflows/local/call_snv/tests/main.nf.test | 2 +- subworkflows/local/call_snv_deepvariant/tests/main.nf.test | 2 +- subworkflows/local/scatter_genome/tests/main.nf.test | 2 +- 8 files changed, 9 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index c44453a09..5441f4256 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "align_mt" - + tag "bwa/mem" tag "bwamem2/mem" tag "sentieon/bwamem" @@ -14,7 +14,7 @@ nextflow_workflow { tag "picard/addorreplacereadgroups" tag "picard/markduplicates" tag "samtools/sort" - + config "./nextflow.config" test("align mt - bwamem2") { diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index efd9ac4a2..b218ac4cf 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { tag "sentieon/dedup" tag "sentieon/readwriter" tag "samtools/view" - + config "./nextflow.config" test("align sentieon") { diff --git a/subworkflows/local/annotate_structural_variants/tests/main.nf.test b/subworkflows/local/annotate_structural_variants/tests/main.nf.test index 978c80c32..279486d02 100644 --- a/subworkflows/local/annotate_structural_variants/tests/main.nf.test +++ b/subworkflows/local/annotate_structural_variants/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "annotate_structural_variants" - + tag "svdb/query" tag "picard/sortvcf" tag "bcftools/view" diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test b/subworkflows/local/call_mobile_elements/tests/main.nf.test index c25f9457a..143f8259d 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { tag "retroseq/call" tag "samtools/view" tag "tabix/tabix" - tag "svdb/merge" + tag "svdb/merge" test("CALL_MOBILE_ELEMENTS - stub") { diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 298e271e3..983e98df9 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { tag "samtools/sort" tag "svdb/merge" tag "tabix/tabix" - + config "./nextflow.config" test("CALL_REPEAT_EXPANSIONS") { diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 9ec028ea8..441187295 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_workflow { tag "call_snv_sentieon" tag "call_snv_MT" tag "postprocess_MT_calls" - + tag "gatk4_selectvariants" tag "bcftools_concat" diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 799a20c43..adafadd4a 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -3,7 +3,7 @@ nextflow_workflow { name "Test Workflow CALL_SNV_DEEPVARIANT" script "subworkflows/local/call_snv_deepvariant/main.nf" workflow "CALL_SNV_DEEPVARIANT" - + tag "subworkflows" tag "call_snv_deepvariant" diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 8ea9a772c..48c96384e 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "scatter_genome" - + tag "gawk" tag "gatk4_splitintervals" From 671c8e04d37ef2752713fdf49ea1b637722f1e78 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 10:53:25 +0100 Subject: [PATCH 555/872] Update tiddit [skip ci] --- conf/modules/raredisease.config | 10 ++++ modules.json | 4 +- modules/nf-core/tiddit/cov/environment.yml | 2 +- modules/nf-core/tiddit/cov/main.nf | 4 +- .../tiddit/cov/tests/main.nf.test.snap | 38 +++++++------- modules/nf-core/tiddit/sv/environment.yml | 2 +- modules/nf-core/tiddit/sv/main.nf | 4 +- .../nf-core/tiddit/sv/tests/main.nf.test.snap | 52 +++++++++---------- 8 files changed, 63 insertions(+), 53 deletions(-) diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config index b6890afcd..5ef1734b4 100644 --- a/conf/modules/raredisease.config +++ b/conf/modules/raredisease.config @@ -55,6 +55,16 @@ process { } } +// +// Peddy options +// + +process { + withName: 'PEDDY' { + ext.args = { params.genome.equals("GRCh38") ? "--sites hg38" : "" } + } +} + // // Multiqc options // diff --git a/modules.json b/modules.json index 987c2d9e8..2b63a0294 100644 --- a/modules.json +++ b/modules.json @@ -528,12 +528,12 @@ }, "tiddit/cov": { "branch": "master", - "git_sha": "d0afa49c7c23c9e99a47af9bafb4cee449853560", + "git_sha": "c00e3ab203bdbce7a6ed6b9cd0a3f6406e2f3d8b", "installed_by": ["modules"] }, "tiddit/sv": { "branch": "master", - "git_sha": "7d7b05291926e7bce86096a0ed49499c200924a5", + "git_sha": "c00e3ab203bdbce7a6ed6b9cd0a3f6406e2f3d8b", "installed_by": ["modules"] }, "ucsc/wigtobigwig": { diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index df74ec81e..d00f5e363 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.9.4 + - bioconda::tiddit=3.9.5 diff --git a/modules/nf-core/tiddit/cov/main.nf b/modules/nf-core/tiddit/cov/main.nf index 690a8b62b..6ef2f8525 100644 --- a/modules/nf-core/tiddit/cov/main.nf +++ b/modules/nf-core/tiddit/cov/main.nf @@ -4,8 +4,8 @@ process TIDDIT_COV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : - 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6a/6a427ef9929eb787b83224b3c8dd5d1dd7f7897e6921c60ecc5e58ef705daf6b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.5--3fb6c287f34e6ab0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap index 977b8c768..c5c6f8c32 100644 --- a/modules/nf-core/tiddit/cov/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/cov/tests/main.nf.test.snap @@ -15,15 +15,15 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], - "timestamp": "2026-02-11T20:36:08.358493", + "timestamp": "2026-03-23T15:59:36.336058", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - cram - wig": { @@ -42,15 +42,15 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], - "timestamp": "2026-02-11T20:36:03.766699", + "timestamp": "2026-03-23T15:59:31.464109", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - stub": { @@ -78,7 +78,7 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ], "cov": [ @@ -94,7 +94,7 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ], "wig": [ @@ -108,7 +108,7 @@ ] } ], - "timestamp": "2026-02-16T11:40:15.064301", + "timestamp": "2026-03-23T15:59:42.352822", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -130,15 +130,15 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], - "timestamp": "2026-02-11T20:35:59.061703", + "timestamp": "2026-03-23T15:59:26.294427", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "homo_sapiens - cram - bed": { @@ -157,15 +157,15 @@ [ "TIDDIT_COV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], - "timestamp": "2026-02-11T20:35:54.066148", + "timestamp": "2026-03-23T15:59:20.487446", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index df74ec81e..d00f5e363 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::tiddit=3.9.4 + - bioconda::tiddit=3.9.5 diff --git a/modules/nf-core/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf index 429695e21..ff097942d 100644 --- a/modules/nf-core/tiddit/sv/main.nf +++ b/modules/nf-core/tiddit/sv/main.nf @@ -4,8 +4,8 @@ process TIDDIT_SV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/89080e08e55823dbdb424407a4e9eefbc669e2b0e841f142a1014204659df87b/data' : - 'community.wave.seqera.io/library/tiddit:3.9.4--11a71ebb5fd55c20' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6a/6a427ef9929eb787b83224b3c8dd5d1dd7f7897e6921c60ecc5e58ef705daf6b/data' : + 'community.wave.seqera.io/library/tiddit:3.9.5--3fb6c287f34e6ab0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap index 6927d6916..92da4db74 100644 --- a/modules/nf-core/tiddit/sv/tests/main.nf.test.snap +++ b/modules/nf-core/tiddit/sv/tests/main.nf.test.snap @@ -22,7 +22,7 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ], "ploidy": [ @@ -45,16 +45,16 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], + "timestamp": "2026-03-23T16:00:24.346829", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T13:40:16.597914" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam - bwa": { "content": [ @@ -64,16 +64,16 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], + "timestamp": "2026-03-23T15:59:52.928838", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T21:38:47.040361" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "human - cram - bwa": { "content": [ @@ -83,16 +83,16 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], + "timestamp": "2026-03-23T16:00:10.285571", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T21:37:13.220785" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 - bam - no_bwa": { "content": [ @@ -102,16 +102,16 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], + "timestamp": "2026-03-23T16:00:01.097762", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T21:38:54.658816" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "human - cram - no_bwa": { "content": [ @@ -121,15 +121,15 @@ [ "TIDDIT_SV", "tiddit", - "3.9.4" + "3.9.5" ] ] } ], + "timestamp": "2026-03-23T16:00:18.226844", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-11T21:39:11.028105" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From be0f6a1aaa68787aa66f9a2e45bf400866b8b181 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 11:15:41 +0100 Subject: [PATCH 556/872] Update CHANGELOG.md --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d4b03041..3191aa59f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) - Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) +- Add CAT_FASTQ before SEQTK_SAMPLE in call_sv_MT to merge reads across lanes before subsampling for MitoSalt [#799](https://github.com/nf-core/raredisease/pull/799) +- Add new local SPLIT_CHR module to split reference FASTA by chromosome for CNVnator, and pass genome flag to all CNVnator steps [#799](https://github.com/nf-core/raredisease/pull/799) +- Add peddy --sites hg38 argument when running with GRCh38 [#799](https://github.com/nf-core/raredisease/pull/799) ### `Changed` @@ -43,6 +46,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791) +- Remove redundant ZIP_TABIX steps after VCFANNO in annotate_genome_snvs and annotate_mt_snvs by using VCFANNO's direct tbi output [#799](https://github.com/nf-core/raredisease/pull/799) +- Collect genome fasta/fai channel in call_sv_tiddit to prevent per-sample re-emission [#799](https://github.com/nf-core/raredisease/pull/799) +- Update cadd_resources channel to use channelFromPathWithMeta and set channelFromSamplesheet calls for svdb/ME resources as non-mandatory [#799](https://github.com/nf-core/raredisease/pull/799) ### `Fixed` @@ -91,7 +97,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | sentieon | 202503 | 202503.02 | | stranger | 0.9.4 | 0.10.0 | | svdb | 2.8.3 | 2.8.4 | -| tiddit | 3.6.1 | 3.9.4 | +| tiddit | 3.6.1 | 3.9.5 | | ucsc | 447 | 482 | | vcfanno | 0.3.5 | 0.3.7 | | vcf2cytosure | 0.9.1 | 0.9.3 | From d13cb3ea58a0b937d8c609a9b1ed92fa5f64aceb Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 12:04:22 +0100 Subject: [PATCH 557/872] updates from review --- README.md | 3 + conf/modules/call_sv_MT.config | 12 ++-- docs/output.md | 14 ++-- main.nf | 60 +++++++++++++++++ modules/local/prep_mitosalt/main.nf | 34 ++++------ subworkflows/local/annotate_mt_snvs/main.nf | 4 +- .../local/call_structural_variants/main.nf | 37 ++--------- .../tests/main.nf.test | 31 +++------ subworkflows/local/call_sv_MT/main.nf | 45 ++++--------- .../local/call_sv_MT/tests/main.nf.test | 29 +++----- workflows/raredisease.nf | 66 +++++++++++++------ 11 files changed, 175 insertions(+), 160 deletions(-) diff --git a/README.md b/README.md index 28d82f736..6bc759894 100644 --- a/README.md +++ b/README.md @@ -90,6 +90,9 @@ On release, automated continuous integration tests run the pipeline on a full-si - [CNVnator](https://github.com/abyzovlab/CNVnator) - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk) - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller) +- Mitochondrial SV calling: + - [MitoSAlt](https://mitosalt.sourceforge.io/) + - [Saltshaker](https://github.com/aksenia/saltshaker) **5. Annotation - SNV:** diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index c9535499b..1c56b31f7 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -27,10 +27,14 @@ process { } withName: '.*CALL_SV_MT:SALTSHAKER_CLASSIFY' { - ext.args = { "--blacklist --vcf --dominant-fraction ${params.saltshaker_dominant_fraction} \ - --radius ${params.saltshaker_group_radius} --high-het ${params.saltshaker_high_heteroplasmy} \ - --multiple-threshold ${params.saltshaker_multiple_threshold} --noise ${params.saltshaker_noise_threshold}" - } + ext.args = { [ + "--blacklist --vcf", + "--dominant-fraction ${params.saltshaker_dominant_fraction}", + "--radius ${params.saltshaker_group_radius}", + "--high-het ${params.saltshaker_high_heteroplasmy}", + "--multiple-threshold ${params.saltshaker_multiple_threshold}", + "--noise ${params.saltshaker_noise_threshold}" + ].join(' ') } } withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { diff --git a/docs/output.md b/docs/output.md index a0bae4571..08ad21919 100644 --- a/docs/output.md +++ b/docs/output.md @@ -475,17 +475,17 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen [MT deletion script](https://github.com/dnil/mitosign/blob/master/run_mt_del_check.sh) lists the fraction of mitochondrially aligning read pairs (per 1000) that appear discordant, as defined by an insert size of more than 1.2 kb (and less than 15 kb due to the circular nature of the genome) using samtools. -- `call_sv/mitochondria` +- `call_sv` - `_mitochondria_deletions.txt`: file containing deletions. -##### eKLIPse +##### Saltshaker -[eKLIPse](https://github.com/dooguypapua/eKLIPse) allows the detection and quantification of large mtDNA rearrangements. +[MitoSAlt](https://mitosalt.sourceforge.io/) allows the detection and quantification of mtDNA strucutral variants. +[Saltshaker](https://github.com/aksenia/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. -- `call_sv/mitochondria` - - `eKLIPse__deletions.csv`: file containing all predicted deletions. - - `eKLIPse__genes.csv`: file summarizing cumulated deletions per mtDNA gene. - - `eKLIPse_.png`: circos plot. +- `call_sv` + - `.saltshaker_classify.txt`: report containing case-level classification of mitochondrial deletions. + - `.saltshaker.png`: circos plot. #### Annotation diff --git a/main.nf b/main.nf index 44e5463ef..2a90eaa7d 100644 --- a/main.nf +++ b/main.nf @@ -62,12 +62,32 @@ workflow NFCORE_RAREDISEASE { val_gens_pon_male val_gnomad_af val_gnomad_af_idx + val_heavy_strand_origin_end + val_heavy_strand_origin_start val_homoplasmy_af_threshold val_intervals_wgs val_intervals_y val_known_dbsnp val_known_dbsnp_tbi + val_light_strand_origin_end + val_light_strand_origin_start val_mbuffer_mem + val_mito_length + val_mito_name + val_mitosalt_breakspan + val_mitosalt_breakthreshold + val_mitosalt_cluster_threshold + val_mitosalt_deletion_threshold_max + val_mitosalt_deletion_threshold_min + val_mitosalt_evalue_threshold + val_mitosalt_exclude + val_mitosalt_flank + val_mitosalt_heteroplasmy_limit + val_mitosalt_paired_distance + val_mitosalt_score_threshold + val_mitosalt_sizelimit + val_mitosalt_split_distance_threshold + val_mitosalt_split_length val_ml_model val_mobile_element_references val_mobile_element_svdb_annotations @@ -453,8 +473,28 @@ workflow NFCORE_RAREDISEASE { val_concatenate_snv_calls, val_extract_alignments, val_genome, + val_heavy_strand_origin_end, + val_heavy_strand_origin_start, val_homoplasmy_af_threshold, + val_light_strand_origin_end, + val_light_strand_origin_start, val_mbuffer_mem, + val_mito_length, + val_mito_name, + val_mitosalt_breakspan, + val_mitosalt_breakthreshold, + val_mitosalt_cluster_threshold, + val_mitosalt_deletion_threshold_max, + val_mitosalt_deletion_threshold_min, + val_mitosalt_evalue_threshold, + val_mitosalt_exclude, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, + val_mitosalt_paired_distance, + val_mitosalt_score_threshold, + val_mitosalt_sizelimit, + val_mitosalt_split_distance_threshold, + val_mitosalt_split_length, val_mt_aligner, val_mt_subsample_approach, val_mt_subsample_rd, @@ -527,12 +567,32 @@ workflow { params.gens_pon_male, params.gnomad_af, params.gnomad_af_idx, + params.heavy_strand_origin_end, + params.heavy_strand_origin_start, params.homoplasmy_af_threshold, params.intervals_wgs, params.intervals_y, params.known_dbsnp, params.known_dbsnp_tbi, + params.light_strand_origin_end, + params.light_strand_origin_start, params.mbuffer_mem, + params.mito_length, + params.mito_name, + params.mitosalt_breakspan, + params.mitosalt_breakthreshold, + params.mitosalt_cluster_threshold, + params.mitosalt_deletion_threshold_max, + params.mitosalt_deletion_threshold_min, + params.mitosalt_evalue_threshold, + params.mitosalt_exclude, + params.mitosalt_flank, + params.mitosalt_heteroplasmy_limit, + params.mitosalt_paired_distance, + params.mitosalt_score_threshold, + params.mitosalt_sizelimit, + params.mitosalt_split_distance_threshold, + params.mitosalt_split_length, params.ml_model, params.mobile_element_references, params.mobile_element_svdb_annotations, diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf index 83455fd3c..47b0e3fd9 100644 --- a/modules/local/prep_mitosalt/main.nf +++ b/modules/local/prep_mitosalt/main.nf @@ -4,26 +4,18 @@ process PREP_MITOSALT { input: path chrsizes - tuple val(meta2), path(genomefai) - tuple val(meta), path(hisat2index) - tuple val(meta4), path(mtfai) - tuple val(meta5), path(mtfasta) - tuple val(meta3), path(lastindex) - val breakspan - val breakthreshold - val cluster_threshold - val deletion_threshold_max - val deletion_threshold_min - val evalue_threshold - val exclude + tuple val(meta), path(genomefai) + tuple val(meta2), path(hisat2index) + tuple val(breakspan), val(breakthreshold), val(cluster_threshold), + val(deletion_threshold_max), val(deletion_threshold_min), val(evalue_threshold), + val(exclude), val(paired_distance), val(score_threshold), + val(sizelimit), val(split_distance_threshold), val(split_length) + tuple val(meta3), path(mtfai) + tuple val(meta4), path(mtfasta) + tuple val(meta5), path(lastindex) val flank - val hplimit - val mito_name - val paired_distance - val score_threshold - val sizelimit - val split_distance_threshold - val split_length + val heteroplasmy_limit + val mitochondria_name output: path "mitosalt_config.txt", emit: msconfig @@ -52,7 +44,7 @@ process PREP_MITOSALT { echo "gsize = ${chrsizes}" >> mitosalt_config.txt echo "MT_fasta = ${mtfasta}" >> mitosalt_config.txt echo "threads = 1" >> mitosalt_config.txt - echo "refchr = ${mito_name}" >> mitosalt_config.txt + echo "refchr = ${mitochondria_name}" >> mitosalt_config.txt echo "msize = 16569" >> mitosalt_config.txt echo "exclude = ${exclude}" >> mitosalt_config.txt echo "orihs = 16081" >> mitosalt_config.txt @@ -69,7 +61,7 @@ process PREP_MITOSALT { echo "cluster_threshold = ${cluster_threshold}" >> mitosalt_config.txt echo "breakspan = ${breakspan}" >> mitosalt_config.txt echo "sizelimit = ${sizelimit}" >> mitosalt_config.txt - echo "hplimit = ${hplimit}" >> mitosalt_config.txt + echo "hplimit = ${heteroplasmy_limit}" >> mitosalt_config.txt echo "flank = ${flank}" >> mitosalt_config.txt echo "split_distance_threshold = ${split_distance_threshold}" >> mitosalt_config.txt echo "dna = yes" >> mitosalt_config.txt diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index fc02ec005..a389db581 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -40,8 +40,6 @@ workflow ANNOTATE_MT_SNVS { VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ch_vcfanno_vcf = VCFANNO_MT.out.vcf - // Annotating with CADD if (!val_cadd_resources.equals(null)) { ANNOTATE_CADD ( @@ -56,7 +54,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_vcf = channel.empty() } - ch_vcfanno_vcf + VCFANNO_MT.out.vcf .join(ch_cadd_vcf, remainder: true) .branch { meta, vcfanno, cadd -> vcfanno: cadd.equals(null) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index a546736a8..bed4ae939 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -36,26 +36,15 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] + ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end - val_mito_length // string: [mandatory] mito_length - val_mito_name // string: [mandatory] mito_name - val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan - val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold - val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold - val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max - val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min - val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold - val_mitosalt_exclude // string: [mandatory] mitosalt_exclude + val_mitochondria_length // string: [mandatory] mito_length + val_mitochondria_name // string: [mandatory] mito_name val_mitosalt_flank // string: [mandatory] mitosalt_flank val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit - val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance - val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold - val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit - val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold - val_mitosalt_split_length // string: [mandatory] mitosalt_split_length val_run_mt_for_wes // boolean: [mandatory] run_mt_for_wes main: @@ -109,33 +98,21 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_reads, ch_subdepth, ch_svcaller_priority, + ch_mitosalt_config, val_heavy_strand_origin_start, val_heavy_strand_origin_end, val_light_strand_origin_start, val_light_strand_origin_end, - val_mito_length, - val_mito_name, - val_mitosalt_breakspan, - val_mitosalt_breakthreshold, - val_mitosalt_cluster_threshold, - val_mitosalt_deletion_threshold_max, - val_mitosalt_deletion_threshold_min, - val_mitosalt_evalue_threshold, - val_mitosalt_exclude, + val_mitochondria_length, + val_mitochondria_name, val_mitosalt_flank, val_mitosalt_heteroplasmy_limit, - val_mitosalt_paired_distance, - val_mitosalt_score_threshold, - val_mitosalt_sizelimit, - val_mitosalt_split_distance_threshold, - val_mitosalt_split_length ) - .set {ch_sv_mt_out} + .set { ch_sv_mt_out } ch_sv_mt_out.saltshaker_vcf .collect{ _meta, vcf -> vcf } .set { ch_saltshaker_vcf } - ch_saltshaker_vcf.view() ch_publish_mt = ch_sv_mt_out.publish ch_svcaller_priority = ch_sv_mt_out.updated_priority } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 16f7b8845..b1968b435 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -56,27 +56,16 @@ nextflow_workflow { ] ]) input[22] = channel.value(10000000) - input[23] = 16081 - input[24] = 407 - input[25] = 5730 - input[26] = 5763 - input[27] = 16569 - input[28] = 'MT' - input[29] = 15 - input[30] = 2 - input[31] = 5 - input[32] = 30000 - input[33] = 30 - input[34] = 0.00001 - input[35] = 5 - input[36] = 15 - input[37] = 0.01 - input[38] = 1000 - input[39] = 80 - input[40] = 10000 - input[41] = 5 - input[42] = 15 - input[43] = true + input[23] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[24] = 16081 + input[25] = 407 + input[26] = 5730 + input[27] = 5763 + input[28] = 16569 + input[29] = 'MT' + input[30] = 15 + input[31] = 0.01 + input[32] = true """ } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 1c8ec1e1c..3f28d0a3b 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -25,26 +25,15 @@ workflow CALL_SV_MT { ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] + ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end - val_mito_length // string: [mandatory] mito_length - val_mito_name // string: [mandatory] mito_name - val_mitosalt_breakspan // string: [mandatory] mitosalt_breakspan - val_mitosalt_breakthreshold // string: [mandatory] mitosalt_breakthreshold - val_mitosalt_cluster_threshold // string: [mandatory] mitosalt_cluster_threshold - val_mitosalt_deletion_threshold_max // string: [mandatory] mitosalt_deletion_threshold_max - val_mitosalt_deletion_threshold_min // string: [mandatory] mitosalt_deletion_threshold_min - val_mitosalt_evalue_threshold // string: [mandatory] mitosalt_evalue_threshold - val_mitosalt_exclude // string: [mandatory] mitosalt_exclude + val_mitochondria_length // string: [mandatory] mito_length + val_mitochondria_name // string: [mandatory] mito_name val_mitosalt_flank // string: [mandatory] mitosalt_flank val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit - val_mitosalt_paired_distance // string: [mandatory] mitosalt_paired_distance - val_mitosalt_score_threshold // string: [mandatory] mitosalt_score_threshold - val_mitosalt_sizelimit // string: [mandatory] mitosalt_sizelimit - val_mitosalt_split_distance_threshold // string: [mandatory] mitosalt_split_distance_threshold - val_mitosalt_split_length // string: [mandatory] mitosalt_split_length main: ch_saltshaker_txt = channel.empty() @@ -60,24 +49,13 @@ workflow CALL_SV_MT { ch_genome_chrsizes, ch_genome_fai, ch_genome_hisat2index, + ch_mitosalt_config, ch_mt_fai, ch_mt_fasta, ch_mt_lastdb, - val_mitosalt_breakspan, - val_mitosalt_breakthreshold, - val_mitosalt_cluster_threshold, - val_mitosalt_deletion_threshold_max, - val_mitosalt_deletion_threshold_min, - val_mitosalt_evalue_threshold, - val_mitosalt_exclude, val_mitosalt_flank, val_mitosalt_heteroplasmy_limit, - val_mito_name, - val_mitosalt_paired_distance, - val_mitosalt_score_threshold, - val_mitosalt_sizelimit, - val_mitosalt_split_distance_threshold, - val_mitosalt_split_length + val_mitochondria_name ) MITOSALT( @@ -93,18 +71,18 @@ workflow CALL_SV_MT { MITOSALT.out.cluster .filter{ _meta, out -> out.countLines() > 0 } - .set{ch_cluster} + .set{ ch_cluster } MITOSALT.out.breakpoint .join(ch_cluster) - .set{ch_saltshaker_in} + .set{ ch_saltshaker_in } SALTSHAKER_CALL( ch_saltshaker_in, ch_mt_fasta, val_mitosalt_flank, val_mitosalt_heteroplasmy_limit, - val_mito_length, + val_mitochondria_length, val_heavy_strand_origin_start, val_heavy_strand_origin_end, val_light_strand_origin_start, @@ -113,7 +91,7 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY( SALTSHAKER_CALL.out.call, - val_mito_name + val_mitochondria_name ) ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf @@ -124,10 +102,11 @@ workflow CALL_SV_MT { ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot SALTSHAKER_CLASSIFY.out.vcf - .collect{_meta, vcf -> vcf} + .collect{ _meta, vcf -> vcf } .toList() .set { ch_vcf_file_list } + // Only set the channel if ch_vcf_file_list was made (ie combined channel has two elements) ch_case_info .combine(ch_vcf_file_list) .filter{ it -> it.size() == 2} @@ -137,7 +116,7 @@ workflow CALL_SV_MT { .set {ch_saltshaker_vcf} // Update priority list when we know saltshaker will run ch_svcaller_priority = ch_svcaller_priority - .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) + .concat(ch_saltshaker_vcf.map{ _meta -> ["mitosalt"] }) .collect() } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index abfb895d9..ecc97601e 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -39,26 +39,15 @@ nextflow_workflow { ]) input[10] = channel.value(10000000) input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[12] = 16081 - input[13] = 407 - input[14] = 5730 - input[15] = 5763 - input[16] = 16569 - input[17] = 'chrM' - input[18] = 15 - input[19] = 2 - input[20] = 2 - input[21] = 30000 - input[22] = 30 - input[23] = 0.00001 - input[24] = 5 - input[25] = 15 - input[26] = 0.01 - input[27] = 1000 - input[28] = 80 - input[29] = 10000 - input[30] = 5 - input[31] = 15 + input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[13] = 16081 + input[14] = 407 + input[15] = 5730 + input[16] = 5763 + input[17] = 16569 + input[18] = 'chrM' + input[19] = 15 + input[20] = 0.01 """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0f600b2fa..da355169e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -184,8 +184,28 @@ workflow RAREDISEASE { val_concatenate_snv_calls val_extract_alignments val_genome + val_heavy_strand_origin_end + val_heavy_strand_origin_start val_homoplasmy_af_threshold + val_light_strand_origin_end + val_light_strand_origin_start val_mbuffer_mem + val_mito_length + val_mito_name + val_mitosalt_breakspan + val_mitosalt_breakthreshold + val_mitosalt_cluster_threshold + val_mitosalt_deletion_threshold_max + val_mitosalt_deletion_threshold_min + val_mitosalt_evalue_threshold + val_mitosalt_exclude + val_mitosalt_flank + val_mitosalt_heteroplasmy_limit + val_mitosalt_paired_distance + val_mitosalt_score_threshold + val_mitosalt_sizelimit + val_mitosalt_split_distance_threshold + val_mitosalt_split_length val_mt_aligner val_mt_subsample_approach val_mt_subsample_rd @@ -209,7 +229,6 @@ workflow RAREDISEASE { ch_qc_bam_publish = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() - ch_call_sv_mt_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_subsample_publish = channel.empty() @@ -572,6 +591,21 @@ workflow RAREDISEASE { */ if (!skip_sv_calling) { + val_mitosalt_breakspan + .concat(val_mitosalt_breakthreshold) + .concat(val_mitosalt_cluster_threshold) + .concat(val_mitosalt_deletion_threshold_max) + .concat(val_mitosalt_deletion_threshold_min) + .concat(val_mitosalt_evalue_threshold) + .concat(val_mitosalt_exclude) + .concat(val_mitosalt_paired_distance) + .concat(val_mitosalt_score_threshold) + .concat(val_mitosalt_sizelimit) + .concat(val_mitosalt_split_distance_threshold) + .concat(val_mitosalt_split_length) + .collect() + .set{ ch_mitosalt_config } + CALL_STRUCTURAL_VARIANTS ( ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bai, @@ -596,26 +630,16 @@ workflow RAREDISEASE { ch_mt_lastdb, ch_input_fastqs, ch_subdepth, - params.heavy_strand_origin_start, - params.heavy_strand_origin_end, - params.light_strand_origin_start, - params.light_strand_origin_end, - params.mito_length, - params.mito_name, - params.mitosalt_breakspan, - params.mitosalt_breakthreshold, - params.mitosalt_cluster_threshold, - params.mitosalt_deletion_threshold_max, - params.mitosalt_deletion_threshold_min, - params.mitosalt_evalue_threshold, - params.mitosalt_exclude, - params.mitosalt_flank, - params.mitosalt_heteroplasmy_limit, - params.mitosalt_paired_distance, - params.mitosalt_score_threshold, - params.mitosalt_sizelimit, - params.mitosalt_split_distance_threshold, - params.mitosalt_split_length, + ch_mitosalt_config, + val_heavy_strand_origin_start, + val_heavy_strand_origin_end, + val_light_strand_origin_start, + val_light_strand_origin_end, + val_mito_length, + val_mito_name, + val_mitosalt_breakspan, + val_mitosalt_flank, + val_mitosalt_heteroplasmy_limit, val_run_mt_for_wes ) ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish From ffded9b43d3ea1fbd0bebc2c5a9c01013bdfd684 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 12:16:36 +0100 Subject: [PATCH 558/872] fix channel of combined values --- workflows/raredisease.nf | 25 ++++++++++++------------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index da355169e..fa141a19e 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -591,19 +591,18 @@ workflow RAREDISEASE { */ if (!skip_sv_calling) { - val_mitosalt_breakspan - .concat(val_mitosalt_breakthreshold) - .concat(val_mitosalt_cluster_threshold) - .concat(val_mitosalt_deletion_threshold_max) - .concat(val_mitosalt_deletion_threshold_min) - .concat(val_mitosalt_evalue_threshold) - .concat(val_mitosalt_exclude) - .concat(val_mitosalt_paired_distance) - .concat(val_mitosalt_score_threshold) - .concat(val_mitosalt_sizelimit) - .concat(val_mitosalt_split_distance_threshold) - .concat(val_mitosalt_split_length) - .collect() + channel.of(val_mitosalt_breakspan, + val_mitosalt_breakthreshold, + val_mitosalt_cluster_threshold, + val_mitosalt_deletion_threshold_max, + val_mitosalt_deletion_threshold_min, + val_mitosalt_evalue_threshold, + val_mitosalt_exclude, + val_mitosalt_paired_distance, + val_mitosalt_score_threshold, + val_mitosalt_sizelimit, + val_mitosalt_split_distance_threshold, + val_mitosalt_split_length) .set{ ch_mitosalt_config } CALL_STRUCTURAL_VARIANTS ( From 53a5c93c0d944e7038bc0875ed4c15704eda4616 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 12:23:21 +0100 Subject: [PATCH 559/872] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d4b03041..407dec929 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) - Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) +- Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) ### `Changed` @@ -43,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791) +- Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove /mitochondria and /genome [#775](https://github.com/nf-core/raredisease/pull/775) ### `Fixed` From ab3e86876c2c8b7a9b0d086acc95520a16c9b753 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 12:44:56 +0100 Subject: [PATCH 560/872] update changelog and call_sv test --- CHANGELOG.md | 4 +++- .../local/call_structural_variants/tests/main.nf.test | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 407dec929..be8f2817d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) - Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) +- Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) ### `Changed` @@ -44,7 +45,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791) -- Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove /mitochondria and /genome [#775](https://github.com/nf-core/raredisease/pull/775) +- Run MitoSAlt.pl from bin rather than within container [#775](https://github.com/nf-core/raredisease/pull/775) +- Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove mitochondria/ and genome/ [#775](https://github.com/nf-core/raredisease/pull/775) ### `Fixed` diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index b1968b435..2ff584b2f 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -66,7 +66,6 @@ nextflow_workflow { input[30] = 15 input[31] = 0.01 input[32] = true - """ } } From 9fe000f4f05b21e5205aefdf55fa30201f7f1c0f Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Fri, 27 Mar 2026 12:52:58 +0100 Subject: [PATCH 561/872] put singularity pull timeout back in test config --- conf/test.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/test.config b/conf/test.config index f22ee64b0..ee863b84e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,6 +22,8 @@ env { MPLCONFIGDIR="." } +singularity.pullTimeout='2h' + params { config_profile_name = 'Test profile - default' config_profile_description = 'Minimal test dataset to check pipeline function' From 70c6247c01395a7a387f478996b148ca9faf5741 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Fri, 27 Mar 2026 12:56:50 +0100 Subject: [PATCH 562/872] clarify comment for saltshaker VCF priority list Clarify comment about updating priority list for saltshaker VCF. --- subworkflows/local/call_sv_MT/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 3f28d0a3b..52694f95b 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -114,7 +114,8 @@ workflow CALL_SV_MT { SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf .set {ch_saltshaker_vcf} - // Update priority list when we know saltshaker will run + // Update priority list when we know saltshaker will run (ie saltshaker vcf is created) + // Updated priority list will be used when saltshaker vcf is merged with other SV vcfs ch_svcaller_priority = ch_svcaller_priority .concat(ch_saltshaker_vcf.map{ _meta -> ["mitosalt"] }) .collect() From 51d097f277882a8f72c41654bfce8148fc20a2bd Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 13:16:46 +0100 Subject: [PATCH 563/872] fix sv inputs --- subworkflows/local/call_sv_MT/main.nf | 2 +- workflows/raredisease.nf | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 3f28d0a3b..9a59de47b 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -116,7 +116,7 @@ workflow CALL_SV_MT { .set {ch_saltshaker_vcf} // Update priority list when we know saltshaker will run ch_svcaller_priority = ch_svcaller_priority - .concat(ch_saltshaker_vcf.map{ _meta -> ["mitosalt"] }) + .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) .collect() } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index fa141a19e..e65248ac4 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -636,7 +636,6 @@ workflow RAREDISEASE { val_light_strand_origin_end, val_mito_length, val_mito_name, - val_mitosalt_breakspan, val_mitosalt_flank, val_mitosalt_heteroplasmy_limit, val_run_mt_for_wes From 2b16ab6e273b0b3ace22f64eb99325f4ce2259a8 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 27 Mar 2026 13:53:10 +0100 Subject: [PATCH 564/872] clearer sv_MT comments and new snaps --- subworkflows/local/call_sv_MT/main.nf | 8 +++++--- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 525947e5d..bf12b839c 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -77,6 +77,7 @@ workflow CALL_SV_MT { .join(ch_cluster) .set{ ch_saltshaker_in } + // Saltshaker modules will only run if mitosalt called SVs and created a cluster file SALTSHAKER_CALL( ch_saltshaker_in, ch_mt_fasta, @@ -106,7 +107,8 @@ workflow CALL_SV_MT { .toList() .set { ch_vcf_file_list } - // Only set the channel if ch_vcf_file_list was made (ie combined channel has two elements) + // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs + // exist, combined channel has two elements) to avoid a merge error ch_case_info .combine(ch_vcf_file_list) .filter{ it -> it.size() == 2} @@ -114,8 +116,8 @@ workflow CALL_SV_MT { SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf .set {ch_saltshaker_vcf} - // Update priority list when we know saltshaker will run (ie saltshaker vcf is created) - // Updated priority list will be used when saltshaker vcf is merged with other SV vcfs + // Saltshaker only runs if there are mitosalt calls. We update priority list when the + // saltshaker vcf is created so the priority matches the list of vcfs that will be merged later ch_svcaller_priority = ch_svcaller_priority .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) .collect() diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index b95de6087..ba430f635 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 770, + 781, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -1014,6 +1014,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-25T13:30:33.907974648" + "timestamp": "2026-03-27T13:49:42.531336219" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 413bcd76d..ae298c820 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 354, + 365, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -714,6 +714,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-25T12:48:18.971209768" + "timestamp": "2026-03-27T13:51:49.424910007" } } \ No newline at end of file From 3c1d831084595948084e35f745b46a3411d766b5 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 27 Mar 2026 13:00:04 +0000 Subject: [PATCH 565/872] [automated] Fix code linting --- subworkflows/local/call_sv_MT/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index bf12b839c..bb6d5d6f8 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -107,7 +107,7 @@ workflow CALL_SV_MT { .toList() .set { ch_vcf_file_list } - // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs + // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs // exist, combined channel has two elements) to avoid a merge error ch_case_info .combine(ch_vcf_file_list) @@ -116,7 +116,7 @@ workflow CALL_SV_MT { SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf .set {ch_saltshaker_vcf} - // Saltshaker only runs if there are mitosalt calls. We update priority list when the + // Saltshaker only runs if there are mitosalt calls. We update priority list when the // saltshaker vcf is created so the priority matches the list of vcfs that will be merged later ch_svcaller_priority = ch_svcaller_priority .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) From 67d44e0c5224d310fc9ee2bc537e22d4f3557b63 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 14:50:50 +0100 Subject: [PATCH 566/872] Update test and snapshots --- .../local/annotate_cadd/tests/main.nf.test | 4 +- .../annotate_cadd/tests/main.nf.test.snap | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 18 +-------- tests/default.nf.test.snap | 38 +++++++++---------- tests/test_bam.nf.test.snap | 25 +++++------- tests/test_singleton.nf.test.snap | 32 ++++++++-------- 6 files changed, 47 insertions(+), 72 deletions(-) diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test index 3dfdf1f18..473dce793 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[2] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() input[3] = channel.of([ [id:'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -50,7 +50,7 @@ nextflow_workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[2] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() input[3] = channel.of([ [id:'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap index 6e6570c31..7e4551e80 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test.snap @@ -87,7 +87,7 @@ ] } ], - "timestamp": "2026-03-04T13:59:33.695957972", + "timestamp": "2026-03-27T13:31:28.294196962", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 8efaafae7..d3f42b85e 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -11,8 +11,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -32,8 +30,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -76,8 +72,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -95,8 +89,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -136,8 +128,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -157,8 +147,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -201,8 +189,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -220,8 +206,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -254,7 +238,7 @@ ] ] ], - "timestamp": "2026-03-17T23:49:47.786799067", + "timestamp": "2026-03-27T13:26:15.956675827", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dcae17c82..4baa5e444 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -80,6 +80,9 @@ "CAT_CAT_BAIT": { "pigz": 2.8 }, + "CAT_FASTQ": { + "cat": 9.5 + }, "CHROMOGRAPH_AUTOZYG": { "chromograph": "1.3.1" }, @@ -118,11 +121,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "addmostsevereconsequence": 1.1, + "addmostsevereconsequence": "1.2.0", "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "addmostseverepli": 1.1, + "addmostseverepli": "1.2.0", "bgzip": 1.21 }, "DEEPVARIANT": { @@ -366,6 +369,9 @@ "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 }, + "SPLIT_CHR": { + "bioawk": 1.0 + }, "SPLIT_MULTIALLELICS_EXP": { "bcftools": 1.22 }, @@ -444,13 +450,13 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_SV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "UCSC_WIGTOBIGWIG": { "ucsc": 482 @@ -479,14 +485,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -675,14 +673,14 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.breakpoint", - "call_sv/mitochondria/earlycasualcaiman_LNUMBER1.cluster", + "call_sv/mitochondria/earlycasualcaiman.breakpoint", + "call_sv/mitochondria/earlycasualcaiman.cluster", "call_sv/mitochondria/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER3.cluster", + "call_sv/mitochondria/hugelymodelbat.breakpoint", + "call_sv/mitochondria/hugelymodelbat.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.breakpoint", - "call_sv/mitochondria/slowlycivilbuck_LNUMBER2.cluster", + "call_sv/mitochondria/slowlycivilbuck.breakpoint", + "call_sv/mitochondria/slowlycivilbuck.cluster", "call_sv/mitochondria/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -1091,7 +1089,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:52:17.64647915", + "timestamp": "2026-03-27T14:13:41.066875777", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9d91e0519..5b68d5f67 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 773, + 777, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -115,11 +115,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "addmostsevereconsequence": 1.1, + "addmostsevereconsequence": "1.2.0", "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "addmostseverepli": 1.1, + "addmostseverepli": "1.2.0", "bgzip": 1.21 }, "DEEPVARIANT": { @@ -339,6 +339,9 @@ "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 }, + "SPLIT_CHR": { + "bioawk": 1.0 + }, "SPLIT_MULTIALLELICS_EXP": { "bcftools": 1.22 }, @@ -414,13 +417,13 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_SV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "UCSC_WIGTOBIGWIG": { "ucsc": 482 @@ -449,14 +452,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -1020,7 +1015,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:58:22.361988613", + "timestamp": "2026-03-27T14:19:45.963121816", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index c86d7ea91..cb02fcb17 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 353, + 352, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -78,6 +78,9 @@ "CAT_CAT_BAIT": { "pigz": 2.8 }, + "CAT_FASTQ": { + "cat": 9.5 + }, "CHROMOGRAPH_AUTOZYG": { "chromograph": "1.3.1" }, @@ -110,11 +113,11 @@ "coreutils": 9.5 }, "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { - "addmostsevereconsequence": 1.1, + "addmostsevereconsequence": "1.2.0", "bgzip": 1.21 }, "CUSTOM_ADDMOSTSEVEREPLI": { - "addmostseverepli": 1.1, + "addmostseverepli": "1.2.0", "bgzip": 1.21 }, "DEEPVARIANT": { @@ -358,6 +361,9 @@ "SPLIT_AND_FILTER_SV_VCF": { "bcftools": 1.22 }, + "SPLIT_CHR": { + "bioawk": 1.0 + }, "SPLIT_MULTIALLELICS_EXP": { "bcftools": 1.22 }, @@ -433,13 +439,13 @@ "tabix": 1.21 }, "TIDDIT_COV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_COV_VCF2CYTOSURE": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "TIDDIT_SV": { - "tiddit": "3.9.4" + "tiddit": "3.9.5" }, "UCSC_WIGTOBIGWIG": { "ucsc": 482 @@ -462,14 +468,6 @@ "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO": { - "bgzip": 1.21, - "tabix": 1.21 - }, - "ZIP_TABIX_VCFANNO_MT": { - "bgzip": 1.21, - "tabix": 1.21 } }, [ @@ -540,8 +538,8 @@ "call_sv/genome/justhusky_sv.vcf.gz", "call_sv/genome/justhusky_sv.vcf.gz.tbi", "call_sv/mitochondria", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.breakpoint", - "call_sv/mitochondria/hugelymodelbat_LNUMBER1.cluster", + "call_sv/mitochondria/hugelymodelbat.breakpoint", + "call_sv/mitochondria/hugelymodelbat.cluster", "call_sv/mitochondria/hugelymodelbat_mitochondria_deletions.txt", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", @@ -710,7 +708,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-17T17:02:07.664289531", + "timestamp": "2026-03-27T14:23:26.834404268", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 03be9f9e3c72896b8a88c8bb190fbdd4449ccee1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 16:57:03 +0100 Subject: [PATCH 567/872] remove haplogrep and qualimap --- CITATIONS.md | 8 - README.md | 2 - assets/multiqc_config.yml | 3 - conf/modules/annotate_mt_snvs.config | 5 - conf/modules/qc_bam.config | 4 - conf/test.config | 2 +- conf/test_bam.config | 2 +- conf/test_sentieon.config | 2 +- conf/test_singleton.config | 2 +- docs/output.md | 31 +-- docs/usage.md | 6 +- main.nf | 4 - modules.json | 10 - .../haplogrep3/classify/environment.yml | 7 - modules/nf-core/haplogrep3/classify/main.nf | 37 ---- modules/nf-core/haplogrep3/classify/meta.yml | 65 ------- .../haplogrep3/classify/tests/main.nf.test | 59 ------ .../classify/tests/main.nf.test.snap | 88 --------- .../haplogrep3/classify/tests/nextflow.config | 5 - .../nf-core/qualimap/bamqc/environment.yml | 7 - modules/nf-core/qualimap/bamqc/main.nf | 113 ----------- modules/nf-core/qualimap/bamqc/meta.yml | 70 ------- .../nf-core/qualimap/bamqc/tests/main.nf.test | 61 ------ .../qualimap/bamqc/tests/main.nf.test.snap | 179 ------------------ nextflow_schema.json | 2 +- subworkflows/local/annotate_mt_snvs/main.nf | 15 -- .../local/annotate_mt_snvs/tests/main.nf.test | 9 +- .../annotate_mt_snvs/tests/main.nf.test.snap | 56 +----- .../annotate_mt_snvs/tests/nextflow.config | 5 - subworkflows/local/qc_bam/main.nf | 8 - subworkflows/local/qc_bam/tests/main.nf.test | 2 - .../local/qc_bam/tests/main.nf.test.snap | 111 +---------- .../local/qc_bam/tests/nextflow.config | 4 - .../utils_nfcore_raredisease_pipeline/main.nf | 13 -- tests/default.nf.test.snap | 171 +---------------- tests/test_bam.nf.test.snap | 173 +---------------- tests/test_singleton.nf.test.snap | 65 +------ workflows/raredisease.nf | 7 +- 38 files changed, 32 insertions(+), 1381 deletions(-) delete mode 100644 modules/nf-core/haplogrep3/classify/environment.yml delete mode 100644 modules/nf-core/haplogrep3/classify/main.nf delete mode 100644 modules/nf-core/haplogrep3/classify/meta.yml delete mode 100644 modules/nf-core/haplogrep3/classify/tests/main.nf.test delete mode 100644 modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap delete mode 100644 modules/nf-core/haplogrep3/classify/tests/nextflow.config delete mode 100644 modules/nf-core/qualimap/bamqc/environment.yml delete mode 100644 modules/nf-core/qualimap/bamqc/main.nf delete mode 100644 modules/nf-core/qualimap/bamqc/meta.yml delete mode 100644 modules/nf-core/qualimap/bamqc/tests/main.nf.test delete mode 100644 modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap diff --git a/CITATIONS.md b/CITATIONS.md index 02b84e877..89784db51 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -74,10 +74,6 @@ > Yun T, Li H, Chang PC, Lin MF, Carroll A, McLean CY. Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Robinson P, ed. Bioinformatics. 2021;36(24):5582-5589. doi:10.1093/bioinformatics/btaa1081 -- [HaploGrep 3](https://academic.oup.com/nar/article/51/W1/W263/7177898) - - > Schönherr S, Weissensteiner H, Kronenberg F, Forer L. Haplogrep 3 an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 2023;51(W1):W263-W268. doi:10.1093/nar/gkad284 - - [Manta](https://academic.oup.com/bioinformatics/article/32/8/1220/1743909?login=true) > Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220-1222. doi:10.1093/bioinformatics/btv710 @@ -98,10 +94,6 @@ - [Picard](https://broadinstitute.github.io/picard/) -- [Qualimap](https://academic.oup.com/bioinformatics/article/32/2/292/1744356?login=true) - - > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32(2):292-294. doi:10.1093/bioinformatics/btv566 - - [RetroSeq](https://academic.oup.com/bioinformatics/article/29/3/389/257479) > Thomas M. Keane, Kim Wong, David J. Adams, RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics.2013 Feb 1;29(3):389-90. doi: 10.1093/bioinformatics/bts697 diff --git a/README.md b/README.md index 28d82f736..f2364f2e8 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,6 @@ On release, automated continuous integration tests run the pipeline on a full-si - [Mosdepth](https://github.com/brentp/mosdepth) - [MultiQC](http://multiqc.info/) - [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/) -- [Qualimap](http://qualimap.conesalab.org/) - [Sambamba](https://github.com/biod/sambamba) - [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/) - [TIDDIT's cov](https://github.com/J35P312/) @@ -109,7 +108,6 @@ On release, automated continuous integration tests run the pipeline on a full-si - [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-) - Annotation: - - [HaploGrep3](https://github.com/genepi/haplogrep3) - [vcfanno](https://github.com/brentp/vcfanno) - [CADD](https://cadd.gs.washington.edu/) - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 2e69f6a3d..a90329141 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -20,7 +20,6 @@ export_plots: true run_modules: - fastqc - fastp - - qualimap - picard - mosdepth - ngsbits @@ -35,8 +34,6 @@ module_order: - "*.zip" - picard: name: "Picard" - - qualimap: - name: "Qualimap" - fastp: name: "fastp" - mosdepth: diff --git a/conf/modules/annotate_mt_snvs.config b/conf/modules/annotate_mt_snvs.config index d9b2844a0..adddea74b 100644 --- a/conf/modules/annotate_mt_snvs.config +++ b/conf/modules/annotate_mt_snvs.config @@ -52,9 +52,4 @@ process { ext.args = "--output-type z --write-index=tbi" ext.args2 = { "-i 'FMT/AF>=${params.homoplasmy_af_threshold} && FMT/DP>=100'" } } - - withName: '.*ANNOTATE_MT_SNVS:HAPLOGREP3_CLASSIFY_MT' { - ext.args = '--tree phylotree-rsrs@17.1' - ext.prefix = { "${meta.prefix}_haplogrep" } - } } diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index d0905762b..52444ff73 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -26,10 +26,6 @@ process { ext.prefix = { "${meta.id}_hsmetrics" } } - withName: '.*QC_BAM:QUALIMAP_BAMQC' { - ext.prefix = { "${meta.id}_qualimap" } - } - withName: '.*QC_BAM:TIDDIT_COV' { ext.args = '-z 500 -w' ext.prefix = { "${meta.id}_tidditcov" } diff --git a/conf/test.config b/conf/test.config index ee863b84e..90f2691f2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -32,7 +32,7 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' - skip_tools = 'fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,ngsbits' + skip_tools = 'fastp,gens,peddy,germlinecnvcaller,ngsbits' input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' diff --git a/conf/test_bam.config b/conf/test_bam.config index 8e90c1a5b..46d398682 100644 --- a/conf/test_bam.config +++ b/conf/test_bam.config @@ -30,7 +30,7 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + skip_tools = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits" input = params.pipelines_testdata_base_path + 'testdata/samplesheet_bam.csv' diff --git a/conf/test_sentieon.config b/conf/test_sentieon.config index 330be5a04..9b56b62ef 100644 --- a/conf/test_sentieon.config +++ b/conf/test_sentieon.config @@ -29,7 +29,7 @@ params { igenomes_ignore = true mito_name = 'MT' - skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + skip_tools = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits" // Input data pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' diff --git a/conf/test_singleton.config b/conf/test_singleton.config index 559e1d6da..3810dbf06 100644 --- a/conf/test_singleton.config +++ b/conf/test_singleton.config @@ -30,7 +30,7 @@ params { mito_name = 'MT' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - skip_tools = "fastp,gens,haplogrep3,peddy,germlinecnvcaller,qualimap,eklipse,ngsbits" + skip_tools = "fastp,gens,peddy,germlinecnvcaller,eklipse,ngsbits" input = params.pipelines_testdata_base_path + 'testdata/samplesheet_single.csv' fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' diff --git a/docs/output.md b/docs/output.md index a0bae4571..ae45a606d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -28,7 +28,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - [Mosdepth](#mosdepth) - [Picard tools](#picard-tools) - - [Qualimap](#qualimap) - [Chromograph coverage](#chromograph-coverage) - [Sention WgsMetricsAlgo](#sention-wgsmetricsalgo) - [TIDDIT's cov and UCSC WigToBigWig](#tiddits-cov-and-ucsc-wigtobigwig) @@ -63,7 +62,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [MT deletion script](#mt-deletion-script) - [eKLIPse](#eklipse) - [Annotation](#annotation) - - [HaploGrep2](#haplogrep2) - [vcfanno](#vcfanno-1) - [CADD](#cadd-1) - [VEP](#vep-2) @@ -183,7 +181,7 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
    Output files -- `{outputdir}/qc_bam/_qualimap/` +- `{outputdir}/qc_bam/` - `_hsmetrics.CollectHsMetrics.coverage_metrics`: - `_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics`: - `_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics`: @@ -194,21 +192,6 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m - `_wgsmetrics_y.CollectWgsMetrics.coverage_metrics`:
    -##### Qualimap - -[Qualimap](http://qualimap.conesalab.org/) also allows you to assess the alignment coverage. Qualimap results are used by MultiQC to generate the following plots. - -- Coverage histogram -- Cumulative genome coverage -- Insert size histogram -- GC content distribution - -
    -Output files - -- `{outputdir}/qc_bam/_qualimap/` this directory includes a qualimap report and associated raw statistic files. You can open the .html file in your internet browser to see the in-depth report. -
    - ##### Chromograph coverage [Chromograph](https://github.com/Clinical-Genomics/chromograph) is a python package to create PNG images from genetics data such as BED and WIG files. @@ -489,18 +472,6 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen #### Annotation -##### HaploGrep2 - -[HaploGrep2](https://github.com/seppinho/haplogrep-cmd) allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations in mitochondria. Haplogrep generates a text report, which is published by default. - -
    -Output files - -- `annotate_snv/mitochondria` - - `*haplogrep.txt`: file containing haplogroup information. - -
    - ##### vcfanno [vcfanno](https://github.com/brentp/vcfanno) allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF. Values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns. The output files are not published in the output folder, and is passed to vep for further annotation. diff --git a/docs/usage.md b/docs/usage.md index f605967ad..b34f80285 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -171,9 +171,9 @@ Note that the pipeline is modular in architecture. It offers you the flexibility The pipeline is modular — individual tools and subworkflows can be skipped using `--skip_tools` and `--skip_subworkflows` (comma-separated). The valid values are: -| `--skip_tools` | -| ----------------------------------------------------------------------------------------------------------------------------------- | -| `fastp`, `fastqc`, `gens`, `germlinecnvcaller`, `haplogrep3`, `ngsbits`, `peddy`, `qualimap`, `smncopynumbercaller`, `vcf2cytosure` | +| `--skip_tools` | +| --------------------------------------------------------------------------------------------------------- | +| `fastp`, `fastqc`, `gens`, `germlinecnvcaller`, `ngsbits`, `peddy`, `smncopynumbercaller`, `vcf2cytosure` | | `--skip_subworkflows` | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | diff --git a/main.nf b/main.nf index 44e5463ef..f1b99e54c 100644 --- a/main.nf +++ b/main.nf @@ -291,10 +291,8 @@ workflow NFCORE_RAREDISEASE { skip_fastqc = parseSkipList(val_skip_tools, 'fastqc') skip_gens = parseSkipList(val_skip_tools, 'gens') skip_germlinecnvcaller = parseSkipList(val_skip_tools, 'germlinecnvcaller') - skip_haplogrep3 = parseSkipList(val_skip_tools, 'haplogrep3') skip_ngsbits = parseSkipList(val_skip_tools, 'ngsbits') skip_peddy = parseSkipList(val_skip_tools, 'peddy') - skip_qualimap = parseSkipList(val_skip_tools, 'qualimap') skip_smncopynumbercaller = parseSkipList(val_skip_tools, 'smncopynumbercaller') skip_vcf2cytosure = parseSkipList(val_skip_tools, 'vcf2cytosure') @@ -441,10 +439,8 @@ workflow NFCORE_RAREDISEASE { skip_fastqc, skip_gens, skip_germlinecnvcaller, - skip_haplogrep3, skip_ngsbits, skip_peddy, - skip_qualimap, skip_smncopynumbercaller, skip_vcf2cytosure, val_aligner, diff --git a/modules.json b/modules.json index 52b5ec8b0..64f726b7d 100644 --- a/modules.json +++ b/modules.json @@ -291,11 +291,6 @@ "git_sha": "824f8012c9ede97642fd23371c8784fb71074c63", "installed_by": ["modules"] }, - "haplogrep3/classify": { - "branch": "master", - "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7", - "installed_by": ["modules"] - }, "hisat2/build": { "branch": "master", "git_sha": "66391ca86ea6a081d288afe6a93d242fefcd8c2c", @@ -371,11 +366,6 @@ "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859", "installed_by": ["modules"] }, - "qualimap/bamqc": { - "branch": "master", - "git_sha": "aa50b51492f79e0bf3ca9ca6e34640e3435b60ba", - "installed_by": ["modules"] - }, "rhocall/annotate": { "branch": "master", "git_sha": "f6cba554dee5a4e180a40f5b1d5df651848d95b9", diff --git a/modules/nf-core/haplogrep3/classify/environment.yml b/modules/nf-core/haplogrep3/classify/environment.yml deleted file mode 100644 index c219ac43c..000000000 --- a/modules/nf-core/haplogrep3/classify/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::haplogrep3=3.2.2 diff --git a/modules/nf-core/haplogrep3/classify/main.nf b/modules/nf-core/haplogrep3/classify/main.nf deleted file mode 100644 index 712146369..000000000 --- a/modules/nf-core/haplogrep3/classify/main.nf +++ /dev/null @@ -1,37 +0,0 @@ -process HAPLOGREP3_CLASSIFY { - tag "$meta.id" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/haplogrep3:3.2.2--hdfd78af_0': - 'biocontainers/haplogrep3:3.2.2--hdfd78af_0' }" - - input: - tuple val(meta), path(inputfile) - - output: - tuple val(meta) , path("*.txt") , emit: txt - tuple val("${task.process}"), val('haplogrep3'), eval("haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'"), emit: versions_haplogrep3, topic: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - haplogrep3 \\ - classify \\ - $args \\ - --in $inputfile \\ - --out ${prefix}.txt - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.txt - """ - -} diff --git a/modules/nf-core/haplogrep3/classify/meta.yml b/modules/nf-core/haplogrep3/classify/meta.yml deleted file mode 100644 index 54b7efdf7..000000000 --- a/modules/nf-core/haplogrep3/classify/meta.yml +++ /dev/null @@ -1,65 +0,0 @@ -name: "haplogrep3_classify" -description: classification into haplogroups -keywords: - - haplogroups - - classify - - mtDNA -tools: - - "haplogrep3": - description: "A tool for mtDNA haplogroup classification." - homepage: "https://github.com/genepi/haplogrep3" - documentation: "https://github.com/genepi/haplogrep3" - tool_dev_url: "https://github.com/genepi/haplogrep3" - licence: ["MIT"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputfile: - type: file - description: valid options are hsd, vcf, or fasta files - pattern: "*.{vcf,vcf.gz,fasta,hsd}" - ontologies: [] -output: - txt: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.txt": - type: file - description: text file with classification information - pattern: "*.{txt}" - ontologies: [] - versions_haplogrep3: - - - ${task.process}: - type: string - description: The process the versions were collected from - - haplogrep3: - type: string - description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': - type: eval - description: The expression to obtain the version of the tool - -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - haplogrep3: - type: string - description: The tool name - - haplogrep3 | sed -n 's/.*Haplogrep 3 \([0-9.]\+\).*/\1/p': - type: eval - description: The expression to obtain the version of the tool - -authors: - - "@lucpen" -maintainers: - - "@lucpen" - - "@ramprasadn" diff --git a/modules/nf-core/haplogrep3/classify/tests/main.nf.test b/modules/nf-core/haplogrep3/classify/tests/main.nf.test deleted file mode 100644 index 654124c52..000000000 --- a/modules/nf-core/haplogrep3/classify/tests/main.nf.test +++ /dev/null @@ -1,59 +0,0 @@ - -nextflow_process { - - name "Test Process HAPLOGREP3_CLASSIFY" - script "../main.nf" - process "HAPLOGREP3_CLASSIFY" - - tag "modules" - tag "modules_nfcore" - tag "haplogrep3" - tag "haplogrep3/classify" - - test("test-haplogrep3-classify") { - - config './nextflow.config' - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test-haplogrep3-classify-stub") { - - options '-stub' - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} diff --git a/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap b/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap deleted file mode 100644 index cce1f8715..000000000 --- a/modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "test-haplogrep3-classify-stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "HAPLOGREP3_CLASSIFY", - "haplogrep3", - "3.2.2" - ] - ], - "txt": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_haplogrep3": [ - [ - "HAPLOGREP3_CLASSIFY", - "haplogrep3", - "3.2.2" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-08T14:14:20.562672125" - }, - "test-haplogrep3-classify": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt:md5,fb242df629aa6168371d1d742f0fb179" - ] - ], - "1": [ - [ - "HAPLOGREP3_CLASSIFY", - "haplogrep3", - "3.2.2" - ] - ], - "txt": [ - [ - { - "id": "test", - "single_end": false - }, - "test.txt:md5,fb242df629aa6168371d1d742f0fb179" - ] - ], - "versions_haplogrep3": [ - [ - "HAPLOGREP3_CLASSIFY", - "haplogrep3", - "3.2.2" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2025-12-08T14:14:10.117489085" - } -} \ No newline at end of file diff --git a/modules/nf-core/haplogrep3/classify/tests/nextflow.config b/modules/nf-core/haplogrep3/classify/tests/nextflow.config deleted file mode 100644 index 7f57266a1..000000000 --- a/modules/nf-core/haplogrep3/classify/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: HAPLOGREP3_CLASSIFY { - ext.args = '--tree phylotree-rsrs@17.1' - } -} diff --git a/modules/nf-core/qualimap/bamqc/environment.yml b/modules/nf-core/qualimap/bamqc/environment.yml deleted file mode 100644 index 4574291d3..000000000 --- a/modules/nf-core/qualimap/bamqc/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::qualimap=2.3 diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf deleted file mode 100644 index 5d7109bed..000000000 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ /dev/null @@ -1,113 +0,0 @@ -process QUALIMAP_BAMQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2b/2b795495fdae4cb3319d19ed4a694302366aa574ba15a0613b85c602f0de4911/data' : - 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' }" - - input: - tuple val(meta), path(bam) - path gff - - output: - tuple val(meta), path("${prefix}"), emit: results - tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - - def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' - def memory = (task.memory.mega*0.8).intValue() + 'M' - def regions = gff ? "--gff $gff" : '' - - def strandedness = 'non-strand-specific' - if (meta.strandedness == 'forward') { - strandedness = 'strand-specific-forward' - } else if (meta.strandedness == 'reverse') { - strandedness = 'strand-specific-reverse' - } - """ - unset DISPLAY - mkdir -p tmp - export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp - qualimap \\ - --java-mem-size=$memory \\ - bamqc \\ - $args \\ - -bam $bam \\ - $regions \\ - -p $strandedness \\ - $collect_pairs \\ - -outdir $prefix \\ - -nt $task.cpus - """ - - stub: - prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" - """ - mkdir -p $prefix/css - mkdir $prefix/images_qualimapReport - mkdir $prefix/raw_data_qualimapReport - cd $prefix/css - touch agogo.css - touch basic.css - touch bgtop.png - touch comment-close.png - touch doctools.js - touch down-pressed.png - touch jquery.js - touch plus.png - touch qualimap_logo_small.png - touch searchtools.js - touch up.png - touch websupport.js - touch ajax-loader.gif - touch bgfooter.png - touch comment-bright.png - touch comment.png - touch down.png - touch file.png - touch minus.png - touch pygments.css - touch report.css - touch underscore.js - touch up-pressed.png - cd ../images_qualimapReport/ - touch genome_coverage_0to50_histogram.png - touch genome_coverage_quotes.png - touch genome_insert_size_across_reference.png - touch genome_mapping_quality_histogram.png - touch genome_uniq_read_starts_histogram.png - touch genome_coverage_across_reference.png - touch genome_gc_content_per_window.png - touch genome_insert_size_histogram.png - touch genome_reads_clipping_profile.png - touch genome_coverage_histogram.png - touch genome_homopolymer_indels.png - touch genome_mapping_quality_across_reference.png - touch genome_reads_content_per_read_position.png - cd ../raw_data_qualimapReport - touch coverage_across_reference.txt - touch genome_fraction_coverage.txt - touch insert_size_histogram.txt - touch mapped_reads_nucleotide_content.txt - touch coverage_histogram.txt - touch homopolymer_indels.txt - touch mapped_reads_clipping_profile.txt - touch mapping_quality_across_reference.txt - touch duplication_rate_histogram.txt - touch insert_size_across_reference.txt - touch mapped_reads_gc-content_distribution.txt - touch mapping_quality_histogram.txt - cd ../ - touch genome_results.txt - touch qualimapReport.html - cd ../ - """ -} diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml deleted file mode 100644 index e93a99137..000000000 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ /dev/null @@ -1,70 +0,0 @@ -name: qualimap_bamqc -description: Evaluate alignment data -keywords: - - quality control - - qc - - bam -tools: - - qualimap: - description: | - Qualimap 2 is a platform-independent application written in - Java and R that provides both a Graphical User Interface and - a command-line interface to facilitate the quality control of - alignment sequencing data and its derivatives like feature counts. - homepage: http://qualimap.bioinfo.cipf.es/ - documentation: http://qualimap.conesalab.org/doc_html/index.html - doi: 10.1093/bioinformatics/bts503 - licence: ["GPL-2.0-only"] - identifier: biotools:qualimap -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - ontologies: [] - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" - ontologies: [] -output: - results: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}: - type: directory - description: Qualimap results dir - pattern: "*/*" - versions_qualimap: - - - ${task.process}: - type: string - description: The name of the process - - qualimap: - type: string - description: The name of the tool - - qualimap -h | sed -n 's/^QualiMap v.//p': - type: eval - description: The expression to obtain the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The name of the process - - qualimap: - type: string - description: The name of the tool - - qualimap -h | sed -n 's/^QualiMap v.//p': - type: eval - description: The expression to obtain the version of the tool -authors: - - "@phue" -maintainers: - - "@phue" diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test deleted file mode 100644 index 7deb086dd..000000000 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test +++ /dev/null @@ -1,61 +0,0 @@ -nextflow_process { - - name "Test Process QUALIMAP_BAMQC" - script "../main.nf" - process "QUALIMAP_BAMQC" - tag "modules" - tag "modules_nfcore" - tag "qualimap" - tag "qualimap/bamqc" - - test("homo_sapiens [bam]") { - when { - process { - """ - gff = [] - - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - input[1] = gff - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot( - file("${process.out.results[0][1]}/qualimapReport.html").name, - path("${process.out.results[0][1]}/genome_results.txt"), - process.out.findAll {key, value -> key.startsWith("versions")}) - .match() } - ) - } - } - - test("homo_sapiens [bam] - stub") { - options "-stub" - when { - process { - """ - gff = [] - - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - input[1] = gff - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap deleted file mode 100644 index 0f67dee18..000000000 --- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap +++ /dev/null @@ -1,179 +0,0 @@ -{ - "homo_sapiens [bam] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - [ - "agogo.css:md5,d41d8cd98f00b204e9800998ecf8427e", - "ajax-loader.gif:md5,d41d8cd98f00b204e9800998ecf8427e", - "basic.css:md5,d41d8cd98f00b204e9800998ecf8427e", - "bgfooter.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "bgtop.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "comment-bright.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "comment-close.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "comment.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "doctools.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "down-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "down.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "file.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "minus.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "plus.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "pygments.css:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_logo_small.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "report.css:md5,d41d8cd98f00b204e9800998ecf8427e", - "searchtools.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "underscore.js:md5,d41d8cd98f00b204e9800998ecf8427e", - "up-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "up.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "websupport.js:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "genome_results.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - [ - "genome_coverage_0to50_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_coverage_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_coverage_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e", - 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"qualimap", - "2.3" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T22:03:27.280522" - }, - "homo_sapiens [bam]": { - "content": [ - "qualimapReport.html", - "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3", - { - "versions_qualimap": [ - [ - "QUALIMAP_BAMQC", - "qualimap", - "2.3" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T22:12:46.38879" - } -} \ No newline at end of file diff --git a/nextflow_schema.json b/nextflow_schema.json index c4113ff6c..9ae5d3a9e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -599,7 +599,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified tools.", "help_text": "Multiple tools can be specified, separated by commas.", - "pattern": "^((fastp|gens|germlinecnvcaller|haplogrep3|peddy|smncopynumbercaller|vcf2cytosure|fastqc|qualimap|ngsbits)?,?)*(? return [meta, vcf, []] } .set { ch_vep_in } @@ -87,14 +82,6 @@ workflow ANNOTATE_MT_SNVS { ch_vcf = ENSEMBLVEP_MT.out.vcf ch_tbi = ENSEMBLVEP_MT.out.tbi - // Running haplogrep3 - ch_haplog_publish = channel.empty() - if (!skip_haplogrep3) { - HAPLOGREP3_CLASSIFY_MT(ch_haplogrep_in) - ch_haplog = HAPLOGREP3_CLASSIFY_MT.out.txt - ch_haplog_publish = HAPLOGREP3_CLASSIFY_MT.out.txt - } - if (val_homoplasmy_af_threshold<1) { BCFTOOLS_PLUGINSETGT ( ENSEMBLVEP_MT.out.vcf.map { meta, vcf -> return [meta, vcf, []] }, @@ -109,11 +96,9 @@ workflow ANNOTATE_MT_SNVS { ch_publish = ENSEMBLVEP_MT.out.vcf .mix(ENSEMBLVEP_MT.out.tbi) - .mix(ch_haplog_publish) .map { meta, value -> ['annotate_snv/mitochondria/', [meta, value]] } emit: - haplog = ch_haplog // channel: [ val(meta), path(txt) ] publish = ch_publish // channel: [ val(destination), val(value) ] report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] tbi = ch_tbi // channel: [ val(meta), path(tbi) ] diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 8bf721bf9..a06af9131 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -29,11 +29,10 @@ nextflow_workflow { input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() input[10] = channel.value([]) - input[11] = false - input[12] = null - input[13] = 'GRCh37' - input[14] = 1.0 - input[15] = 107 + input[11] = null + input[12] = 'GRCh37' + input[13] = 1.0 + input[14] = 107 """ } } diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index ad603f11d..0dd128e2a 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -4,19 +4,6 @@ [ [ "0", - [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "1", [ [ "annotate_snv/mitochondria/", @@ -39,22 +26,11 @@ }, "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] ] ] ], [ - "2", + "1", [ [ { @@ -69,7 +45,7 @@ ] ], [ - "3", + "2", [ [ { @@ -82,7 +58,7 @@ ] ], [ - "4", + "3", [ [ { @@ -94,19 +70,6 @@ ] ] ], - [ - "haplog", - [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], [ "publish", [ @@ -131,17 +94,6 @@ }, "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep_haplogrep.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] ] ] ], @@ -188,7 +140,7 @@ ] ] ], - "timestamp": "2026-03-17T22:54:47.201373396", + "timestamp": "2026-03-27T16:43:51.626374218", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/annotate_mt_snvs/tests/nextflow.config b/subworkflows/local/annotate_mt_snvs/tests/nextflow.config index 6d30464f6..a31fa13b0 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/nextflow.config +++ b/subworkflows/local/annotate_mt_snvs/tests/nextflow.config @@ -26,11 +26,6 @@ process { ext.prefix = { "${meta.prefix}" } } - withName: 'HAPLOGREP3_CLASSIFY_MT' { - ext.args = '--tree phylotree-rsrs@17.1' - ext.prefix = { "${meta.prefix}_haplogrep" } - } - withName: 'BCFTOOLS_PLUGINSETGT' { ext.prefix = { "${meta.prefix}_mt_modifiedgt" } ext.args = "--output-type z --write-index=tbi" diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 35d00c4d4..3b57f6900 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -5,7 +5,6 @@ include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../../modules/nf-core/chromograph/main' -include { QUALIMAP_BAMQC } from '../../../modules/nf-core/qualimap/bamqc/main' include { TIDDIT_COV } from '../../../modules/nf-core/tiddit/cov/main' include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' include { SAMBAMBA_DEPTH } from '../../../modules/nf-core/sambamba/depth/main' @@ -38,13 +37,11 @@ workflow QC_BAM { val_aligner // string: "bwa", "bwamem2", "bwameme", or "sentieon" val_target_bed // string: path to target bed file skip_ngsbits // boolean - skip_qualimap // boolean main: ch_cov = channel.empty() ch_cov_y = channel.empty() ch_hsmetrics = channel.empty() - ch_qualimap = channel.empty() ch_ngsbits = channel.empty() PICARD_COLLECTMULTIPLEMETRICS (ch_bam_bai, ch_genome_fasta, ch_genome_fai) @@ -57,9 +54,6 @@ workflow QC_BAM { if (val_target_bed) { ch_hsmetrics = PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[:],[]], [[:],[]]).metrics } - if (!skip_qualimap) { - ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results - } TIDDIT_COV (ch_bam_bai, [[],[]]) // 2nd pos. arg is req. only for cram input @@ -122,7 +116,6 @@ workflow QC_BAM { .mix(VERIFYBAMID_VERIFYBAMID2.out.mu) .mix(VERIFYBAMID_VERIFYBAMID2.out.ancestry) .mix(ch_hsmetrics) - .mix(ch_qualimap) .mix(ch_cov) .mix(ch_cov_y) .map { meta, value -> ['qc_bam/', [meta, value]] } @@ -132,7 +125,6 @@ workflow QC_BAM { emit: multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] - qualimap_results = ch_qualimap // channel: [ val(meta), path(qualimap_dir) ] tiddit_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] bigwig = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] d4 = MOSDEPTH.out.per_base_d4 // channel: [ val(meta), path(d4) ] diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 79bbaaedc..41b7112fa 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -45,7 +45,6 @@ nextflow_workflow { input[15] = 'bwamem2' input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' input[17] = true - input[18] = false """ } } @@ -126,7 +125,6 @@ nextflow_workflow { input[15] = 'sentieon' input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' input[17] = true - input[18] = false """ } } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index dcacf5eaf..f9bd22357 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -17,7 +17,6 @@ "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_qualimap", "earlycasualcaiman_tidditcov.bw", "earlycasualcaiman_tidditcov.wig", "earlycasualcaiman_tidditcov_1.png", @@ -118,7 +117,7 @@ ] ] ], - "timestamp": "2026-03-13T15:34:21.197802663", + "timestamp": "2026-03-27T16:45:40.990778813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -127,123 +126,31 @@ "QC_BAM - test, sentieon": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - 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"earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.txt" + ], [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ ], [ - "earlycasualcaiman_wgsmetrics.txt" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" - ] + ] ], - "timestamp": "2026-03-13T15:35:09.991615599", + "timestamp": "2026-03-27T16:46:27.678545975", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/qc_bam/tests/nextflow.config b/subworkflows/local/qc_bam/tests/nextflow.config index 4f1859433..f33ab2dc8 100644 --- a/subworkflows/local/qc_bam/tests/nextflow.config +++ b/subworkflows/local/qc_bam/tests/nextflow.config @@ -10,10 +10,6 @@ process { ext.prefix = { "${meta.id}_hsmetrics" } } - withName: '.*QC_BAM:QUALIMAP_BAMQC' { - ext.prefix = { "${meta.id}_qualimap" } - } - withName: '.*QC_BAM:TIDDIT_COV' { ext.args = '-z 500 -w' ext.prefix = { "${meta.id}_tidditcov" } diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index 4b9472567..ad87a4dc8 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -511,12 +511,6 @@ def toolCitationText() { "Vcfanno (Pedersen et al., 2016),", "Genmod (Magnusson et al., 2018)," ] - if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) { - mt_annotation_text += [ - "HaploGrep3 (Schönherr et al., 2023)," - ] - - } } if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('me_annotation')) && params.analysis_type.equals("wgs")) { me_annotation_text = [ @@ -532,7 +526,6 @@ def toolCitationText() { } qc_bam_text = [ "Picard (Broad Institute, 2023)", - "Qualimap (Okonechnikov et al., 2016),", "Sambamba (Tarasov et al., 2015),", "TIDDIT (Eisfeldt et al., 2017),", "UCSC Bigwig and Bigbed (Kent et al., 2010),", @@ -641,11 +634,6 @@ def toolBibliographyText() { "
  • McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016). The Ensembl Variant Effect Predictor. Genome Biology, 17(1), 122. https://doi.org/10.1186/s13059-016-0974-4
    • ", "
  • Magnusson, M., Hughes, T., Glabilloy, & Bitdeli Chef. (2018). genmod: Version 3.7.3 (3.7.3) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3841142
    • " ] - if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) { - mt_annotation_text += [ - "
  • Schönherr, S., Weissensteiner, H., Kronenberg, F., & Forer, L. (2023). Haplogrep 3 an interactive haplogroup classification and analysis platform. Nucleic Acids Research, 51(W1), W263-W268. https://doi.org/10.1093/nar/gkad284
    • " - ] - } } if (!(params.skip_subworkflows && params.skip_subworkflows.split(',').contains('me_annotation')) && params.analysis_type.equals("wgs")) { me_annotation_text = [ @@ -661,7 +649,6 @@ def toolBibliographyText() { } qc_bam_text = [ "
  • Broad Institute. (2023). Picard Tools. In Broad Institute, GitHub repository. http://broadinstitute.github.io/picard/
    • ", - "
  • Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics, 32(2), 292–294. https://doi.org/10.1093/bioinformatics/btv566
    • ", "
  • Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: Fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032–2034. https://doi.org/10.1093/bioinformatics/btv098
    • ", "
  • Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6, 664. https://doi.org/10.12688/f1000research.11168.2
    • ", "
  • Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S., & Karolchik, D. (2010). BigWig and BigBed: Enabling browsing of large distributed datasets. Bioinformatics, 26(17), 2204–2207. https://doi.org/10.1093/bioinformatics/btq351
    • ", diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dcae17c82..99ef960d2 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -228,9 +228,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOGREP3_CLASSIFY_MT": { - "haplogrep3": "3.2.2" - }, "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, @@ -294,9 +291,6 @@ "PICARD_SORTVCF": { "picard": "3.4.0" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 - }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.22 }, @@ -655,7 +649,6 @@ "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", @@ -719,60 +712,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - "qc_bam/earlycasualcaiman/css/minus.png", - "qc_bam/earlycasualcaiman/css/plus.png", - "qc_bam/earlycasualcaiman/css/pygments.css", - "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", - "qc_bam/earlycasualcaiman/css/report.css", - "qc_bam/earlycasualcaiman/css/searchtools.js", - "qc_bam/earlycasualcaiman/css/underscore.js", - "qc_bam/earlycasualcaiman/css/up-pressed.png", - "qc_bam/earlycasualcaiman/css/up.png", - "qc_bam/earlycasualcaiman/css/websupport.js", - "qc_bam/earlycasualcaiman/genome_results.txt", - "qc_bam/earlycasualcaiman/images_qualimapReport", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/earlycasualcaiman/qualimapReport.html", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", @@ -826,60 +765,6 @@ "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat", - "qc_bam/hugelymodelbat/css", - "qc_bam/hugelymodelbat/css/agogo.css", - "qc_bam/hugelymodelbat/css/ajax-loader.gif", - "qc_bam/hugelymodelbat/css/basic.css", - "qc_bam/hugelymodelbat/css/bgfooter.png", - "qc_bam/hugelymodelbat/css/bgtop.png", - "qc_bam/hugelymodelbat/css/comment-bright.png", - "qc_bam/hugelymodelbat/css/comment-close.png", - "qc_bam/hugelymodelbat/css/comment.png", - "qc_bam/hugelymodelbat/css/doctools.js", - "qc_bam/hugelymodelbat/css/down-pressed.png", - "qc_bam/hugelymodelbat/css/down.png", - "qc_bam/hugelymodelbat/css/file.png", - "qc_bam/hugelymodelbat/css/jquery.js", - "qc_bam/hugelymodelbat/css/minus.png", - "qc_bam/hugelymodelbat/css/plus.png", - "qc_bam/hugelymodelbat/css/pygments.css", - "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", - "qc_bam/hugelymodelbat/css/report.css", - "qc_bam/hugelymodelbat/css/searchtools.js", - "qc_bam/hugelymodelbat/css/underscore.js", - "qc_bam/hugelymodelbat/css/up-pressed.png", - "qc_bam/hugelymodelbat/css/up.png", - "qc_bam/hugelymodelbat/css/websupport.js", - "qc_bam/hugelymodelbat/genome_results.txt", - "qc_bam/hugelymodelbat/images_qualimapReport", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/hugelymodelbat/qualimapReport.html", - "qc_bam/hugelymodelbat/raw_data_qualimapReport", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -933,60 +818,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck", - "qc_bam/slowlycivilbuck/css", - "qc_bam/slowlycivilbuck/css/agogo.css", - "qc_bam/slowlycivilbuck/css/ajax-loader.gif", - "qc_bam/slowlycivilbuck/css/basic.css", - "qc_bam/slowlycivilbuck/css/bgfooter.png", - "qc_bam/slowlycivilbuck/css/bgtop.png", - "qc_bam/slowlycivilbuck/css/comment-bright.png", - "qc_bam/slowlycivilbuck/css/comment-close.png", - "qc_bam/slowlycivilbuck/css/comment.png", - "qc_bam/slowlycivilbuck/css/doctools.js", - "qc_bam/slowlycivilbuck/css/down-pressed.png", - "qc_bam/slowlycivilbuck/css/down.png", - "qc_bam/slowlycivilbuck/css/file.png", - "qc_bam/slowlycivilbuck/css/jquery.js", - "qc_bam/slowlycivilbuck/css/minus.png", - "qc_bam/slowlycivilbuck/css/plus.png", - "qc_bam/slowlycivilbuck/css/pygments.css", - "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", - "qc_bam/slowlycivilbuck/css/report.css", - "qc_bam/slowlycivilbuck/css/searchtools.js", - "qc_bam/slowlycivilbuck/css/underscore.js", - "qc_bam/slowlycivilbuck/css/up-pressed.png", - "qc_bam/slowlycivilbuck/css/up.png", - "qc_bam/slowlycivilbuck/css/websupport.js", - "qc_bam/slowlycivilbuck/genome_results.txt", - "qc_bam/slowlycivilbuck/images_qualimapReport", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/slowlycivilbuck/qualimapReport.html", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", @@ -1091,7 +922,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:52:17.64647915", + "timestamp": "2026-03-27T15:19:46.941799577", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 9d91e0519..fc6a2dbd0 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 773, + 769, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -219,9 +219,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOGREP3_CLASSIFY_MT": { - "haplogrep3": "3.2.2" - }, "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, @@ -279,9 +276,6 @@ "PICARD_SORTVCF": { "picard": "3.4.0" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 - }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.22 }, @@ -616,7 +610,6 @@ "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", @@ -664,60 +657,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman", - "qc_bam/earlycasualcaiman/css", - "qc_bam/earlycasualcaiman/css/agogo.css", - "qc_bam/earlycasualcaiman/css/ajax-loader.gif", - "qc_bam/earlycasualcaiman/css/basic.css", - "qc_bam/earlycasualcaiman/css/bgfooter.png", - "qc_bam/earlycasualcaiman/css/bgtop.png", - "qc_bam/earlycasualcaiman/css/comment-bright.png", - "qc_bam/earlycasualcaiman/css/comment-close.png", - "qc_bam/earlycasualcaiman/css/comment.png", - "qc_bam/earlycasualcaiman/css/doctools.js", - "qc_bam/earlycasualcaiman/css/down-pressed.png", - "qc_bam/earlycasualcaiman/css/down.png", - "qc_bam/earlycasualcaiman/css/file.png", - "qc_bam/earlycasualcaiman/css/jquery.js", - "qc_bam/earlycasualcaiman/css/minus.png", - "qc_bam/earlycasualcaiman/css/plus.png", - "qc_bam/earlycasualcaiman/css/pygments.css", - "qc_bam/earlycasualcaiman/css/qualimap_logo_small.png", - "qc_bam/earlycasualcaiman/css/report.css", - "qc_bam/earlycasualcaiman/css/searchtools.js", - "qc_bam/earlycasualcaiman/css/underscore.js", - "qc_bam/earlycasualcaiman/css/up-pressed.png", - "qc_bam/earlycasualcaiman/css/up.png", - "qc_bam/earlycasualcaiman/css/websupport.js", - "qc_bam/earlycasualcaiman/genome_results.txt", - "qc_bam/earlycasualcaiman/images_qualimapReport", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/earlycasualcaiman/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/earlycasualcaiman/qualimapReport.html", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/earlycasualcaiman/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", @@ -771,60 +710,6 @@ "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/hugelymodelbat", - "qc_bam/hugelymodelbat/css", - "qc_bam/hugelymodelbat/css/agogo.css", - "qc_bam/hugelymodelbat/css/ajax-loader.gif", - "qc_bam/hugelymodelbat/css/basic.css", - "qc_bam/hugelymodelbat/css/bgfooter.png", - "qc_bam/hugelymodelbat/css/bgtop.png", - "qc_bam/hugelymodelbat/css/comment-bright.png", - "qc_bam/hugelymodelbat/css/comment-close.png", - "qc_bam/hugelymodelbat/css/comment.png", - "qc_bam/hugelymodelbat/css/doctools.js", - "qc_bam/hugelymodelbat/css/down-pressed.png", - "qc_bam/hugelymodelbat/css/down.png", - "qc_bam/hugelymodelbat/css/file.png", - "qc_bam/hugelymodelbat/css/jquery.js", - "qc_bam/hugelymodelbat/css/minus.png", - "qc_bam/hugelymodelbat/css/plus.png", - "qc_bam/hugelymodelbat/css/pygments.css", - "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", - "qc_bam/hugelymodelbat/css/report.css", - "qc_bam/hugelymodelbat/css/searchtools.js", - "qc_bam/hugelymodelbat/css/underscore.js", - "qc_bam/hugelymodelbat/css/up-pressed.png", - "qc_bam/hugelymodelbat/css/up.png", - "qc_bam/hugelymodelbat/css/websupport.js", - "qc_bam/hugelymodelbat/genome_results.txt", - "qc_bam/hugelymodelbat/images_qualimapReport", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/hugelymodelbat/qualimapReport.html", - "qc_bam/hugelymodelbat/raw_data_qualimapReport", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -878,60 +763,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck", - "qc_bam/slowlycivilbuck/css", - "qc_bam/slowlycivilbuck/css/agogo.css", - "qc_bam/slowlycivilbuck/css/ajax-loader.gif", - "qc_bam/slowlycivilbuck/css/basic.css", - "qc_bam/slowlycivilbuck/css/bgfooter.png", - "qc_bam/slowlycivilbuck/css/bgtop.png", - "qc_bam/slowlycivilbuck/css/comment-bright.png", - "qc_bam/slowlycivilbuck/css/comment-close.png", - "qc_bam/slowlycivilbuck/css/comment.png", - "qc_bam/slowlycivilbuck/css/doctools.js", - "qc_bam/slowlycivilbuck/css/down-pressed.png", - "qc_bam/slowlycivilbuck/css/down.png", - "qc_bam/slowlycivilbuck/css/file.png", - "qc_bam/slowlycivilbuck/css/jquery.js", - "qc_bam/slowlycivilbuck/css/minus.png", - "qc_bam/slowlycivilbuck/css/plus.png", - "qc_bam/slowlycivilbuck/css/pygments.css", - "qc_bam/slowlycivilbuck/css/qualimap_logo_small.png", - "qc_bam/slowlycivilbuck/css/report.css", - "qc_bam/slowlycivilbuck/css/searchtools.js", - "qc_bam/slowlycivilbuck/css/underscore.js", - "qc_bam/slowlycivilbuck/css/up-pressed.png", - "qc_bam/slowlycivilbuck/css/up.png", - "qc_bam/slowlycivilbuck/css/websupport.js", - "qc_bam/slowlycivilbuck/genome_results.txt", - "qc_bam/slowlycivilbuck/images_qualimapReport", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/slowlycivilbuck/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/slowlycivilbuck/qualimapReport.html", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/slowlycivilbuck/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", @@ -1020,7 +851,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-17T16:58:22.361988613", + "timestamp": "2026-03-27T15:28:24.531728352", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index c86d7ea91..559b0dad1 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 353, + 351, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -220,9 +220,6 @@ "GLNEXUS": { "glnexus": "1.4.1" }, - "HAPLOGREP3_CLASSIFY_MT": { - "haplogrep3": "3.2.2" - }, "HISAT2_INDEX_GENOME": { "hisat2": "2.2.1" }, @@ -286,9 +283,6 @@ "PICARD_SORTVCF": { "picard": "3.4.0" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 - }, "REMOVE_DUPLICATES_GL": { "bcftools": 1.22 }, @@ -520,7 +514,6 @@ "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", - "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep_haplogrep.txt", "annotate_sv", "annotate_sv/justhusky_svdbquery_vep.vcf.gz", "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", @@ -570,60 +563,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/hugelymodelbat", - "qc_bam/hugelymodelbat/css", - "qc_bam/hugelymodelbat/css/agogo.css", - "qc_bam/hugelymodelbat/css/ajax-loader.gif", - "qc_bam/hugelymodelbat/css/basic.css", - "qc_bam/hugelymodelbat/css/bgfooter.png", - "qc_bam/hugelymodelbat/css/bgtop.png", - "qc_bam/hugelymodelbat/css/comment-bright.png", - "qc_bam/hugelymodelbat/css/comment-close.png", - "qc_bam/hugelymodelbat/css/comment.png", - "qc_bam/hugelymodelbat/css/doctools.js", - "qc_bam/hugelymodelbat/css/down-pressed.png", - "qc_bam/hugelymodelbat/css/down.png", - "qc_bam/hugelymodelbat/css/file.png", - "qc_bam/hugelymodelbat/css/jquery.js", - "qc_bam/hugelymodelbat/css/minus.png", - "qc_bam/hugelymodelbat/css/plus.png", - "qc_bam/hugelymodelbat/css/pygments.css", - "qc_bam/hugelymodelbat/css/qualimap_logo_small.png", - "qc_bam/hugelymodelbat/css/report.css", - "qc_bam/hugelymodelbat/css/searchtools.js", - "qc_bam/hugelymodelbat/css/underscore.js", - "qc_bam/hugelymodelbat/css/up-pressed.png", - "qc_bam/hugelymodelbat/css/up.png", - "qc_bam/hugelymodelbat/css/websupport.js", - "qc_bam/hugelymodelbat/genome_results.txt", - "qc_bam/hugelymodelbat/images_qualimapReport", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_0to50_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_coverage_quotes.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_gc_content_per_window.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_homopolymer_indels.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_insert_size_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_across_reference.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_mapping_quality_histogram.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_clipping_profile.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_reads_content_per_read_position.png", - "qc_bam/hugelymodelbat/images_qualimapReport/genome_uniq_read_starts_histogram.png", - "qc_bam/hugelymodelbat/qualimapReport.html", - "qc_bam/hugelymodelbat/raw_data_qualimapReport", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/coverage_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/homopolymer_indels.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/insert_size_histogram.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qc_bam/hugelymodelbat/raw_data_qualimapReport/mapping_quality_histogram.txt", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -710,7 +649,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-17T17:02:07.664289531", + "timestamp": "2026-03-27T15:32:27.001538758", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 93220ee89..684b4a09d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -173,10 +173,8 @@ workflow RAREDISEASE { skip_fastqc skip_gens skip_germlinecnvcaller - skip_haplogrep3 skip_ngsbits skip_peddy - skip_qualimap skip_smncopynumbercaller skip_vcf2cytosure val_aligner @@ -336,8 +334,7 @@ workflow RAREDISEASE { val_analysis_type, val_aligner, val_target_bed, - skip_ngsbits, - skip_qualimap + skip_ngsbits ) ch_qc_bam_publish = QC_BAM.out.publish @@ -510,7 +507,6 @@ workflow RAREDISEASE { ch_vcfanno_toml, ch_vep_cache, ch_vep_extra_files, - skip_haplogrep3, val_cadd_resources, val_genome, val_homoplasmy_af_threshold, @@ -938,7 +934,6 @@ workflow RAREDISEASE { ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) From 1467433b1e012fc2006552f0c5ee729a49d20f53 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 17:11:46 +0100 Subject: [PATCH 568/872] update snap & changlog --- CHANGELOG.md | 3 + .../local/qc_bam/tests/main.nf.test.snap | 107 ++++++++++++++++-- 2 files changed, 102 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d4b03041..d594cf2be 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#789](https://github.com/nf-core/raredisease/pull/789) - Remove redundant TABIX processes, and update configs for nf-test [#790](https://github.com/nf-core/raredisease/pull/790) - Migrate file publishing from publishDir to a centralized output {} block for some workflows [#791](https://github.com/nf-core/raredisease/pull/791) +- Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801) ### `Fixed` @@ -78,6 +79,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | gens-preproc | 1.0.11 | | | gens/preparecovandbaf | | 1.1.5 | | haplocheck | 1.3.3 | | +| haplogrep3 | 3.2.2 | | | hmtnote | 0.7.2 | | | htslib | 1.20 | 1.21 | | MitoSalt | | 1.1.1 | @@ -86,6 +88,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | ngsbits | 202411 | 202512 | | picard | 3.3.0 | 3.4.0 | | pigz | 2.3.4 | 2.8 | +| qualimap | 2.3 | | | sambamba | | 1.0.1 | | samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index f9bd22357..42f458e1c 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -126,31 +126,122 @@ "QC_BAM - test, sentieon": { "content": [ [ - + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png", + "earlycasualcaiman_wgsmetrics.txt" ], [ - + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ], [ - + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ ], [ - + "earlycasualcaiman_wgsmetrics.txt" ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + ] ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + ] ] ], - "timestamp": "2026-03-27T16:46:27.678545975", + "timestamp": "2026-03-27T17:07:36.836738984", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 5e31da2d33034176da5a284ffa39b8f9796bc97b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 27 Mar 2026 17:14:58 +0100 Subject: [PATCH 569/872] change to dev From d7be8912a5c02d2a682be952fc3244531deb1e8c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 30 Mar 2026 14:22:45 +0200 Subject: [PATCH 570/872] Review suggestions --- subworkflows/local/annotate_genome_snvs/main.nf | 3 ++- subworkflows/local/annotate_mt_snvs/main.nf | 4 +--- subworkflows/local/call_sv_MT/main.nf | 9 +++++---- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 61e5c2263..5ca1797bd 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -101,9 +101,10 @@ workflow ANNOTATE_GENOME_SNVS { .join(VCFANNO.out.tbi, failOnMismatch:true, failOnDuplicate:true) .set { ch_bcftools_view_in } + // filter on frequencies BCFTOOLS_VIEW( ch_bcftools_view_in, - [], [], []) // filter on frequencies + [], [], []) // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index ef7660272..975f96f89 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -36,8 +36,6 @@ workflow ANNOTATE_MT_SNVS { VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) - ch_vcfanno_vcf = VCFANNO_MT.out.vcf - // Annotating with CADD if (!val_cadd_resources.equals(null)) { ANNOTATE_CADD ( @@ -52,7 +50,7 @@ workflow ANNOTATE_MT_SNVS { ch_cadd_vcf = channel.empty() } - ch_vcfanno_vcf + VCFANNO_MT.out.vcf .join(ch_cadd_vcf, remainder: true) .branch { meta, vcfanno, cadd -> vcfanno: cadd.equals(null) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index aa5210788..e1149e276 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -1,5 +1,6 @@ // -// Call SV MT +// Calls SV MT, concatenates FASTQs per sample, then runs MitoSalt and SaltShaker. +// Also detects the number of discordant pairs using the mitodel script. // include { MT_DELETION } from '../../../modules/local/mt_deletion_script' @@ -43,10 +44,10 @@ workflow CALL_SV_MT { ch_reads .map { meta, reads -> - def groupKey = meta.sample - return [groupKey, meta, reads] + def sample_group_key = meta.sample + return [sample_group_key, meta, reads] } - .groupTuple(by: 0) + .groupTuple() .map { sample_id, meta_list, reads_list -> def combined_meta = meta_list[0].clone() combined_meta.id = sample_id From c34fb816bb6294672730baf4a1bc3e7e772a3226 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 30 Mar 2026 14:24:21 +0200 Subject: [PATCH 571/872] Added sub test to scatter_genome subworkflow --- .../local/scatter_genome/tests/main.nf.test | 29 ++++++++ .../scatter_genome/tests/main.nf.test.snap | 71 +++++++++++++++++++ 2 files changed, 100 insertions(+) diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 4845e81c4..3c2afcfe9 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -32,4 +32,33 @@ nextflow_workflow { } + test("Should run without failures, stub") { + + options "-stub" + + when { + params { + pipelines_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + fasta = params.pipelines_testdata_base_path + 'reference/reference.fasta' + fai = params.pipelines_testdata_base_path + 'reference/reference.fasta.fai' + dict = params.pipelines_testdata_base_path + 'reference/reference.dict' + scatter_count = 20 + } + workflow { + """ + input[0] = channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() + input[1] = channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() + input[2] = channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() + input[3] = "processed_references" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 095562f2d..823e91d1a 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -1,4 +1,75 @@ { + "Should run without failures, stub": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "bed": [ + [ + { + "id": "genome" + }, + "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "split_intervals": [ + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-03-30T10:55:18.112519", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ { From 8631f9d23331f261a0dad6fbf7c5fdc7f056ae53 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic <164479386+emmadizdarevic@users.noreply.github.com> Date: Mon, 30 Mar 2026 14:47:57 +0200 Subject: [PATCH 572/872] Update subworkflows/local/annotate_genome_snvs/tests/main.nf.test Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- subworkflows/local/annotate_genome_snvs/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index cb11eff34..323262893 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_workflow { tag "subworkflows" tag "annotate_genome_snvs" - tag"annotate_cadd" + tag "annotate_cadd" tag "annotate_rhocallviz" tag "vcfanno" From b661a8bdcbe084d2feb606e06a193f0a0dc88ec3 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic <164479386+emmadizdarevic@users.noreply.github.com> Date: Mon, 30 Mar 2026 14:48:09 +0200 Subject: [PATCH 573/872] Update subworkflows/local/annotate_mobile_elements/tests/main.nf.test Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- subworkflows/local/annotate_mobile_elements/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test index fb46452da..5aa86d4e3 100644 --- a/subworkflows/local/annotate_mobile_elements/tests/main.nf.test +++ b/subworkflows/local/annotate_mobile_elements/tests/main.nf.test @@ -7,7 +7,7 @@ nextflow_workflow { tag "subworkflows" tag "annotate_mobile_elements" - tag"bcftools/view" + tag "bcftools/view" tag "ensemblvep/vep" tag "picard/sortvcf" tag "svdb/query" From 00d42fd0b53274000b9ca80cc49d577203cadd4c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 30 Mar 2026 15:29:12 +0200 Subject: [PATCH 574/872] Move params to main.nf --- main.nf | 2 + .../local/call_structural_variants/main.nf | 2 + .../tests/main.nf.test | 37 ++++++++++--------- .../tests/main.nf.test.snap | 4 +- subworkflows/local/call_sv_MT/main.nf | 3 +- .../local/call_sv_MT/tests/main.nf.test | 19 +++++----- .../local/call_sv_MT/tests/main.nf.test.snap | 4 +- workflows/raredisease.nf | 2 + 8 files changed, 41 insertions(+), 32 deletions(-) diff --git a/main.nf b/main.nf index f4a168e81..ec6a77e09 100644 --- a/main.nf +++ b/main.nf @@ -311,6 +311,7 @@ workflow NFCORE_RAREDISEASE { skip_fastqc = parseSkipList(val_skip_tools, 'fastqc') skip_gens = parseSkipList(val_skip_tools, 'gens') skip_germlinecnvcaller = parseSkipList(val_skip_tools, 'germlinecnvcaller') + skip_mitosalt = parseSkipList(val_skip_tools, 'mitosalt') skip_ngsbits = parseSkipList(val_skip_tools, 'ngsbits') skip_peddy = parseSkipList(val_skip_tools, 'peddy') skip_smncopynumbercaller = parseSkipList(val_skip_tools, 'smncopynumbercaller') @@ -459,6 +460,7 @@ workflow NFCORE_RAREDISEASE { skip_fastqc, skip_gens, skip_germlinecnvcaller, + skip_mitosalt, skip_ngsbits, skip_peddy, skip_smncopynumbercaller, diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index bed4ae939..bc225c1da 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -28,6 +28,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] val_analysis_type // string: "wes", "wgs", or "mito" skip_germlinecnvcaller // boolean + skip_mitosalt // boolean ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] @@ -99,6 +100,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_subdepth, ch_svcaller_priority, ch_mitosalt_config, + skip_mitosalt, val_heavy_strand_origin_start, val_heavy_strand_origin_end, val_light_strand_origin_start, diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 2ff584b2f..39d604023 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -38,34 +38,35 @@ nextflow_workflow { input[12] = channel.of([[id:'gcnvcaller'], []]) input[13] = 'wgs' input[14] = true - input[15] = channel.of([ + input[15] = false + input[16] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[16] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)) - input[17] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[18] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[20] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[21] = channel.of([ + input[17] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)) + input[18] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[21] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[22] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[22] = channel.value(10000000) - input[23] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[24] = 16081 - input[25] = 407 - input[26] = 5730 - input[27] = 5763 - input[28] = 16569 - input[29] = 'MT' - input[30] = 15 - input[31] = 0.01 - input[32] = true + input[23] = channel.value(10000000) + input[24] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[25] = 16081 + input[26] = 407 + input[27] = 5730 + input[28] = 5763 + input[29] = 16569 + input[30] = 'MT' + input[31] = 15 + input[32] = 0.01 + input[33] = true """ } } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 120b54b2c..74bde0944 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -16,10 +16,10 @@ "justhusky_sv.vcf.gz.tbi" ] ], + "timestamp": "2026-03-25T16:02:32.429241176", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-25T16:02:32.429241176" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index bb6d5d6f8..c16c6090f 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -26,6 +26,7 @@ workflow CALL_SV_MT { ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] + skip_mitosalt // Boolean val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start @@ -40,7 +41,7 @@ workflow CALL_SV_MT { ch_saltshaker_vcf = channel.empty() ch_saltshaker_plot = channel.empty() - if (!(params.skip_tools && params.skip_tools.split(',').contains('mitosalt'))) { + if (!skip_mitosalt) { ch_reads_subdepth = ch_reads.combine(ch_subdepth) SEQTK_SAMPLE (ch_reads_subdepth) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index ecc97601e..c522e95e0 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -37,17 +37,18 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[10] = channel.value(10000000) + input[10] = channel.value(10000000) input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[13] = 16081 - input[14] = 407 - input[15] = 5730 - input[16] = 5763 - input[17] = 16569 - input[18] = 'chrM' - input[19] = 15 - input[20] = 0.01 + input[13] = false + input[14] = 16081 + input[15] = 407 + input[16] = 5730 + input[17] = 5763 + input[18] = 16569 + input[19] = 'chrM' + input[20] = 15 + input[21] = 0.01 """ } } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index ffff40473..16dac4ed5 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -316,10 +316,10 @@ ] ] ], + "timestamp": "2026-03-25T15:53:51.569932008", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-25T15:53:51.569932008" + } } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index caae0090b..ee36f9196 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -172,6 +172,7 @@ workflow RAREDISEASE { skip_fastqc skip_gens skip_germlinecnvcaller + skip_mitosalt skip_ngsbits skip_peddy skip_smncopynumbercaller @@ -617,6 +618,7 @@ workflow RAREDISEASE { ch_gcnvcaller_model, val_analysis_type, skip_germlinecnvcaller, + skip_mitosalt, ch_mapped.mt_bam_bai, ch_genome_chrsizes, ch_genome_hisat2index, From c652cf41af9a0bbaf2d71f952636032dd7cbcc83 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 30 Mar 2026 16:43:11 +0200 Subject: [PATCH 575/872] Added changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d4b03041..ee3698f32 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) - Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) +- Test tags for dependent modules in subworkflow tests [#800](https://github.com/nf-core/raredisease/pull/800/changes#top) +- Stub test for scatter_genome subworkflow [#802](https://github.com/nf-core/raredisease/pull/802) ### `Changed` From 1e883246de098ff288198c0d51b7c106afe9849e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 30 Mar 2026 17:04:57 +0200 Subject: [PATCH 576/872] Update snapshot --- tests/default.nf.test.snap | 5 ++--- tests/test_bam.nf.test.snap | 9 ++++----- tests/test_singleton.nf.test.snap | 9 ++++----- 3 files changed, 10 insertions(+), 13 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d9943ffc9..71292f130 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -922,11 +922,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-27T15:19:46.941799577", + "timestamp": "2026-03-25T12:44:18.757225141", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-25T12:44:18.757225141" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 44215ffaf..b975f82a2 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 769, + 777, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -841,11 +841,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-27T15:28:24.531728352", + "timestamp": "2026-03-30T16:58:17.703462431", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T13:49:42.531336219" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e56391d1f..86b829ae2 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 351, + 363, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -649,11 +649,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-27T15:32:27.001538758", + "timestamp": "2026-03-30T17:02:07.692317187", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T13:51:49.424910007" + } } } \ No newline at end of file From bd6161861324dcaac926ecb31952f81d5ca24611 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic <164479386+emmadizdarevic@users.noreply.github.com> Date: Mon, 30 Mar 2026 17:09:44 +0200 Subject: [PATCH 577/872] Update CHANGELOG.md Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98f077069..821fbf832 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tests for some of the subworkflows [#780](https://github.com/nf-core/raredisease/pull/780) - Tests for some of the subworkflows [#782](https://github.com/nf-core/raredisease/pull/782) - Tests for some of the subworkflows [#783](https://github.com/nf-core/raredisease/pull/783) -- Test tags for dependent modules in subworkflow tests [#800](https://github.com/nf-core/raredisease/pull/800/changes#top) +- Test tags for dependent modules in subworkflow tests [#800](https://github.com/nf-core/raredisease/pull/800) - Stub test for scatter_genome subworkflow [#802](https://github.com/nf-core/raredisease/pull/802) ### `Changed` From 94e788a068c45ac4b2e1b3928d3d67a604043bb1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 30 Mar 2026 20:21:05 +0200 Subject: [PATCH 578/872] Update snapshot --- subworkflows/local/call_sv_MT/tests/main.nf.test.snap | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index c7174c099..f612a8558 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -247,8 +247,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -268,8 +266,6 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, @@ -304,9 +300,9 @@ ] ] ], - "timestamp": "2026-03-25T15:53:51.569932008", + "timestamp": "2026-03-30T20:20:40.266229001", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" } } From 9a0c8b8cfb28f0d4e66c5caf2c57207b3684f975 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 31 Mar 2026 22:46:55 +0200 Subject: [PATCH 579/872] Fix intervals error for wes --- subworkflows/local/prepare_references/main.nf | 126 +++++++++--------- 1 file changed, 65 insertions(+), 61 deletions(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 5eb8bfbbf..a3a99851d 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -60,32 +60,33 @@ workflow PREPARE_REFERENCES { main: - ch_bait_intervals = channel.empty() - ch_bwa = channel.empty() - ch_genome_bwameme_index = channel.empty() - ch_genome_bwamem2_index = channel.empty() - ch_genome_hisat2_index = channel.empty() - ch_mt_last_index = channel.empty() - ch_gnomad_af_idx = channel.empty() - ch_dbsnp = channel.value([[:],[]]) - ch_dbsnp_tbi = channel.value([[:],[]]) - ch_mt_bwa_index = channel.empty() - ch_mt_bwamem2_index = channel.empty() - ch_mtshift_bwa_index = channel.empty() - ch_mtshift_bwamem2_index = channel.empty() - ch_mtshift_backchain = channel.empty() - ch_mtshift_dict = channel.empty() - ch_mtshift_fai = channel.empty() - ch_mtshift_fasta = channel.empty() - ch_mt_dict = channel.empty() - ch_mt_fai = channel.empty() - ch_mt_fasta = channel.empty() - ch_sdf = channel.empty() - ch_shiftfasta_mtintervals = channel.empty() - ch_target_bed_gz_tbi = channel.value([[:],[],[]]) - ch_target_intervals = channel.empty() - ch_vcfanno_extra = channel.value([[]]) - ch_vep_resources = channel.value([[]]) + ch_bait_intervals = channel.empty() + ch_bwa = channel.empty() + ch_genome_bwameme_index = channel.empty() + ch_genome_bwamem2_index = channel.empty() + ch_genome_hisat2_index = channel.empty() + ch_mt_last_index = channel.empty() + ch_gnomad_af_idx = channel.empty() + ch_dbsnp = channel.value([[:],[]]) + ch_dbsnp_tbi = channel.value([[:],[]]) + ch_mt_bwa_index = channel.empty() + ch_mt_bwamem2_index = channel.empty() + ch_mtshift_bwa_index = channel.empty() + ch_mtshift_bwamem2_index = channel.empty() + ch_mtshift_backchain = channel.empty() + ch_mtshift_dict = channel.empty() + ch_mtshift_fai = channel.empty() + ch_mtshift_fasta = channel.empty() + ch_mt_dict = channel.empty() + ch_mt_fai = channel.empty() + ch_mt_fasta = channel.empty() + ch_sdf = channel.empty() + ch_shiftfasta_mtintervals = channel.empty() + ch_shiftfasta_mtshiftintervals = channel.empty() + ch_target_bed_gz_tbi = channel.value([[:],[],[]]) + ch_target_intervals = channel.empty() + ch_vcfanno_extra = channel.value([[]]) + ch_vep_resources = channel.value([[]]) ch_genome_fasta = channel.fromPath(val_fasta).map { it -> [[id:it.simpleName], it] }.collect() // @@ -163,7 +164,10 @@ workflow PREPARE_REFERENCES { ind = files.findIndexValues {file -> !(file.toString().endsWith("shifted.intervals"))} files[ind] } - .set {ch_shiftfasta_mtintervals} + .set {ch_mtintervals} + ch_shiftfasta_mtintervals = ch_mtintervals.intervals.collect() + ch_shiftfasta_mtshiftintervals = ch_mtintervals.shift_intervals.collect() + } // @@ -299,8 +303,8 @@ workflow PREPARE_REFERENCES { .mix( ch_bait_intervals .mix(ch_chrom_sizes) - .mix(ch_shiftfasta_mtintervals.intervals) - .mix(ch_shiftfasta_mtintervals.shift_intervals) + .mix(ch_shiftfasta_mtintervals) + .mix(ch_shiftfasta_mtshiftintervals) .mix(ch_target_intervals) .mix(ch_gnomad_af_idx) .mix(ch_vcfanno_extra) @@ -310,36 +314,36 @@ workflow PREPARE_REFERENCES { } emit: - bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] - dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] - dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] - genome_bwa_index = ch_bwa // channel:[ val(meta), path(index) ] - genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] - genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] - genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] - genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] - genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] - genome_hisat2_index = ch_genome_hisat2_index // channel: [ val(meta), path(index) ] - genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] - gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] - mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] - mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] - mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] - mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] - mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] - mt_intervals = ch_shiftfasta_mtintervals.intervals.collect() // channel:[ path(intervals) ] - mt_last_index = ch_mt_last_index // channel: [ val(meta), path(index) ] - mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] - mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] - mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] - mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] - mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] - mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] - mtshift_intervals = ch_shiftfasta_mtintervals.shift_intervals.collect() // channel:[ path(intervals) ] - sdf = ch_sdf // channel:[ val (meta), path(sdf) ] - target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] - target_intervals = ch_target_intervals // channel:[ path(interval_list) ] - vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] - vep_resources = ch_vep_resources // channel:[ path(cache) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] + dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] + dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] + genome_bwa_index = ch_bwa // channel:[ val(meta), path(index) ] + genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] + genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] + genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] + genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] + genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] + genome_hisat2_index = ch_genome_hisat2_index // channel: [ val(meta), path(index) ] + genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] + gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] + mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] + mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] + mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] + mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] + mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] + mt_intervals = ch_shiftfasta_mtintervals // channel:[ path(intervals) ] + mt_last_index = ch_mt_last_index // channel: [ val(meta), path(index) ] + mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] + mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] + mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] + mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] + mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] + mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] + mtshift_intervals = ch_shiftfasta_mtshiftintervals // channel:[ path(intervals) ] + sdf = ch_sdf // channel:[ val (meta), path(sdf) ] + target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] + target_intervals = ch_target_intervals // channel:[ path(interval_list) ] + vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] + vep_resources = ch_vep_resources // channel:[ path(cache) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } From 529433172a97b3a4c074d2ae57640790e219e0e7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 1 Apr 2026 01:29:59 +0200 Subject: [PATCH 580/872] Update main.nf --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 1ec15d4c9..eccf5b0e3 100644 --- a/main.nf +++ b/main.nf @@ -250,7 +250,7 @@ workflow NFCORE_RAREDISEASE { // Using channelFromSamplesheet helper. Returns either an empty channel or validated channel. ch_me_references = channelFromSamplesheet(val_mobile_element_references, "${projectDir}/assets/mobile_element_references_schema.json", false) ch_me_svdb_resources = channelFromSamplesheet(val_mobile_element_svdb_annotations, "${projectDir}/assets/svdb_query_vcf_schema.json", false) - ch_sample_id_map = channelFromSamplesheet(val_sample_id_map, "${projectDir}/assets/sample_id_map.json") + ch_sample_id_map = channelFromSamplesheet(val_sample_id_map, "${projectDir}/assets/sample_id_map.json", false) ch_svdb_bedpedbs = channelFromSamplesheet(val_svdb_query_bedpedbs, "${projectDir}/assets/svdb_query_bedpe_schema.json", false) ch_svdb_dbs = channelFromSamplesheet(val_svdb_query_dbs, "${projectDir}/assets/svdb_query_vcf_schema.json", false) From f0ee26c8d02585ce5ee0e4ced83ab092272175e3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 7 Apr 2026 21:28:04 +0200 Subject: [PATCH 581/872] sort input parameters in sv calling subworkflow --- CHANGELOG.md | 1 + .../local/call_structural_variants/main.nf | 34 +++++----- .../tests/main.nf.test | 62 +++++++++---------- workflows/raredisease.nf | 34 +++++----- 4 files changed, 66 insertions(+), 65 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c7472f1b..0ca989fce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Sort parameters of `CALL_STRUCTURAL_VARIANTS` and `CALL_SV_MANTA` alphabetically [[#](https://github.com/nf-core/raredisease/pull/)] - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index bc225c1da..19abff24f 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -13,35 +13,35 @@ include { TABIX_TABIX } from '../../../modules/nf-core/tabix/ workflow CALL_STRUCTURAL_VARIANTS { take: - ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] - ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_bwa_index // channel: [mandatory] [ val(meta), path(index)] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] - ch_genome_dictionary // channel: [optional; used by mandatory for GATK's cnvcaller][ val(meta), path(dict) ] - ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] - ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] - ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_gcnvcaller_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(gcnvcaller_model) ] - val_analysis_type // string: "wes", "wgs", or "mito" - skip_germlinecnvcaller // boolean - skip_mitosalt // boolean - ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] + ch_genome_bai // channel: [mandatory] [ val(meta), path(bai) ] + ch_genome_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_genome_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] + ch_genome_dictionary // channel: [optional; used by mandatory for GATK's cnvcaller][ val(meta), path(dict) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] + ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] + ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] + ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] - ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] - val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start + ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] + ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] + skip_germlinecnvcaller // boolean + skip_mitosalt // boolean + val_analysis_type // string: "wes", "wgs", or "mito" val_heavy_strand_origin_end // string: [mandatory] mitochondira_heavy_strand_origin_end - val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start + val_heavy_strand_origin_start // string: [mandatory] mitochondira_heavy_strand_origin_start val_light_strand_origin_end // string: [mandatory] mitochondira_light_strand_origin_end + val_light_strand_origin_start // string: [mandatory] mitochondira_light_strand_origin_start val_mitochondria_length // string: [mandatory] mito_length val_mitochondria_name // string: [mandatory] mito_name val_mitosalt_flank // string: [mandatory] mitosalt_flank diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 09da4d44e..f2d69db9d 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -21,55 +21,55 @@ nextflow_workflow { when { workflow { """ - input[0] = channel.of([ + input[0] = channel.of([[id:'bwa'], []]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of([[id:'gcnvcaller'], []]) + input[3] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[1] = channel.of([ + input[4] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true) ]) - input[2] = channel.of([ + input[5] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[3] = channel.of([[id:'bwa'], []]) - input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[6] = channel.of([id:'justhusky']) - input[7] = channel.of([[id:'target'], [], []]) - input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() - input[9] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[10] = channel.of([[]]) - input[11] = channel.of([[id:'ploidy'], []]) - input[12] = channel.of([[id:'gcnvcaller'], []]) - input[13] = 'wgs' - input[14] = true - input[15] = false - input[16] = channel.of([ + input[6] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)) + input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() + input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[12] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[17] = channel.from(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)) - input[18] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[19] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[20] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[21] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[22] = channel.of([ + input[13] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[15] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[16] = channel.of([[id:'ploidy'], []]) + input[17] = channel.of([[]]) + input[18] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[23] = channel.value(10000000) - input[24] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[25] = 16081 - input[26] = 407 - input[27] = 5730 - input[28] = 5763 + input[19] = channel.value(10000000) + input[20] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[21] = channel.of([[id:'target'], [], []]) + input[22] = true + input[23] = false + input[24] = 'wgs' + input[25] = 407 + input[26] = 16081 + input[27] = 5763 + input[28] = 5730 input[29] = 16569 input[30] = 'MT' input[31] = 15 diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ee36f9196..cdeba0f99 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -603,35 +603,35 @@ workflow RAREDISEASE { .set{ ch_mitosalt_config } CALL_STRUCTURAL_VARIANTS ( - ch_mapped.genome_marked_bam, - ch_mapped.genome_marked_bai, - ch_mapped.genome_marked_bam_bai, ch_genome_bwaindex, - ch_genome_fasta, - ch_genome_fai, ch_case_info, - ch_target_bed, - ch_genome_dictionary, - ch_svcaller_priority, - ch_readcount_intervals, - ch_ploidy_model, ch_gcnvcaller_model, - val_analysis_type, - skip_germlinecnvcaller, - skip_mitosalt, - ch_mapped.mt_bam_bai, + ch_mapped.genome_marked_bai, + ch_mapped.genome_marked_bam, + ch_mapped.genome_marked_bam_bai, ch_genome_chrsizes, + ch_genome_dictionary, + ch_genome_fai, + ch_genome_fasta, ch_genome_hisat2index, + ch_mitosalt_config, + ch_mapped.mt_bam_bai, ch_mt_fai, ch_mt_fasta, ch_mt_lastdb, + ch_ploidy_model, + ch_readcount_intervals, ch_input_fastqs, ch_subdepth, - ch_mitosalt_config, - val_heavy_strand_origin_start, + ch_svcaller_priority, + ch_target_bed, + skip_germlinecnvcaller, + skip_mitosalt, + val_analysis_type, val_heavy_strand_origin_end, - val_light_strand_origin_start, + val_heavy_strand_origin_start, val_light_strand_origin_end, + val_light_strand_origin_start, val_mito_length, val_mito_name, val_mitosalt_flank, From 08c8d58ecd547c281c074bc2bc8aae409c53f2e1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 7 Apr 2026 23:20:38 +0200 Subject: [PATCH 582/872] exclude alt --- conf/modules/align.config | 13 +++++- main.nf | 3 ++ nextflow.config | 1 + nextflow_schema.json | 5 +++ subworkflows/local/align/main.nf | 22 +++++++++-- subworkflows/local/align/tests/main.nf.test | 44 ++++++++++++--------- tests/default.nf.test.snap | 2 +- workflows/raredisease.nf | 2 + 8 files changed, 66 insertions(+), 26 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 7cc52726f..000ddb41d 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -21,8 +21,17 @@ process{ ].join(' ').trim() } } - withName: '.*ALIGN:SAMTOOLS_VIEW' { + withName: '.*ALIGN:SAMTOOLS_VIEW_CONVERTTOCRAM' { ext.args = { '--output-fmt cram' } - ext.prefix = { "${meta.id}_sort_md" } + ext.prefix = { params.exclude_alt ? "${meta.id}_sort_md_primary_contigs" : "${meta.id}_sort_md" } + } + + withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { + ext.args2 = { + params.genome == 'GRCh38' + ? ((1..22).collect { "chr${it}" } + ['chrX', 'chrY', 'chrM']).join(' ') + : ((1..22).collect { "${it}" } + ['X', 'Y', 'MT' ]).join(' ') + } + ext.prefix = { "${meta.id}_sort_md_primary_contigs" } } } diff --git a/main.nf b/main.nf index eccf5b0e3..5e903f2e2 100644 --- a/main.nf +++ b/main.nf @@ -51,6 +51,7 @@ workflow NFCORE_RAREDISEASE { val_cadd_resources val_call_interval val_concatenate_snv_calls + val_exclude_alt val_extract_alignments val_fai val_fasta @@ -469,6 +470,7 @@ workflow NFCORE_RAREDISEASE { val_analysis_type, val_cadd_resources, val_concatenate_snv_calls, + val_exclude_alt, val_extract_alignments, val_genome, val_heavy_strand_origin_end, @@ -554,6 +556,7 @@ workflow { params.cadd_resources, params.call_interval, params.concatenate_snv_calls, + params.exclude_alt, params.extract_alignments, params.fai, params.fasta, diff --git a/nextflow.config b/nextflow.config index a5b0cc24a..ea44923dc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,6 +29,7 @@ params { analysis_type = 'wgs' bait_padding = 100 concatenate_snv_calls = false + exclude_alt = false extract_alignments = false mt_subsample_approach = 'reads' mt_subsample_reads = 18000 diff --git a/nextflow_schema.json b/nextflow_schema.json index e1df3010e..76a10d9a5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -536,6 +536,11 @@ "description": "Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls", "fa_icon": "fas fa-toggle-on" }, + "exclude_alt": { + "type": "boolean", + "description": "After aligning the reads to a reference, remove alignments to alt contigs using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM).", + "fa_icon": "fas fa-toggle-on" + }, "extract_alignments": { "type": "boolean", "description": "After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.", diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f61c92e04..db9be1170 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -5,7 +5,8 @@ include { FASTP } from '../../../modules/nf-core/fastp/main' include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' include { ALIGN_SENTIEON } from '../align_sentieon' -include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_CONVERTTOCRAM } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' include { ALIGN_MT } from '../align_MT' include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' @@ -33,6 +34,7 @@ workflow ALIGN { skip_fastp // boolean val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_exclude_alt // boolean val_extract_alignments // boolean val_mbuffer_mem // integer: [mandatory] memory in megabytes val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' @@ -120,6 +122,18 @@ workflow ALIGN { ch_genome_marked_bai = channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + if (val_exclude_alt) { + SAMTOOLS_VIEW_EXCLUDE_ALT( + ch_genome_marked_bam_bai, + ch_genome_fasta.map { meta, fasta -> [meta, fasta, []] }, + [], + 'bai' + ) + ch_genome_marked_bam = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam + ch_genome_marked_bai = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai + ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + } + // PREPARING READS FOR MT ALIGNMENT if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { @@ -160,9 +174,9 @@ workflow ALIGN { } if (val_save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) - ch_cram_publish = SAMTOOLS_VIEW.out.cram - .mix(SAMTOOLS_VIEW.out.crai) + SAMTOOLS_VIEW_CONVERTTOCRAM( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_publish = SAMTOOLS_VIEW_CONVERTTOCRAM.out.cram + .mix(SAMTOOLS_VIEW_CONVERTTOCRAM.out.crai) .map { meta, value -> ['alignment/', [meta, value]] } } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index afb6b485d..2ba598e1f 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_workflow { tag "fastp" tag "samtools/view" + tag "samtools/view_exclude_alt" config "./nextflow.config" @@ -60,6 +61,8 @@ nextflow_workflow { when { params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + exclude_alt = true + genome = "GRCh38" platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -110,13 +113,14 @@ nextflow_workflow { input[18] = false input[19] = "bwamem2" input[20] = "wgs" - input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = true + input[21] = true + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true """ } } @@ -215,12 +219,13 @@ nextflow_workflow { input[19] = "bwamem2" input[20] = "wes" input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = false + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = false """ } } @@ -311,12 +316,13 @@ nextflow_workflow { input[19] = "bwameme" input[20] = "wgs" input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = true + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true """ } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index aa47538f1..1adf9d2f3 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -928,7 +928,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-30T18:50:54.008055201", + "timestamp": "2026-04-07T22:49:04.94908105", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index cdeba0f99..da7fc7f47 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -181,6 +181,7 @@ workflow RAREDISEASE { val_analysis_type val_cadd_resources val_concatenate_snv_calls + val_exclude_alt val_extract_alignments val_genome val_heavy_strand_origin_end @@ -305,6 +306,7 @@ workflow RAREDISEASE { skip_fastp, val_aligner, val_analysis_type, + val_exclude_alt, val_extract_alignments, val_mbuffer_mem, val_mt_aligner, From 6000085d64e5eceaadd824dda4a2ba94f72b35d5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 10:10:51 +0200 Subject: [PATCH 583/872] Add exlude alt --- conf/modules/align.config | 13 +++++- docs/output.md | 4 +- docs/usage.md | 2 + main.nf | 3 ++ nextflow.config | 1 + nextflow_schema.json | 5 +++ subworkflows/local/align/main.nf | 22 +++++++++-- subworkflows/local/align/tests/main.nf.test | 44 ++++++++++++--------- tests/default.nf.test.snap | 2 +- workflows/raredisease.nf | 2 + 10 files changed, 70 insertions(+), 28 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 7cc52726f..000ddb41d 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -21,8 +21,17 @@ process{ ].join(' ').trim() } } - withName: '.*ALIGN:SAMTOOLS_VIEW' { + withName: '.*ALIGN:SAMTOOLS_VIEW_CONVERTTOCRAM' { ext.args = { '--output-fmt cram' } - ext.prefix = { "${meta.id}_sort_md" } + ext.prefix = { params.exclude_alt ? "${meta.id}_sort_md_primary_contigs" : "${meta.id}_sort_md" } + } + + withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { + ext.args2 = { + params.genome == 'GRCh38' + ? ((1..22).collect { "chr${it}" } + ['chrX', 'chrY', 'chrM']).join(' ') + : ((1..22).collect { "${it}" } + ['X', 'Y', 'MT' ]).join(' ') + } + ext.prefix = { "${meta.id}_sort_md_primary_contigs" } } } diff --git a/docs/output.md b/docs/output.md index 00b5a4572..c748f17f3 100644 --- a/docs/output.md +++ b/docs/output.md @@ -106,7 +106,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files from Alignment - `{outputdir}/alignment/` - - `*.bam|*.cram`: Alignment file in bam/cram format. + - `*.bam|*.cram`: Alignment file in bam/cram format. When `--exclude_alt` is set, the file is filtered to primary chromosomes only (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM), which will also restrict variant calling to those chromosomes. - `*.bai|*.crai`: Index of the corresponding bam/cram file. - `*.txt`: Text file containing the dedup metrics. @@ -119,7 +119,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files from Alignment - `{outputdir}/alignment/` - - `*.bam|*.cram`: Alignment file in bam/cram format. + - `*.bam|*.cram`: Alignment file in bam/cram format. When `--exclude_alt` is set, the file is filtered to primary chromosomes only (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM), which will also restrict variant calling to those chromosomes. - `*.bai|*.crai`: Index of the corresponding bam/cram file. - `*.metrics`: Text file containing the dedup metrics. diff --git a/docs/usage.md b/docs/usage.md index b34f80285..54c39bd50 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -210,6 +210,7 @@ The mandatory and optional parameters for each category are tabulated below. | | min_trimmed_length6 | | | extract_alignments | | | restrict_to_contigs7 | +| | exclude_alt8 | 1Default value is bwamem2. Other alternatives are bwa, bwameme and sentieon (requires valid Sentieon license ).
    2Analysis set reference genome in fasta format, first 25 contigs need to be chromosome 1-22, X, Y and the mitochondria.
    @@ -218,6 +219,7 @@ The mandatory and optional parameters for each category are tabulated below. 5Used only by Sentieon.
    6Default value is 40. Used only by fastp.
    7Used to limit your analysis to specific contigs. Can be used to remove alignments to unplaced contigs to minimize potential errors. This parameter should be used in conjunction with the `extract_alignments` parameter.
    +8When set to true, alignments to alt/unplaced contigs are removed after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that this will affect all downstream variant calling, as variants will only be called on these primary chromosomes.
    ##### 2. QC stats from the alignment files diff --git a/main.nf b/main.nf index eccf5b0e3..5e903f2e2 100644 --- a/main.nf +++ b/main.nf @@ -51,6 +51,7 @@ workflow NFCORE_RAREDISEASE { val_cadd_resources val_call_interval val_concatenate_snv_calls + val_exclude_alt val_extract_alignments val_fai val_fasta @@ -469,6 +470,7 @@ workflow NFCORE_RAREDISEASE { val_analysis_type, val_cadd_resources, val_concatenate_snv_calls, + val_exclude_alt, val_extract_alignments, val_genome, val_heavy_strand_origin_end, @@ -554,6 +556,7 @@ workflow { params.cadd_resources, params.call_interval, params.concatenate_snv_calls, + params.exclude_alt, params.extract_alignments, params.fai, params.fasta, diff --git a/nextflow.config b/nextflow.config index a5b0cc24a..ea44923dc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,6 +29,7 @@ params { analysis_type = 'wgs' bait_padding = 100 concatenate_snv_calls = false + exclude_alt = false extract_alignments = false mt_subsample_approach = 'reads' mt_subsample_reads = 18000 diff --git a/nextflow_schema.json b/nextflow_schema.json index e1df3010e..76a10d9a5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -536,6 +536,11 @@ "description": "Specifies whether to generate a concatenated VCF file containing both nuclear & mitochondrial snv calls", "fa_icon": "fas fa-toggle-on" }, + "exclude_alt": { + "type": "boolean", + "description": "After aligning the reads to a reference, remove alignments to alt contigs using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM).", + "fa_icon": "fas fa-toggle-on" + }, "extract_alignments": { "type": "boolean", "description": "After aligning the reads to a reference, extract alignments from specific regions/contigs and restrict the analysis to those regions/contigs.", diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f61c92e04..db9be1170 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -5,7 +5,8 @@ include { FASTP } from '../../../modules/nf-core/fastp/main' include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' include { ALIGN_SENTIEON } from '../align_sentieon' -include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_CONVERTTOCRAM } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' include { ALIGN_MT } from '../align_MT' include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' @@ -33,6 +34,7 @@ workflow ALIGN { skip_fastp // boolean val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_exclude_alt // boolean val_extract_alignments // boolean val_mbuffer_mem // integer: [mandatory] memory in megabytes val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' @@ -120,6 +122,18 @@ workflow ALIGN { ch_genome_marked_bai = channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + if (val_exclude_alt) { + SAMTOOLS_VIEW_EXCLUDE_ALT( + ch_genome_marked_bam_bai, + ch_genome_fasta.map { meta, fasta -> [meta, fasta, []] }, + [], + 'bai' + ) + ch_genome_marked_bam = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam + ch_genome_marked_bai = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai + ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + } + // PREPARING READS FOR MT ALIGNMENT if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { @@ -160,9 +174,9 @@ workflow ALIGN { } if (val_save_mapped_as_cram) { - SAMTOOLS_VIEW( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) - ch_cram_publish = SAMTOOLS_VIEW.out.cram - .mix(SAMTOOLS_VIEW.out.crai) + SAMTOOLS_VIEW_CONVERTTOCRAM( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_publish = SAMTOOLS_VIEW_CONVERTTOCRAM.out.cram + .mix(SAMTOOLS_VIEW_CONVERTTOCRAM.out.crai) .map { meta, value -> ['alignment/', [meta, value]] } } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index afb6b485d..2ba598e1f 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -13,6 +13,7 @@ nextflow_workflow { tag "fastp" tag "samtools/view" + tag "samtools/view_exclude_alt" config "./nextflow.config" @@ -60,6 +61,8 @@ nextflow_workflow { when { params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + exclude_alt = true + genome = "GRCh38" platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -110,13 +113,14 @@ nextflow_workflow { input[18] = false input[19] = "bwamem2" input[20] = "wgs" - input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = true + input[21] = true + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true """ } } @@ -215,12 +219,13 @@ nextflow_workflow { input[19] = "bwamem2" input[20] = "wes" input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = false + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = false """ } } @@ -311,12 +316,13 @@ nextflow_workflow { input[19] = "bwameme" input[20] = "wgs" input[21] = false - input[22] = 3072 - input[23] = "bwamem2" - input[24] = "illumina" - input[25] = false - input[26] = 4 - input[27] = true + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true """ } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index aa47538f1..1adf9d2f3 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -928,7 +928,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-30T18:50:54.008055201", + "timestamp": "2026-04-07T22:49:04.94908105", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index cdeba0f99..da7fc7f47 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -181,6 +181,7 @@ workflow RAREDISEASE { val_analysis_type val_cadd_resources val_concatenate_snv_calls + val_exclude_alt val_extract_alignments val_genome val_heavy_strand_origin_end @@ -305,6 +306,7 @@ workflow RAREDISEASE { skip_fastp, val_aligner, val_analysis_type, + val_exclude_alt, val_extract_alignments, val_mbuffer_mem, val_mt_aligner, From 0e76060601603cbc0cd955b5f527f965b20d3148 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 10:18:11 +0200 Subject: [PATCH 584/872] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ca989fce..f9bb04713 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add peddy --sites hg38 argument when running with GRCh38 [#799](https://github.com/nf-core/raredisease/pull/799) - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) +- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [[#](https://github.com/nf-core/raredisease/pull/)] ### `Changed` @@ -72,6 +73,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | bwa_as_fallback | | | | multiqc_samples | | | homoplasmy_af_threshold | +| | exclude_alt | ### Tool updates From b669b4d423bcb103299564499a8dc48d0923eb7e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 13:49:21 +0200 Subject: [PATCH 585/872] Fix tests --- subworkflows/local/align/main.nf | 34 +++++++++++-------- subworkflows/local/align/tests/main.nf.test | 2 +- .../local/align/tests/main.nf.test.snap | 26 +++++++------- .../local/align/tests/nextflow.config | 13 +++++-- 4 files changed, 45 insertions(+), 30 deletions(-) diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index db9be1170..340c6a4e1 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -118,22 +118,28 @@ workflow ALIGN { ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai } - ch_genome_marked_bam = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) - ch_genome_marked_bai = channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) - ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) - - if (val_exclude_alt) { - SAMTOOLS_VIEW_EXCLUDE_ALT( - ch_genome_marked_bam_bai, - ch_genome_fasta.map { meta, fasta -> [meta, fasta, []] }, - [], - 'bai' - ) - ch_genome_marked_bam = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam - ch_genome_marked_bai = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai - ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + ch_genome_marked_bam_initial = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) + ch_genome_marked_bai_initial = channel.empty().mix(ch_bwamem2_bai, ch_sentieon_bai, ch_input_bai) + ch_genome_marked_bam_bai_initial = ch_genome_marked_bam_initial.join(ch_genome_marked_bai_initial, failOnMismatch:true, failOnDuplicate:true) + + ch_branched = ch_genome_marked_bam_bai_initial.branch { meta, bam, bai -> + exclude_alt: val_exclude_alt + return [meta, bam, bai] + keep_all: true + return [meta, bam, bai] } + SAMTOOLS_VIEW_EXCLUDE_ALT( + ch_branched.exclude_alt, + ch_genome_fasta.map { meta, fasta -> [meta, fasta, []] }, + [], + 'bai' + ) + + ch_genome_marked_bam = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam : ch_branched.keep_all.map { meta, bam, bai -> [meta, bam] } + ch_genome_marked_bai = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai : ch_branched.keep_all.map { meta, bam, bai -> [meta, bai] } + ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) + // PREPARING READS FOR MT ALIGNMENT if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 2ba598e1f..cc6664a86 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -62,7 +62,7 @@ nextflow_workflow { params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' exclude_alt = true - genome = "GRCh38" + genome = "GRCh37" platform = "illumina" min_trimmed_length = 50 mito_name = "MT" diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index d1d0c7003..60d6419a7 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -7,22 +7,22 @@ "earlycasualcaiman.fastp.log", "earlycasualcaiman_R1.fastp.fastq.gz", "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sort_md.cram", - "earlycasualcaiman_sort_md.cram.crai", + "earlycasualcaiman_sort_md_primary_contigs.cram", + "earlycasualcaiman_sort_md_primary_contigs.cram.crai", "hugelymodelbat.fastp.html", "hugelymodelbat.fastp.json", "hugelymodelbat.fastp.log", "hugelymodelbat_R1.fastp.fastq.gz", "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sort_md.cram", - "hugelymodelbat_sort_md.cram.crai", + "hugelymodelbat_sort_md_primary_contigs.cram", + "hugelymodelbat_sort_md_primary_contigs.cram.crai", "slowlycivilbuck.fastp.html", "slowlycivilbuck.fastp.json", "slowlycivilbuck.fastp.log", "slowlycivilbuck_R1.fastp.fastq.gz", "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai" + "slowlycivilbuck_sort_md_primary_contigs.cram", + "slowlycivilbuck_sort_md_primary_contigs.cram.crai" ], [ [ @@ -41,8 +41,8 @@ "case_id": "justhusky" } }, - "d948b0bd18f6f6526f5d8832465e1542", - "earlycasualcaiman_sorted_md.bam.bai" + "bb547b29eca1afded4229826c774fc90", + "earlycasualcaiman_sort_md_primary_contigs.bam.bai" ], [ { @@ -60,8 +60,8 @@ "case_id": "justhusky" } }, - "2530fd24192b09084f45011703bd4954", - "hugelymodelbat_sorted_md.bam.bai" + "6f48b21e58c7450dd4db0bfc1268d687", + "hugelymodelbat_sort_md_primary_contigs.bam.bai" ], [ { @@ -79,8 +79,8 @@ "case_id": "justhusky" } }, - "cc1385671a27d394f628d2d7868eba80", - "slowlycivilbuck_sorted_md.bam.bai" + "e8431e5dc096f9636efd37ebfe9a5883", + "slowlycivilbuck_sort_md_primary_contigs.bam.bai" ] ], [ @@ -261,7 +261,7 @@ ] ] ], - "timestamp": "2026-03-13T14:53:02.154281647", + "timestamp": "2026-04-08T13:33:51.233648996", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index 4f13ba425..a36ae41b7 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -12,9 +12,18 @@ process { ].join(' ').trim() } } - withName: 'SAMTOOLS_VIEW' { + withName: 'SAMTOOLS_VIEW_CONVERTTOCRAM' { ext.args = { '--output-fmt cram' } - ext.prefix = { "${meta.id}_sorted_md" } + ext.prefix = { params.exclude_alt ? "${meta.id}_sorted_md_primary_contigs" : "${meta.id}_sorted_md" } + } + + withName: 'SAMTOOLS_VIEW_EXCLUDE_ALT' { + ext.args2 = { + params.genome == 'GRCh38' + ? ((1..22).collect { "chr${it}" } + ['chrX', 'chrY', 'chrM']).join(' ') + : ((1..22).collect { "${it}" } + ['X', 'Y', 'MT' ]).join(' ') + } + ext.prefix = { "${meta.id}_sorted_md_primary_contigs" } } withName: 'BWAMEM2_MEM' { From 55e9f8f20c730a5379c4cda8c07f93522a6e79d2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 13:54:11 +0200 Subject: [PATCH 586/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f9bb04713..43154de10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add peddy --sites hg38 argument when running with GRCh38 [#799](https://github.com/nf-core/raredisease/pull/799) - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) -- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [[#](https://github.com/nf-core/raredisease/pull/)] +- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] ### `Changed` From f790998d9dc875a59b0244f267fc361c4fdc3f19 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 14:26:47 +0200 Subject: [PATCH 587/872] Update config --- CHANGELOG.md | 1 + nextflow.config | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 43154de10..612330288 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -56,6 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Run MitoSAlt.pl from bin rather than within container [#775](https://github.com/nf-core/raredisease/pull/775) - Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove mitochondria/ and genome/ [#775](https://github.com/nf-core/raredisease/pull/775) - Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801) +- Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from the config since this has to be set outside the subworkflow [#804](https://github.com/nf-core/raredisease/pull/804) ### `Fixed` diff --git a/nextflow.config b/nextflow.config index ea44923dc..f284e10b1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -345,7 +345,6 @@ env { R_PROFILE_USER = "/.Rprofile" R_ENVIRON_USER = "/.Renviron" JULIA_DEPOT_PATH = "/usr/local/share/julia" - NXF_SINGULARITY_NEW_PID_NAMESPACE = false } // Set bash options From a61f969ee704b5507e107f4a50271c9d43d3958c Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 8 Apr 2026 15:19:48 +0200 Subject: [PATCH 588/872] Added stubtest for align_bwa_bwamem2_bwameme --- .../tests/main.nf.test | 104 ++++ .../tests/main.nf.test.snap | 454 +++++++++++++++++- 2 files changed, 556 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 7e64d0355..62cfd8893 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -138,4 +138,108 @@ nextflow_workflow { } } + test("align bwamem2, stub") { + + setup { + run("BWAMEM2_INDEX") { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = [[:],[]] + input[1] = BWAMEM2_INDEX.out.index + input[2] = [[:],[]] + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[6] = "bwamem2" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + } + + test("align bwameme, stub") { + + setup { + run("BWAMEME_INDEX") { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = [[:],[]] + input[1] = [[:],[]] + input[2] = BWAMEME_INDEX.out.index + input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[5] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[6] = "bwameme" + input[7] = true + input[8] = 3072 + input[9] = "illumina" + input[10] = 4 + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + } + } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 7632f79b8..abcf802fa 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -37,7 +37,457 @@ ] ] ], - "timestamp": "2026-03-13T15:04:33.885203481", + "timestamp": "2026-04-08T14:47:44.537374", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align bwamem2, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T14:48:42.172404", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align bwameme, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "stats": [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T14:49:01.39982", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -81,7 +531,7 @@ ] ] ], - "timestamp": "2026-03-13T15:05:20.75721248", + "timestamp": "2026-04-08T14:48:21.046802", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 8888e71ba405c161e053325bd737848a1163cdf5 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 8 Apr 2026 16:18:10 +0200 Subject: [PATCH 589/872] Added stubtest for align_MT --- .../local/align_MT/tests/main.nf.test | 142 ++++++ .../local/align_MT/tests/main.nf.test.snap | 422 ++++++++++++++++++ 2 files changed, 564 insertions(+) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 5441f4256..3318b260c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -150,4 +150,146 @@ nextflow_workflow { } } + + + test("align mt - bwamem2, stub") { + + setup { + run("BWAMEM2_INDEX", alias: 'MT_MEM2') { + script "modules/nf-core/bwamem2/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + outdir = "$outputDir" + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = [[:],[]] + input[1] = MT_MEM2.out.index.collect() + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[6] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[7] = "bwamem2" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + + test("align mt - bwa, stub") { + + setup { + run("BWA_INDEX", alias: 'MT_BWA') { + script "modules/nf-core/bwa/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'mt'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference_mt.fa', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + outdir = "$outputDir" + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + } + workflow { + """ + input[0] = MT_BWA.out.index.collect() + input[1] = [[:],[]] + input[2] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)]]) + input[3] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]]) + input[4] = channel.value([[id:'mt'], [file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]]) + input[5] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mt_2.fastq.gz', checkIfExists: true)] + ] + ) + input[6] = channel.of( + [ + [ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/hugelymodelbat_mtreverted.bam', checkIfExists: true)] + ], + [ + [ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ file(params.pipelines_testdata_base_path + '/testdata/slowlycivilbuck_mtreverted.bam', checkIfExists: true)] + ] + ) + input[7] = 'bwa' + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } diff --git a/subworkflows/local/align_MT/tests/main.nf.test.snap b/subworkflows/local/align_MT/tests/main.nf.test.snap index 53cd47acd..f122b005c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test.snap +++ b/subworkflows/local/align_MT/tests/main.nf.test.snap @@ -1,4 +1,426 @@ { + "align mt - bwamem2, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T15:49:24.73309", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "align mt - bwa, stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck_sorted_merged_md_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-04-08T15:51:10.749046", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "align mt - bwamem2": { "content": [ { From ef61d0e40117eeebcc524256e7fb503b242c86e9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 16:45:56 +0200 Subject: [PATCH 590/872] Fix warnings --- nextflow.config | 1 + nextflow_schema.json | 5 +++++ workflows/raredisease.nf | 4 ++-- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index f284e10b1..8c2963df3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -59,6 +59,7 @@ params { gnomad_af = null gnomad_af_idx = null hisat2 = null + hisat2_build_memory = null intervals_wgs = null intervals_y = null known_dbsnp = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 76a10d9a5..dfc782826 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -761,6 +761,11 @@ "hisat2": { "type": "string" }, + "hisat2_build_memory": { + "type": "string", + "description": "Minimum memory required to build HISAT2 index with splice sites and exons. If available memory is below this threshold, a simpler index is built without splice sites.", + "fa_icon": "fas fa-memory" + }, "mitosalt_breakspan": { "type": "integer", "default": 15, diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index da7fc7f47..a772557ef 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -590,7 +590,7 @@ workflow RAREDISEASE { */ if (!skip_sv_calling) { - channel.of(val_mitosalt_breakspan, + channel.of([val_mitosalt_breakspan, val_mitosalt_breakthreshold, val_mitosalt_cluster_threshold, val_mitosalt_deletion_threshold_max, @@ -601,7 +601,7 @@ workflow RAREDISEASE { val_mitosalt_score_threshold, val_mitosalt_sizelimit, val_mitosalt_split_distance_threshold, - val_mitosalt_split_length) + val_mitosalt_split_length]) .set{ ch_mitosalt_config } CALL_STRUCTURAL_VARIANTS ( From 0713998ccc855e6430eb7428ff953f0839aa05bd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 17:04:46 +0200 Subject: [PATCH 591/872] Fix syntax warnings --- conf/modules/align.config | 4 +- main.nf | 2 +- subworkflows/local/align/main.nf | 4 +- .../local/align/tests/nextflow.config | 4 +- .../annotate_structural_variants/main.nf | 2 +- .../local/call_structural_variants/main.nf | 2 +- subworkflows/local/call_sv_MT/main.nf | 2 +- subworkflows/local/call_sv_cnvnator/main.nf | 1 - .../local/call_sv_cnvnator/tests/main.nf.test | 6 +- subworkflows/local/qc_bam/main.nf | 1 - subworkflows/local/qc_bam/tests/main.nf.test | 64 ++++++++----------- .../nf-core/utils_nfschema_plugin/main.nf | 2 +- workflows/raredisease.nf | 1 - 13 files changed, 39 insertions(+), 56 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 000ddb41d..dc52fa708 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -29,8 +29,8 @@ process{ withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { ext.args2 = { params.genome == 'GRCh38' - ? ((1..22).collect { "chr${it}" } + ['chrX', 'chrY', 'chrM']).join(' ') - : ((1..22).collect { "${it}" } + ['X', 'Y', 'MT' ]).join(' ') + ? ((1..22).collect { n -> "chr${n}" } + ['chrX', 'chrY', 'chrM']).join(' ') + : ((1..22).collect { n -> "${n}" } + ['X', 'Y', 'MT' ]).join(' ') } ext.prefix = { "${meta.id}_sort_md_primary_contigs" } } diff --git a/main.nf b/main.nf index 5e903f2e2..ff805ea88 100644 --- a/main.nf +++ b/main.nf @@ -666,7 +666,7 @@ workflow { output { subworkflow_results { - path { destination, value -> destination } + path { destination, _value -> destination } } } diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 1e34145f3..c31251d21 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -136,8 +136,8 @@ workflow ALIGN { 'bai' ) - ch_genome_marked_bam = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam : ch_branched.keep_all.map { meta, bam, bai -> [meta, bam] } - ch_genome_marked_bai = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai : ch_branched.keep_all.map { meta, bam, bai -> [meta, bai] } + ch_genome_marked_bam = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam : ch_branched.keep_all.map { meta, bam, _bai -> [meta, bam] } + ch_genome_marked_bai = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai : ch_branched.keep_all.map { meta, _bam, bai -> [meta, bai] } ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) if (val_exclude_alt) { diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index a36ae41b7..cd1d005a5 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -20,8 +20,8 @@ process { withName: 'SAMTOOLS_VIEW_EXCLUDE_ALT' { ext.args2 = { params.genome == 'GRCh38' - ? ((1..22).collect { "chr${it}" } + ['chrX', 'chrY', 'chrM']).join(' ') - : ((1..22).collect { "${it}" } + ['X', 'Y', 'MT' ]).join(' ') + ? ((1..22).collect { n -> "chr${n}" } + ['chrX', 'chrY', 'chrM']).join(' ') + : ((1..22).collect { n -> "${n}" } + ['X', 'Y', 'MT' ]).join(' ') } ext.prefix = { "${meta.id}_sorted_md_primary_contigs" } } diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index 3c226a9d8..b24d7f4f9 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -95,7 +95,7 @@ workflow ANNOTATE_STRUCTURAL_VARIANTS { ch_publish = ENSEMBLVEP_SV.out.vcf .mix(ENSEMBLVEP_SV.out.tbi) - .mix(ENSEMBLVEP_SV.out.report.map{ meta, process, vep, html -> return [meta, html] }) + .mix(ENSEMBLVEP_SV.out.report.map{ meta, _process, _vep, html -> return [meta, html] }) .map { meta, value -> ['annotate_sv/', [meta, value]] } emit: diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 19abff24f..84994cc96 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -71,7 +71,7 @@ workflow CALL_STRUCTURAL_VARIANTS { .collect{ _meta, vcf -> vcf } .set { ch_tiddit_vcf } - CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_genome_fai, ch_case_info) + CALL_SV_CNVNATOR (ch_genome_bam_bai, ch_genome_fasta, ch_case_info) .vcf .collect{ _meta, vcf -> vcf } .set { ch_cnvnator_vcf } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 9f31c4cdc..38fffa551 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -142,7 +142,7 @@ workflow CALL_SV_MT { // Saltshaker only runs if there are mitosalt calls. We update priority list when the // saltshaker vcf is created so the priority matches the list of vcfs that will be merged later ch_svcaller_priority = ch_svcaller_priority - .concat(ch_saltshaker_vcf.map{ _ -> ["mitosalt"] }) + .concat(ch_saltshaker_vcf.map{ _it -> ["mitosalt"] }) .collect() } diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 0516419b4..6355fd953 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -17,7 +17,6 @@ workflow CALL_SV_CNVNATOR { take: ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_case_info // channel: [mandatory] [ val(case_info) ] main: diff --git a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test index e83917364..aae06a47f 100644 --- a/subworkflows/local/call_sv_cnvnator/tests/main.nf.test +++ b/subworkflows/local/call_sv_cnvnator/tests/main.nf.test @@ -29,8 +29,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ) input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[3] = channel.of([id:'justhusky']) + input[2] = channel.of([id:'justhusky']) """ } } @@ -61,8 +60,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ) input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[3] = channel.of([id:'justhusky']) + input[2] = channel.of([id:'justhusky']) """ } } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 3b57f6900..b63fa5b8a 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -19,7 +19,6 @@ include { VERIFYBAMID_VERIFYBAMID2 } from '../.. workflow QC_BAM { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_bait_intervals // channel: [mandatory] [ path(intervals_list) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 184eabc40..522858f9e 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -32,34 +32,28 @@ nextflow_workflow { workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'bwamem2' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'bwamem2' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } @@ -112,34 +106,28 @@ nextflow_workflow { workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'sentieon' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'sentieon' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8d..e69b7aaec 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + params.help instanceof String && params.help != "true" ? params.help : "", ) exit 0 } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a772557ef..a51f5d23c 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -338,7 +338,6 @@ workflow RAREDISEASE { // BAM QUALITY CHECK // QC_BAM ( - ch_mapped.genome_marked_bam, ch_mapped.genome_marked_bam_bai, ch_bait_intervals, ch_genome_chrsizes, From 4c8e6ecdd4d93550c3e9dfd37f19b95c1c0e40c5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 18:31:17 +0200 Subject: [PATCH 592/872] Update filter logic to fetch pairs as well. --- conf/modules/align.config | 1 + subworkflows/local/align/main.nf | 12 ------------ subworkflows/local/align/tests/nextflow.config | 1 + 3 files changed, 2 insertions(+), 12 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index dc52fa708..64628c2bd 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -27,6 +27,7 @@ process{ } withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { + ext.args = { '--fetch-pairs' } ext.args2 = { params.genome == 'GRCh38' ? ((1..22).collect { n -> "chr${n}" } + ['chrX', 'chrY', 'chrM']).join(' ') diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index c31251d21..b889566d9 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -140,18 +140,6 @@ workflow ALIGN { ch_genome_marked_bai = val_exclude_alt ? SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai : ch_branched.keep_all.map { meta, _bam, bai -> [meta, bai] } ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) - if (val_exclude_alt) { - SAMTOOLS_VIEW_EXCLUDE_ALT( - ch_genome_marked_bam_bai, - ch_genome_fasta.map { meta, fasta -> [meta, fasta, []] }, - [], - 'bai' - ) - ch_genome_marked_bam = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bam - ch_genome_marked_bai = SAMTOOLS_VIEW_EXCLUDE_ALT.out.bai - ch_genome_marked_bam_bai = ch_genome_marked_bam.join(ch_genome_marked_bai, failOnMismatch:true, failOnDuplicate:true) - } - // PREPARING READS FOR MT ALIGNMENT if (val_analysis_type.matches("wgs|mito") || val_run_mt_for_wes) { diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index cd1d005a5..f626ed73b 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -18,6 +18,7 @@ process { } withName: 'SAMTOOLS_VIEW_EXCLUDE_ALT' { + ext.args = { '--fetch-pairs' } ext.args2 = { params.genome == 'GRCh38' ? ((1..22).collect { n -> "chr${n}" } + ['chrX', 'chrY', 'chrM']).join(' ') From 15ea02993d431be5202d576b00a4de655e10d359 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 8 Apr 2026 19:01:14 +0200 Subject: [PATCH 593/872] Fix ml model default --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 8c2963df3..fab089aaa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,7 +123,7 @@ params { vep_cache_version = 112 // sentieon Defaults - ml_model = '' + ml_model = null // Dnascope SNV calling sentieon_dnascope_pcr_indel_model = 'CONSERVATIVE' From 456776cff6549967b36d74a51e84414bd7c7a365 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 13 Apr 2026 12:08:45 +0200 Subject: [PATCH 594/872] Update upd logic --- CHANGELOG.md | 1 + .../local/annotate_genome_snvs/main.nf | 23 +- .../annotate_genome_snvs/tests/main.nf.test | 64 ++- .../tests/main.nf.test.snap | 495 +++++++++++++++++- workflows/raredisease.nf | 1 + 5 files changed, 561 insertions(+), 23 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 612330288..0a5a54861 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] +- Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#805](https://github.com/nf-core/raredisease/pull/805) ### `Changed` diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 5ca1797bd..6f490d13a 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -35,14 +35,16 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] + val_analysis_type // string: wgs, wes, or mito val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 val_vep_cache_version // string: vep version ex: 107 main: - ch_cadd_vcf = channel.empty() - ch_vcf_scatter_in = channel.empty() - ch_vep_in = channel.empty() + ch_cadd_vcf = channel.empty() + ch_vcf_scatter_in = channel.empty() + ch_vep_in = channel.empty() + ch_chromograph_publish = channel.empty() ch_vcf .filter { meta, _vcf, _tbi -> @@ -176,10 +178,14 @@ workflow ANNOTATE_GENOME_SNVS { } .set { ch_upd_in } - UPD_SITES(ch_upd_in) - UPD_REGIONS(ch_upd_in) - CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed) - CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]]) + if (val_analysis_type.equals("wgs")) { + UPD_SITES(ch_upd_in) + UPD_REGIONS(ch_upd_in) + CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed) + CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]]) + ch_chromograph_publish = CHROMOGRAPH_SITES.out.plots + .mix(CHROMOGRAPH_REGIONS.out.plots) + } BCFTOOLS_CONCAT.out.vcf .map { meta, vcf -> [meta - meta.subMap('prefix'), vcf] } @@ -193,8 +199,7 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) - ch_publish = CHROMOGRAPH_SITES.out.plots - .mix(CHROMOGRAPH_REGIONS.out.plots) + ch_publish = ch_chromograph_publish .mix(ch_concat_vcf_out) .mix(ch_concat_tbi_out) .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 323262893..0b6b95c53 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_workflow { config "./nextflow.config" - test("ANNOTATE_GENOME_SNVS - GRCh37, stub") { + test("ANNOTATE_GENOME_SNVS - GRCh37, wgs, stub") { options "-stub" @@ -38,7 +38,7 @@ nextflow_workflow { input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) input[8] = channel.of([ - [id:'justhusky', probands:['earlycasualcaiman'], upd_children:[], mother:'', father:''], + [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) @@ -48,9 +48,10 @@ nextflow_workflow { input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() input[14] = channel.value([]) - input[15] = null - input[16] = 'GRCh37' - input[17] = 107 + input[15] = 'wgs' + input[16] = null + input[17] = 'GRCh37' + input[18] = 107 """ } } @@ -76,4 +77,57 @@ nextflow_workflow { ) } } + + test("ANNOTATE_GENOME_SNVS - GRCh37, wes, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[1] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = channel.value([[],[]]) + input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([ + [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ]) + input[9] = channel.value([[]]) + input[10] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[11] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[14] = channel.value([]) + input[15] = 'wes' + input[16] = null + input[17] = 'GRCh37' + input[18] = 107 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } + ).match() } + ) + } + } } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index a5435526a..bbcbf5aa3 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "ANNOTATE_GENOME_SNVS - GRCh37, stub": { + "ANNOTATE_GENOME_SNVS - GRCh37, wes, stub": { "content": [ [ [ @@ -12,7 +12,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -31,7 +31,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -138,7 +138,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -155,7 +155,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -263,7 +263,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -280,7 +280,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -300,7 +300,7 @@ "earlycasualcaiman" ], "upd_children": [ - + "earlycasualcaiman" ], "mother": "", "father": "" @@ -319,7 +319,484 @@ "earlycasualcaiman" ], "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ] + ], + "timestamp": "2026-04-13T12:05:20.748196158", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "ANNOTATE_GENOME_SNVS - GRCh37, wgs, stub": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + 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"earlycasualcaiman_upd_sites.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + "annotate_snv/genome/", + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + [ + "tbi", + [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" + ], + "mother": "", + "father": "" + }, + "justhusky_rhocall_filter_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "vcf_ann", + [ + [ + { + "id": "justhusky", + "probands": [ + "earlycasualcaiman" + ], + "upd_children": [ + "earlycasualcaiman" ], "mother": "", "father": "" @@ -330,7 +807,7 @@ ] ] ], - "timestamp": "2026-03-17T22:35:10.37613529", + "timestamp": "2026-04-13T12:04:20.194067577", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a51f5d23c..a80ecce95 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -457,6 +457,7 @@ workflow RAREDISEASE { ch_vcfanno_toml, ch_vep_cache, ch_vep_extra_files, + val_analysis_type, val_cadd_resources, val_genome, val_vep_cache_version From 7c635b9f7cbe9f0db53947c97425fe73fa6912ad Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 13 Apr 2026 12:13:14 +0200 Subject: [PATCH 595/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a5a54861..f0f41604a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,7 +27,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] -- Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#805](https://github.com/nf-core/raredisease/pull/805) ### `Changed` @@ -58,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Include mitochonrdial SV calls in combined SV vcf, change call_sv output directory structure to remove mitochondria/ and genome/ [#775](https://github.com/nf-core/raredisease/pull/775) - Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801) - Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from the config since this has to be set outside the subworkflow [#804](https://github.com/nf-core/raredisease/pull/804) +- Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#806](https://github.com/nf-core/raredisease/pull/806) ### `Fixed` From e76f126aa7c4f48877264d28d30a492030ff802f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 13 Apr 2026 14:21:40 +0200 Subject: [PATCH 596/872] Update snapshot --- tests/default.nf.test.snap | 6 +----- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1adf9d2f3..0535fb641 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -674,14 +674,10 @@ "call_sv/earlycasualcaiman.saltshaker.png", "call_sv/earlycasualcaiman.saltshaker_classify.txt", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/hugelymodelbat.saltshaker.png", - "call_sv/hugelymodelbat.saltshaker_classify.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", - "call_sv/slowlycivilbuck.saltshaker.png", - "call_sv/slowlycivilbuck.saltshaker_classify.txt", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -928,7 +924,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-07T22:49:04.94908105", + "timestamp": "2026-04-13T14:02:49.746679555", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 57706f08e..25e6c4651 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 784, + 773, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -844,7 +844,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-03-30T18:57:15.672289796", + "timestamp": "2026-04-13T13:41:50.485130892", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 2960126f9..1337bdffe 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 365, + 354, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -655,7 +655,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-03-30T19:01:02.542705551", + "timestamp": "2026-04-13T13:45:35.515919262", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 874d2a2c56e218b47456892942557976f57e7696 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 13 Apr 2026 16:49:07 +0200 Subject: [PATCH 597/872] Add save mapped options --- CHANGELOG.md | 4 +++ conf/modules/align.config | 9 ++++-- docs/output.md | 4 +-- main.nf | 16 ++++++++-- nextflow.config | 3 +- nextflow_schema.json | 9 ++++-- ro-crate-metadata.json | 2 +- subworkflows/local/align/main.nf | 31 +++++++++++++------ subworkflows/local/align/tests/main.nf.test | 6 ++-- .../local/align_sentieon/tests/main.nf.test | 3 +- workflows/raredisease.nf | 6 ++-- 11 files changed, 68 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 612330288..3ccd56b27 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] +- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) ### `Changed` @@ -75,6 +76,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | | multiqc_samples | | | homoplasmy_af_threshold | | | exclude_alt | +| save_mapped_as_cram | | +| | save_all_mapped_as_cram | +| | save_noalt_mapped_as_cram | ### Tool updates diff --git a/conf/modules/align.config b/conf/modules/align.config index 64628c2bd..074fd09c1 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -21,9 +21,14 @@ process{ ].join(' ').trim() } } - withName: '.*ALIGN:SAMTOOLS_VIEW_CONVERTTOCRAM' { + withName: '.*ALIGN:CONVERTTOCRAM_ALTFILTERED' { ext.args = { '--output-fmt cram' } - ext.prefix = { params.exclude_alt ? "${meta.id}_sort_md_primary_contigs" : "${meta.id}_sort_md" } + ext.prefix = { "${meta.id}_sort_md_primary_contigs" } + } + + withName: '.*ALIGN:CONVERTTOCRAM_UNFILTERED' { + ext.args = { '--output-fmt cram' } + ext.prefix = { "${meta.id}_sort_md" } } withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { diff --git a/docs/output.md b/docs/output.md index c748f17f3..b9900eb37 100644 --- a/docs/output.md +++ b/docs/output.md @@ -100,7 +100,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ##### Picard's MarkDuplicates -[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2, bwameme and bwa are processed by this tool. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true. +[Picard MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) is used for marking PCR duplicates that can occur during library amplification. This is essential as the presence of such duplicates results in false inflated coverages, which in turn can lead to overly-confident genotyping calls during variant calling. Only reads aligned by Bwa-mem2, bwameme and bwa are processed by this tool. By default, alignment files are published in bam format. To publish cram files instead, use `--save_all_mapped_as_cram` for the full (unfiltered) alignment, or `--save_noalt_mapped_as_cram` for the alt-filtered alignment (requires `--exclude_alt`).
    Output files from Alignment @@ -113,7 +113,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ##### Sentieon Dedup -[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm. By default, alignment files are published in bam format. If you would like to store cram files instead, set `--save_mapped_as_cram` to true. +[Sentieon Dedup](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/#remove-or-mark-duplicates) is the algorithm used by Sentieon's driver to remove duplicate reads. Only reads aligned by Sentieon's implementation of bwa are processed by this algorithm. By default, alignment files are published in bam format. To publish cram files instead, use `--save_all_mapped_as_cram` for the full (unfiltered) alignment, or `--save_noalt_mapped_as_cram` for the alt-filtered alignment (requires `--exclude_alt`).
    Output files from Alignment diff --git a/main.nf b/main.nf index ff805ea88..a068f44d2 100644 --- a/main.nf +++ b/main.nf @@ -110,7 +110,8 @@ workflow NFCORE_RAREDISEASE { val_sambamba_regions val_sample_id_map val_samtools_sort_threads - val_save_mapped_as_cram + val_save_all_mapped_as_cram + val_save_noalt_mapped_as_cram val_save_reference val_score_config_mt val_score_config_snv @@ -331,6 +332,13 @@ workflow NFCORE_RAREDISEASE { skip_sv_calling = parseSkipList(val_skip_subworkflows, 'sv_calling') skip_generate_clinical_set = parseSkipList(val_skip_subworkflows, 'generate_clinical_set') + // + // Validate parameter combinations + // + if (val_save_noalt_mapped_as_cram && !val_exclude_alt) { + error("save_noalt_mapped_as_cram requires exclude_alt to be set to true") + } + // // SV caller priority // @@ -504,7 +512,8 @@ workflow NFCORE_RAREDISEASE { val_run_rtgvcfeval, val_sample_id_map, val_samtools_sort_threads, - val_save_mapped_as_cram, + val_save_all_mapped_as_cram, + val_save_noalt_mapped_as_cram, val_svdb_query_bedpedbs, val_svdb_query_dbs, val_target_bed, @@ -615,7 +624,8 @@ workflow { params.sambamba_regions, params.sample_id_map, params.samtools_sort_threads, - params.save_mapped_as_cram, + params.save_all_mapped_as_cram, + params.save_noalt_mapped_as_cram, params.save_reference, params.score_config_mt, params.score_config_snv, diff --git a/nextflow.config b/nextflow.config index fab089aaa..aa280a8b4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,7 +36,8 @@ params { restrict_to_contigs = null run_mt_for_wes = false run_rtgvcfeval = false - save_mapped_as_cram = false + save_all_mapped_as_cram = false + save_noalt_mapped_as_cram = false scatter_count = 20 skip_tools = null skip_subworkflows = null diff --git a/nextflow_schema.json b/nextflow_schema.json index dfc782826..ec4b4fd34 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -581,9 +581,14 @@ "description": "Specifies whether to run rtgtools' vcfeval", "fa_icon": "fas fa-toggle-on" }, - "save_mapped_as_cram": { + "save_all_mapped_as_cram": { "type": "boolean", - "description": "Specifies whether to generate and publish alignment files as cram instead of bam", + "description": "Specifies whether to generate and publish all (unfiltered) alignment files as cram instead of bam", + "fa_icon": "fas fa-toggle-on" + }, + "save_noalt_mapped_as_cram": { + "type": "boolean", + "description": "Specifies whether to generate and publish alt-filtered alignment files as cram instead of bam. Requires exclude_alt to be set to true.", "fa_icon": "fas fa-toggle-on" }, "scatter_count": { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d2187ded7..325d4688d 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-03-13T22:32:54+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://github.com/aksenia/saltshaker)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index b889566d9..593de277f 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -5,8 +5,9 @@ include { FASTP } from '../../../modules/nf-core/fastp/main' include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' include { ALIGN_SENTIEON } from '../align_sentieon' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_CONVERTTOCRAM } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as CONVERTTOCRAM_ALTFILTERED } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as CONVERTTOCRAM_UNFILTERED } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' include { ALIGN_MT } from '../align_MT' include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' @@ -41,7 +42,8 @@ workflow ALIGN { val_platform // string: [mandatory] illumina or a different technology val_run_mt_for_wes // boolean val_samtools_sort_threads // integer: [mandatory] number of sorting threads - val_save_mapped_as_cram // boolean + val_save_all_mapped_as_cram // boolean + val_save_noalt_mapped_as_cram // boolean main: ch_bwamem2_bam = channel.empty() @@ -54,7 +56,9 @@ workflow ALIGN { ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() + ch_cram_altfiltered = channel.empty() ch_cram_publish = channel.empty() + ch_cram_unfiltered = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) @@ -179,15 +183,24 @@ workflow ALIGN { .join(ALIGN_MT_SHIFT.out.marked_bai, failOnMismatch:true, failOnDuplicate:true) // Only for SNV calling } - if (val_save_mapped_as_cram) { - SAMTOOLS_VIEW_CONVERTTOCRAM( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) - ch_cram_publish = SAMTOOLS_VIEW_CONVERTTOCRAM.out.cram - .mix(SAMTOOLS_VIEW_CONVERTTOCRAM.out.crai) - .map { meta, value -> ['alignment/', [meta, value]] } + if (val_save_noalt_mapped_as_cram) { + CONVERTTOCRAM_ALTFILTERED( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_altfiltered = CONVERTTOCRAM_ALTFILTERED.out.cram + .mix(CONVERTTOCRAM_ALTFILTERED.out.crai) } + if (val_save_all_mapped_as_cram) { + CONVERTTOCRAM_UNFILTERED( ch_genome_marked_bam_bai_initial, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) + ch_cram_unfiltered = CONVERTTOCRAM_UNFILTERED.out.cram + .mix(CONVERTTOCRAM_UNFILTERED.out.crai) + } + + ch_cram_publish = ch_cram_altfiltered + .mix(ch_cram_unfiltered) + .map { meta, value -> ['alignment/', [meta, value]] } + ch_bam_publish = channel.empty() - if (!val_save_mapped_as_cram) { + if (!val_save_noalt_mapped_as_cram && !val_save_all_mapped_as_cram) { if (val_aligner.matches("bwamem2|bwa|bwameme")) { ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.publish } else if (val_aligner.equals("sentieon")) { diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index cc6664a86..bd3480ba4 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -167,7 +167,8 @@ nextflow_workflow { when { params { pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' - save_mapped_as_cram = true + save_noalt_mapped_as_cram = false + save_all_mapped_as_cram = true platform = "illumina" min_trimmed_length = 50 mito_name = "MT" @@ -225,7 +226,8 @@ nextflow_workflow { input[25] = "illumina" input[26] = false input[27] = 4 - input[28] = false + input[28] = true + input[29] = false """ } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index b218ac4cf..63b4b6f97 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -35,7 +35,8 @@ nextflow_workflow { params { aligner = "sentieon" sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - save_mapped_as_cram = true + save_noalt_mapped_as_cram = false + save_all_mapped_as_cram = true } workflow { """ diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a51f5d23c..8272d1068 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -215,7 +215,8 @@ workflow RAREDISEASE { val_run_rtgvcfeval val_sample_id_map val_samtools_sort_threads - val_save_mapped_as_cram + val_save_all_mapped_as_cram + val_save_noalt_mapped_as_cram val_svdb_query_bedpedbs val_svdb_query_dbs val_target_bed @@ -313,7 +314,8 @@ workflow RAREDISEASE { val_platform, val_run_mt_for_wes, val_samtools_sort_threads, - val_save_mapped_as_cram + val_save_all_mapped_as_cram, + val_save_noalt_mapped_as_cram ) .set { ch_mapped } ch_align_publish = ALIGN.out.publish From 7d714b4482da560fb7921e7695728ca6b7a70d1a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 13 Apr 2026 21:01:28 +0200 Subject: [PATCH 598/872] Update main.nf.test --- subworkflows/local/align/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index bd3480ba4..79db336ed 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -101,7 +101,7 @@ nextflow_workflow { ] ) input[8] = channel.empty() - input[9] = MT_MEM2.out.index.collect() + input[9] = .out.index.collect() input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() From cf8587695d130b90ffbe24156e7330527f0fdfd6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 08:47:53 +0200 Subject: [PATCH 599/872] Update config --- conf/modules/align.config | 6 +++--- docs/output.md | 6 ++++-- subworkflows/local/align/tests/nextflow.config | 9 +++++++-- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/conf/modules/align.config b/conf/modules/align.config index 074fd09c1..cf3dcac18 100644 --- a/conf/modules/align.config +++ b/conf/modules/align.config @@ -23,12 +23,12 @@ process{ withName: '.*ALIGN:CONVERTTOCRAM_ALTFILTERED' { ext.args = { '--output-fmt cram' } - ext.prefix = { "${meta.id}_sort_md_primary_contigs" } + ext.prefix = { "${meta.id}_sorted_md_primary_contigs" } } withName: '.*ALIGN:CONVERTTOCRAM_UNFILTERED' { ext.args = { '--output-fmt cram' } - ext.prefix = { "${meta.id}_sort_md" } + ext.prefix = { "${meta.id}_sorted_md" } } withName: '.*ALIGN:SAMTOOLS_VIEW_EXCLUDE_ALT' { @@ -38,6 +38,6 @@ process{ ? ((1..22).collect { n -> "chr${n}" } + ['chrX', 'chrY', 'chrM']).join(' ') : ((1..22).collect { n -> "${n}" } + ['X', 'Y', 'MT' ]).join(' ') } - ext.prefix = { "${meta.id}_sort_md_primary_contigs" } + ext.prefix = { "${meta.id}_sorted_md_primary_contigs" } } } diff --git a/docs/output.md b/docs/output.md index b9900eb37..f8e5f5a31 100644 --- a/docs/output.md +++ b/docs/output.md @@ -106,7 +106,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files from Alignment - `{outputdir}/alignment/` - - `*.bam|*.cram`: Alignment file in bam/cram format. When `--exclude_alt` is set, the file is filtered to primary chromosomes only (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM), which will also restrict variant calling to those chromosomes. + - `*_sorted_md.bam|*_sorted_md.cram`: Full (unfiltered) alignment file. Published as bam by default, or as cram when `--save_all_mapped_as_cram` is set. + - `*_sorted_md_primary_contigs.cram`: Alt-filtered alignment file in cram format. Published when `--save_noalt_mapped_as_cram` is set (requires `--exclude_alt`). Contains only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). - `*.bai|*.crai`: Index of the corresponding bam/cram file. - `*.txt`: Text file containing the dedup metrics.
    @@ -119,7 +120,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files from Alignment - `{outputdir}/alignment/` - - `*.bam|*.cram`: Alignment file in bam/cram format. When `--exclude_alt` is set, the file is filtered to primary chromosomes only (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM), which will also restrict variant calling to those chromosomes. + - `*_sorted_md.bam|*_sorted_md.cram`: Full (unfiltered) alignment file. Published as bam by default, or as cram when `--save_all_mapped_as_cram` is set. + - `*_sorted_md_primary_contigs.cram`: Alt-filtered alignment file in cram format. Published when `--save_noalt_mapped_as_cram` is set (requires `--exclude_alt`). Contains only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). - `*.bai|*.crai`: Index of the corresponding bam/cram file. - `*.metrics`: Text file containing the dedup metrics.
    diff --git a/subworkflows/local/align/tests/nextflow.config b/subworkflows/local/align/tests/nextflow.config index f626ed73b..5a3bc1cdf 100644 --- a/subworkflows/local/align/tests/nextflow.config +++ b/subworkflows/local/align/tests/nextflow.config @@ -12,9 +12,14 @@ process { ].join(' ').trim() } } - withName: 'SAMTOOLS_VIEW_CONVERTTOCRAM' { + withName: 'CONVERTTOCRAM_ALTFILTERED' { ext.args = { '--output-fmt cram' } - ext.prefix = { params.exclude_alt ? "${meta.id}_sorted_md_primary_contigs" : "${meta.id}_sorted_md" } + ext.prefix = { "${meta.id}_sorted_md_primary_contigs" } + } + + withName: 'CONVERTTOCRAM_UNFILTERED' { + ext.args = { '--output-fmt cram' } + ext.prefix = { "${meta.id}_sorted_md" } } withName: 'SAMTOOLS_VIEW_EXCLUDE_ALT' { From 210a3ed3fd21f4cde4d5e0d80bed29c0376845bc Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 09:00:20 +0200 Subject: [PATCH 600/872] Fix bug --- subworkflows/local/align/tests/main.nf.test | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 79db336ed..bc411292d 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -101,7 +101,7 @@ nextflow_workflow { ] ) input[8] = channel.empty() - input[9] = .out.index.collect() + input[9] = MT_MEM2.out.index.collect() input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() @@ -121,6 +121,7 @@ nextflow_workflow { input[26] = false input[27] = 4 input[28] = true + input[29] = false """ } } From e6c93da5fe5fedfd75829fc8c0cb47d851a1ac16 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 09:27:30 +0200 Subject: [PATCH 601/872] Update main.nf.test --- subworkflows/local/align/tests/main.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index bc411292d..ebb3a9fbe 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -326,6 +326,7 @@ nextflow_workflow { input[26] = false input[27] = 4 input[28] = true + input[29] = false """ } } From 90fa56787b1b9dd0bd8e69fd38c4d374d9fd42c1 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 14 Apr 2026 10:40:13 +0200 Subject: [PATCH 602/872] add saltshaker to html local module --- modules/local/saltshaker_to_html/main.nf | 29 ++++++++++++++++++++++++ subworkflows/local/call_sv_MT/main.nf | 8 +++++++ 2 files changed, 37 insertions(+) create mode 100644 modules/local/saltshaker_to_html/main.nf diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf new file mode 100644 index 000000000..413477c80 --- /dev/null +++ b/modules/local/saltshaker_to_html/main.nf @@ -0,0 +1,29 @@ +process SALTSHAKER_TO_HTML { + tag "$meta.id" + label "process_low" + + input: + tuple val(meta), path(classify) + + output: + tuple val(meta), path("*.html"), emit: classify_html + + script: + """ + python3 << 'EOF' + import re + def saltshaker_txt_to_html(txt_file): + with open(txt_file) as f: + content = f.read() + html_content = re.sub(r'\\t', '', content) + html_content = re.sub(r'\\n', '', html_content) + return html_content + + html = saltshaker_txt_to_html("${classify}") + with open("${classify.baseName}.html", 'w') as f: + f.write('') + f.write(html) + f.write('
    ') + EOF + """ +} diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 38fffa551..085060430 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -10,6 +10,7 @@ include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' +include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' @@ -120,6 +121,11 @@ workflow CALL_SV_MT { ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + SALTSHAKER_TO_HTML( + ch_saltshaker_txt, + ) + ch_saltshaker_html = SALTSHAKER_TO_HTML.out.classify_html + SALTSHAKER_PLOT( SALTSHAKER_CLASSIFY.out.classify ) @@ -149,6 +155,7 @@ workflow CALL_SV_MT { MT_DELETION(ch_bam_bai, ch_genome_fasta) ch_publish = ch_saltshaker_txt + .mix(ch_saltshaker_html) .mix(ch_saltshaker_vcf) .mix(ch_saltshaker_plot) .mix(MT_DELETION.out.mt_del_result) @@ -157,6 +164,7 @@ workflow CALL_SV_MT { emit: saltshaker_txt = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] updated_priority = ch_svcaller_priority // channel: [ val(["caller1", "caller2", ...]) ] - includes "mitosalt" if it ran From 5b3b1f1d31c99c095553df8f81c53abd417e8686 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 10:59:44 +0200 Subject: [PATCH 603/872] Update main.nf.test --- subworkflows/local/align/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index ebb3a9fbe..7a8e427ac 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -121,7 +121,7 @@ nextflow_workflow { input[26] = false input[27] = 4 input[28] = true - input[29] = false + input[29] = true """ } } From 780ddb4eba6f7cf5d53885a56bbfd8583b45499a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 11:07:59 +0200 Subject: [PATCH 604/872] Publish deepvariant report --- conf/modules/call_snv_deepvariant.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules/call_snv_deepvariant.config b/conf/modules/call_snv_deepvariant.config index 93b5b32f6..b97ff6d74 100644 --- a/conf/modules/call_snv_deepvariant.config +++ b/conf/modules/call_snv_deepvariant.config @@ -19,6 +19,7 @@ process { withName: '.*CALL_SNV_DEEPVARIANT:DEEPVARIANT' { ext.args = { [ + "--vcf_stats_report=true", "--model_type=${params.analysis_type.toUpperCase()}", meta.sex == 1 ? params.genome == 'GRCh37' ? '--haploid_contigs="X,Y"' : '--haploid_contigs="chrX,chrY"' : '' ].join(' ') } From 83487e7dc89649e30a619690cb86979af507fa1b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 14 Apr 2026 11:36:17 +0200 Subject: [PATCH 605/872] update snap --- .../local/align/tests/main.nf.test.snap | 57 ++++++++++--------- 1 file changed, 30 insertions(+), 27 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 60d6419a7..e56d30a3b 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -7,22 +7,28 @@ "earlycasualcaiman.fastp.log", "earlycasualcaiman_R1.fastp.fastq.gz", "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sort_md_primary_contigs.cram", - "earlycasualcaiman_sort_md_primary_contigs.cram.crai", + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "earlycasualcaiman_sorted_md_primary_contigs.cram", + "earlycasualcaiman_sorted_md_primary_contigs.cram.crai", "hugelymodelbat.fastp.html", "hugelymodelbat.fastp.json", "hugelymodelbat.fastp.log", "hugelymodelbat_R1.fastp.fastq.gz", "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sort_md_primary_contigs.cram", - "hugelymodelbat_sort_md_primary_contigs.cram.crai", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "hugelymodelbat_sorted_md_primary_contigs.cram", + "hugelymodelbat_sorted_md_primary_contigs.cram.crai", "slowlycivilbuck.fastp.html", "slowlycivilbuck.fastp.json", "slowlycivilbuck.fastp.log", "slowlycivilbuck_R1.fastp.fastq.gz", "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sort_md_primary_contigs.cram", - "slowlycivilbuck_sort_md_primary_contigs.cram.crai" + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai", + "slowlycivilbuck_sorted_md_primary_contigs.cram", + "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" ], [ [ @@ -42,7 +48,7 @@ } }, "bb547b29eca1afded4229826c774fc90", - "earlycasualcaiman_sort_md_primary_contigs.bam.bai" + "earlycasualcaiman_sorted_md_primary_contigs.bam.bai" ], [ { @@ -61,7 +67,7 @@ } }, "6f48b21e58c7450dd4db0bfc1268d687", - "hugelymodelbat_sort_md_primary_contigs.bam.bai" + "hugelymodelbat_sorted_md_primary_contigs.bam.bai" ], [ { @@ -80,7 +86,7 @@ } }, "e8431e5dc096f9636efd37ebfe9a5883", - "slowlycivilbuck_sort_md_primary_contigs.bam.bai" + "slowlycivilbuck_sorted_md_primary_contigs.bam.bai" ] ], [ @@ -261,7 +267,7 @@ ] ] ], - "timestamp": "2026-04-08T13:33:51.233648996", + "timestamp": "2026-04-14T11:13:27.943707346", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -270,12 +276,12 @@ "align bwameme - wgs": { "content": [ [ - "earlycasualcaiman_sort_md.cram", - "earlycasualcaiman_sort_md.cram.crai", - "hugelymodelbat_sort_md.cram", - "hugelymodelbat_sort_md.cram.crai", - "slowlycivilbuck_sort_md.cram", - "slowlycivilbuck_sort_md.cram.crai" + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" ], [ [ @@ -399,7 +405,7 @@ ] ], - "timestamp": "2026-03-13T14:59:34.430725854", + "timestamp": "2026-04-14T09:52:25.609505795", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -413,25 +419,22 @@ "earlycasualcaiman.fastp.log", "earlycasualcaiman_R1.fastp.fastq.gz", "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.bam", - "earlycasualcaiman_sorted_md.bam.bai", - "earlycasualcaiman_sorted_md.metrics.txt", + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", "hugelymodelbat.fastp.html", "hugelymodelbat.fastp.json", "hugelymodelbat.fastp.log", "hugelymodelbat_R1.fastp.fastq.gz", "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.bam", - "hugelymodelbat_sorted_md.bam.bai", - "hugelymodelbat_sorted_md.metrics.txt", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", "slowlycivilbuck.fastp.html", "slowlycivilbuck.fastp.json", "slowlycivilbuck.fastp.log", "slowlycivilbuck_R1.fastp.fastq.gz", "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.bam", - "slowlycivilbuck_sorted_md.bam.bai", - "slowlycivilbuck_sorted_md.metrics.txt" + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" ], [ [ @@ -502,7 +505,7 @@ ] ], - "timestamp": "2026-03-13T14:53:37.576915277", + "timestamp": "2026-04-14T08:57:37.024004334", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 24200cd5f6f33f85e765c4171913ae72a093bc04 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 14 Apr 2026 09:43:38 +0000 Subject: [PATCH 606/872] [automated] Fix code linting --- CHANGELOG.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ccd56b27..bc6ad7bee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -69,16 +69,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| --------------- | ----------------------- | -| | sambamba_regions | -| bwa_as_fallback | | -| | multiqc_samples | -| | homoplasmy_af_threshold | -| | exclude_alt | -| save_mapped_as_cram | | -| | save_all_mapped_as_cram | -| | save_noalt_mapped_as_cram | +| Old parameter | New parameter | +| ------------------- | ------------------------- | +| | sambamba_regions | +| bwa_as_fallback | | +| | multiqc_samples | +| | homoplasmy_af_threshold | +| | exclude_alt | +| save_mapped_as_cram | | +| | save_all_mapped_as_cram | +| | save_noalt_mapped_as_cram | ### Tool updates From 1e70f5a8e0e59e789146107a962f2d80b91210a4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 14 Apr 2026 14:53:45 +0200 Subject: [PATCH 607/872] fix formatting and update snaps --- modules/local/saltshaker_to_html/main.nf | 9 ++++----- tests/default.nf.test.snap | 11 ++++++----- tests/test_bam.nf.test.snap | 6 +++--- tests/test_singleton.nf.test.snap | 9 +++++---- 4 files changed, 18 insertions(+), 17 deletions(-) diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 413477c80..64c1dfd8e 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -15,15 +15,14 @@ process SALTSHAKER_TO_HTML { def saltshaker_txt_to_html(txt_file): with open(txt_file) as f: content = f.read() - html_content = re.sub(r'\\t', '', content) - html_content = re.sub(r'\\n', '', html_content) + html_content = re.sub(r'\\n', '
    ', content) return html_content html = saltshaker_txt_to_html("${classify}") with open("${classify.baseName}.html", 'w') as f: - f.write('') - f.write(html) - f.write('
    ') + f.write('') + f.write(f'
    {html}
    ') + f.write('') EOF """ } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0535fb641..c3e0989f4 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -671,13 +671,14 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/earlycasualcaiman.saltshaker.png", - "call_sv/earlycasualcaiman.saltshaker_classify.txt", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck.saltshaker.png", + "call_sv/slowlycivilbuck.saltshaker_classify.html", + "call_sv/slowlycivilbuck.saltshaker_classify.txt", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -924,10 +925,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-13T14:02:49.746679555", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-14T14:44:52.328631143" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 25e6c4651..2fb2629fd 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -844,10 +844,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-13T13:41:50.485130892", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-14T14:47:13.174933057" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 1337bdffe..a6a3947de 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 354, + 355, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -537,6 +537,7 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/hugelymodelbat.saltshaker_classify.html", "call_sv/hugelymodelbat.saltshaker_classify.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", @@ -655,10 +656,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-04-13T13:45:35.515919262", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-14T14:51:08.261564117" } } \ No newline at end of file From fcc241d9e0ea8c96141dca75b42a14514c054c71 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 14 Apr 2026 15:09:14 +0200 Subject: [PATCH 608/872] remove txt classification from outputs --- subworkflows/local/call_sv_MT/main.nf | 4 +--- tests/default.nf.test.snap | 7 +++---- tests/test_singleton.nf.test.snap | 3 +-- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 085060430..723d89777 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -154,15 +154,13 @@ workflow CALL_SV_MT { } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_saltshaker_txt - .mix(ch_saltshaker_html) + ch_publish = ch_saltshaker_html .mix(ch_saltshaker_vcf) .mix(ch_saltshaker_plot) .mix(MT_DELETION.out.mt_del_result) .map { meta, value -> ['call_sv/', [meta, value]] } emit: - saltshaker_txt = ch_saltshaker_txt // channel: [ val(meta), path(txt) ] saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c3e0989f4..e0e924241 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -671,14 +671,13 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", + "call_sv/earlycasualcaiman.saltshaker.png", + "call_sv/earlycasualcaiman.saltshaker_classify.html", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", - "call_sv/slowlycivilbuck.saltshaker.png", - "call_sv/slowlycivilbuck.saltshaker_classify.html", - "call_sv/slowlycivilbuck.saltshaker_classify.txt", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -929,6 +928,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T14:44:52.328631143" + "timestamp": "2026-04-14T14:58:54.280831107" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a6a3947de..4af8437b5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -538,7 +538,6 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat.saltshaker_classify.html", - "call_sv/hugelymodelbat.saltshaker_classify.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", @@ -660,6 +659,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T14:51:08.261564117" + "timestamp": "2026-04-14T15:03:52.559527073" } } \ No newline at end of file From 377a3e37d9e5b0c05ee998395cfde99da658a367 Mon Sep 17 00:00:00 2001 From: peterpru Date: Tue, 14 Apr 2026 15:28:10 +0200 Subject: [PATCH 609/872] add genome 38 flag --- conf/modules/generate_cytosure_files.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/modules/generate_cytosure_files.config b/conf/modules/generate_cytosure_files.config index dd8f71ee1..969d726cf 100644 --- a/conf/modules/generate_cytosure_files.config +++ b/conf/modules/generate_cytosure_files.config @@ -42,7 +42,8 @@ process { ext.args = { [ meta.sex == 1 ? '--sex male' : '--sex female', '--size 5000', - '--maxbnd 5000' + '--maxbnd 5000', + params.genome.equals("GRCh38") ? "--genome 38" : "" ].join(' ') } ext.prefix = { "${meta.custid}" ? "${meta.custid}" : "${meta.id}" } } From 5f82831247bc3c467641f80b2e1fe401b3fbf925 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 14 Apr 2026 15:39:33 +0200 Subject: [PATCH 610/872] update docs --- CHANGELOG.md | 1 + docs/output.md | 5 +++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f0f41604a..9666e2f45 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,6 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801) - Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from the config since this has to be set outside the subworkflow [#804](https://github.com/nf-core/raredisease/pull/804) - Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#806](https://github.com/nf-core/raredisease/pull/806) +- Change saltshaker classification output from txt to html [#808](https://github.com/nf-core/raredisease/pull/808) ### `Fixed` diff --git a/docs/output.md b/docs/output.md index c748f17f3..28b529bed 100644 --- a/docs/output.md +++ b/docs/output.md @@ -60,7 +60,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Mitochondrial analysis](#mitochondrial-analysis) - [Alignment and variant calling](#alignment-and-variant-calling) - [MT deletion script](#mt-deletion-script) - - [eKLIPse](#eklipse) + - [MitoSAlt](#mitosalt) + - [saltshaker](#saltshaker) - [Annotation](#annotation) - [vcfanno](#vcfanno-1) - [CADD](#cadd-1) @@ -467,7 +468,7 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen [Saltshaker](https://github.com/aksenia/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. - `call_sv` - - `.saltshaker_classify.txt`: report containing case-level classification of mitochondrial deletions. + - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. - `.saltshaker.png`: circos plot. #### Annotation From c1b9430887b96e7ea446d502e9ca1df1a64dcf7a Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 14 Apr 2026 15:54:05 +0200 Subject: [PATCH 611/872] update subworkflow snapshots --- .../tests/main.nf.test.snap | 6 +-- .../local/call_sv_MT/tests/main.nf.test.snap | 42 +++++++++---------- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 74bde0944..d3b9e9234 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -3,7 +3,7 @@ "content": [ [ "earlycasualcaiman.saltshaker.png", - "earlycasualcaiman.saltshaker_classify.txt", + "earlycasualcaiman.saltshaker_classify.html", "earlycasualcaiman_mitochondria_deletions.txt", "justhusky_saltshaker.vcf.gz", "justhusky_sv.vcf.gz", @@ -16,10 +16,10 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-03-25T16:02:32.429241176", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-14T15:51:47.077800376" } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index f612a8558..8d7ae6e46 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -7,17 +7,9 @@ [ [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" + "id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -26,9 +18,17 @@ [ [ { - "id": "justhusky" + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], @@ -117,7 +117,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], [ @@ -205,7 +205,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], [ @@ -239,7 +239,7 @@ ] ], [ - "saltshaker_plot", + "saltshaker_html", [ [ { @@ -253,12 +253,12 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], [ - "saltshaker_txt", + "saltshaker_plot", [ [ { @@ -272,7 +272,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -300,10 +300,10 @@ ] ] ], - "timestamp": "2026-03-30T20:20:40.266229001", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-04-14T15:53:31.425509861" } } \ No newline at end of file From 490b687dbd3d0d525cc5f7d805f333abadc53b33 Mon Sep 17 00:00:00 2001 From: Story Benjamin Date: Sat, 18 Apr 2026 14:47:55 +0200 Subject: [PATCH 612/872] fix: sort BAM/BAI inputs to Manta for deterministic sample order --- CHANGELOG.md | 1 + subworkflows/local/call_sv_manta/main.nf | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dd0496f5e..5a2f30ec5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- Ensure deterministic sample ordering in Manta SV output by sorting BAM/BAI channel inputs [#815](https://github.com/nf-core/raredisease/pull/815) - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 5cef7a157..e0f1d717b 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -16,11 +16,13 @@ workflow CALL_SV_MANTA { val_analysis_type // string: "wes", "wgs", or "mito" main: - ch_bam.collect{_meta, bam -> bam} + ch_bam.map{ _meta, bam -> bam } + .collect(sort: { a, b -> a.getName() <=> b.getName() }) .toList() .set { bam_file_list } - ch_bai.collect{_meta, bai -> bai} + ch_bai.map{ _meta, bai -> bai } + .collect(sort: { a, b -> a.getName() <=> b.getName() }) .toList() .set { bai_file_list } From 6474379f045d30b085caaf911976307dc34c43e7 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 20 Apr 2026 15:24:11 +0200 Subject: [PATCH 613/872] Added stubtest for call_repeat_expansions --- .../call_repeat_expansions/tests/main.nf.test | 30 ++++ .../tests/main.nf.test.snap | 145 ++++++++++++++++++ 2 files changed, 175 insertions(+) diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index 983e98df9..b708a4535 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -51,4 +51,34 @@ nextflow_workflow { } + + test("CALL_REPEAT_EXPANSIONS, stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[1] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + '/reference/variant_catalog.json', checkIfExists: true)).collect() + input[2] = channel.of([id:'justhusky']) + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 58e9e8bd7..7839b9b18 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -1,4 +1,149 @@ { + "CALL_REPEAT_EXPANSIONS, stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "publish": [ + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "repeat_expansions/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "timestamp": "2026-04-20T14:48:04.074693", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "CALL_REPEAT_EXPANSIONS": { "content": [ [ From 5b3e2705787af4563bfb16d55ae36b41a8efd88c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 20 Apr 2026 16:04:14 +0200 Subject: [PATCH 614/872] index as bash variable --- modules/local/prep_mitosalt/main.nf | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/modules/local/prep_mitosalt/main.nf b/modules/local/prep_mitosalt/main.nf index 47b0e3fd9..fa749e0ca 100644 --- a/modules/local/prep_mitosalt/main.nf +++ b/modules/local/prep_mitosalt/main.nf @@ -22,6 +22,9 @@ process PREP_MITOSALT { script: """ + hisat2path=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'` + lastpath=`find -L ./ -name "*.prj" | sed 's/.prj//'` + echo "hisat2 = hisat2" > mitosalt_config.txt echo "lastal = lastal" >> mitosalt_config.txt echo "lastsp = last-split" >> mitosalt_config.txt @@ -37,9 +40,9 @@ process PREP_MITOSALT { echo "randomBed = randomBed" >> mitosalt_config.txt echo "groupBy = groupBy" >> mitosalt_config.txt echo "bg2bw = bedGraphToBigWig" >> mitosalt_config.txt - echo "hsindex = ${hisat2index}/reference" >> mitosalt_config.txt + echo "hsindex = \$hisat2path" >> mitosalt_config.txt echo "faindex = ${genomefai}" >> mitosalt_config.txt - echo "lastindex = ${lastindex}/reference" >> mitosalt_config.txt + echo "lastindex = \$lastpath" >> mitosalt_config.txt echo "mtfaindex = ${mtfai}" >> mitosalt_config.txt echo "gsize = ${chrsizes}" >> mitosalt_config.txt echo "MT_fasta = ${mtfasta}" >> mitosalt_config.txt From a571cd9cd2febacf8e68ca12516179efbea6056b Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 20 Apr 2026 16:44:11 +0200 Subject: [PATCH 615/872] Added the stub test for align_sentieon --- .../local/align_sentieon/tests/main.nf.test | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index b218ac4cf..3f7c79ac5 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -75,4 +75,53 @@ nextflow_workflow { } + test("align sentieon, stub") { + + setup { + run("SENTIEON_BWAINDEX") { + script "modules/nf-core/sentieon/bwaindex/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + options "-stub" + + when { + params { + aligner = "sentieon" + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + save_mapped_as_cram = true + } + workflow { + """ + input[0] = SENTIEON_BWAINDEX.out.index + input[1] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[2] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[4] = false + input[5] = "illumina" + """ + } + } + + then { + assert workflow.success + assert snapshot(workflow.out).match() + } + + } + } From 200dde09c01e41fe4a93a57642750edd30023039 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 20 Apr 2026 16:51:07 +0200 Subject: [PATCH 616/872] Updated snapshot for align_sentieon --- .../align_sentieon/tests/main.nf.test.snap | 419 +++++++++++++++++- 1 file changed, 417 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b538612cb..b6ef91ad3 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,4 +1,419 @@ { + "align sentieon, stub": { + "content": [ + { + "0": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "aln_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_summary": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "is_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bai": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "marked_bam": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mq_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "publish": [ + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "alignment/", + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "qd_metrics": [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-20T16:45:49.119367273" + }, "align sentieon": { "content": [ [ @@ -129,10 +544,10 @@ "test_dedup.score" ] ], - "timestamp": "2026-03-14T00:02:24.597092362", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-14T00:02:24.597092362" } } \ No newline at end of file From 0e497d01ceda0cef67c73ef23fdc570ab30c6979 Mon Sep 17 00:00:00 2001 From: xtruka Date: Tue, 21 Apr 2026 09:41:32 +0200 Subject: [PATCH 617/872] fix(call_snv_sentieon): swap ch_genome_fai and ch_genome_fasta to alphabetical order --- CHANGELOG.md | 2 +- subworkflows/local/call_snv_sentieon/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dd0496f5e..68356b8f4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -58,7 +58,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Remove Qualimap and Haplogrep3 as they were made redundant by Picard and VerifyBamID2 [#801](https://github.com/nf-core/raredisease/pull/801) ### `Fixed` - +- Fixed argument order of `ch_genome_fai` and `ch_genome_fasta` in the `CALL_SNV_SENTIEON` subworkflow [#811](https://github.com/nf-core/raredisease/pull/811) - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index aacbcab54..75a78412f 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -21,8 +21,8 @@ workflow CALL_SNV_SENTIEON { ch_dbsnp_index // channel: [mandatory] [ val(meta), path(tbi) ] ch_foundin_header // channel: [mandatory] [ path(header) ] ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_ml_model // channel: [mandatory] [ val(meta), path(model) ] ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] From 522fead18478e5e60d2d818392d030fe86daddf6 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Tue, 21 Apr 2026 10:47:04 +0200 Subject: [PATCH 618/872] Added stubtest for qc_bam --- subworkflows/local/qc_bam/tests/main.nf.test | 105 +++++++++++++++++++ 1 file changed, 105 insertions(+) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 184eabc40..889de7da2 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -102,6 +102,59 @@ nextflow_workflow { } + test("QC_BAM - test, bwamem2, stub") { + + options "-stub" + + when { + params { + skip_tools = null + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[14] = 'wgs' + input[15] = 'bwamem2' + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + + } + test("QC_BAM - test, sentieon") { when { @@ -182,4 +235,56 @@ nextflow_workflow { } } + test("QC_BAM - test, sentieon, stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + skip_tools = null + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] + ] + ) + input[1] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], + [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] + ] + ) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[7] = channel.empty() + input[8] = channel.of('xy') + input[9] = channel.empty() + input[10] = channel.empty() + input[11] = channel.empty() + input[12] = channel.empty() + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[14] = 'wgs' + input[15] = 'sentieon' + input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[17] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + } From ca40cb9184c3365a3bfba8e3224f1191406c38f1 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Tue, 21 Apr 2026 10:55:44 +0200 Subject: [PATCH 619/872] Added snapshot got qc_bam --- .../local/qc_bam/tests/main.nf.test.snap | 2234 ++++++++++++++++- 1 file changed, 2230 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 42f458e1c..b833f5520 100644 --- 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"'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_wgsmetrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bed:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "qc_bam/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "qc_bam/", - [ - { - - }, - [ - "earlycasualcaiman_tidditcov.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_tidditcov.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], - "self_sm": [ - - ], - "sex_check": [ - - ], - "tiddit_wig": [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-21T10:54:33.661317026" - }, "QC_BAM - test, bwamem2": { "content": [ [ @@ -2343,11 +117,11 @@ ] ] ], + "timestamp": "2026-03-27T16:45:40.990778813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:45:40.990778813" + } }, "QC_BAM - test, sentieon": { "content": [ @@ -2467,10 +241,10 @@ ] ] ], + "timestamp": "2026-03-27T17:07:36.836738984", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T17:07:36.836738984" + } } } \ No newline at end of file From 4a36d4d8bd70f1dd0930a64232b1dae087e53592 Mon Sep 17 00:00:00 2001 From: xtruka Date: Wed, 22 Apr 2026 12:52:35 +0200 Subject: [PATCH 621/872] Update utils_nfschema_plugin subworkflow to match remote --- subworkflows/nf-core/utils_nfschema_plugin/main.nf | 3 +-- .../nf-core/utils_nfschema_plugin/tests/nextflow.config | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8d..1df8b76fb 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + (params.help instanceof String && params.help != "true") ? params.help : "", ) exit 0 } @@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN { emit: dummy_emit = true } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 8d8c73718..f6537cc33 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.5.1" + id "nf-schema@2.6.1" } validation { From 46a2d19d3bcd2d93a7ddadd5b8d816f4e321faa1 Mon Sep 17 00:00:00 2001 From: xtruka Date: Wed, 22 Apr 2026 14:32:13 +0200 Subject: [PATCH 622/872] Apply pre-commit prettier fixes --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index afe035947..fcf49a678 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -64,6 +64,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Change saltshaker classification output from txt to html [#808](https://github.com/nf-core/raredisease/pull/808) ### `Fixed` + - Fixed argument order of `ch_genome_fai` and `ch_genome_fasta` in the `CALL_SNV_SENTIEON` subworkflow [#811](https://github.com/nf-core/raredisease/pull/811) - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) From 3b75c84a0a527549005cdfc5feb3669f9002b735 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 22 Apr 2026 13:36:03 +0000 Subject: [PATCH 623/872] [automated] Fix code linting --- subworkflows/local/align_MT/tests/main.nf.test | 2 +- subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test | 2 +- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- subworkflows/local/qc_bam/tests/main.nf.test | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/align_MT/tests/main.nf.test b/subworkflows/local/align_MT/tests/main.nf.test index 3318b260c..986daca5c 100644 --- a/subworkflows/local/align_MT/tests/main.nf.test +++ b/subworkflows/local/align_MT/tests/main.nf.test @@ -239,7 +239,7 @@ nextflow_workflow { } options "-stub" - + when { params { outdir = "$outputDir" diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 62cfd8893..3a5de492a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -207,7 +207,7 @@ nextflow_workflow { } options "-stub" - + when { params { sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 22bc04d78..5849342f3 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -91,7 +91,7 @@ nextflow_workflow { } } } - + options "-stub" when { diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 0b2559070..739c3ad18 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -226,7 +226,7 @@ nextflow_workflow { test("QC_BAM - test, sentieon, stub") { options "-stub" - + when { params { outdir = "$outputDir" From 22577c14ca3bba746b79b28785e446afd4fa2fac Mon Sep 17 00:00:00 2001 From: xtruka Date: Wed, 22 Apr 2026 18:14:02 +0200 Subject: [PATCH 624/872] Update nf-test snapshots for fasta/fai order fix --- subworkflows/local/call_snv/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index ebe790f53..d43eef332 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "justhusky_snv.vcf.gz", "justhusky_snv.vcf.gz.tbi" ], - "dfc0eeae02f4c1f04034e0fff555bf50", + "dc179c28435ffe6d3127fde7ca401337", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ "justhusky_snv.vcf.gz.tbi" @@ -16,9 +16,9 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-03-17T23:03:58.765265498", + "timestamp": "2026-04-22T18:04:13.466587948", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, From 98f7fce15ace80e2c0dea34c2fb1f225775c6e89 Mon Sep 17 00:00:00 2001 From: xtruka Date: Wed, 22 Apr 2026 18:59:39 +0200 Subject: [PATCH 625/872] Revert call_snv snapshot to docker hash --- subworkflows/local/call_snv/tests/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index d43eef332..d7b46c267 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "justhusky_snv.vcf.gz", "justhusky_snv.vcf.gz.tbi" ], - "dc179c28435ffe6d3127fde7ca401337", + "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ "justhusky_snv.vcf.gz.tbi" From 3eb7ca86c9b41240ff055a2ef32a0c7727480c05 Mon Sep 17 00:00:00 2001 From: xtruka Date: Wed, 22 Apr 2026 19:12:40 +0200 Subject: [PATCH 626/872] Update call_snv snapshot to correct hash after upstream merge --- subworkflows/local/call_snv/tests/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index d7b46c267..d43eef332 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "justhusky_snv.vcf.gz", "justhusky_snv.vcf.gz.tbi" ], - "dfc0eeae02f4c1f04034e0fff555bf50", + "dc179c28435ffe6d3127fde7ca401337", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ "justhusky_snv.vcf.gz.tbi" From f2e9cb70af4d7543f149a67a9579a02eb3b0cf2a Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Thu, 23 Apr 2026 10:16:53 +0200 Subject: [PATCH 627/872] Added stub test for prepare_references --- .../prepare_references/tests/main.nf.test | 81 ++ .../tests/main.nf.test.snap | 1245 +++++++++++++++++ 2 files changed, 1326 insertions(+) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 56e9d6831..85dea279c 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -108,4 +108,85 @@ nextflow_workflow { } + test("Should run without failures, stub") { + + options "-stub" + + when { + params { + variant_caller = "deepvariant" + mito_name = "MT" + bait_padding = 100 + } + workflow { + """ + input[0] = "bwamem2" + input[1] = "wgs" + input[2] = null + input[3] = null + input[4] = null + input[5] = null + input[6] = params.pipelines_testdata_base_path + 'reference/reference.fasta' + input[7] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[8] = null + input[9] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[10] = null + input[11] = "bwa" + input[12] = null + input[13] = false + input[14] = false + input[15] = null + input[16] = null + input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[18] = null + input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' + input[20] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List && !sortKey.isEmpty()) { + def next = sortKey[-1] + if (next instanceof List && next.every { !(it instanceof List) }) { + // Leaf list: could be [meta, path] or [file1, file2, ...]. + // For directory outputs (e.g. BWA/BWAMEM2/HISAT2 index folders), + // nf-test represents the value as a Path at sort time rather than + // expanding it to a file list. List the directory contents to + // produce a stable, unique sort key across same-named directories. + return next.findAll { !(it instanceof Map) } + .collect { v -> + def s = v.toString() + if (s.contains(':md5,')) { + return s.split(':md5,')[0].tokenize('/').last() ?: '' + } + try { + def f = new File(s) + if (f.isDirectory()) { + return f.listFiles()?.collect { it.name }?.sort()?.join(',') ?: s.tokenize('/').last() ?: '' + } + } catch (e) {} + return s.tokenize('/').last() ?: '' + } + .sort() + .join(',') + } + sortKey = next + } + def parts = sortKey.toString().split(':md5,')[0].tokenize('/') + parts ? parts[-1] : '' + } + [name, sorted_channel] + }.sort { it[0] } + ).match() } + ) + } + + } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index ee140eaa3..49c454958 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -1,4 +1,1249 @@ { + "Should run without failures, stub": { + "content": [ + [ + [ + "0", + [ + [ + "target_bait.intervals_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "dbsnp_-138-" + }, + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + ] + ] + ], + [ + "10", + [ + [ + { + "id": "reference" + }, + "reference.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "11", + [ + [ + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "gnomad_reformated.tab.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "12", + [ + [ + { + "id": "reference" + }, + [ + "reference_mt.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + 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"references/", + [ + { + "id": "reference" + }, + "reference.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + [ + "reference.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + [ + "reference.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + [ + "reference.shifted.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + [ + "reference_mt.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_mt.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_mt.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_mt.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_mt.fa.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + [ + "reference_shift.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_shift.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_shift.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_shift.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "reference_shift.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_shift.back_chain:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_shift.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_shift.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + { + "id": "reference" + }, + "reference_shift.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + [ + "target_bait.intervals_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + { + "id": "target" + }, + "target_pad100.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "target_pad100.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "references/", + [ + [ + "target_target.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "references/", + [ + [ + [ + + ] + ] + ] + ] + ] + ], + [ + "sdf", + [ + + ] + ], + [ + "target_bed", + [ + [ + { + "id": "target" + }, + "target_pad100.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "target_pad100.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "target_intervals", + [ + [ + "target_target.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "vcfanno_extra", + [ + [ + [ + + ] + ] + ] + ], + [ + "vep_resources", + [ + [ + [ + + ] + ] + ] + ] + ] + ], + "timestamp": "2026-04-23T09:48:42.84565", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "Should run without failures": { "content": [ [ From 61680d08cc42a22c5d3c96c6fe4919c6c27ac4ab Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 23 Apr 2026 11:00:35 +0200 Subject: [PATCH 628/872] Update schema --- assets/sample_id_map.json | 22 ++++++++++++++++++---- assets/schema_input.json | 4 ++-- 2 files changed, 20 insertions(+), 6 deletions(-) diff --git a/assets/sample_id_map.json b/assets/sample_id_map.json index 1110f959f..ffe19f809 100644 --- a/assets/sample_id_map.json +++ b/assets/sample_id_map.json @@ -8,13 +8,27 @@ "type": "object", "properties": { "customer_id": { - "type": "string", - "pattern": "^\\S+$", + "anyOf": [ + { + "type": "integer" + }, + { + "type": "string", + "pattern": "^\\S+$" + } + ], "errorMessage": "Customer id cannot contain spaces" }, "internal_id": { - "type": "string", - "pattern": "^\\S+$", + "anyOf": [ + { + "type": "integer" + }, + { + "type": "string", + "pattern": "^\\S+$" + } + ], "errorMessage": "Internal id cannot contain spaces", "meta": ["id"] } diff --git a/assets/schema_input.json b/assets/schema_input.json index b3d7517ea..902e67881 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -14,7 +14,7 @@ "errorMessage": "Sample name must be provided and must be a string that cannot contain spaces" }, "lane": { - "oneOf": [ + "anyOf": [ { "type": "integer" }, @@ -69,7 +69,7 @@ "exists": true }, "sex": { - "oneOf": [ + "anyOf": [ { "type": "integer", "enum": [0, 1, 2] From e7d742b98e8702bdfc85677d776b37fb09ed6969 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 24 Apr 2026 11:26:59 +0200 Subject: [PATCH 629/872] Add sanity checks for vcfanno databases --- CHANGELOG.md | 6 +- docs/usage.md | 3 +- main.nf | 3 + .../environment.yml | 8 ++ .../sanity_check_vcfanno_databases/main.nf | 34 ++++++++ .../usr/bin/sanity_check_vcfanno_databases.py | 77 +++++++++++++++++++ nextflow.config | 35 +++++---- nextflow_schema.json | 5 ++ .../local/annotate_genome_snvs/main.nf | 49 +++++++----- .../annotate_genome_snvs/tests/main.nf.test | 7 +- workflows/raredisease.nf | 2 + 11 files changed, 187 insertions(+), 42 deletions(-) create mode 100644 modules/local/sanity_check_vcfanno_databases/environment.yml create mode 100644 modules/local/sanity_check_vcfanno_databases/main.nf create mode 100644 modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py diff --git a/CHANGELOG.md b/CHANGELOG.md index d75ef8794..218ac7b39 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) +- Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno ### `Changed` @@ -83,8 +84,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | | homoplasmy_af_threshold | | | exclude_alt | | save_mapped_as_cram | | -| | save_all_mapped_as_cram | -| | save_noalt_mapped_as_cram | +| | save_all_mapped_as_cram | +| | save_noalt_mapped_as_cram | +| | run_vcfanno_db_sanity_check | ### Tool updates diff --git a/docs/usage.md b/docs/usage.md index 54c39bd50..0a17c0194 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -287,7 +287,7 @@ The mandatory and optional parameters for each category are tabulated below. | vcfanno_resources2 | vcfanno_lua | | vcfanno_toml3 | vep_filters/vep_filters_scout_fmt10 | | vep_cache_version | cadd_resources11 | -| vep_cache4 | | +| vep_cache4 | run_vcfanno_db_sanity_check12 | | gnomad_af5 | | | score_config_snv6 | | | variant_consequences_snv7 | | @@ -307,6 +307,7 @@ no header and the following columns: `CHROM POS REF_ALLELE,ALT_ALLELE AF`. Sampl 9Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
    10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into candidate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set. To skip this splitting entirely, add `generate_clinical_set` to `--skip_subworkflows`.
    11Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
    +12When set to `true`, each vcfanno database file listed in `vcfanno_resources` is checked for records (non-header lines). Any database with zero records is removed from the vcfanno TOML config before annotation runs. Default: `false`.
    :::note We use CADD only to annotate small indels. To annotate SNVs with precomputed CADD scores, pass the file containing CADD scores as a resource to vcfanno instead. Files containing the precomputed CADD scores for SNVs can be downloaded from [here](https://cadd.gs.washington.edu/download) (download files listed under the description: "All possible SNVs of GRCh3<7/8>/hg3<7/8>") diff --git a/main.nf b/main.nf index a068f44d2..789a3d62a 100644 --- a/main.nf +++ b/main.nf @@ -107,6 +107,7 @@ workflow NFCORE_RAREDISEASE { val_rtg_truthvcfs val_run_mt_for_wes val_run_rtgvcfeval + val_run_vcfanno_db_sanity_check val_sambamba_regions val_sample_id_map val_samtools_sort_threads @@ -510,6 +511,7 @@ workflow NFCORE_RAREDISEASE { val_platform, val_run_mt_for_wes, val_run_rtgvcfeval, + val_run_vcfanno_db_sanity_check, val_sample_id_map, val_samtools_sort_threads, val_save_all_mapped_as_cram, @@ -621,6 +623,7 @@ workflow { params.rtg_truthvcfs, params.run_mt_for_wes, params.run_rtgvcfeval, + params.run_vcfanno_db_sanity_check, params.sambamba_regions, params.sample_id_map, params.samtools_sort_threads, diff --git a/modules/local/sanity_check_vcfanno_databases/environment.yml b/modules/local/sanity_check_vcfanno_databases/environment.yml new file mode 100644 index 000000000..c38e0465e --- /dev/null +++ b/modules/local/sanity_check_vcfanno_databases/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.23 + - conda-forge::python=3.14.3 diff --git a/modules/local/sanity_check_vcfanno_databases/main.nf b/modules/local/sanity_check_vcfanno_databases/main.nf new file mode 100644 index 000000000..9c53bce0a --- /dev/null +++ b/modules/local/sanity_check_vcfanno_databases/main.nf @@ -0,0 +1,34 @@ +process SANITY_CHECK_VCFANNO_DATABASES { + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2f/2fdb3ffa4bac62e98ec062e991217df2ab96e67bbd45a502bd25ff2effecb96e/data': + 'community.wave.seqera.io/library/htslib_python:d1e4474cbf76f4e9' }" + + input: + path(toml) + path(databases) + + output: + path("*_filtered.toml") , emit: toml + tuple val("${task.process}"), val('sanity_check_vcfanno_databases'), val("1.0"), topic: versions , emit: versions_sanity_check_vcfanno_databases + tuple val("${task.process}"), val('python'), eval("python -V | sed 's/Python //'"), topic: versions , emit: versions_python + + when: + task.ext.when == null || task.ext.when + + script: + """ + sanity_check_vcfanno_databases.py \\ + --toml ${toml} \\ + --databases ${databases} + + """ + + stub: + """ + touch ${toml.baseName}_filtered.toml + + """ +} diff --git a/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py b/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py new file mode 100644 index 000000000..7da092ab9 --- /dev/null +++ b/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py @@ -0,0 +1,77 @@ +#!/usr/bin/env python3 + +# Written by Ramprasad Neethiraj and released under the MIT license. +# See git repository (https://github.com/nf-core/raredisease) for full license text. + +import argparse +import gzip +import re +import sys +from pathlib import Path + + +INDEX_SUFFIXES = {".tbi", ".csi", ".bai"} + + +def has_records(path: Path) -> bool: + if path.suffix in INDEX_SUFFIXES: + return True + open_fn = gzip.open if path.suffix in {".gz", ".bgz"} else open + with open_fn(path, "rt") as fh: + for line in fh: + if not line.startswith("#") and line.strip(): + return True + return False + + +def split_toml(content: str): + """Return (header, blocks) where blocks is a list of [[annotation]] block strings.""" + parts = re.split(r"(?=\[\[annotation\]\])", content) + return parts[0], parts[1:] + + +def block_filename(block: str) -> str | None: + match = re.search(r'^file\s*=\s*["\']([^"\']+)["\']', block, re.MULTILINE) + if match: + return Path(match.group(1)).name + return None + + +def main(): + parser = argparse.ArgumentParser( + description="Check vcfanno database files and remove zero-record entries from the TOML" + ) + parser.add_argument("--toml", required=True, help="Path to vcfanno TOML config file") + parser.add_argument( + "--databases", + nargs="+", + required=True, + help="Paths to vcfanno database files", + ) + args = parser.parse_args() + + empty_basenames = set() + for db in args.databases: + path = Path(db) + if not has_records(path): + print(f"WARNING: {path.name} has zero records — removing from TOML", file=sys.stderr) + empty_basenames.add(path.name) + else: + print(f"{path.name}: has records") + + toml_path = Path(args.toml) + content = toml_path.read_text() + header, blocks = split_toml(content) + + filtered_blocks = [b for b in blocks if block_filename(b) not in empty_basenames] + removed = len(blocks) - len(filtered_blocks) + if removed: + print(f"Removed {removed} annotation block(s) from TOML.", file=sys.stderr) + + output_path = Path(toml_path.stem + "_filtered.toml") + output_path.write_text(header + "".join(filtered_blocks)) + print(f"Filtered TOML written to {output_path}") + + +if __name__ == "__main__": + main() diff --git a/nextflow.config b/nextflow.config index aa280a8b4..7de7a6548 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,23 +26,24 @@ params { mito_length = 16569 // Main options - analysis_type = 'wgs' - bait_padding = 100 - concatenate_snv_calls = false - exclude_alt = false - extract_alignments = false - mt_subsample_approach = 'reads' - mt_subsample_reads = 18000 - restrict_to_contigs = null - run_mt_for_wes = false - run_rtgvcfeval = false - save_all_mapped_as_cram = false - save_noalt_mapped_as_cram = false - scatter_count = 20 - skip_tools = null - skip_subworkflows = null - cadd_resources = null - platform = 'illumina' + analysis_type = 'wgs' + bait_padding = 100 + concatenate_snv_calls = false + exclude_alt = false + extract_alignments = false + mt_subsample_approach = 'reads' + mt_subsample_reads = 18000 + restrict_to_contigs = null + run_mt_for_wes = false + run_rtgvcfeval = false + run_vcfanno_db_sanity_check = false + save_all_mapped_as_cram = false + save_noalt_mapped_as_cram = false + scatter_count = 20 + skip_tools = null + skip_subworkflows = null + cadd_resources = null + platform = 'illumina' // reference file options fasta = null diff --git a/nextflow_schema.json b/nextflow_schema.json index ec4b4fd34..7a7a3a629 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -581,6 +581,11 @@ "description": "Specifies whether to run rtgtools' vcfeval", "fa_icon": "fas fa-toggle-on" }, + "run_vcfanno_db_sanity_check": { + "type": "boolean", + "description": "Specifies whether to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno", + "fa_icon": "fas fa-toggle-on" + }, "save_all_mapped_as_cram": { "type": "boolean", "description": "Specifies whether to generate and publish all (unfiltered) alignment files as cram instead of bam", diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 6f490d13a..616a82b6d 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -16,29 +16,31 @@ include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' include { ANNOTATE_CADD } from '../annotate_cadd' include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' +include { SANITY_CHECK_VCFANNO_DATABASES } from '../../../modules/local/sanity_check_vcfanno_databases/main' workflow ANNOTATE_GENOME_SNVS { take: - ch_cadd_header // channel: [mandatory] [ path(txt) ] - ch_cadd_resources // channel: [mandatory] [ path(annotation) ] - ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] - ch_genome_fai // channel: [mandatory] [ path(fai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_gnomad_af // channel: [optional] [ path(tab), path(tbi) ] - ch_samples // channel: [mandatory] [ val(sample_meta) ] - ch_split_intervals // channel: [mandatory] [ path(intervals) ] - ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] - ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] - ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] - ch_vep_cache // channel: [mandatory] [ path(cache) ] - ch_vep_extra_files // channel: [mandatory] [ path(files) ] - val_analysis_type // string: wgs, wes, or mito - val_cadd_resources // string: path to cadd resources file - val_genome // string: GRCh37 or GRCh38 - val_vep_cache_version // string: vep version ex: 107 + ch_cadd_header // channel: [mandatory] [ path(txt) ] + ch_cadd_resources // channel: [mandatory] [ path(annotation) ] + ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] + ch_genome_fai // channel: [mandatory] [ path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_gnomad_af // channel: [optional] [ path(tab), path(tbi) ] + ch_samples // channel: [mandatory] [ val(sample_meta) ] + ch_split_intervals // channel: [mandatory] [ path(intervals) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] + ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] + ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] + ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] + ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] + ch_vep_cache // channel: [mandatory] [ path(cache) ] + ch_vep_extra_files // channel: [mandatory] [ path(files) ] + val_analysis_type // string: wgs, wes, or mito + val_cadd_resources // string: path to cadd resources file + val_genome // string: GRCh37 or GRCh38 + val_run_vcfanno_db_sanity_check // boolean: run sanity check on vcfanno databases + val_vep_cache_version // string: vep version ex: 107 main: ch_cadd_vcf = channel.empty() @@ -97,7 +99,14 @@ workflow ANNOTATE_GENOME_SNVS { .combine(ch_vcfanno_extra) .set { ch_vcfanno_in } - VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) + if (val_run_vcfanno_db_sanity_check) { + SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_vcfanno_resources) + ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml + } else { + ch_vcfanno_toml_final = ch_vcfanno_toml + } + + VCFANNO (ch_vcfanno_in, ch_vcfanno_toml_final, ch_vcfanno_lua, ch_vcfanno_resources) VCFANNO.out.vcf .join(VCFANNO.out.tbi, failOnMismatch:true, failOnDuplicate:true) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 0b6b95c53..6a579463c 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -19,6 +19,7 @@ nextflow_workflow { tag "ensemblvep/vep" tag "tabix/bgziptabix" tag "gatk4/selectvariants" + tag "sanity_check_vcfanno_databases" config "./nextflow.config" @@ -51,7 +52,8 @@ nextflow_workflow { input[15] = 'wgs' input[16] = null input[17] = 'GRCh37' - input[18] = 107 + input[18] = true + input[19] = 107 """ } } @@ -107,7 +109,8 @@ nextflow_workflow { input[15] = 'wes' input[16] = null input[17] = 'GRCh37' - input[18] = 107 + input[18] = true + input[19] = 107 """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 276c971ed..31042b757 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -213,6 +213,7 @@ workflow RAREDISEASE { val_platform val_run_mt_for_wes val_run_rtgvcfeval + val_run_vcfanno_db_sanity_check val_sample_id_map val_samtools_sort_threads val_save_all_mapped_as_cram @@ -462,6 +463,7 @@ workflow RAREDISEASE { val_analysis_type, val_cadd_resources, val_genome, + val_run_vcfanno_db_sanity_check, val_vep_cache_version ).set { ch_snv_annotate } ch_annotate_genome_snvs_publish = ANNOTATE_GENOME_SNVS.out.publish From 87e4407db08234b6ac9ca159ffb8d0085ec75971 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Fri, 24 Apr 2026 12:16:22 +0200 Subject: [PATCH 630/872] Updated the stub test channels to match full --- subworkflows/local/qc_bam/tests/main.nf.test | 66 ++++++++------------ 1 file changed, 27 insertions(+), 39 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 739c3ad18..3f1ac7d91 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -108,34 +108,28 @@ nextflow_workflow { workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'bwamem2' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'bwamem2' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } @@ -232,37 +226,31 @@ nextflow_workflow { outdir = "$outputDir" skip_tools = null } - workflow { + workflow { """ input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)] - ] - ) - input[1] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true)], [file(params.pipelines_testdata_base_path + '/testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true)] ] ) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() - input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() - input[7] = channel.empty() - input[8] = channel.of('xy') + input[1] = channel.of(file(params.pipelines_testdata_base_path + 'reference/bait.interval_list', checkIfExists: true)).collect() + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[5] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)).collect() + input[6] = channel.empty() + input[7] = channel.of('xy') + input[8] = channel.empty() input[9] = channel.empty() input[10] = channel.empty() input[11] = channel.empty() - input[12] = channel.empty() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() - input[14] = 'wgs' - input[15] = 'sentieon' - input[16] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[17] = true + input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target.interval_list', checkIfExists: true)).collect() + input[13] = 'wgs' + input[14] = 'sentieon' + input[15] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[16] = true """ } } From cfddc967bef024902a05b26f11c19f3045839a67 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 24 Apr 2026 13:56:29 +0200 Subject: [PATCH 631/872] publish deepvar report --- subworkflows/local/call_snv/main.nf | 43 ++++++++++--------- .../local/call_snv_deepvariant/main.nf | 5 +++ 2 files changed, 28 insertions(+), 20 deletions(-) diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 543e259a1..4308f9a8d 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -42,19 +42,20 @@ workflow CALL_SNV { val_variant_caller // string: 'deepvariant' or 'sentieon' main: - ch_deepvar_vcf = channel.empty() - ch_deepvar_tbi = channel.empty() - ch_deepvar_gvcf = channel.empty() - ch_deepvar_gtbi = channel.empty() - ch_mt_vcf = channel.empty() - ch_mt_tabix = channel.empty() - ch_mt_vcf_tabix = channel.empty() - ch_sentieon_vcf = channel.empty() - ch_sentieon_tbi = channel.empty() - ch_sentieon_gvcf = channel.empty() - ch_sentieon_gtbi = channel.empty() ch_concat_publish = channel.empty() + ch_deepvar_vcf = channel.empty() + ch_deepvar_tbi = channel.empty() + ch_deepvar_gvcf = channel.empty() + ch_deepvar_gtbi = channel.empty() + ch_deepvar_publish = channel.empty() ch_mt_snv_publish = channel.empty() + ch_mt_tabix = channel.empty() + ch_mt_vcf = channel.empty() + ch_mt_vcf_tabix = channel.empty() + ch_sentieon_vcf = channel.empty() + ch_sentieon_tbi = channel.empty() + ch_sentieon_gvcf = channel.empty() + ch_sentieon_gtbi = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( @@ -68,10 +69,11 @@ workflow CALL_SNV { ch_target_bed, val_analysis_type ) - ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf - ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix - ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf - ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix + ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf + ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix + ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf + ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix + ch_deepvar_publish = CALL_SNV_DEEPVARIANT.out.publish } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, @@ -135,9 +137,9 @@ workflow CALL_SNV { ch_mtshift_backchain, CALL_SNV_MT_SHIFT.out.vcf ) - ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf - ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi - ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) + ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf + ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi + ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.publish } @@ -153,7 +155,8 @@ workflow CALL_SNV { } ch_publish = GATK4_SELECTVARIANTS.out.vcf - .mix(GATK4_SELECTVARIANTS.out.tbi) + .mix(GATK4_SELECTVARIANTS.out.tbi + .mix(ch_deepvar_report) .map { meta, value -> ['call_snv/genome/', [meta, value]] } .mix(ch_concat_publish) .mix(ch_mt_snv_publish) @@ -167,5 +170,5 @@ workflow CALL_SNV { mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] mt_vcf_tbi = ch_mt_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 9aadc6aaa..869df2ec5 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -24,6 +24,8 @@ workflow CALL_SNV_DEEPVARIANT { main: + ch_publish = channel.empty() + if (val_analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) ch_bam_bai @@ -78,9 +80,12 @@ workflow CALL_SNV_DEEPVARIANT { BCFTOOLS_ANNOTATE(ch_annotate_in) + ch_publish = DEEPVARIANT.out.report + emit: gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] + publish = ch_publish // channel: [ val(meta), path(report) ] tabix = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] } From 4830299ea6cbb2d5c3b6238abb62cd76e168167a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 24 Apr 2026 14:43:23 +0200 Subject: [PATCH 632/872] fix permissions --- .../resources/usr/bin/sanity_check_vcfanno_databases.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py diff --git a/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py b/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py old mode 100644 new mode 100755 From c4e96feb09b2a35ea9328a5ff62a746fecd82127 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 25 Apr 2026 10:39:53 +0200 Subject: [PATCH 633/872] fix bug --- subworkflows/local/call_snv/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 4308f9a8d..3bf48c34f 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -155,8 +155,8 @@ workflow CALL_SNV { } ch_publish = GATK4_SELECTVARIANTS.out.vcf - .mix(GATK4_SELECTVARIANTS.out.tbi - .mix(ch_deepvar_report) + .mix(GATK4_SELECTVARIANTS.out.tbi) + .mix(ch_deepvar_publish) .map { meta, value -> ['call_snv/genome/', [meta, value]] } .mix(ch_concat_publish) .mix(ch_mt_snv_publish) From 0fe4f183858b42614235a566e6a3a22cb4250bf0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 25 Apr 2026 10:41:05 +0200 Subject: [PATCH 634/872] Update main.nf --- subworkflows/local/call_snv/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 4308f9a8d..3bf48c34f 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -155,8 +155,8 @@ workflow CALL_SNV { } ch_publish = GATK4_SELECTVARIANTS.out.vcf - .mix(GATK4_SELECTVARIANTS.out.tbi - .mix(ch_deepvar_report) + .mix(GATK4_SELECTVARIANTS.out.tbi) + .mix(ch_deepvar_publish) .map { meta, value -> ['call_snv/genome/', [meta, value]] } .mix(ch_concat_publish) .mix(ch_mt_snv_publish) From 8db7babba4b7b3c7103c47f697ae63a86452f925 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 25 Apr 2026 23:20:43 +0200 Subject: [PATCH 635/872] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 218ac7b39..0cebabd6d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,11 +30,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) -- Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno +- Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#802](https://github.com/nf-core/raredisease/pull/821) ### `Changed` -- Sort parameters of `CALL_STRUCTURAL_VARIANTS` and `CALL_SV_MANTA` alphabetically [[#](https://github.com/nf-core/raredisease/pull/)] - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) @@ -63,6 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from the config since this has to be set outside the subworkflow [#804](https://github.com/nf-core/raredisease/pull/804) - Run UPD_SITES, UPD_REGIONS, and CHROMOGRAPH for UPD only when analysis type is WGS [#806](https://github.com/nf-core/raredisease/pull/806) - Change saltshaker classification output from txt to html [#808](https://github.com/nf-core/raredisease/pull/808) +- Sort parameters of `CALL_STRUCTURAL_VARIANTS` and `CALL_SV_MANTA` alphabetically [#821](https://github.com/nf-core/raredisease/pull/821) ### `Fixed` From cc6eb7a34701417e8f1d82df77d4d2d5982833a2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Sat, 25 Apr 2026 21:22:18 +0000 Subject: [PATCH 636/872] [automated] Fix code linting --- CHANGELOG.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cebabd6d..9c826aadf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,17 +76,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------------- | ------------------------- | -| | sambamba_regions | -| bwa_as_fallback | | -| | multiqc_samples | -| | homoplasmy_af_threshold | -| | exclude_alt | -| save_mapped_as_cram | | -| | save_all_mapped_as_cram | -| | save_noalt_mapped_as_cram | -| | run_vcfanno_db_sanity_check | +| Old parameter | New parameter | +| ------------------- | --------------------------- | +| | sambamba_regions | +| bwa_as_fallback | | +| | multiqc_samples | +| | homoplasmy_af_threshold | +| | exclude_alt | +| save_mapped_as_cram | | +| | save_all_mapped_as_cram | +| | save_noalt_mapped_as_cram | +| | run_vcfanno_db_sanity_check | ### Tool updates From 295cd34633d0a0982302a499830161417059b200 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 26 Apr 2026 22:32:41 +0200 Subject: [PATCH 637/872] update snap --- .../local/call_snv/tests/main.nf.test.snap | 7 ++++--- .../call_snv_deepvariant/tests/main.nf.test.snap | 16 ++++++++++++++-- 2 files changed, 18 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index d43eef332..9991ce273 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -2,12 +2,13 @@ "CALL_SNV - deepvariant wgs": { "content": [ [ + "earlycasualcaiman_deepvar.visual_report.html", "justhusky_mitochondria.vcf.gz", "justhusky_mitochondria.vcf.gz.tbi", "justhusky_snv.vcf.gz", "justhusky_snv.vcf.gz.tbi" ], - "dc179c28435ffe6d3127fde7ca401337", + "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", [ "justhusky_snv.vcf.gz.tbi" @@ -16,9 +17,9 @@ "justhusky_mitochondria.vcf.gz" ] ], - "timestamp": "2026-04-22T18:04:13.466587948", + "timestamp": "2026-04-26T11:22:45.301474135", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } }, diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index e7c2ff4fd..6f17d088b 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -46,6 +46,12 @@ ], [ "2", + [ + + ] + ], + [ + "3", [ [ { @@ -56,7 +62,7 @@ ] ], [ - "3", + "4", [ [ { @@ -108,6 +114,12 @@ ] ] ], + [ + "publish", + [ + + ] + ], [ "tabix", [ @@ -132,7 +144,7 @@ ] ] ], - "timestamp": "2026-03-17T23:21:43.293315837", + "timestamp": "2026-04-26T11:35:57.486021267", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 739b570c47a11e71c1f17c24ae9779b693dc4bd9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Apr 2026 12:11:00 +0200 Subject: [PATCH 638/872] add skip split multiallelics parameter --- CHANGELOG.md | 25 ++++++++++--------- docs/usage.md | 16 ++++++------ main.nf | 3 +++ nextflow.config | 5 ++-- nextflow_schema.json | 6 +++++ subworkflows/local/call_snv/main.nf | 15 ++++++----- .../local/call_snv_deepvariant/main.nf | 19 ++++++++------ .../call_snv_deepvariant/tests/main.nf.test | 2 ++ subworkflows/local/call_snv_sentieon/main.nf | 20 +++++++++------ .../call_snv_sentieon/tests/main.nf.test | 2 ++ workflows/raredisease.nf | 2 ++ 11 files changed, 74 insertions(+), 41 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 218ac7b39..3d6aaa8a1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,7 +34,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Sort parameters of `CALL_STRUCTURAL_VARIANTS` and `CALL_SV_MANTA` alphabetically [[#](https://github.com/nf-core/raredisease/pull/)] - Use distinct output filenames for bcfools (in call_mobile_elements subworkflow) and svdb (in call_sv_tiddit subworkflow) [#716](https://github.com/nf-core/raredisease/pull/716) - Use nf-core's most severe consequence & pli scripts instead of local ones [#732](https://github.com/nf-core/raredisease/pull/732) - Use nf-core's VCF_FILTER_BCFTOOLS_ENSEMBLVEP subworkflow to generate clinical set instead of a local subworkflow [#727](https://github.com/nf-core/raredisease/pull/727) @@ -67,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - Fixed argument order of `ch_genome_fai` and `ch_genome_fasta` in the `CALL_SNV_SENTIEON` subworkflow [#811](https://github.com/nf-core/raredisease/pull/811) +- Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#8](https://github.com/nf-core/raredisease/pull/8) - Ensure deterministic sample ordering in Manta SV output by sorting BAM/BAI channel inputs [#815](https://github.com/nf-core/raredisease/pull/815) - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) @@ -76,17 +76,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| ------------------- | ------------------------- | -| | sambamba_regions | -| bwa_as_fallback | | -| | multiqc_samples | -| | homoplasmy_af_threshold | -| | exclude_alt | -| save_mapped_as_cram | | -| | save_all_mapped_as_cram | -| | save_noalt_mapped_as_cram | -| | run_vcfanno_db_sanity_check | +| Old parameter | New parameter | +| ------------------- | --------------------------- | +| | sambamba_regions | +| bwa_as_fallback | | +| | multiqc_samples | +| | homoplasmy_af_threshold | +| | exclude_alt | +| save_mapped_as_cram | | +| | save_all_mapped_as_cram | +| | save_noalt_mapped_as_cram | +| | run_vcfanno_db_sanity_check | +| | skip_split_multiallelics | ### Tool updates diff --git a/docs/usage.md b/docs/usage.md index 0a17c0194..a3811b3e9 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -246,18 +246,20 @@ The mandatory and optional parameters for each category are tabulated below. ##### 4. Variant calling - SNV -| Mandatory | Optional | -| -------------------------- | --------------------------- | -| variant_caller1 | known_dbsnp2 | -| ml_model2 | known_dbsnp_tbi2 | -| analysis_type3 | call_interval2 | -| | known_dbsnp_tbi2 | -| | par_bed4 | +| Mandatory | Optional | +| -------------------------- | ------------------------------------- | +| variant_caller1 | known_dbsnp2 | +| ml_model2 | known_dbsnp_tbi2 | +| analysis_type3 | call_interval2 | +| | known_dbsnp_tbi2 | +| | par_bed4 | +| | skip_split_multiallelics5 | 1Default variant caller is DeepVariant, but you have the option to use Sentieon as well.
    2These parameters are only used by Sentieon.
    3Default is `WGS`, but you have the option to choose `WES` and `mito` as well.
    4This parameter is only used by Deepvariant.
    +5Skips `bcftools norm --multiallelics -both` in both DeepVariant and Sentieon SNV calling. Recommended for single-interval runs to avoid indel quality degradation. See [#813](https://github.com/nf-core/raredisease/issues/813) for details.
    ##### 5. Variant calling - Structural variants diff --git a/main.nf b/main.nf index 789a3d62a..f847e20e6 100644 --- a/main.nf +++ b/main.nf @@ -51,6 +51,7 @@ workflow NFCORE_RAREDISEASE { val_cadd_resources val_call_interval val_concatenate_snv_calls + val_skip_split_multiallelics val_exclude_alt val_extract_alignments val_fai @@ -479,6 +480,7 @@ workflow NFCORE_RAREDISEASE { val_analysis_type, val_cadd_resources, val_concatenate_snv_calls, + val_skip_split_multiallelics, val_exclude_alt, val_extract_alignments, val_genome, @@ -567,6 +569,7 @@ workflow { params.cadd_resources, params.call_interval, params.concatenate_snv_calls, + params.skip_split_multiallelics, params.exclude_alt, params.extract_alignments, params.fai, diff --git a/nextflow.config b/nextflow.config index 7de7a6548..cd152e33e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -28,6 +28,7 @@ params { // Main options analysis_type = 'wgs' bait_padding = 100 + cadd_resources = null concatenate_snv_calls = false exclude_alt = false extract_alignments = false @@ -40,9 +41,9 @@ params { save_all_mapped_as_cram = false save_noalt_mapped_as_cram = false scatter_count = 20 - skip_tools = null + skip_split_multiallelics = false skip_subworkflows = null - cadd_resources = null + skip_tools = null platform = 'illumina' // reference file options diff --git a/nextflow_schema.json b/nextflow_schema.json index 7a7a3a629..c1289e4f3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -602,6 +602,12 @@ "description": "Number of intervals to split your genome into (used to parallelize annotations)", "fa_icon": "fas fa-less-than" }, + "skip_split_multiallelics": { + "type": "boolean", + "fa_icon": "fas fa-forward", + "description": "Skip the split multiallelics step in SNV calling.", + "help_text": "Skips bcftools norm --multiallelics -both in CALL_SNV_SENTIEON and CALL_SNV_DEEPVARIANT. Useful for single-interval runs where the step is unnecessary and can degrade indel quality." + }, "skip_subworkflows": { "type": "string", "fa_icon": "fas fa-forward", diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 3bf48c34f..c7e0cb799 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -36,10 +36,11 @@ workflow CALL_SNV { ch_par_bed // channel: [optional] [ val(meta), path(bed) ] ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] - val_analysis_type // string: 'wgs', 'wes', or 'mito' - val_concatenate_snv_calls // boolean - val_run_mt_for_wes // boolean - val_variant_caller // string: 'deepvariant' or 'sentieon' + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_concatenate_snv_calls // boolean + val_run_mt_for_wes // boolean + val_skip_split_multiallelics // boolean + val_variant_caller // string: 'deepvariant' or 'sentieon' main: ch_concat_publish = channel.empty() @@ -67,7 +68,8 @@ workflow CALL_SNV { ch_genome_fasta, ch_par_bed, ch_target_bed, - val_analysis_type + val_analysis_type, + val_skip_split_multiallelics ) ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix @@ -86,7 +88,8 @@ workflow CALL_SNV { ch_genome_fai, ch_genome_fasta, ch_ml_model, - ch_pcr_indel_model + ch_pcr_indel_model, + val_skip_split_multiallelics ) ch_sentieon_vcf = CALL_SNV_SENTIEON.out.vcf ch_sentieon_tbi = CALL_SNV_SENTIEON.out.tabix diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 869df2ec5..9cffeebe0 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -18,9 +18,10 @@ workflow CALL_SNV_DEEPVARIANT { ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_par_bed // channel: [optional] [ val(meta), path(bed) ] - ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] - val_analysis_type // boolean + ch_par_bed // channel: [optional] [ val(meta), path(bed) ] + ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ] + val_analysis_type // boolean + val_skip_split_multiallelics // boolean main: @@ -55,11 +56,15 @@ workflow CALL_SNV_DEEPVARIANT { ch_split_multi_in = GLNEXUS.out.bcf .map{ meta, bcf -> return [meta, bcf, []] } - SPLIT_MULTIALLELICS_GL (ch_split_multi_in, ch_genome_fasta) - ch_remove_dup_in = SPLIT_MULTIALLELICS_GL.out.vcf - .map{ meta, vcf -> - return [meta, vcf, []] } + if (!val_skip_split_multiallelics) { + SPLIT_MULTIALLELICS_GL (ch_split_multi_in, ch_genome_fasta) + ch_remove_dup_in = SPLIT_MULTIALLELICS_GL.out.vcf + .map{ meta, vcf -> + return [meta, vcf, []] } + } else { + ch_remove_dup_in = ch_split_multi_in + } REMOVE_DUPLICATES_GL (ch_remove_dup_in, ch_genome_fasta) ch_genome_chrsizes.flatten().map{chromsizes -> diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index adafadd4a..5ea64aa2f 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -37,6 +37,7 @@ nextflow_workflow { input[6] = channel.of([[id:'par'], []]) input[7] = channel.of([[id:'target'], [], []]) input[8] = 'wgs' + input[9] = false """ } } @@ -73,6 +74,7 @@ nextflow_workflow { input[6] = channel.of([[id:'par'], []]) input[7] = channel.of([[id:'target'], [], []]) input[8] = 'wgs' + input[9] = false """ } } diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index 75a78412f..b4e54e633 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -23,8 +23,9 @@ workflow CALL_SNV_SENTIEON { ch_genome_chrsizes // channel: [mandatory] [ path(chrsizes) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_ml_model // channel: [mandatory] [ val(meta), path(model) ] - ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] + ch_ml_model // channel: [mandatory] [ val(meta), path(model) ] + ch_pcr_indel_model // channel: [optional] [ val(sentieon_dnascope_pcr_indel_model) ] + val_skip_split_multiallelics // boolean main: // Combine bam and intervals @@ -79,11 +80,16 @@ workflow CALL_SNV_SENTIEON { ch_vcf_idx_case = ch_vcf_idx_merge_in.single.mix(ch_split_multi_in) - SPLIT_MULTIALLELICS_SEN(ch_vcf_idx_case, ch_genome_fasta) - - ch_remove_dup_in = SPLIT_MULTIALLELICS_SEN.out.vcf - .map{meta, vcf -> - return [meta, vcf, []]} + if (!val_skip_split_multiallelics) { + SPLIT_MULTIALLELICS_SEN(ch_vcf_idx_case, ch_genome_fasta) + ch_remove_dup_in = SPLIT_MULTIALLELICS_SEN.out.vcf + .map{meta, vcf -> + return [meta, vcf, []]} + } else { + ch_remove_dup_in = ch_vcf_idx_case + .map{meta, vcf, _idx -> + return [meta, vcf, []]} + } REMOVE_DUPLICATES_SEN(ch_remove_dup_in, ch_genome_fasta) diff --git a/subworkflows/local/call_snv_sentieon/tests/main.nf.test b/subworkflows/local/call_snv_sentieon/tests/main.nf.test index b80e0d774..9011c759f 100644 --- a/subworkflows/local/call_snv_sentieon/tests/main.nf.test +++ b/subworkflows/local/call_snv_sentieon/tests/main.nf.test @@ -39,6 +39,7 @@ nextflow_workflow { input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'model'], []]) input[10] = channel.value([]) + input[11] = false """ } } @@ -80,6 +81,7 @@ nextflow_workflow { input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'model'], []]) input[10] = channel.value([]) + input[11] = false """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 31042b757..400ce17ce 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -181,6 +181,7 @@ workflow RAREDISEASE { val_analysis_type val_cadd_resources val_concatenate_snv_calls + val_skip_split_multiallelics val_exclude_alt val_extract_alignments val_genome @@ -434,6 +435,7 @@ workflow RAREDISEASE { ch_target_bed, val_analysis_type, val_concatenate_snv_calls, + val_skip_split_multiallelics, val_run_mt_for_wes, val_variant_caller ) From e2f9a36d2b650482f23a7df4d79137cf83806a77 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Apr 2026 12:20:26 +0200 Subject: [PATCH 639/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 788efd879..882750e44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) +- Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) ### `Changed` @@ -67,7 +68,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - Fixed argument order of `ch_genome_fai` and `ch_genome_fasta` in the `CALL_SNV_SENTIEON` subworkflow [#811](https://github.com/nf-core/raredisease/pull/811) -- Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#8](https://github.com/nf-core/raredisease/pull/8) - Ensure deterministic sample ordering in Manta SV output by sorting BAM/BAI channel inputs [#815](https://github.com/nf-core/raredisease/pull/815) - Fixed inconsistencies in JSON schema [#714](https://github.com/nf-core/raredisease/pull/714) - Fixed conda declaration in the add_varcallername_to_bed module [#733](https://github.com/nf-core/raredisease/pull/733) From 15e0381e5af62cfc6df27c9020692f6fcaa7e411 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Apr 2026 14:05:10 +0200 Subject: [PATCH 640/872] Update main.nf.test --- subworkflows/local/call_snv/tests/main.nf.test | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 441187295..1c0a323c9 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -59,7 +59,8 @@ nextflow_workflow { input[24] = 'wgs' input[25] = false input[26] = false - input[27] = 'deepvariant' + input[27] = false + input[28] = 'deepvariant' """ } } @@ -127,7 +128,8 @@ nextflow_workflow { input[24] = 'wgs' input[25] = false input[26] = false - input[27] = 'deepvariant' + input[27] = false + input[28] = 'deepvariant' """ } } From d771f2f7d9d242f07a5dea22e2b150133f2b27e7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 27 Apr 2026 14:50:55 +0200 Subject: [PATCH 641/872] Fix linting --- docs/usage.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a3811b3e9..c25bb64ac 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -246,14 +246,14 @@ The mandatory and optional parameters for each category are tabulated below. ##### 4. Variant calling - SNV -| Mandatory | Optional | -| -------------------------- | ------------------------------------- | -| variant_caller1 | known_dbsnp2 | -| ml_model2 | known_dbsnp_tbi2 | -| analysis_type3 | call_interval2 | -| | known_dbsnp_tbi2 | -| | par_bed4 | -| | skip_split_multiallelics5 | +| Mandatory | Optional | +| -------------------------- | ------------------------------------ | +| variant_caller1 | known_dbsnp2 | +| ml_model2 | known_dbsnp_tbi2 | +| analysis_type3 | call_interval2 | +| | known_dbsnp_tbi2 | +| | par_bed4 | +| | skip_split_multiallelics5 | 1Default variant caller is DeepVariant, but you have the option to use Sentieon as well.
    2These parameters are only used by Sentieon.
    From cf755c4bd5f93c9880b90060fefb5348bfbc9f0b Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 27 Apr 2026 15:53:41 +0200 Subject: [PATCH 642/872] Modified assertion for the sub tests and updated snapshot --- subworkflows/local/qc_bam/tests/main.nf.test | 19 ++- .../local/qc_bam/tests/main.nf.test.snap | 134 +++++++++++++++++- 2 files changed, 145 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 3f1ac7d91..0b630a835 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -137,7 +137,13 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() + } ) } @@ -258,9 +264,14 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out).match() } + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ).match() + } ) } - } - +} } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 42f458e1c..a13789caf 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -1,4 +1,130 @@ { + "QC_BAM - test, bwamem2, stub": { + "content": [ + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.per-base.d4", + "earlycasualcaiman_mosdepth.quantized.bed.gz", + "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "earlycasualcaiman_mosdepth.region.dist.txt", + "earlycasualcaiman_mosdepth.regions.bed.gz", + "earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "earlycasualcaiman_mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.thresholds.bed.gz", + "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bed", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png", + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-27T15:31:05.442602988" + }, + "QC_BAM - test, sentieon, stub": { + "content": [ + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_mosdepth.per-base.d4", + "earlycasualcaiman_mosdepth.quantized.bed.gz", + "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "earlycasualcaiman_mosdepth.region.dist.txt", + "earlycasualcaiman_mosdepth.regions.bed.gz", + "earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "earlycasualcaiman_mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.thresholds.bed.gz", + "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bed", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png", + "earlycasualcaiman_wgsmetrics.txt" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-04-27T15:38:50.479811008" + }, "QC_BAM - test, bwamem2": { "content": [ [ @@ -117,11 +243,11 @@ ] ] ], - "timestamp": "2026-03-27T16:45:40.990778813", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T16:45:40.990778813" }, "QC_BAM - test, sentieon": { "content": [ @@ -241,10 +367,10 @@ ] ] ], - "timestamp": "2026-03-27T17:07:36.836738984", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T17:07:36.836738984" } } \ No newline at end of file From 974e1a53e95bb34cd9ffca100f7dccce61e47046 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 28 Apr 2026 11:21:04 +0000 Subject: [PATCH 643/872] Template update for nf-core/tools version 4.0.0 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 125 -- .github/PULL_REQUEST_TEMPLATE.md | 4 +- .github/actions/get-shards/action.yml | 2 +- .github/actions/nf-test/action.yml | 10 +- .github/workflows/awsfulltest.yml | 25 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 14 +- .github/workflows/fix_linting.yml | 22 +- .github/workflows/linting.yml | 34 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/nf-test.yml | 8 +- .github/workflows/release-announcements.yml | 4 +- .../workflows/template-version-comment.yml | 6 +- .gitignore | 1 + .nf-core.yml | 2 +- .pre-commit-config.yaml | 16 +- .prettierignore | 2 - README.md | 12 +- assets/adaptivecard.json | 67 - assets/slackreport.json | 34 - conf/base.config | 2 +- conf/containers_conda_lock_files_amd64.config | 2 + conf/containers_conda_lock_files_arm64.config | 2 + conf/containers_docker_amd64.config | 2 + conf/containers_docker_arm64.config | 2 + .../containers_singularity_https_amd64.config | 2 + .../containers_singularity_https_arm64.config | 2 + conf/containers_singularity_oras_amd64.config | 2 + conf/containers_singularity_oras_arm64.config | 2 + docs/CONTRIBUTING.md | 185 ++ docs/usage.md | 8 +- main.nf | 7 +- modules.json | 8 +- .../linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt | 822 +++++++++ .../linux_arm64-bd-e455e32f745abe68_1.txt | 769 ++++++++ modules/nf-core/fastqc/main.nf | 43 +- modules/nf-core/fastqc/meta.yml | 51 +- modules/nf-core/fastqc/tests/main.nf.test | 12 +- .../nf-core/fastqc/tests/main.nf.test.snap | 228 ++- .../linux_amd64-bd-c1f4a7982b743963_1.txt | 1552 +++++++++++++++++ .../linux_amd64-bd-db7c73dae76bc9e6_1.txt | 126 ++ .../linux_arm64-bd-40bf3b435e89dc22_1.txt | 1502 ++++++++++++++++ .../linux_arm64-bd-d167b8012595a136_1.txt | 125 ++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 51 +- modules/nf-core/multiqc/meta.yml | 165 +- .../multiqc/tests/custom_prefix.config | 5 + modules/nf-core/multiqc/tests/main.nf.test | 191 +- .../nf-core/multiqc/tests/main.nf.test.snap | 435 ++++- modules/nf-core/multiqc/tests/nextflow.config | 1 + nextflow.config | 8 +- nextflow_schema.json | 7 - nf-test.config | 26 +- ro-crate-metadata.json | 30 +- .../utils_nfcore_raredisease_pipeline/main.nf | 17 +- .../nf-core/utils_nfcore_pipeline/main.nf | 66 +- .../utils_nfcore_pipeline/tests/main.nf.test | 29 + .../tests/main.nf.test.snap | 19 + .../nf-core/utils_nfschema_plugin/main.nf | 3 +- .../tests/nextflow.config | 2 +- tests/default.nf.test | 14 +- tests/nextflow.config | 2 +- workflows/raredisease.nf | 84 +- 66 files changed, 6276 insertions(+), 738 deletions(-) delete mode 100644 .github/CONTRIBUTING.md delete mode 100644 assets/adaptivecard.json delete mode 100644 assets/slackreport.json create mode 100644 conf/containers_conda_lock_files_amd64.config create mode 100644 conf/containers_conda_lock_files_arm64.config create mode 100644 conf/containers_docker_amd64.config create mode 100644 conf/containers_docker_arm64.config create mode 100644 conf/containers_singularity_https_amd64.config create mode 100644 conf/containers_singularity_https_arm64.config create mode 100644 conf/containers_singularity_oras_amd64.config create mode 100644 conf/containers_singularity_oras_arm64.config create mode 100644 docs/CONTRIBUTING.md create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt create mode 100644 modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c1f4a7982b743963_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-40bf3b435e89dc22_1.txt create mode 100644 modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt create mode 100644 modules/nf-core/multiqc/tests/custom_prefix.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 97c8c97fe..237c9ed08 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,4 +1,5 @@ { + "$schema": "https://raw.githubusercontent.com/devcontainers/spec/main/schemas/devContainer.schema.json", "name": "nfcore", "image": "nfcore/devcontainer:latest", diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 23e34a03f..000000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,125 +0,0 @@ -# `nf-core/raredisease`: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/raredisease. - -We try to manage the required tasks for nf-core/raredisease using GitHub issues, you probably came to this page when creating one. -Please use the pre-filled template to save time. - -However, don't be put off by this template - other more general issues and suggestions are welcome! -Contributions to the code are even more welcome ;) - -> [!NOTE] -> If you need help using or modifying nf-core/raredisease then the best place to ask is on the nf-core Slack [#raredisease](https://nfcore.slack.com/channels/raredisease) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/raredisease, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/raredisease issues](https://github.com/nf-core/raredisease/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/raredisease repository](https://github.com/nf-core/raredisease) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: - -```bash -nf-test test --profile debug,test,docker --verbose -``` - -When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. -Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- Open a pull-request from `patch` to `main`/`master` with the changes. - -## Getting help - -For further information/help, please consult the [nf-core/raredisease documentation](https://nf-co.re/raredisease/usage) and don't hesitate to get in touch on the nf-core Slack [#raredisease](https://nfcore.slack.com/channels/raredisease) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the `nf-core/raredisease` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel. -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). -6. Add sanity checks and validation for all relevant parameters. -7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test in the `tests` directory. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. - -Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. - -The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` - -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## GitHub Codespaces - -This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. - -To get started: - -- Open the repo in [Codespaces](https://github.com/nf-core/raredisease/codespaces) -- Tools installed - - nf-core - - Nextflow - -Devcontainer specs: - -- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 3691cefcd..4fe1d1426 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/raredisease/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/raredisease/tree/master/docs/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/raredisease/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/raredisease/tree/master/docs/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/raredisease _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml index 34085279f..e2833ee97 100644 --- a/.github/actions/get-shards/action.yml +++ b/.github/actions/get-shards/action.yml @@ -21,7 +21,7 @@ runs: using: "composite" steps: - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: ${{ env.NFT_VER }} - name: Get number of shards diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c76..ad686e8e8 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -20,24 +20,24 @@ runs: using: "composite" steps: - name: Setup Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 with: version: "${{ env.NXF_VERSION }}" - name: Set up Python - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" - name: Install nf-test - uses: nf-core/setup-nf-test@v1 + uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 with: version: "${{ env.NFT_VER }}" install-pdiff: true - name: Setup apptainer if: contains(inputs.profile, 'singularity') - uses: eWaterCycle/setup-apptainer@main + uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2 - name: Set up Singularity if: contains(inputs.profile, 'singularity') @@ -48,7 +48,7 @@ runs: - name: Conda setup if: contains(inputs.profile, 'conda') - uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4 with: auto-update-conda: true conda-solver: libmamba diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 5cc5ff209..cda3bb0dd 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -23,7 +23,7 @@ jobs: echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -33,14 +33,33 @@ jobs: compute_env: ${{ vars.TOWER_COMPUTE_ENV }} revision: ${{ steps.revision.outputs.revision }} workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/raredisease/work-${{ steps.revision.outputs.revision }} + nextflow_config: | + plugins { + id 'nf-slack@0.5.0' + } + slack { + enabled = true + bot { + token = '${{ secrets.NFSLACK_BOT_TOKEN }}' + channel = 'raredisease' + } + onStart { + enabled = false + } + onComplete { + message = ':white_check_mark: *raredisease/test_full* completed successfully! :tada:' + } + onError { + message = ':x: *raredisease/test_full* failed :crying_cat_face:' + } + } parameters: | { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/raredisease/results-${{ steps.revision.outputs.revision }}" } profiles: test_full - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index ce658b626..3a35ecdb4 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Seqera Platform CLI tool action - name: Launch workflow via Seqera Platform - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@51565b514bff1827cf34620de25d0055759f1fc9 # v2 with: workspace_id: ${{ vars.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: Seqera Platform debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index a7f9e1bad..6629f3ef5 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -21,7 +21,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 with: message: | ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 6adb0fff4..172de6f37 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 + - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 45884ff90..5b6592c1e 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -39,12 +39,12 @@ jobs: needs: configure steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" @@ -54,10 +54,16 @@ jobs: with: apptainer-version: 1.3.4 + - name: Read .nf-core.yml + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Make a cache directory for the container images run: | @@ -127,7 +133,7 @@ jobs: fi - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: nextflow_logfile.txt path: .nextflow.log* diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index ebf4b81c9..1e256aebb 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -31,22 +31,18 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - # Install and run pre-commit - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - id: pre-commit - run: pre-commit run --all-files + # Install and run prek + - name: Run prek + id: prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 continue-on-error: true # indication that the linting has finished - name: react if linting finished succesfully - if: steps.pre-commit.outcome == 'success' + if: steps.prek.outcome == 'success' uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 with: comment-id: ${{ github.event.comment.id }} @@ -54,7 +50,7 @@ jobs: - name: Commit & push changes id: commit-and-push - if: steps.pre-commit.outcome == 'failure' + if: steps.prek.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7a527a346..bfe46c98f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,33 +11,31 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - - name: Set up Python 3.14 - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 - with: - python-version: "3.14" - - - name: Install pre-commit - run: pip install pre-commit + - name: Install Nextflow + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run prek + uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 + - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 with: python-version: "3.14" architecture: "x64" + - name: Setup uv + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 + - name: read .nf-core.yml uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml @@ -45,12 +43,10 @@ jobs: config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' }} + if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -58,7 +54,7 @@ jobs: run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Run nf-core pipelines lint --release - if: ${{ github.base_ref == 'master' }} + if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} @@ -71,7 +67,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index e6e9bc269..2bc3c07fd 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 + uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 + uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index c98d76ec7..efd72d653 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -18,7 +18,7 @@ concurrency: env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - NFT_VER: "0.9.3" + NFT_VER: "0.9.4" NFT_WORKDIR: "~" NXF_ANSI_LOG: false NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity @@ -40,7 +40,7 @@ jobs: rm -rf ./* || true rm -rf ./.??* || true ls -la ./ - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 @@ -78,14 +78,14 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "25.04.0" + - "25.10.4" - "latest-everything" env: NXF_ANSI_LOG: false TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} steps: - - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: fetch-depth: 0 diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 431d3d445..78d5dbe05 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -18,7 +18,7 @@ jobs: id: get_description run: | echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT - - uses: rzr/fediverse-action@master + - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) @@ -34,7 +34,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 + - uses: zentered/bluesky-post-action@5a91cc2ad10a304a4e96c16182dbe4918710bcf6 # v0.4.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml index e8560fc7c..ea30827ec 100644 --- a/.github/workflows/template-version-comment.yml +++ b/.github/workflows/template-version-comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 with: ref: ${{ github.event.pull_request.head.sha }} @@ -29,7 +29,7 @@ jobs: run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3 if: | contains(env.OUTPUT, 'nf-core') with: @@ -42,5 +42,5 @@ jobs: > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. > Please update your pipeline to the latest version. > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview). # diff --git a/.gitignore b/.gitignore index a42ce0162..cc2b1a778 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc null/ +.lineage/ diff --git a/.nf-core.yml b/.nf-core.yml index c30136f84..4b01d75e6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,7 +8,7 @@ lint: - docs/images/nf-core-raredisease_logo_light.png - assets/nf-core-raredisease_logo_light.png modules_config: false -nf_core_version: 3.5.1 +nf_core_version: 4.0.0 repository_type: pipeline template: author: Clinical Genomics Stockholm diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d06777a8f..f51e1a28d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.6.2 + - prettier@3.8.3 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: @@ -13,15 +13,21 @@ repos: exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ - id: end-of-file-fixer exclude: | (?x)^( .*ro-crate-metadata.json$| - modules/nf-core/.*| - subworkflows/nf-core/.*| + modules/(?!local/).*| + subworkflows/(?!local/).*| .*\.snap$ )$ + - repo: https://github.com/seqeralabs/nf-lint-pre-commit + rev: v0.3.0 + hooks: + - id: nextflow-lint + files: '\.nf$|nextflow\.config$' + args: ["-output", "json"] diff --git a/.prettierignore b/.prettierignore index dd749d43d..63cde500e 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,4 @@ email_template.html -adaptivecard.json -slackreport.json .nextflow* work/ data/ diff --git a/README.md b/README.md index 69f34e906..d7dace8d4 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -30,13 +30,13 @@ --> + workflows use the "tube map" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples. --> 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data. diff --git a/docs/usage.md b/docs/usage.md index 4d6a6b2d4..616541dc0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -76,7 +76,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > [!WARNING] -> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/running/run-pipelines#configuring-pipelines), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -173,19 +173,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. +To change the resource requests, please see the [max resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#set-max-resources) and [customise process resources](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources) section of the nf-core website. ### Custom Containers In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. -To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#update-tool-versions) section of the nf-core website. ### Custom Tool Arguments A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#modifying-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/main.nf b/main.nf index 68e9a1bd2..eca89f320 100644 --- a/main.nf +++ b/main.nf @@ -51,7 +51,11 @@ workflow NFCORE_RAREDISEASE { // WORKFLOW: Run pipeline // RAREDISEASE ( - samplesheet + samplesheet, + params.multiqc_config, + params.multiqc_logo, + params.multiqc_methods_description, + params.outdir, ) emit: multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html @@ -95,7 +99,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_RAREDISEASE.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 618ec0652..8319fdaa6 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", + "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", "installed_by": ["modules"] } } @@ -26,12 +26,12 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", + "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", + "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt new file mode 100644 index 000000000..7770ccd5f --- /dev/null +++ b/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt @@ -0,0 +1,822 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda +- conda: 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conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' + : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads, stageAs: '?/*') output: tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions + tuple val(meta), path("*.zip"), emit: zip + tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null + // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label + def memory_in_mb = task.memory + ? (task.memory.toUnit('MB') / task.cpus).intValue() + : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : '' """ printf "%s %s\\n" ${rename_to} | while read old_name new_name; do @@ -41,13 +44,8 @@ process FASTQC { fastqc \\ ${args} \\ --threads ${task.cpus} \\ - --memory ${fastqc_memory} \\ + ${fastqc_memory_arg} \\ ${renamed_files} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ stub: @@ -55,10 +53,5 @@ process FASTQC { """ touch ${prefix}.html touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index c8d9d025a..2f6cfef6d 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -53,13 +53,28 @@ output: description: FastQC report archive pattern: "*_{fastqc.zip}" ontologies: [] + versions_fastqc: + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//": + type: eval + description: The expression to obtain the version of the tool + +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The process the versions were collected from + - fastqc: + type: string + description: The tool name + - fastqc --version | sed "/FastQC v/!d; s/.*v//": + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@grst" @@ -70,3 +85,27 @@ maintainers: - "@grst" - "@ewels" - "@FelixKrueger" +containers: + docker: + linux/arm64: + name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68 + build_id: bd-e455e32f745abe68_1 + scan_id: sc-f102f736465af88c_1 + linux/amd64: + name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2 + build_id: bd-5cb1a2fa2f18c7c2_1 + scan_id: sc-0c0466326b6b77d2_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd + build_id: bd-5c4bd442468d75dd_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data + linux/arm64: + name: oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035 + build_id: bd-127a87fc06499035_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data + conda: + linux/amd64: + lock_file: modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt + linux/arm64: + lock_file: modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a074..66c44da9b 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -30,7 +30,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -58,7 +58,7 @@ nextflow_process { { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -82,7 +82,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -106,7 +106,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -142,7 +142,7 @@ nextflow_process { { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } @@ -166,7 +166,7 @@ nextflow_process { { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(sanitizeOutput(process.out).findAll { key, val -> key != 'html' && key != 'zip' }).match() } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db3092f..c8ee120f5 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,15 +1,21 @@ { "sarscov2 custom_prefix": { "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] + ] + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "25.10.0" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2025-10-28T16:39:14.518503" }, "sarscov2 single-end [fastq] - stub": { "content": [ @@ -33,7 +39,11 @@ ] ], "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "html": [ [ @@ -44,8 +54,12 @@ "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + "versions_fastqc": [ + [ + "FASTQC", + "fastqc", + "0.12.1" + ] ], "zip": [ [ @@ -59,10 +73,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": 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create an environment using: +# $ conda create --name --file +# platform: linux-aarch64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958 +https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d +https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6 +https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d +https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1 +https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc +https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.45.1-default_h1979696_102.conda#a21644fc4a83da26452a718dc9468d5f 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+https://conda.anaconda.org/conda-forge/noarch/polars-1.40.0-pyh58ad624_0.conda#fd16be490f5403adfbf27dd4901bbe34 +https://conda.anaconda.org/conda-forge/linux-aarch64/polars-runtime-compat-1.40.0-py310hf00a4a2_0.conda#a82af0fcbb72db253dc89a7a45279372 +https://conda.anaconda.org/conda-forge/noarch/polars-lts-cpu-1.34.0.deprecated-hc364b38_0.conda#ef0340e75068ac8ff96462749b5c98e7 +https://conda.anaconda.org/conda-forge/linux-aarch64/yaml-0.2.5-h80f16a2_3.conda#032d8030e4a24fe1f72c74423a46fb88 +https://conda.anaconda.org/conda-forge/linux-aarch64/pyyaml-6.0.3-py314h807365f_1.conda#9ae2c92975118058bd720e9ba2bb7c58 +https://conda.anaconda.org/conda-forge/noarch/pyaml-env-1.2.2-pyhd8ed1ab_0.conda#e17be1016bcc3516827b836cd3e4d9dc +https://conda.anaconda.org/conda-forge/linux-aarch64/pydantic-core-2.46.3-py314h451b6cc_0.conda#1a2cb55be9a153ad6203bff6b787c240 +https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6 +https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98 +https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c +https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2 +https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac +https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130 +https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59 +https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0 +https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66 +https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9 +https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a +https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864 +https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6 +https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206 +https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b +https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873 +https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f +https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index d02016a00..37e7612d4 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.32 + - bioconda::multiqc=1.34 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index c1158fb08..e80e8cd8d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,24 +1,21 @@ process MULTIQC { + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : - 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' + : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) + tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions + tuple val(meta), path("*.html"), emit: report + tuple val(meta), path("*_data"), emit: data + tuple val(meta), path("*_plots"), emit: plots, optional: true + // MultiQC should not push its versions to the `versions` topic. Its input depends on the versions topic to be resolved thus outputting to the topic will let the pipeline hang forever + tuple val("${task.process}"), val('multiqc'), eval('multiqc --version | sed "s/.* //g"'), emit: versions when: task.ext.when == null || task.ext.when @@ -26,38 +23,28 @@ process MULTIQC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def config = multiqc_config ? multiqc_config instanceof List ? "--config ${multiqc_config.join(' --config ')}" : "--config ${multiqc_config}" : "" def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' def replace = replace_names ? "--replace-names ${replace_names}" : '' def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ + ${args} \\ + ${config} \\ + ${prefix} \\ + ${logo} \\ + ${replace} \\ + ${samples} \\ . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ stub: """ mkdir multiqc_data + touch multiqc_data/.stub mkdir multiqc_plots + touch multiqc_plots/.stub touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS """ } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ce30eb732..2facc627b 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report +description: Aggregate results from bioinformatics analyses across many samples + into a single report keywords: - QC - bioinformatics tools @@ -12,74 +12,91 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + licence: + - "GPL-3.0-or-later" identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - ontologies: [] - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - ontologies: [] - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 # TSV -output: - report: - - "*multiqc_report.html": + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - multiqc_files: type: file - description: MultiQC report file - pattern: "multiqc_report.html" + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC ontologies: [] - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - plots: - - "*_plots": + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 + - multiqc_logo: type: file - description: Plots created by MultiQC - pattern: "*_data" + description: Optional logo file for MultiQC + pattern: "*.{png}" ontologies: [] - versions: - - versions.yml: + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 + - sample_names: type: file - description: File containing software versions - pattern: "versions.yml" + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - edam: http://edamontology.org/format_3475 +output: + report: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*.html": + type: file + description: MultiQC report file + pattern: ".html" + ontologies: [] + data: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1', single_end:false ] + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_plots" + ontologies: [] + versions: + - - ${task.process}: + type: string + description: The process the versions were collected from + - multiqc: + type: string + description: The tool name + - multiqc --version | sed "s/.* //g": + type: eval + description: The expression to obtain the version of the tool authors: - "@abhi18av" - "@bunop" @@ -90,3 +107,27 @@ maintainers: - "@bunop" - "@drpatelh" - "@jfy133" +containers: + conda: + linux/amd64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt + linux/arm64: + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt + docker: + linux/amd64: + name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 + build_id: bd-db7c73dae76bc9e6_1 + scan_id: sc-66fc7138dbf1cf48_1 + linux/arm64: + name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 + build_id: bd-d167b8012595a136_1 + scan_id: sc-ac701dfa631a2af9_1 + singularity: + linux/amd64: + name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 + build_id: bd-4fc8657c816047c0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data + linux/arm64: + name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 + build_id: bd-7fbd82d945c06726_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data diff --git a/modules/nf-core/multiqc/tests/custom_prefix.config b/modules/nf-core/multiqc/tests/custom_prefix.config new file mode 100644 index 000000000..b30b1358b --- /dev/null +++ b/modules/nf-core/multiqc/tests/custom_prefix.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = "custom_prefix" + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 33316a7dd..4cbdb95d4 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -15,25 +15,84 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] - custom prefix") { + config "./custom_prefix.config" + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) + """ + } } + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } } test("sarscov2 single-end [fastqc] [config]") { @@ -41,23 +100,85 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + [], + [], + [] + ]) """ } } then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() + } + } + + test("sarscov2 single-end [fastqc] [multiple configs]") { + + when { + process { + """ + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [ + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) + ], + [], + [], + [] + ]) + """ + } + } + + then { + assert process.success + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -68,25 +189,23 @@ nextflow_process { when { process { """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + input[0] = channel.of([ + [ id: 'FASTQC' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), + [], + [], + [], + [] + ]) """ } } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } + { assert snapshot(sanitizeOutput(process.out)).match() } ) } - } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index a88bafd67..7c2f370f3 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,41 +1,422 @@ { - "multiqc_versions_single": { + "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:33:24.356715" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_stub": { + "sarscov2 single-end [fastqc]": { "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:34:11.103619" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, - "multiqc_versions_config": { + "sarscov2 single-end [fastqc] - stub": { "content": [ - [ - "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" - ] + { + "data": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "plots": [ + [ + { + "id": "FASTQC" + }, + [ + ".stub:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "report": [ + [ + { + "id": "FASTQC" + }, + "multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { - "nf-test": "0.9.3", - "nextflow": "24.10.4" - }, - "timestamp": "2025-10-27T13:34:04.615233" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] [config]": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:30.372239611", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 single-end [fastqc] - custom prefix": { + "content": [ + { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", + "versions": [ + [ + "MULTIQC", + "multiqc", + "1.34" + ] + ] + } + ], + "timestamp": "2026-03-17T16:15:18.189023981", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config index c537a6a3e..374dfef2c 100644 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: 'MULTIQC' { ext.prefix = null + ext.args = '-p' } } diff --git a/nextflow.config b/nextflow.config index 670d8aea1..d10bddda8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -32,7 +32,6 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false @@ -53,6 +52,10 @@ params { validate_params = true } +// Backwards compatibility for publishDir syntax +outputDir = params.outdir +workflow.output.mode = params.publish_dir_mode + // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -251,7 +254,7 @@ manifest { description = """call and score variants from WGS/WES of rare disease patients""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=25.04.0' + nextflowVersion = '!>=25.10.4' version = '2.7.0dev' doi = '' } @@ -265,6 +268,5 @@ validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs } - // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 365fd7129..4f86ae951 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -180,13 +180,6 @@ "fa_icon": "fas fa-palette", "hidden": true }, - "hook_url": { - "type": "string", - "description": "Incoming hook URL for messaging service", - "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", - "hidden": true - }, "multiqc_config": { "type": "string", "format": "file-path", diff --git a/nf-test.config b/nf-test.config index 3a1fff59f..f7aaeb4a1 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,21 +1,35 @@ config { // location for all nf-test tests - testsDir "." + testsDir = "." // nf-test directory including temporary files for each test - workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" + workDir = System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "tests/nextflow.config" + configFile = "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' + ignore = [ + 'modules/nf-core/**/tests/*', + 'subworkflows/nf-core/**/tests/*', + ] // run all test with defined profile(s) from the main nextflow.config - profile "test" + profile = "test" // list of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' + triggers = [ + '.github/actions/nf-test/action.yml', + '.github/workflows/nf-test.yml', + 'assets/schema_input.json', + 'bin/*', + 'conf/test.config', + 'nextflow.config', + 'nextflow_schema.json', + 'nf-test.config', + 'tests/.nftignore', + 'tests/nextflow.config', + ] // load the necessary plugins plugins { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index f4579141e..828d8a6e6 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-11-20T09:31:56+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-28T11:20:55+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#6f2bb14f-9d35-4e7a-bdb2-b3f8a0952d05" + "@id": "#9ef09118-0930-47d1-ad79-681897eb2572" } ], "name": "nf-core/raredisease" @@ -112,7 +112,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -122,8 +122,13 @@ { "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "contributor": [ + { + "@id": "#43cd2794-2544-43e3-bff1-c22b2c4e90af" + } + ], "dateCreated": "", - "dateModified": "2025-11-20T09:31:56Z", + "dateModified": "2026-04-28T11:20:55Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -158,14 +163,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.10.4" }, { - "@id": "#6f2bb14f-9d35-4e7a-bdb2-b3f8a0952d05", + "@id": "#9ef09118-0930-47d1-ad79-681897eb2572", "@type": "TestSuite", "instance": [ { - "@id": "#7f2b0b84-cc76-45e2-964b-48cad7249f4f" + "@id": "#9d02ecc1-065e-4b66-a104-c2d4d511429e" } ], "mainEntity": { @@ -174,7 +179,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#7f2b0b84-cc76-45e2-964b-48cad7249f4f", + "@id": "#9d02ecc1-065e-4b66-a104-c2d4d511429e", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -301,6 +306,11 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#43cd2794-2544-43e3-bff1-c22b2c4e90af", + "@type": "Person", + "name": "Clinical Genomics Stockholm" } ] } diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index d02b07c24..4ed3e39db 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -14,7 +14,6 @@ include { samplesheetToList } from 'plugin/nf-schema' include { paramsHelp } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' @@ -54,6 +53,9 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // + + def before_text = "" + def after_text = "" before_text = """ -\033[2m----------------------------------------------------\033[0m- \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m @@ -71,6 +73,10 @@ workflow PIPELINE_INITIALISATION { * Software dependencies https://github.com/nf-core/raredisease/blob/master/CITATIONS.md """ + if (monochrome_logs) { + before_text = before_text.replaceAll(/\033\[[0-9;]*m/, '') + } + command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " UTILS_NFSCHEMA_PLUGIN ( @@ -102,7 +108,7 @@ workflow PIPELINE_INITIALISATION { // channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -140,7 +146,6 @@ workflow PIPELINE_COMPLETION { plaintext_email // boolean: Send plain-text email instead of HTML outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: @@ -164,13 +169,11 @@ workflow PIPELINE_COMPLETION { } completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } + } workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting" } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 2f30e9a46..afca54390 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -17,7 +17,7 @@ workflow UTILS_NFCORE_PIPELINE { checkProfileProvided(nextflow_cli_args) emit: - valid_config + valid_config = valid_config } /* @@ -353,67 +353,3 @@ def completionSummary(monochrome_logs=true) { log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } - -// -// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack -// -def imNotification(summary_params, hook_url) { - def summary = [:] - summary_params - .keySet() - .sort() - .each { group -> - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) { - misc_fields['repository'] = workflow.repository - } - if (workflow.commitId) { - misc_fields['commitid'] = workflow.commitId - } - if (workflow.revision) { - misc_fields['revision'] = workflow.revision - } - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = getWorkflowVersion() - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("${workflow.projectDir}/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection() - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")) - def postRC = post.getResponseCode() - if (!postRC.equals(200)) { - log.warn(post.getErrorStream().getText()) - } -} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test new file mode 100644 index 000000000..8940d32d1 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap new file mode 100644 index 000000000..859d1030f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index ee4738c8d..1df8b76fb 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -38,7 +38,7 @@ workflow UTILS_NFSCHEMA_PLUGIN { } log.info paramsHelp( help_options, - params.help instanceof String ? params.help : "", + (params.help instanceof String && params.help != "true") ? params.help : "", ) exit 0 } @@ -71,4 +71,3 @@ workflow UTILS_NFSCHEMA_PLUGIN { emit: dummy_emit = true } - diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 8d8c73718..f6537cc33 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.5.1" + id "nf-schema@2.6.1" } validation { diff --git a/tests/default.nf.test b/tests/default.nf.test index c1bc745ca..2ee6145d4 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,19 +13,19 @@ nextflow_pipeline { } then { - // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // stable_path: All files + folders in ${params.outdir}/ with a stable path (including file name) + def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_content: All files in ${params.outdir}/ with stable content + def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assert workflow.success assertAll( - { assert workflow.success}, { assert snapshot( // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_raredisease_software_mqc_versions.yml"), // All stable path name, with a relative path - stable_name, + stable_path, // All files with stable contents - stable_path + stable_content ).match() } ) } diff --git a/tests/nextflow.config b/tests/nextflow.config index f46754286..693f4a91e 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,7 +8,7 @@ // Or any resources requirements params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/' } aws.client.anonymous = true // fixes S3 access issues on self-hosted runners diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 16b2f11ba..f84a00c52 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -20,23 +20,25 @@ workflow RAREDISEASE { take: ch_samplesheet // channel: samplesheet read in from --input + multiqc_config + multiqc_logo + multiqc_methods_description + outdir + main: - ch_versions = channel.empty() - ch_multiqc_files = channel.empty() + def ch_versions = channel.empty() + def ch_multiqc_files = channel.empty() // // MODULE: Run FastQC // - FASTQC ( - ch_samplesheet - ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + FASTQC(ch_samplesheet) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map{ _meta, file -> file }) // // Collate and save software versions // - def topic_versions = Channel.topic("versions") + def topic_versions = channel.topic("versions") .distinct() .branch { entry -> versions_file: entry instanceof Path @@ -53,59 +55,43 @@ workflow RAREDISEASE { "${process}:\n${tool_versions.join('\n')}" } - softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) + def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${params.outdir}/pipeline_info", + storeDir: "${outdir}/pipeline_info", name: 'nf_core_' + 'raredisease_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true - ).set { ch_collated_versions } - + ) // // MODULE: MultiQC // - ch_multiqc_config = channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - channel.fromPath(params.multiqc_config, checkIfExists: true) : - channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - channel.fromPath(params.multiqc_logo, checkIfExists: true) : - channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix( - ch_methods_description.collectFile( - name: 'methods_description_mqc.yaml', - sort: true - ) - ) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] + def ch_summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def ch_workflow_summary = channel.value(paramsSummaryMultiqc(ch_summary_params)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + def ch_multiqc_custom_methods_description = multiqc_methods_description + ? file(multiqc_methods_description, checkIfExists: true) + : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true) + def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) + MULTIQC( + ch_multiqc_files.flatten().collect().map { files -> + [ + [id: 'raredisease'], + files, + multiqc_config + ? file(multiqc_config, checkIfExists: true) + : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), + multiqc_logo ? file(multiqc_logo, checkIfExists: true) : [], + [], + [], + ] + } ) - - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.map { _meta, report -> [report] }.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] - } /* From 57532eb1a8809e9bf6cb0ae296996c8810897c7e Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Tue, 28 Apr 2026 14:20:24 +0200 Subject: [PATCH 644/872] Modified stub test for align_sentieon and added new snapshot --- .../local/align_sentieon/tests/main.nf.test | 15 +- .../align_sentieon/tests/main.nf.test.snap | 533 +++++------------- 2 files changed, 141 insertions(+), 407 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 5849342f3..b6c800a74 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -120,7 +120,20 @@ nextflow_workflow { then { assert workflow.success - assert snapshot(workflow.out).match() + assert snapshot( + workflow.out.marked_bam, + workflow.out.marked_bai, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort() + ) } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b6ef91ad3..a18f76244 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -1,418 +1,139 @@ { "align sentieon, stub": { "content": [ - { - "0": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "5": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "6": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "8": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "aln_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gc_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "gc_summary": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "is_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "marked_bai": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "marked_bam": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "mq_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "qd_metrics": [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_datametrics_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "test_dedup.bam", + "test_dedup.bam.bai", + "test_dedup.bam.metrics", + "test_dedup.bam.metrics.multiqc.tsv", + "test_dedup.score" + ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-20T16:45:49.119367273" + "timestamp": "2026-04-28T13:54:38.517974195" }, "align sentieon": { "content": [ From 6be949293e0ff51e699f56f7d469a7686a27a92e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Apr 2026 09:49:33 +0200 Subject: [PATCH 645/872] add concat_saltshaker module --- modules/local/concat_saltshaker/main.nf | 15 +++++++++++++++ subworkflows/local/call_sv_MT/main.nf | 17 ++++++++++++++++- 2 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 modules/local/concat_saltshaker/main.nf diff --git a/modules/local/concat_saltshaker/main.nf b/modules/local/concat_saltshaker/main.nf new file mode 100644 index 000000000..6e3e453b3 --- /dev/null +++ b/modules/local/concat_saltshaker/main.nf @@ -0,0 +1,15 @@ +process CONCAT_SALTSHAKER { + tag "$meta.id" + label "process_low" + + input: + tuple val(meta), path(txts) + + output: + tuple val(meta), path("*.txt"), emit: txt + + script: + """ + cat ${txts.join(' ')} > ${meta.id}_saltshaker_classify.txt + """ +} diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 723d89777..90c420d98 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -9,6 +9,7 @@ include { MITOSALT } from '../../../modules/local/mitosalt/main' include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' +include { CONCAT_SALTSHAKER } from '../../../modules/local/concat_saltshaker/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' @@ -118,9 +119,23 @@ workflow CALL_SV_MT { SALTSHAKER_CALL.out.call, val_mitochondria_name ) - ch_saltshaker_txt = SALTSHAKER_CLASSIFY.out.txt ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + SALTSHAKER_CLASSIFY.out.txt + .map{ _meta, txt -> txt } + .toSortedList{ a, b -> a.name <=> b.name } + .toList() + .set{ ch_saltshaker_files } + + ch_case_info + .combine(ch_saltshaker_files) + .set { ch_saltshaker_txts } + + CONCAT_SALTSHAKER( + ch_saltshaker_txts + ) + ch_saltshaker_txt = CONCAT_SALTSHAKER.out.txt + SALTSHAKER_TO_HTML( ch_saltshaker_txt, ) From f200370c6cbf22d4cdf487440ab53734fa6979b7 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Wed, 29 Apr 2026 10:28:07 +0200 Subject: [PATCH 646/872] Fixed assertion in align_sentieon --- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index b6c800a74..4aab03722 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -133,7 +133,7 @@ nextflow_workflow { .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } .collect { new File(it).name } .sort() - ) + ).match() } } From c5e322e674e5c639a49bbf6e90335d91ce553c99 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Apr 2026 11:31:59 +0200 Subject: [PATCH 647/872] update snaps --- .../tests/main.nf.test.snap | 4 +- .../local/call_sv_MT/tests/main.nf.test.snap | 66 +++++-------------- tests/default.nf.test.snap | 4 +- tests/test_bam.nf.test.snap | 5 +- tests/test_singleton.nf.test.snap | 6 +- 5 files changed, 27 insertions(+), 58 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index d3b9e9234..8a3520523 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -3,9 +3,9 @@ "content": [ [ "earlycasualcaiman.saltshaker.png", - "earlycasualcaiman.saltshaker_classify.html", "earlycasualcaiman_mitochondria_deletions.txt", "justhusky_saltshaker.vcf.gz", + "justhusky_saltshaker_classify.html", "justhusky_sv.vcf.gz", "justhusky_sv.vcf.gz.tbi" ], @@ -20,6 +20,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T15:51:47.077800376" + "timestamp": "2026-04-29T11:30:52.489871467" } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 8d7ae6e46..bd59ef6f2 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -18,17 +18,9 @@ [ [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" + "id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], @@ -111,32 +103,24 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ "call_sv/", [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" + "id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -145,7 +129,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ] @@ -199,32 +183,24 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ "call_sv/", [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" + "id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], [ @@ -233,7 +209,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ] @@ -243,17 +219,9 @@ [ [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" + "id": "justhusky" }, - "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], @@ -304,6 +272,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T15:53:31.425509861" + "timestamp": "2026-04-29T11:28:53.502143977" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e0e924241..3cee417f7 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -672,10 +672,10 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/earlycasualcaiman.saltshaker.png", - "call_sv/earlycasualcaiman.saltshaker_classify.html", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", + "call_sv/justhusky_saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", @@ -928,6 +928,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T14:58:54.280831107" + "timestamp": "2026-04-29T11:19:25.324404145" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 2fb2629fd..4ba2da711 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 773, + 775, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -622,6 +622,7 @@ "call_sv", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", @@ -848,6 +849,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T14:47:13.174933057" + "timestamp": "2026-04-29T11:21:47.405969864" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 4af8437b5..ae84ad3e7 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 355, + 356, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -537,9 +537,9 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/hugelymodelbat.saltshaker.png", - "call_sv/hugelymodelbat.saltshaker_classify.html", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", + "call_sv/justhusky_saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "fastqc", @@ -659,6 +659,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-14T15:03:52.559527073" + "timestamp": "2026-04-29T11:23:42.947508416" } } \ No newline at end of file From 8226075360ef4ee372095fd169ce39146df697cd Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 29 Apr 2026 13:10:11 +0200 Subject: [PATCH 648/872] Added stub test for align wes, and updated the CHANGELOG --- CHANGELOG.md | 3 +- subworkflows/local/align/tests/main.nf.test | 103 +++++++- .../local/align/tests/main.nf.test.snap | 242 +++++++++++++++++- 3 files changed, 344 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d75ef8794..f198068b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,7 +29,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] -- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) +- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), +- Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) ### `Changed` diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 7a8e427ac..44bee596a 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -147,7 +147,7 @@ nextflow_workflow { ) } } - test("align bwamem2 - wes") { + test("align bwamem2 - wes, stub") { options "-stub" @@ -350,4 +350,105 @@ nextflow_workflow { ) } } + + + + test("align bwameme - wes, stub") { + + options "-stub" + + setup { + run("BWAMEME_INDEX", alias: 'GENOME_MEME') { + script "modules/nf-core/bwameme/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'genome'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta', checkIfExists: true) + ]) + """ + } + } + } + + + when { + params { + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' + platform = "illumina" + min_trimmed_length = 50 + mito_name = "MT" + outdir = "$outputDir" + } + workflow { + """ + input[0] = channel.empty() + input[1] = channel.empty() + input[2] = channel.empty() + input[3] = GENOME_MEME.out.index.collect() + input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[7] = channel.fromList([ + [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", 'lane':1, 'sex':1, 'phenotype':2, 'paternal':'earlycasualcaiman', 'maternal':'slowlycivilbuck', 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_hugelymodelbat_XXXXXX_2.fastq.gz', checkIfExists: true) + ]], + [[ id:'slowlycivilbuck', sample:'slowlycivilbuck', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:slowlycivilbuck\\\\tPL:illumina\\\\tSM:slowlycivilbuck'", 'lane':1, 'sex':2, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map + [ + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) + ]] + ]) + input[8] = channel.empty() + input[9] = MT_MEM2.out.index.collect() + input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[13] = channel.empty() + input[14] = SHIFTMT_MEM2.out.index.collect() + input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[18] = true + input[19] = "bwameme" + input[20] = "wgs" + input[21] = false + input[22] = false + input[23] = 3072 + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = 4 + input[28] = true + input[29] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), + workflow.out.genome_marked_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mt_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + workflow.out.mtshift_bam_bai + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } + ).match() + } + ) + } + } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index e56d30a3b..922cdc8ee 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1,4 +1,104 @@ { + "align bwamem2 - wes, stub": { + "content": [ + [ + "earlycasualcaiman.fastp.html", + "earlycasualcaiman.fastp.json", + "earlycasualcaiman.fastp.log", + "earlycasualcaiman_R1.fastp.fastq.gz", + "earlycasualcaiman_R2.fastp.fastq.gz", + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "hugelymodelbat.fastp.html", + "hugelymodelbat.fastp.json", + "hugelymodelbat.fastp.log", + "hugelymodelbat_R1.fastp.fastq.gz", + "hugelymodelbat_R2.fastp.fastq.gz", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "slowlycivilbuck.fastp.html", + "slowlycivilbuck.fastp.json", + "slowlycivilbuck.fastp.log", + "slowlycivilbuck_R1.fastp.fastq.gz", + "slowlycivilbuck_R2.fastp.fastq.gz", + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_md.bam.bai" + ] + ], + [ + + ], + [ + + ], + [ + + ] + ], + "timestamp": "2026-04-29T10:49:41.402548", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "align bwamem2 - wgs": { "content": [ [ @@ -267,7 +367,7 @@ ] ] ], - "timestamp": "2026-04-14T11:13:27.943707346", + "timestamp": "2026-04-29T10:48:31.959971", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -405,7 +505,7 @@ ] ], - "timestamp": "2026-04-14T09:52:25.609505795", + "timestamp": "2026-04-29T11:06:56.369571", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -510,5 +610,143 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "align bwameme - wes, stub": { + "content": [ + [ + "earlycasualcaiman_sorted_md.cram", + "earlycasualcaiman_sorted_md.cram.crai", + "hugelymodelbat_sorted_md.cram", + "hugelymodelbat_sorted_md.cram.crai", + "slowlycivilbuck_sorted_md.cram", + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_md.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_md.bam.bai" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck.bam.bai" + ] + ], + [ + + ] + ], + "timestamp": "2026-04-29T11:13:18.312548", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From c63e96d31e567078d30e759514c6766b66165501 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Apr 2026 14:26:51 +0200 Subject: [PATCH 649/872] update snaps again --- modules/local/concat_saltshaker/main.nf | 2 +- .../tests/main.nf.test.snap | 4 +- .../local/call_sv_MT/tests/main.nf.test.snap | 14 +- tests/default.nf.test.snap | 6 +- tests/test_bam.nf.test.snap | 308 ++++-------------- 5 files changed, 72 insertions(+), 262 deletions(-) diff --git a/modules/local/concat_saltshaker/main.nf b/modules/local/concat_saltshaker/main.nf index 6e3e453b3..004b83dcb 100644 --- a/modules/local/concat_saltshaker/main.nf +++ b/modules/local/concat_saltshaker/main.nf @@ -10,6 +10,6 @@ process CONCAT_SALTSHAKER { script: """ - cat ${txts.join(' ')} > ${meta.id}_saltshaker_classify.txt + cat ${txts.join(' ')} > ${meta.id}.saltshaker_classify.txt """ } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 8a3520523..e6385f20d 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -4,8 +4,8 @@ [ "earlycasualcaiman.saltshaker.png", "earlycasualcaiman_mitochondria_deletions.txt", + "justhusky.saltshaker_classify.html", "justhusky_saltshaker.vcf.gz", - "justhusky_saltshaker_classify.html", "justhusky_sv.vcf.gz", "justhusky_sv.vcf.gz.tbi" ], @@ -20,6 +20,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T11:30:52.489871467" + "timestamp": "2026-04-29T12:10:29.211103134" } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index bd59ef6f2..5743414fe 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -20,7 +20,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], @@ -120,7 +120,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], [ @@ -129,7 +129,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ] @@ -200,7 +200,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], [ @@ -209,7 +209,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ] @@ -221,7 +221,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ] ], @@ -272,6 +272,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T11:28:53.502143977" + "timestamp": "2026-04-29T12:15:25.188690715" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3cee417f7..55ef69084 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -671,13 +671,13 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/earlycasualcaiman.saltshaker.png", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", - "call_sv/justhusky_saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck.saltshaker.png", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -928,6 +928,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T11:19:25.324404145" + "timestamp": "2026-04-29T12:37:38.229711898" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 4ba2da711..d53fd33d2 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 775, + 356, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,9 +16,6 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.22 - }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -67,6 +64,10 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.22.1" + }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.22.1" @@ -77,18 +78,15 @@ "CAT_CAT_BAIT": { "pigz": 2.8 }, + "CAT_FASTQ": { + "cat": 9.5 + }, "CHROMOGRAPH_AUTOZYG": { "chromograph": "1.3.1" }, "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -153,6 +151,12 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, + "FASTP": { + "fastp": "1.0.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -236,9 +240,15 @@ "MANTA": { "manta": "1.6.0" }, + "MARKDUPLICATES": { + "picard": "3.4.0" + }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, "MOSDEPTH": { "mosdepth": "0.3.11" }, @@ -303,6 +313,15 @@ "RHOCALL_VIZ": { "rhocall": "0.5.1" }, + "SALTSHAKER_CALL": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_CLASSIFY": { + "saltshaker": "1.0.1" + }, + "SALTSHAKER_PLOT": { + "saltshaker": "1.0.0" + }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" }, @@ -312,6 +331,12 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_INDEX_ALIGN": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MARKDUP": { + "samtools": "1.22.1" + }, "SAMTOOLS_INDEX_MT": { "samtools": "1.22.1" }, @@ -321,12 +346,18 @@ "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" + }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, "SMNCOPYNUMBERCALLER": { "smncopynumbercaller": "1.1.2" }, @@ -425,12 +456,6 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.3" }, @@ -450,12 +475,11 @@ }, [ "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/hugelymodelbat_sorted_md.bam", + "alignment/hugelymodelbat_sorted_md.bam.bai", + "alignment/hugelymodelbat_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -463,35 +487,6 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -521,87 +516,8 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", @@ -620,21 +536,23 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky_saltshaker_classify.html", + "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", - "call_sv/slowlycivilbuck_mitochondria_deletions.txt", + "fastqc", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -651,59 +569,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.summary.txt", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/earlycasualcaiman_tidditcov.bed", - "qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -757,59 +622,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -824,31 +636,29 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/earlycasualcaiman.cgh", - "vcf2cytosure/hugelymodelbat.cgh", - "vcf2cytosure/slowlycivilbuck.cgh" + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T11:21:47.405969864" + "timestamp": "2026-04-29T14:23:37.468812614" } } \ No newline at end of file From e14a945d539bb75d2af4d755819d25cab391792a Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Wed, 29 Apr 2026 14:28:41 +0200 Subject: [PATCH 650/872] Fixed CHANGELOG with prettier --- CHANGELOG.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b337d7fb2..f1e4934e0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,14 +29,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) - Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] -<<<<<<< HEAD -- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), -- Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) -======= + <<<<<<< HEAD +- Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807), +- # Stub test for all the remaning subworkflows that were lacking it: align_bwa_bwamem2_bwameme, align_MT, align (bwameme - wes), align_sentieon, call_repeat_expansions, prepare_references, qc_bam [#820](https://github.com/nf-core/raredisease/pull/820) - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) ->>>>>>> f200370c6cbf22d4cdf487440ab53734fa6979b7 + > > > > > > > f200370c6cbf22d4cdf487440ab53734fa6979b7 ### `Changed` From 3666250b7fa968f6d7daa9d00cdaeed24d7d11e3 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Apr 2026 14:50:16 +0200 Subject: [PATCH 651/872] singleton snap --- tests/test_singleton.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index ae84ad3e7..527b106e7 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -538,8 +538,8 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", - "call_sv/justhusky_saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "fastqc", @@ -659,6 +659,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T11:23:42.947508416" + "timestamp": "2026-04-29T14:49:58.807870905" } } \ No newline at end of file From ba329e938c4fac2764b5c448f6d072f92b13c269 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 29 Apr 2026 14:53:33 +0200 Subject: [PATCH 652/872] review comments --- .nf-core.yml | 2 +- CHANGELOG.md | 4 +- README.md | 18 +- assets/multiqc_config.yml | 5 +- conf/modules/annotate_genome_snvs.config | 2 +- conf/modules/call_snv_sentieon.config | 4 +- conf/modules/subsample_mt_reads.config | 1 + conf/test.config | 2 - docs/output.md | 23 ++- docs/usage.md | 2 +- .../resources/usr/bin/create_hgncids_file.py | 5 +- .../usr/bin/replace_spaces_in_vcfinfo.py | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 154 ++++++++++++------ subworkflows/local/align/main.nf | 18 +- subworkflows/local/align_MT/main.nf | 4 +- .../local/align_bwa_bwamem2_bwameme/main.nf | 6 +- subworkflows/local/align_sentieon/main.nf | 10 +- subworkflows/local/annotate_cadd/main.nf | 14 +- .../local/annotate_genome_snvs/main.nf | 16 +- subworkflows/local/annotate_mt_snvs/main.nf | 10 +- .../local/annotate_rhocallviz/main.nf | 4 +- .../annotate_structural_variants/main.nf | 6 +- .../local/call_mobile_elements/main.nf | 18 +- subworkflows/local/call_snv/main.nf | 6 +- subworkflows/local/call_snv_MT/main.nf | 4 +- .../local/call_snv_deepvariant/main.nf | 14 +- subworkflows/local/call_snv_sentieon/main.nf | 18 +- .../local/call_structural_variants/main.nf | 14 +- subworkflows/local/call_sv_MT/main.nf | 4 +- subworkflows/local/call_sv_cnvnator/main.nf | 12 +- .../local/call_sv_germlinecnvcaller/main.nf | 4 +- subworkflows/local/call_sv_manta/main.nf | 2 +- subworkflows/local/call_sv_tiddit/main.nf | 4 +- .../local/generate_cytosure_files/main.nf | 2 +- .../local/postprocess_MT_calls/main.nf | 16 +- subworkflows/local/prepare_references/main.nf | 60 +++---- subworkflows/local/qc_bam/main.nf | 26 +-- subworkflows/local/rank_variants/main.nf | 4 +- subworkflows/local/scatter_genome/main.nf | 2 +- subworkflows/local/subsample_mt_reads/main.nf | 6 +- subworkflows/local/variant_evaluation/main.nf | 6 +- 42 files changed, 297 insertions(+), 239 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index c30136f84..0b2f130e4 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 2.7.0dev + version: 3.0.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 882750e44..ca9ff3320 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 2.7.0dev - Semiautomatix [xxxx-xx-xx] +## 3.0.0 - Mario [xxxx-xx-xx] ### `Added` @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add peddy --sites hg38 argument when running with GRCh38 [#799](https://github.com/nf-core/raredisease/pull/799) - Saltshaker for downstream processing of mitochondrial SV calls from MitoSAlt [#775](https://github.com/nf-core/raredisease/pull/775) - Env variable NXF_SINGULARITY_NEW_PID_NAMESPACE = false to accommodate hisat2 running with latest Nextflow and Singularity [#775](https://github.com/nf-core/raredisease/pull/775) -- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803)] +- Parameter `exclude_alt` to filter alignments to alt/unplaced contigs after alignment using samtools view, retaining only primary chromosomes (GRCh37: 1-22,X,Y,MT / GRCh38: chr1-chr22,chrX,chrY,chrM). Note that enabling this will restrict variant calling to these chromosomes [#803](https://github.com/nf-core/raredisease/pull/803) - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) diff --git a/README.md b/README.md index 24483ad33..c4d2274cc 100644 --- a/README.md +++ b/README.md @@ -81,7 +81,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - [DeepVariant](https://github.com/google/deepvariant) - [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/) -**4. Variant calling - SV:** +**6. Variant calling - SV:** - [Manta](https://github.com/Illumina/manta) - [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT) @@ -91,9 +91,9 @@ On release, automated continuous integration tests run the pipeline on a full-si - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller) - Mitochondrial SV calling: - [MitoSAlt](https://mitosalt.sourceforge.io/) - - [Saltshaker](https://github.com/aksenia/saltshaker) + - [Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker) -**5. Annotation - SNV:** +**7. Annotation - SNV:** - [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh) - [vcfanno](https://github.com/brentp/vcfanno) @@ -102,12 +102,12 @@ On release, automated continuous integration tests run the pipeline on a full-si - [UPD](https://github.com/bjhall/upd) - [Chromograph](https://github.com/Clinical-Genomics/chromograph) -**6. Annotation - SV:** +**8. Annotation - SV:** - [SVDB query](https://github.com/J35P312/SVDB#Query) - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) -**7. Mitochondrial analysis:** +**9. Mitochondrial analysis:** - [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-) - Annotation: @@ -115,20 +115,20 @@ On release, automated continuous integration tests run the pipeline on a full-si - [CADD](https://cadd.gs.washington.edu/) - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html) -**8. Variant calling - repeat expansions:** +**10. Variant calling - repeat expansions:** - [Expansion Hunter](https://github.com/Illumina/ExpansionHunter) - [Stranger](https://github.com/Clinical-Genomics/stranger) -**9. Variant calling - mobile elements:** +**11. Variant calling - mobile elements:** - [RetroSeq](https://github.com/tk2/RetroSeq) -**10. Rank variants - SV and SNV:** +**12. Rank variants - SV and SNV:** - [GENMOD](https://github.com/Clinical-Genomics/genmod) -**11. Variant evaluation:** +**13. Variant evaluation:** - [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a90329141..0b6823681 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,10 +2,7 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about - how to interpret these results, please see the documentation. + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-raredisease-methods-description": diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index 5d448dd31..6a1a3736b 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -91,7 +91,7 @@ process { } withName: '.*ANNOTATE_GENOME_SNVS:BCFTOOLS_CONCAT' { - ext.args = { "-Oz --write-index=tbi" } + ext.args = { "--output-type z --write-index=tbi" } ext.prefix = { "${meta.prefix}_vep" } } } diff --git a/conf/modules/call_snv_sentieon.config b/conf/modules/call_snv_sentieon.config index 8ba47353c..39085f55d 100644 --- a/conf/modules/call_snv_sentieon.config +++ b/conf/modules/call_snv_sentieon.config @@ -29,12 +29,12 @@ process { } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:BCF_FILTER_ONE' { - ext.args = "-s 'ML_FAIL' -i 'INFO/ML_PROB <= 0.95' -m x -Oz --write-index=tbi" + ext.args = "-s 'ML_FAIL' -i 'INFO/ML_PROB <= 0.95' -m x --output-type z --write-index=tbi" ext.prefix = { "${meta.id}_mlfiltered_0.95" } } withName: '.*CALL_SNV:CALL_SNV_SENTIEON:BCF_FILTER_TWO' { - ext.args = "-i FILTER='\"PASS\"' -m x -Oz --write-index=tbi" + ext.args = "-i FILTER='\"PASS\"' -m x --output-type z --write-index=tbi" ext.prefix = { "${meta.id}_passed" } } diff --git a/conf/modules/subsample_mt_reads.config b/conf/modules/subsample_mt_reads.config index d8525b521..5c009ba61 100644 --- a/conf/modules/subsample_mt_reads.config +++ b/conf/modules/subsample_mt_reads.config @@ -27,6 +27,7 @@ process { ext.prefix = { "${meta.id}_mt_nodups_collate" } } + // subsample a collated SAM down to approximately mt_subsample_reads reads, while making sure that read pairs are never split withName: '.*SUBSAMPLE_MT_READS:GAWK' { ext.args2 = { "'/^@/ { print; next } count < ${params.mt_subsample_reads} || last == \$1 { print; last = \$1; count++ }'" } ext.prefix = { "${meta.id}_mt_nodups_collate_awk" } diff --git a/conf/test.config b/conf/test.config index 90f2691f2..ca8827f4e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,8 +22,6 @@ env { MPLCONFIGDIR="." } -singularity.pullTimeout='2h' - params { config_profile_name = 'Test profile - default' config_profile_description = 'Minimal test dataset to check pipeline function' diff --git a/docs/output.md b/docs/output.md index edbbaa14b..7e486eb1f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -467,7 +467,7 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen ##### Saltshaker [MitoSAlt](https://mitosalt.sourceforge.io/) allows the detection and quantification of mtDNA strucutral variants. -[Saltshaker](https://github.com/aksenia/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. +[Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. - `call_sv` - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. @@ -607,17 +607,16 @@ The sequencing data can be prepared for visualization of CNVs in [Gens](https:// Output files - `peddy/` - - `*.het_check.csv` - - `*.het_check.png` - - `*.html` - - `*.pca_check.png` - - `*.ped_check.csv` - - `*.ped_check.png` - - `*.ped_check.rel-difference.csv` - - `*.peddy.ped` - - `*.sex_check.csv` - - `*.sex_check.png` - - `*.vs.html` + - `*.het_check.csv`: CSV file containing heterozygosity check results — rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto 1000 Genomes. + - `*.het_check.png`: PNG plot of heterozygosity check results — rate of het calls, allele-balance at het calls, mean and median depth, and a PCA projection onto 1000 Genomes. + - `*.html`: interactive HTML report with plots for sex check (HET rate on chrX), depth and heterozygosity, and pedigree relatedness, plus an interactive pedigree table. + - `*.ped_check.csv`: CSV file containing pedigree check results — pairwise relatedness statistics comparing reported vs. inferred relationships. + - `*.ped_check.png`: PNG plot of pedigree check results — comparison between reported and inferred relatedness. + - `*.ped_check.rel-difference.csv`: CSV file with the comparison between inferred and reported relatedness for sample pairs where they differ. + - `*.peddy.ped`: extended PED file augmented with key columns from the het-check and sex-check results. + - `*.sex_check.csv`: CSV file with sex check results — comparison between the sex reported in the PED file and that inferred from genotypes on the non-PAR regions of the X chromosome. + - `*.sex_check.png`: PNG plot of sex check results — comparison between reported and inferred sex. + - `*.vs.html`: interactive scatter plot of observed vs. expected (pedigree-reported) relatedness for all sample pairs. ### Pipeline information diff --git a/docs/usage.md b/docs/usage.md index c25bb64ac..be1e5cfc0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -307,7 +307,7 @@ no header and the following columns: `CHROM POS REF_ALLELE,ALT_ALLELE AF`. Sampl 7File containing list of SO terms listed in the order of severity from most severe to lease severe for annotating genomic and mitochondrial SNVs. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt). You can learn more about these terms [here](https://grch37.ensembl.org/info/genome/variation/prediction/predicted_data.html). 8A CSV file that describes the files used by VEP's named and custom plugins. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/vep_files.csv).
    9Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
    -10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into candidate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set. To skip this splitting entirely, add `generate_clinical_set` to `--skip_subworkflows`.
    +10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into candidate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set.
    11Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
    12When set to `true`, each vcfanno database file listed in `vcfanno_resources` is checked for records (non-header lines). Any database with zero records is removed from the vcfanno TOML config before annotation runs. Default: `false`.
    diff --git a/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py b/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py index 6f0261922..3bd7f358c 100755 --- a/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py +++ b/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py @@ -8,7 +8,10 @@ def main(): parser = argparse.ArgumentParser( - description="Reformat input file based on meta.id" + description="Extract HGNC IDs from a VEP filter file. Supports Scout gene panel format " + "(tab-delimited, HGNC ID in column 4) and standard format (one HGNC ID per " + "non-comment line). Pass --meta-id scout for Scout format, any other value " + "for standard format." ) parser.add_argument( "--input", diff --git a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py index 23ea6ba63..5263cdc6f 100755 --- a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py +++ b/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py @@ -29,7 +29,7 @@ def main(): else: spl = line.rstrip("\n").split("\t") if len(spl) > 7: - spl[7] = spl[7].replace(" ", "_") + spl[7] = spl[7].replace(" ", "_") #update INFO column output.write("\t".join(spl) + "\n") diff --git a/nextflow.config b/nextflow.config index cd152e33e..0234c8007 100644 --- a/nextflow.config +++ b/nextflow.config @@ -481,7 +481,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '2.7.0dev' + version = '3.0.0' doi = '10.5281/zenodo.7995798' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 325d4688d..11886e712 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -1,6 +1,6 @@ { "@context": [ - "https://w3id.org/ro/crate/1.1/context", + "https://w3id.org/ro/crate/1.2/context", { "GithubService": "https://w3id.org/ro/terms/test#GithubService", "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-03-13T22:32:54+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://github.com/aksenia/saltshaker)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", + "creativeWorkStatus": "Stable", + "datePublished": "2026-04-29T08:07:02+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**6. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker)\n\n**7. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**8. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**9. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**10. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**11. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**12. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**13. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759" + "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541" } ], "name": "nf-core/raredisease" @@ -118,7 +118,7 @@ }, "conformsTo": [ { - "@id": "https://w3id.org/ro/crate/1.1" + "@id": "https://w3id.org/ro/crate/1.2" }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" @@ -132,31 +132,48 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], - "creator": [ + "author": [ { - "@id": "https://orcid.org/0000-0003-1316-2845" + "@id": "https://orcid.org/0000-0001-7313-3734" }, { - "@id": "https://orcid.org/0000-0001-7313-3734" + "@id": "https://orcid.org/0000-0002-2219-0197" + } + ], + "contributor": [ + { + "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3" }, { "@id": "https://orcid.org/0000-0002-5044-7754" }, { - "@id": "https://orcid.org/0009-0005-4189-8704" + "@id": "https://orcid.org/0000-0002-6987-5839" }, { - "@id": "#25568561+projectoriented@users.noreply.github.com" + "@id": "https://orcid.org/0009-0008-1112-841X" }, { - "@id": "https://orcid.org/0000-0002-2219-0197" + "@id": "https://orcid.org/0000-0002-4100-9963" }, { - "@id": "https://orcid.org/0000-0002-4100-9963" + "@id": "#sima.rahimi@med.lu.se" + }, + { + "@id": "https://orcid.org/0000-0002-9594-0710" + }, + { + "@id": "https://orcid.org/0000-0003-2827-9261" + }, + { + "@id": "#eva.caceres@scilifelab.se" + }, + { + "@id": "https://orcid.org/0000-0003-1581-0711" } ], "dateCreated": "", - "dateModified": "2026-03-13T22:32:54Z", + "dateModified": "2026-04-29T10:07:02Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -177,17 +194,8 @@ { "@id": "https://orcid.org/0000-0001-7313-3734" }, - { - "@id": "https://orcid.org/0000-0002-5044-7754" - }, - { - "@id": "#25568561+projectoriented@users.noreply.github.com" - }, { "@id": "https://orcid.org/0000-0002-2219-0197" - }, - { - "@id": "https://orcid.org/0000-0002-4100-9963" } ], "name": [ @@ -201,10 +209,10 @@ }, "url": [ "https://github.com/nf-core/raredisease", - "https://nf-co.re/raredisease/dev/" + "https://nf-co.re/raredisease/3.0.0/" ], "version": [ - "2.7.0dev" + "3.0.0" ] }, { @@ -220,11 +228,11 @@ "version": "!>=25.10.4" }, { - "@id": "#acbb265d-df95-4c8c-b241-9c704c07f759", + "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541", "@type": "TestSuite", "instance": [ { - "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636" + "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24" } ], "mainEntity": { @@ -233,7 +241,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#e2389f87-0193-4a16-a8f1-7dab97ad2636", + "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -372,46 +380,98 @@ "url": "https://nf-co.re/" }, { - "@id": "https://orcid.org/0000-0003-1316-2845", + "@id": "https://orcid.org/0000-0001-7313-3734", "@type": "Person", - "email": "raysloks@gmail.com", - "name": "Emil Bertilsson" + "affiliation": "School of Engineering sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden", + "email": "rne@kth.se", + "name": "Ramprasad Neethiraj", + "url": "https://github.com/ramprasadn" }, { - "@id": "https://orcid.org/0000-0001-7313-3734", + "@id": "https://orcid.org/0000-0002-2219-0197", + "@type": "Person", + "affiliation": "Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden", + "email": "anders.jemt@scilifelab.se", + "name": "Anders Jemt", + "url": "https://github.com/jemten" + }, + { + "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3", "@type": "Person", - "email": "20065894+ramprasadn@users.noreply.github.com", - "name": "Ramprasad Neethiraj" + "email": "25568561+projectoriented@users.noreply.github.com", + "name": "Mei Wu", + "url": "https://github.com/projectoriented" }, { "@id": "https://orcid.org/0000-0002-5044-7754", "@type": "Person", + "affiliation": "Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden", "email": "lucia.pena.perez@scilifelab.se", - "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" + "name": "Lucía Peña-Pérez", + "url": "https://github.com/Lucpen" }, { - "@id": "https://orcid.org/0009-0005-4189-8704", + "@id": "https://orcid.org/0000-0002-6987-5839", "@type": "Person", - "email": "75395041+ieduba@users.noreply.github.com", - "name": "Irene Duba" + "affiliation": "Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden", + "email": "peter.pruisscher@scilifelab.se", + "name": "Peter Pruisscher", + "url": "https://github.com/peterpru" }, { - "@id": "#25568561+projectoriented@users.noreply.github.com", + "@id": "https://orcid.org/0009-0008-1112-841X", "@type": "Person", - "email": "25568561+projectoriented@users.noreply.github.com", - "name": "Mei Wu" + "affiliation": "Danish National Genome Center", + "email": "aspe@clin.au.dk", + "name": "Anders Sune Pedersen", + "url": "https://github.com/asp8200" }, { - "@id": "https://orcid.org/0000-0002-2219-0197", + "@id": "https://orcid.org/0000-0002-4100-9963", "@type": "Person", - "email": "jemten@users.noreply.github.com", - "name": "Anders Jemt" + "affiliation": "Clinical Genomics Gothenburg, Sahlgrenska University Hospital and University of Gothenburg", + "email": "gwenna.breton@gu.se", + "name": "Gwenna Breton", + "url": "https://github.com/Gwennid" }, { - "@id": "https://orcid.org/0000-0002-4100-9963", + "@id": "#sima.rahimi@med.lu.se", + "@type": "Person", + "affiliation": "Clinical Genomics Lund, Lund University", + "email": "sima.rahimi@med.lu.se", + "name": "Sima Rahimi", + "url": "https://github.com/sima-r" + }, + { + "@id": "https://orcid.org/0000-0002-9594-0710", + "@type": "Person", + "affiliation": "Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden", + "email": "felix.lenner@scilifelab.se", + "name": "Felix Lenner", + "url": "https://github.com/fellen31" + }, + { + "@id": "https://orcid.org/0000-0003-2827-9261", + "@type": "Person", + "affiliation": "Seqera", + "email": "maxime.garcia@seqera.io", + "name": "Maxime U Garcia", + "url": "https://github.com/maxulysse" + }, + { + "@id": "#eva.caceres@scilifelab.se", + "@type": "Person", + "affiliation": "Clinical Genomics Stockholm", + "email": "eva.caceres@scilifelab.se", + "name": "Eva Caceres", + "url": "https://github.com/fevac" + }, + { + "@id": "https://orcid.org/0000-0003-1581-0711", "@type": "Person", - "email": "Gwenna.breton@gu.se", - "name": "Gwenna Breton" + "affiliation": "nf-core community", + "name": "and the nf-core/raredisease team", + "url": "https://github.com/nf-core" } ] } \ No newline at end of file diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 593de277f..8faeb99bd 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -2,15 +2,15 @@ // Map to reference // -include { FASTP } from '../../../modules/nf-core/fastp/main' -include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' -include { ALIGN_SENTIEON } from '../align_sentieon' -include { SAMTOOLS_VIEW as CONVERTTOCRAM_ALTFILTERED } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as CONVERTTOCRAM_UNFILTERED } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' -include { ALIGN_MT } from '../align_MT' -include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' -include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' +include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' +include { ALIGN_MT } from '../align_MT' +include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' +include { ALIGN_SENTIEON } from '../align_sentieon' +include { CONVERT_MT_BAM_TO_FASTQ } from '../convert_mt_bam_to_fastq' +include { FASTP } from '../../../modules/nf-core/fastp/main' +include { SAMTOOLS_VIEW as CONVERTTOCRAM_ALTFILTERED } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as CONVERTTOCRAM_UNFILTERED } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' workflow ALIGN { take: diff --git a/subworkflows/local/align_MT/main.nf b/subworkflows/local/align_MT/main.nf index 17de7f7c1..75fe65c74 100644 --- a/subworkflows/local/align_MT/main.nf +++ b/subworkflows/local/align_MT/main.nf @@ -2,13 +2,13 @@ // Align MT // -include { BWA_MEM as BWA_MEM_MT } from '../../../modules/nf-core/bwa/mem/main' -include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT } from '../../../modules/nf-core/sentieon/bwamem/main' include { BWAMEM2_MEM as BWAMEM2_MEM_MT } from '../../../modules/nf-core/bwamem2/mem/main' +include { BWA_MEM as BWA_MEM_MT } from '../../../modules/nf-core/bwa/mem/main' include { GATK4_MERGEBAMALIGNMENT as GATK4_MERGEBAMALIGNMENT_MT } from '../../../modules/nf-core/gatk4/mergebamalignment/main' include { PICARD_ADDORREPLACEREADGROUPS as PICARD_ADDORREPLACEREADGROUPS_MT } from '../../../modules/nf-core/picard/addorreplacereadgroups/main' include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_MT } from '../../../modules/nf-core/picard/markduplicates/main' include { SAMTOOLS_SORT as SAMTOOLS_SORT_MT } from '../../../modules/nf-core/samtools/sort/main' +include { SENTIEON_BWAMEM as SENTIEON_BWAMEM_MT } from '../../../modules/nf-core/sentieon/bwamem/main' workflow ALIGN_MT { take: diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 66eafb804..6ea0434de 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -2,16 +2,16 @@ // Map to reference, fetch stats for each demultiplexed read pair, merge, mark duplicates, and index. // -include { BWA_MEM as BWA } from '../../../modules/nf-core/bwa/mem/main' include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main' include { BWAMEME_MEM } from '../../../modules/nf-core/bwameme/mem/main' +include { BWA_MEM as BWA } from '../../../modules/nf-core/bwa/mem/main' +include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGN } from '../../../modules/nf-core/samtools/index/main' include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_EXTRACT } from '../../../modules/nf-core/samtools/index/main' include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_MARKDUP } from '../../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' include { SAMTOOLS_MERGE } from '../../../modules/nf-core/samtools/merge/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-core/samtools/view/main' -include { PICARD_MARKDUPLICATES as MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' workflow ALIGN_BWA_BWAMEM2_BWAMEME { diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 2038682b5..5269ccb45 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -2,11 +2,11 @@ // A subworkflow to annotate structural variants. // -include { SENTIEON_BWAMEM } from '../../../modules/nf-core/sentieon/bwamem/main' -include { SENTIEON_DATAMETRICS } from '../../../modules/nf-core/sentieon/datametrics/main' -include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main' -include { SENTIEON_READWRITER } from '../../../modules/nf-core/sentieon/readwriter/main' -include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-core/samtools/view/main' +include { SENTIEON_BWAMEM } from '../../../modules/nf-core/sentieon/bwamem/main' +include { SENTIEON_DATAMETRICS } from '../../../modules/nf-core/sentieon/datametrics/main' +include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main' +include { SENTIEON_READWRITER } from '../../../modules/nf-core/sentieon/readwriter/main' workflow ALIGN_SENTIEON { take: diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index a6052fdff..5b8d3369a 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -2,13 +2,13 @@ // A subworkflow to annotate snvs // -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { BCFTOOLS_ANNOTATE as RENAME_CHRNAMES } from '../../../modules/nf-core/bcftools/annotate/main' -include { CADD } from '../../../modules/nf-core/cadd/main' -include { GAWK as REFERENCE_TO_CADD_CHRNAMES } from '../../../modules/nf-core/gawk/main' -include { GAWK as CADD_TO_REFERENCE_CHRNAMES } from '../../../modules/nf-core/gawk/main' -include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/tabix/tabix/main' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_ANNOTATE as RENAME_CHRNAMES } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' +include { CADD } from '../../../modules/nf-core/cadd/main' +include { GAWK as CADD_TO_REFERENCE_CHRNAMES } from '../../../modules/nf-core/gawk/main' +include { GAWK as REFERENCE_TO_CADD_CHRNAMES } from '../../../modules/nf-core/gawk/main' +include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CADD { diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 616a82b6d..bd98a3516 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -2,21 +2,21 @@ // A subworkflow to annotate snvs in the genome // -include { VCFANNO } from '../../../modules/nf-core/vcfanno/main' +include { ANNOTATE_CADD } from '../annotate_cadd' +include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' include { BCFTOOLS_ROH } from '../../../modules/nf-core/bcftools/roh/main' include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { RHOCALL_ANNOTATE } from '../../../modules/nf-core/rhocall/annotate/main' -include { UPD as UPD_SITES } from '../../../modules/nf-core/upd/main' -include { UPD as UPD_REGIONS } from '../../../modules/nf-core/upd/main' -include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../../modules/nf-core/chromograph/main' include { CHROMOGRAPH as CHROMOGRAPH_REGIONS } from '../../../modules/nf-core/chromograph/main' +include { CHROMOGRAPH as CHROMOGRAPH_SITES } from '../../../modules/nf-core/chromograph/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_SNV } from '../../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' -include { ANNOTATE_CADD } from '../annotate_cadd' -include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' +include { RHOCALL_ANNOTATE } from '../../../modules/nf-core/rhocall/annotate/main' include { SANITY_CHECK_VCFANNO_DATABASES } from '../../../modules/local/sanity_check_vcfanno_databases/main' +include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { UPD as UPD_REGIONS } from '../../../modules/nf-core/upd/main' +include { UPD as UPD_SITES } from '../../../modules/nf-core/upd/main' +include { VCFANNO } from '../../../modules/nf-core/vcfanno/main' workflow ANNOTATE_GENOME_SNVS { diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 975f96f89..5b80e5132 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -3,11 +3,11 @@ // -include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt' -include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../../modules/nf-core/tabix/tabix/main' -include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../modules/nf-core/ensemblvep/vep/main' -include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' -include { ANNOTATE_CADD } from '../annotate_cadd' +include { ANNOTATE_CADD } from '../annotate_cadd' +include { BCFTOOLS_PLUGINSETGT } from '../../../modules/nf-core/bcftools/pluginsetgt' +include { ENSEMBLVEP_VEP as ENSEMBLVEP_MT } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_TABIX as TABIX_TABIX_VEP_MT } from '../../../modules/nf-core/tabix/tabix/main' +include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcfanno/main' workflow ANNOTATE_MT_SNVS { take: diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index 9431a4824..d7f50cbe8 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -2,12 +2,12 @@ // A subworkflow to plot binned zygosity and RHO-regions. // -include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_RHOCALL } from '../../../modules/nf-core/bcftools/view/main' include { BCFTOOLS_ROH } from '../../../modules/nf-core/bcftools/roh/main' +include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_RHOCALL } from '../../../modules/nf-core/bcftools/view/main' include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_UNCOMPRESS } from '../../../modules/nf-core/bcftools/view/main' +include { CHROMOGRAPH as CHROMOGRAPH_AUTOZYG } from '../../../modules/nf-core/chromograph/main' include { RHOCALL_VIZ } from '../../../modules/nf-core/rhocall/viz/main' include { UCSC_WIGTOBIGWIG } from '../../../modules/nf-core/ucsc/wigtobigwig/main' -include { CHROMOGRAPH as CHROMOGRAPH_AUTOZYG } from '../../../modules/nf-core/chromograph/main' workflow ANNOTATE_RHOCALLVIZ { diff --git a/subworkflows/local/annotate_structural_variants/main.nf b/subworkflows/local/annotate_structural_variants/main.nf index b24d7f4f9..af846901a 100644 --- a/subworkflows/local/annotate_structural_variants/main.nf +++ b/subworkflows/local/annotate_structural_variants/main.nf @@ -2,11 +2,11 @@ // A subworkflow to annotate structural variants. // -include { SVDB_QUERY as SVDB_QUERY_DB } from '../../../modules/nf-core/svdb/query/main' -include { SVDB_QUERY as SVDB_QUERY_BEDPE } from '../../../modules/nf-core/svdb/query/main' -include { PICARD_SORTVCF } from '../../../modules/nf-core/picard/sortvcf/main' include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../../../modules/nf-core/ensemblvep/vep/main' +include { PICARD_SORTVCF } from '../../../modules/nf-core/picard/sortvcf/main' +include { SVDB_QUERY as SVDB_QUERY_BEDPE } from '../../../modules/nf-core/svdb/query/main' +include { SVDB_QUERY as SVDB_QUERY_DB } from '../../../modules/nf-core/svdb/query/main' workflow ANNOTATE_STRUCTURAL_VARIANTS { diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 896da1068..2f8a46883 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -2,15 +2,15 @@ // A subworkflow to call mobile elements in the genome // -include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_ME } from '../../../modules/nf-core/bcftools/reheader/main' -include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_ME } from '../../../modules/nf-core/bcftools/concat/main' -include { BCFTOOLS_SORT as BCFTOOLS_SORT_ME } from '../../../modules/nf-core/bcftools/sort/main' -include { RETROSEQ_CALL as RETROSEQ_CALL } from '../../../modules/local/retroseq/call/main' -include { RETROSEQ_DISCOVER as RETROSEQ_DISCOVER } from '../../../modules/local/retroseq/discover/main' -include { SAMTOOLS_VIEW as ME_SPLIT_ALIGNMENT } from '../../../modules/nf-core/samtools/view/main' -include { TABIX_TABIX as TABIX_ME } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_ME_SPLIT } from '../../../modules/nf-core/tabix/tabix/main' -include { SVDB_MERGE as SVDB_MERGE_ME } from '../../../modules/nf-core/svdb/merge/main' +include { BCFTOOLS_CONCAT as BCFTOOLS_CONCAT_ME } from '../../../modules/nf-core/bcftools/concat/main' +include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_ME } from '../../../modules/nf-core/bcftools/reheader/main' +include { BCFTOOLS_SORT as BCFTOOLS_SORT_ME } from '../../../modules/nf-core/bcftools/sort/main' +include { RETROSEQ_CALL as RETROSEQ_CALL } from '../../../modules/local/retroseq/call/main' +include { RETROSEQ_DISCOVER as RETROSEQ_DISCOVER } from '../../../modules/local/retroseq/discover/main' +include { SAMTOOLS_VIEW as ME_SPLIT_ALIGNMENT } from '../../../modules/nf-core/samtools/view/main' +include { SVDB_MERGE as SVDB_MERGE_ME } from '../../../modules/nf-core/svdb/merge/main' +include { TABIX_TABIX as TABIX_ME } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_ME_SPLIT } from '../../../modules/nf-core/tabix/tabix/main' workflow CALL_MOBILE_ELEMENTS { diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index c7e0cb799..b36cc1d7d 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -2,13 +2,13 @@ // call Single-nucleotide Varinats // +include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat' include { CALL_SNV_DEEPVARIANT } from '../call_snv_deepvariant' -include { CALL_SNV_SENTIEON } from '../call_snv_sentieon' include { CALL_SNV_MT } from '../call_snv_MT' include { CALL_SNV_MT as CALL_SNV_MT_SHIFT } from '../call_snv_MT' -include { POSTPROCESS_MT_CALLS } from '../postprocess_MT_calls' +include { CALL_SNV_SENTIEON } from '../call_snv_sentieon' include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' -include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat' +include { POSTPROCESS_MT_CALLS } from '../postprocess_MT_calls' workflow CALL_SNV { take: diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index eea854421..8c0b2b176 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -2,8 +2,8 @@ // Call SNV MT // -include { GATK4_MUTECT2 as GATK4_MUTECT2_MT } from '../../../modules/nf-core/gatk4/mutect2/main' -include { GATK4_FILTERMUTECTCALLS as GATK4_FILTERMUTECTCALLS_MT } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' +include { GATK4_FILTERMUTECTCALLS as GATK4_FILTERMUTECTCALLS_MT } from '../../../modules/nf-core/gatk4/filtermutectcalls/main' +include { GATK4_MUTECT2 as GATK4_MUTECT2_MT } from '../../../modules/nf-core/gatk4/mutect2/main' workflow CALL_SNV_MT { take: diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 9cffeebe0..0ac9d70fa 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -2,13 +2,13 @@ // A variant caller workflow for deepvariant // -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_GL } from '../../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as REMOVE_DUPLICATES_GL } from '../../../modules/nf-core/bcftools/norm/main' -include { DEEPVARIANT_RUNDEEPVARIANT as DEEPVARIANT } from '../../../modules/nf-core/deepvariant/rundeepvariant/main' -include { GLNEXUS } from '../../../modules/nf-core/glnexus/main' -include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' -include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' +include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_NORM as REMOVE_DUPLICATES_GL } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_GL } from '../../../modules/nf-core/bcftools/norm/main' +include { DEEPVARIANT_RUNDEEPVARIANT as DEEPVARIANT } from '../../../modules/nf-core/deepvariant/rundeepvariant/main' +include { GLNEXUS } from '../../../modules/nf-core/glnexus/main' +include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' workflow CALL_SNV_DEEPVARIANT { take: diff --git a/subworkflows/local/call_snv_sentieon/main.nf b/subworkflows/local/call_snv_sentieon/main.nf index b4e54e633..15b0b5b78 100644 --- a/subworkflows/local/call_snv_sentieon/main.nf +++ b/subworkflows/local/call_snv_sentieon/main.nf @@ -2,15 +2,15 @@ // A subworkflow to call SNVs by sentieon dnascope with a machine learning model. // -include { SENTIEON_DNASCOPE } from '../../../modules/nf-core/sentieon/dnascope/main' -include { SENTIEON_DNAMODELAPPLY } from '../../../modules/nf-core/sentieon/dnamodelapply/main' -include { BCFTOOLS_MERGE } from '../../../modules/nf-core/bcftools/merge/main' -include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_SEN } from '../../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_NORM as REMOVE_DUPLICATES_SEN } from '../../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_FILTER as BCF_FILTER_ONE } from '../../../modules/nf-core/bcftools/filter/main' -include { BCFTOOLS_FILTER as BCF_FILTER_TWO } from '../../../modules/nf-core/bcftools/filter/main' -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' +include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_FILTER as BCF_FILTER_ONE } from '../../../modules/nf-core/bcftools/filter/main' +include { BCFTOOLS_FILTER as BCF_FILTER_TWO } from '../../../modules/nf-core/bcftools/filter/main' +include { BCFTOOLS_MERGE } from '../../../modules/nf-core/bcftools/merge/main' +include { BCFTOOLS_NORM as REMOVE_DUPLICATES_SEN } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_SEN } from '../../../modules/nf-core/bcftools/norm/main' +include { SENTIEON_DNAMODELAPPLY } from '../../../modules/nf-core/sentieon/dnamodelapply/main' +include { SENTIEON_DNASCOPE } from '../../../modules/nf-core/sentieon/dnascope/main' workflow CALL_SNV_SENTIEON { take: diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 84994cc96..1a7728a2a 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -2,13 +2,13 @@ // A nested subworkflow to call structural variants. // -include { CALL_SV_MANTA } from '../call_sv_manta' -include { CALL_SV_TIDDIT } from '../call_sv_tiddit' -include { CALL_SV_MT } from '../call_sv_MT' -include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' -include { CALL_SV_GERMLINECNVCALLER } from '../call_sv_germlinecnvcaller' -include { CALL_SV_CNVNATOR } from '../call_sv_cnvnator' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' +include { CALL_SV_CNVNATOR } from '../call_sv_cnvnator' +include { CALL_SV_GERMLINECNVCALLER } from '../call_sv_germlinecnvcaller' +include { CALL_SV_MANTA } from '../call_sv_manta' +include { CALL_SV_MT } from '../call_sv_MT' +include { CALL_SV_TIDDIT } from '../call_sv_tiddit' +include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow CALL_STRUCTURAL_VARIANTS { diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 723d89777..9e2c1c720 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -3,10 +3,10 @@ // Also detects the number of discordant pairs using the mitodel script. // +include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' include { MT_DELETION } from '../../../modules/local/mt_deletion_script' include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf index 6355fd953..20db0edca 100644 --- a/subworkflows/local/call_sv_cnvnator/main.nf +++ b/subworkflows/local/call_sv_cnvnator/main.nf @@ -2,16 +2,16 @@ // A subworkflow to call CNVs using cnvnator // -include { SPLIT_CHR } from '../../../modules/local/split_chr/main.nf' -include { CNVNATOR_CNVNATOR as CNVNATOR_RD } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' +include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_CNVNATOR } from '../../../modules/nf-core/bcftools/view/main.nf' +include { CNVNATOR_CNVNATOR as CNVNATOR_CALL } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' include { CNVNATOR_CNVNATOR as CNVNATOR_HIST } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' -include { CNVNATOR_CNVNATOR as CNVNATOR_STAT } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' include { CNVNATOR_CNVNATOR as CNVNATOR_PARTITION } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' -include { CNVNATOR_CNVNATOR as CNVNATOR_CALL } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' +include { CNVNATOR_CNVNATOR as CNVNATOR_RD } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' +include { CNVNATOR_CNVNATOR as CNVNATOR_STAT } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf' include { CNVNATOR_CONVERT2VCF } from '../../../modules/nf-core/cnvnator/convert2vcf/main.nf' -include { TABIX_BGZIPTABIX as INDEX_CNVNATOR } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_CNVNATOR } from '../../../modules/nf-core/bcftools/view/main.nf' +include { SPLIT_CHR } from '../../../modules/local/split_chr/main.nf' include { SVDB_MERGE as SVDB_MERGE_CNVNATOR } from '../../../modules/nf-core/svdb/merge/main' +include { TABIX_BGZIPTABIX as INDEX_CNVNATOR } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow CALL_SV_CNVNATOR { take: diff --git a/subworkflows/local/call_sv_germlinecnvcaller/main.nf b/subworkflows/local/call_sv_germlinecnvcaller/main.nf index aea59f5f3..46eb00212 100644 --- a/subworkflows/local/call_sv_germlinecnvcaller/main.nf +++ b/subworkflows/local/call_sv_germlinecnvcaller/main.nf @@ -2,13 +2,13 @@ // A variant caller workflow for GATK's GermlinceCNVCaller // +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' include { GATK4_COLLECTREADCOUNTS } from '../../../modules/nf-core/gatk4/collectreadcounts/main.nf' include { GATK4_DETERMINEGERMLINECONTIGPLOIDY } from '../../../modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf' include { GATK4_GERMLINECNVCALLER } from '../../../modules/nf-core/gatk4/germlinecnvcaller/main.nf' include { GATK4_POSTPROCESSGERMLINECNVCALLS } from '../../../modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf' -include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view/main' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' include { SVDB_MERGE as SVDB_MERGE_GCNVCALLER } from '../../../modules/nf-core/svdb/merge/main' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow CALL_SV_GERMLINECNVCALLER { take: diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index e0f1d717b..3a514c3ec 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -2,8 +2,8 @@ // A structural variant caller workflow for manta // -include { MANTA_GERMLINE as MANTA } from '../../../modules/nf-core/manta/germline/main' include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_MANTA } from '../../../modules/nf-core/bcftools/view/main.nf' +include { MANTA_GERMLINE as MANTA } from '../../../modules/nf-core/manta/germline/main' workflow CALL_SV_MANTA { take: diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf index f3f7386da..0abe8294e 100644 --- a/subworkflows/local/call_sv_tiddit/main.nf +++ b/subworkflows/local/call_sv_tiddit/main.nf @@ -2,10 +2,10 @@ // A structural variant caller workflow for tiddit // -include { TIDDIT_SV } from '../../../modules/nf-core/tiddit/sv/main' +include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_TIDDIT } from '../../../modules/nf-core/bcftools/view/main.nf' include { SVDB_MERGE as SVDB_MERGE_TIDDIT } from '../../../modules/nf-core/svdb/merge/main' include { TABIX_BGZIPTABIX as INDEX_TIDDIT } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_TIDDIT } from '../../../modules/nf-core/bcftools/view/main.nf' +include { TIDDIT_SV } from '../../../modules/nf-core/tiddit/sv/main' workflow CALL_SV_TIDDIT { take: diff --git a/subworkflows/local/generate_cytosure_files/main.nf b/subworkflows/local/generate_cytosure_files/main.nf index e9a67c6f9..045722f16 100644 --- a/subworkflows/local/generate_cytosure_files/main.nf +++ b/subworkflows/local/generate_cytosure_files/main.nf @@ -2,8 +2,8 @@ // Convert VCF with structural variations to the “.CGH” format used by the CytoSure Interpret Software // -include { BCFTOOLS_VIEW as SPLIT_AND_FILTER_SV_VCF } from '../../../modules/nf-core/bcftools/view/main' include { BCFTOOLS_REHEADER as BCFTOOLS_REHEADER_SV_VCF } from '../../../modules/nf-core/bcftools/reheader/main' +include { BCFTOOLS_VIEW as SPLIT_AND_FILTER_SV_VCF } from '../../../modules/nf-core/bcftools/view/main' include { TIDDIT_COV as TIDDIT_COV_VCF2CYTOSURE } from '../../../modules/nf-core/tiddit/cov/main' include { VCF2CYTOSURE } from '../../../modules/nf-core/vcf2cytosure/main' diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index a9ecdf01b..758e9ec8d 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -2,18 +2,18 @@ // Merge and normalize MT variants // +include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_MT } from '../../../modules/nf-core/bcftools/merge/main' +include { BCFTOOLS_NORM as REMOVE_DUPLICATES_MT } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_MT } from '../../../modules/nf-core/bcftools/norm/main' include { GATK4_MERGEVCFS as GATK4_MERGEVCFS_LIFT_UNLIFT_MT } from '../../../modules/nf-core/gatk4/mergevcfs/main' include { GATK4_VARIANTFILTRATION as GATK4_VARIANTFILTRATION_MT } from '../../../modules/nf-core/gatk4/variantfiltration/main' -include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_MT } from '../../../modules/nf-core/bcftools/norm/main' -include { TABIX_TABIX as TABIX_TABIX_MT } from '../../../modules/nf-core/tabix/tabix/main' -include { BCFTOOLS_NORM as REMOVE_DUPLICATES_MT } from '../../../modules/nf-core/bcftools/norm/main' -include { TABIX_TABIX as TABIX_TABIX_MT2 } from '../../../modules/nf-core/tabix/tabix/main' -include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_MT } from '../../../modules/nf-core/bcftools/merge/main' -include { TABIX_TABIX as TABIX_TABIX_MERGE } from '../../../modules/nf-core/tabix/tabix/main' include { PICARD_LIFTOVERVCF } from '../../../modules/nf-core/picard/liftovervcf/main' -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed' include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_TABIX_MERGE } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_TABIX_MT } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_TABIX_MT2 } from '../../../modules/nf-core/tabix/tabix/main' workflow POSTPROCESS_MT_CALLS { take: diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index a3a99851d..0b180e2b5 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -3,36 +3,36 @@ // Prepare reference files // -include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED } from '../../../modules/nf-core/bedtools/slop/main' -include { BWA_INDEX as BWA_INDEX_GENOME } from '../../../modules/nf-core/bwa/index/main' -include { BWA_INDEX as BWA_INDEX_MT } from '../../../modules/nf-core/bwa/index/main' -include { BWA_INDEX as BWA_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwa/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../../modules/nf-core/bwamem2/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../../modules/nf-core/bwamem2/index/main' -include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwamem2/index/main' -include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME } from '../../../modules/nf-core/bwameme/index/main' -include { CAT_CAT as CAT_CAT_BAIT } from '../../../modules/nf-core/cat/cat/main' -include { GATK4_BEDTOINTERVALLIST as GATK_BILT } from '../../../modules/nf-core/gatk4/bedtointervallist/main' -include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../../modules/nf-core/gatk4/intervallisttools/main' -include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../../modules/nf-core/gatk4/shiftfasta/main' -include { GET_CHROM_SIZES } from '../../../modules/local/get_chrom_sizes' -include { HISAT2_BUILD as HISAT2_INDEX_GENOME } from '../../../modules/nf-core/hisat2/build' -include { LAST_LASTDB as LAST_INDEX_MT } from '../../../modules/nf-core/last/lastdb' -include { RTGTOOLS_FORMAT } from '../../../modules/nf-core/rtgtools/format/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../../modules/nf-core/samtools/faidx/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../../modules/nf-core/samtools/faidx/main' -include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../../modules/nf-core/samtools/faidx/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../../modules/nf-core/sentieon/bwaindex/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../../modules/nf-core/sentieon/bwaindex/main' -include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../../modules/nf-core/sentieon/bwaindex/main' -include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../../modules/nf-core/tabix/tabix/main' -include { UNTAR as UNTAR_VEP_CACHE } from '../../../modules/nf-core/untar/main' +include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED } from '../../../modules/nf-core/bedtools/slop/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwamem2/index/main' +include { BWAMEME_INDEX as BWAMEME_INDEX_GENOME } from '../../../modules/nf-core/bwameme/index/main' +include { BWA_INDEX as BWA_INDEX_GENOME } from '../../../modules/nf-core/bwa/index/main' +include { BWA_INDEX as BWA_INDEX_MT } from '../../../modules/nf-core/bwa/index/main' +include { BWA_INDEX as BWA_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwa/index/main' +include { CAT_CAT as CAT_CAT_BAIT } from '../../../modules/nf-core/cat/cat/main' +include { GATK4_BEDTOINTERVALLIST as GATK_BILT } from '../../../modules/nf-core/gatk4/bedtointervallist/main' +include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_MT } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GATK4_INTERVALLISTTOOLS as GATK_ILT } from '../../../modules/nf-core/gatk4/intervallisttools/main' +include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA } from '../../../modules/nf-core/gatk4/shiftfasta/main' +include { GET_CHROM_SIZES } from '../../../modules/local/get_chrom_sizes' +include { HISAT2_BUILD as HISAT2_INDEX_GENOME } from '../../../modules/nf-core/hisat2/build' +include { LAST_LASTDB as LAST_INDEX_MT } from '../../../modules/nf-core/last/lastdb' +include { RTGTOOLS_FORMAT } from '../../../modules/nf-core/rtgtools/format/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../../modules/nf-core/samtools/faidx/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../../modules/nf-core/samtools/faidx/main' +include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT } from '../../../modules/nf-core/samtools/faidx/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../../modules/nf-core/sentieon/bwaindex/main' +include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_PADDED_BED } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../../modules/nf-core/tabix/tabix/main' +include { UNTAR as UNTAR_VEP_CACHE } from '../../../modules/nf-core/untar/main' workflow PREPARE_REFERENCES { take: diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index b63fa5b8a..fdbca0b2d 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -2,19 +2,19 @@ // A quality check subworkflow for processed bams. // -include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' -include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' -include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../../modules/nf-core/chromograph/main' -include { TIDDIT_COV } from '../../../modules/nf-core/tiddit/cov/main' -include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' -include { SAMBAMBA_DEPTH } from '../../../modules/nf-core/sambamba/depth/main' -include { UCSC_WIGTOBIGWIG } from '../../../modules/nf-core/ucsc/wigtobigwig/main' -include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG } from '../../../modules/nf-core/picard/collectwgsmetrics/main' -include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../../modules/nf-core/picard/collectwgsmetrics/main' -include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG } from '../../../modules/nf-core/sentieon/wgsmetrics/main' -include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../../modules/nf-core/sentieon/wgsmetrics/main' -include { NGSBITS_SAMPLEGENDER } from '../../../modules/nf-core/ngsbits/samplegender/main' -include { VERIFYBAMID_VERIFYBAMID2 } from '../../../modules/nf-core/verifybamid/verifybamid2/main' +include { CHROMOGRAPH as CHROMOGRAPH_COV } from '../../../modules/nf-core/chromograph/main' +include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' +include { NGSBITS_SAMPLEGENDER } from '../../../modules/nf-core/ngsbits/samplegender/main' +include { PICARD_COLLECTHSMETRICS } from '../../../modules/nf-core/picard/collecthsmetrics/main' +include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/nf-core/picard/collectmultiplemetrics/main' +include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_Y } from '../../../modules/nf-core/picard/collectwgsmetrics/main' +include { SAMBAMBA_DEPTH } from '../../../modules/nf-core/sambamba/depth/main' +include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_WG } from '../../../modules/nf-core/sentieon/wgsmetrics/main' +include { SENTIEON_WGSMETRICS as SENTIEON_WGSMETRICS_Y } from '../../../modules/nf-core/sentieon/wgsmetrics/main' +include { TIDDIT_COV } from '../../../modules/nf-core/tiddit/cov/main' +include { UCSC_WIGTOBIGWIG } from '../../../modules/nf-core/ucsc/wigtobigwig/main' +include { VERIFYBAMID_VERIFYBAMID2 } from '../../../modules/nf-core/verifybamid/verifybamid2/main' workflow QC_BAM { diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf index 93b6093b3..f2446196d 100644 --- a/subworkflows/local/rank_variants/main.nf +++ b/subworkflows/local/rank_variants/main.nf @@ -2,11 +2,11 @@ // A subworkflow to score and rank variants. // +include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' include { GENMOD_ANNOTATE } from '../../../modules/nf-core/genmod/annotate/main' +include { GENMOD_COMPOUND } from '../../../modules/nf-core/genmod/compound/main' include { GENMOD_MODELS } from '../../../modules/nf-core/genmod/models/main' include { GENMOD_SCORE } from '../../../modules/nf-core/genmod/score/main' -include { GENMOD_COMPOUND } from '../../../modules/nf-core/genmod/compound/main' -include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow RANK_VARIANTS { diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index a93d8cfaa..b6a258828 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -2,8 +2,8 @@ // A subworkflow to create genome interval files necessary for bam/vcf scatter operations. // -include { GAWK } from '../../../modules/nf-core/gawk' include { GATK4_SPLITINTERVALS } from '../../../modules/nf-core/gatk4/splitintervals/main' +include { GAWK } from '../../../modules/nf-core/gawk' workflow SCATTER_GENOME { diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index 3f75a74d4..cc78d17ee 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -2,11 +2,11 @@ // A subworkflow to subsample MT alignments // -include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as SAM_TO_BAM } from '../../../modules/nf-core/samtools/view/main' +include { GAWK } from '../../../modules/nf-core/gawk/main' include { SAMTOOLS_COLLATE } from '../../../modules/nf-core/samtools/collate/main' include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' -include { GAWK } from '../../../modules/nf-core/gawk/main' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_VIEW as SAM_TO_BAM } from '../../../modules/nf-core/samtools/view/main' workflow SUBSAMPLE_MT_READS { diff --git a/subworkflows/local/variant_evaluation/main.nf b/subworkflows/local/variant_evaluation/main.nf index e2df70802..68cad1d8d 100644 --- a/subworkflows/local/variant_evaluation/main.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -2,9 +2,9 @@ // A subworkflow to evaluate variants using truth vcfs. // -include { RTGTOOLS_VCFEVAL } from '../../../modules/nf-core/rtgtools/vcfeval/main' -include { BCFTOOLS_REHEADER } from '../../../modules/nf-core/bcftools/reheader/main' -include { TABIX_TABIX as TABIX_TRUTHVCF } from '../../../modules/nf-core/tabix/tabix/main' +include { BCFTOOLS_REHEADER } from '../../../modules/nf-core/bcftools/reheader/main' +include { RTGTOOLS_VCFEVAL } from '../../../modules/nf-core/rtgtools/vcfeval/main' +include { TABIX_TABIX as TABIX_TRUTHVCF } from '../../../modules/nf-core/tabix/tabix/main' workflow VARIANT_EVALUATION { From 59c10b0eee9a472fc423cdcfcfaf0d40fa23bc45 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 29 Apr 2026 15:25:47 +0200 Subject: [PATCH 653/872] even more snaps --- tests/default.nf.test.snap | 4 +- tests/test_bam.nf.test.snap | 292 +++++++++++++++++++++++++++-- tests/test_singleton.nf.test.snap | 294 ++++++++++++++++++++++++++++-- 3 files changed, 565 insertions(+), 25 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 55ef69084..2f0b2b959 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -672,12 +672,12 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", - "call_sv/slowlycivilbuck.saltshaker.png", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -928,6 +928,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T12:37:38.229711898" + "timestamp": "2026-04-29T15:18:41.727506862" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index d53fd33d2..092890a2c 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 356, + 808, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,6 +16,9 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.22 + }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -87,6 +90,12 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -376,6 +385,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -456,6 +468,12 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, + "UPD_REGIONS": { + "upd": 0.1 + }, + "UPD_SITES": { + "upd": 0.1 + }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.3" }, @@ -475,11 +493,21 @@ }, [ "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/hugelymodelbat_sorted_md.metrics.txt", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -487,6 +515,35 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", + "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -516,8 +573,87 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", @@ -536,23 +672,33 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", + "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/hugelymodelbat_LNUMBER1", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -569,6 +715,59 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.summary.txt", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/earlycasualcaiman_tidditcov.bed", + "qc_bam/earlycasualcaiman_tidditcov.bw", + "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", + "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -622,6 +821,59 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.summary.txt", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/slowlycivilbuck_tidditcov.bed", + "qc_bam/slowlycivilbuck_tidditcov.bw", + "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -636,29 +888,47 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "vcf2cytosure/earlycasualcaiman.cgh", + "vcf2cytosure/hugelymodelbat.cgh", + "vcf2cytosure/slowlycivilbuck.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T14:23:37.468812614" + "timestamp": "2026-04-29T15:20:46.408600997" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 527b106e7..012c6211a 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 356, + 808, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,6 +16,9 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.22 + }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -87,6 +90,12 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -376,6 +385,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPRING_DECOMPRESS_TO_FQ_PAIR": { + "spring": "1.1.1" + }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -456,6 +468,12 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, + "UPD_REGIONS": { + "upd": 0.1 + }, + "UPD_SITES": { + "upd": 0.1 + }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.3" }, @@ -475,11 +493,21 @@ }, [ "alignment", + "alignment/earlycasualcaiman_mt_subsample.bam", + "alignment/earlycasualcaiman_mt_subsample.bam.bai", + "alignment/earlycasualcaiman_sorted_md.bam", + "alignment/earlycasualcaiman_sorted_md.bam.bai", + "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/hugelymodelbat_sorted_md.metrics.txt", + "alignment/slowlycivilbuck_mt_subsample.bam", + "alignment/slowlycivilbuck_mt_subsample.bam.bai", + "alignment/slowlycivilbuck_sorted_md.bam", + "alignment/slowlycivilbuck_sorted_md.bam.bai", + "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -487,6 +515,35 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", + "annotate_snv/genome/earlycasualcaiman_rhocallviz", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", + "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -516,8 +573,87 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", + "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/genome/slowlycivilbuck_rhocallviz", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", + "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", @@ -536,23 +672,33 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/earlycasualcaiman.saltshaker.png", + "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/hugelymodelbat_LNUMBER1", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", - "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "fastqc/earlycasualcaiman_LNUMBER1", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", + "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", + "fastqc/hugelymodelbat_LNUMBER3", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", + "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", + "fastqc/slowlycivilbuck_LNUMBER2", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", + "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", + "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -569,6 +715,59 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", + "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", + "qc_bam/earlycasualcaiman_mosdepth.summary.txt", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", + "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/earlycasualcaiman_tidditcov.bed", + "qc_bam/earlycasualcaiman_tidditcov.bw", + "qc_bam/earlycasualcaiman_tidditcov.wig", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", + "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", + "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -622,6 +821,59 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", + "qc_bam/slowlycivilbuck_mosdepth.summary.txt", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", + "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/slowlycivilbuck_tidditcov.bed", + "qc_bam/slowlycivilbuck_tidditcov.bw", + "qc_bam/slowlycivilbuck_tidditcov.wig", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", + "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", + "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -636,29 +888,47 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", + "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", + "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", + "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", + "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/hugelymodelbat_LNUMBER1.fastp.html", - "trimming/hugelymodelbat_LNUMBER1.fastp.json", - "trimming/hugelymodelbat_LNUMBER1.fastp.log", - "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1.fastp.html", + "trimming/earlycasualcaiman_LNUMBER1.fastp.json", + "trimming/earlycasualcaiman_LNUMBER1.fastp.log", + "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", + "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3.fastp.html", + "trimming/hugelymodelbat_LNUMBER3.fastp.json", + "trimming/hugelymodelbat_LNUMBER3.fastp.log", + "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2.fastp.html", + "trimming/slowlycivilbuck_LNUMBER2.fastp.json", + "trimming/slowlycivilbuck_LNUMBER2.fastp.log", + "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", + "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/hugelymodelbat.cgh" + "vcf2cytosure/earlycasualcaiman.cgh", + "vcf2cytosure/hugelymodelbat.cgh", + "vcf2cytosure/slowlycivilbuck.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T14:49:58.807870905" + "timestamp": "2026-04-29T15:22:52.823500658" } } \ No newline at end of file From 4fec83951b11bf2024f0885db9741d8c1480f9a2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 29 Apr 2026 22:38:50 +0200 Subject: [PATCH 654/872] update snaps --- tests/default.nf.test.snap | 8 ++++---- tests/test_bam.nf.test.snap | 8 ++++---- tests/test_singleton.nf.test.snap | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e0e924241..938b6899f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -483,7 +483,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v2.7.0dev" + "nf-core/raredisease": "v3.0.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -924,10 +924,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-04-29T22:20:44.976982426", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-14T14:58:54.280831107" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 2fb2629fd..e26145db1 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -441,7 +441,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v2.7.0dev" + "nf-core/raredisease": "v3.0.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -844,10 +844,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], + "timestamp": "2026-04-29T22:26:48.082490207", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-14T14:47:13.174933057" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 4af8437b5..66f438cc4 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -466,7 +466,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v2.7.0dev" + "nf-core/raredisease": "v3.0.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -655,10 +655,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], + "timestamp": "2026-04-29T22:30:32.111448817", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-14T15:03:52.559527073" + } } } \ No newline at end of file From e6e1dca42b07dea70bd766585527ac168b4b283e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 30 Apr 2026 11:08:21 +0200 Subject: [PATCH 655/872] more snaps --- tests/test_bam.nf.test.snap | 84 +-------- tests/test_singleton.nf.test.snap | 294 ++---------------------------- 2 files changed, 14 insertions(+), 364 deletions(-) diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 092890a2c..16290e3be 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 808, + 775, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -67,10 +67,6 @@ "BWAMEM2_INDEX_MT_SHIFT": { "bwamem2": "2.2.1" }, - "BWAMEM2_MEM": { - "bwamem2": "2.2.1", - "samtools": "1.22.1" - }, "BWAMEM2_MEM_MT": { "bwamem2": "2.2.1", "samtools": "1.22.1" @@ -81,9 +77,6 @@ "CAT_CAT_BAIT": { "pigz": 2.8 }, - "CAT_FASTQ": { - "cat": 9.5 - }, "CHROMOGRAPH_AUTOZYG": { "chromograph": "1.3.1" }, @@ -160,12 +153,6 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, - "FASTP": { - "fastp": "1.0.1" - }, - "FASTQC": { - "fastqc": "0.12.1" - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -249,15 +236,9 @@ "MANTA": { "manta": "1.6.0" }, - "MARKDUPLICATES": { - "picard": "3.4.0" - }, "ME_SPLIT_ALIGNMENT": { "samtools": "1.22.1" }, - "MITOSALT": { - "mitosalt": "1.1.1" - }, "MOSDEPTH": { "mosdepth": "0.3.11" }, @@ -322,15 +303,6 @@ "RHOCALL_VIZ": { "rhocall": "0.5.1" }, - "SALTSHAKER_CALL": { - "saltshaker": "1.0.0" - }, - "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.1" - }, - "SALTSHAKER_PLOT": { - "saltshaker": "1.0.0" - }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" }, @@ -340,12 +312,6 @@ "SAMTOOLS_FAIDX_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_INDEX_ALIGN": { - "samtools": "1.22.1" - }, - "SAMTOOLS_INDEX_MARKDUP": { - "samtools": "1.22.1" - }, "SAMTOOLS_INDEX_MT": { "samtools": "1.22.1" }, @@ -355,18 +321,12 @@ "SAMTOOLS_SORT_MT": { "samtools": "1.22.1" }, - "SAMTOOLS_STATS": { - "samtools": "1.22.1" - }, "SAMTOOLS_VIEW": { "samtools": "1.22.1" }, "SAM_TO_BAM": { "samtools": "1.22.1" }, - "SEQTK_SAMPLE": { - "seqtk": "1.4-r122" - }, "SMNCOPYNUMBERCALLER": { "smncopynumbercaller": "1.1.2" }, @@ -385,9 +345,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -495,19 +452,10 @@ "alignment", "alignment/earlycasualcaiman_mt_subsample.bam", "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", - "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", - "alignment/hugelymodelbat_sorted_md.bam", - "alignment/hugelymodelbat_sorted_md.bam.bai", - "alignment/hugelymodelbat_sorted_md.metrics.txt", "alignment/slowlycivilbuck_mt_subsample.bam", "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", - "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -673,23 +621,11 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", - "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", - "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", - "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", @@ -903,22 +839,6 @@ "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", - "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", "vcf2cytosure", "vcf2cytosure/earlycasualcaiman.cgh", "vcf2cytosure/hugelymodelbat.cgh", @@ -929,6 +849,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T15:20:46.408600997" + "timestamp": "2026-04-30T11:05:32.425390809" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 012c6211a..d0201c8d5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 808, + 356, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -16,9 +16,6 @@ "BCFTOOLS_CONCAT_ME": { "bcftools": 1.22 }, - "BCFTOOLS_MERGE_MT": { - "bcftools": 1.22 - }, "BCFTOOLS_REHEADER_EXP": { "bcftools": 1.22 }, @@ -90,12 +87,6 @@ "CHROMOGRAPH_COV": { "chromograph": "1.3.1" }, - "CHROMOGRAPH_REGIONS": { - "chromograph": "1.3.1" - }, - "CHROMOGRAPH_SITES": { - "chromograph": "1.3.1" - }, "CNVNATOR_CALL": { "cnvnator": "0.4.1" }, @@ -385,9 +376,6 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, - "SPRING_DECOMPRESS_TO_FQ_PAIR": { - "spring": "1.1.1" - }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -468,12 +456,6 @@ "UNTAR_VEP_CACHE": { "untar": 1.34 }, - "UPD_REGIONS": { - "upd": 0.1 - }, - "UPD_SITES": { - "upd": 0.1 - }, "VCF2CYTOSURE": { "vcf2cytosure": "0.9.3" }, @@ -493,21 +475,11 @@ }, [ "alignment", - "alignment/earlycasualcaiman_mt_subsample.bam", - "alignment/earlycasualcaiman_mt_subsample.bam.bai", - "alignment/earlycasualcaiman_sorted_md.bam", - "alignment/earlycasualcaiman_sorted_md.bam.bai", - "alignment/earlycasualcaiman_sorted_md.metrics.txt", "alignment/hugelymodelbat_mt_subsample.bam", "alignment/hugelymodelbat_mt_subsample.bam.bai", "alignment/hugelymodelbat_sorted_md.bam", "alignment/hugelymodelbat_sorted_md.bam.bai", "alignment/hugelymodelbat_sorted_md.metrics.txt", - "alignment/slowlycivilbuck_mt_subsample.bam", - "alignment/slowlycivilbuck_mt_subsample.bam.bai", - "alignment/slowlycivilbuck_sorted_md.bam", - "alignment/slowlycivilbuck_sorted_md.bam.bai", - "alignment/slowlycivilbuck_sorted_md.metrics.txt", "annotate_mobile_elements", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz", "annotate_mobile_elements/justhusky_me_pli_clinical.vcf.gz.tbi", @@ -515,35 +487,6 @@ "annotate_mobile_elements/justhusky_me_pli_research.vcf.gz.tbi", "annotate_snv", "annotate_snv/genome", - "annotate_snv/genome/earlycasualcaiman_rhocallviz", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr1.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr10.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr11.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr12.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr13.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr14.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr15.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr16.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr17.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr18.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr19.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr2.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr20.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr21.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr22.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr3.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr4.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr5.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr6.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr7.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr8.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chr9.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrM.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrX.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz.bed_chrY.png", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bed", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.bw", - "annotate_snv/genome/earlycasualcaiman_rhocallviz/earlycasualcaiman_rhocallviz.wig", "annotate_snv/genome/hugelymodelbat_rhocallviz", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr1.png", "annotate_snv/genome/hugelymodelbat_rhocallviz.bed_chr10.png", @@ -573,87 +516,8 @@ "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_regions.bed_chrY.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr1.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr10.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr11.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr12.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr13.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr14.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr15.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr16.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr17.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr18.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr19.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr2.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr20.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr21.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr22.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr3.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr4.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr5.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr6.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr7.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr8.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chr9.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrM.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrX.png", - "annotate_snv/genome/hugelymodelbat_upd_sites.bed_chrY.png", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", - "annotate_snv/genome/slowlycivilbuck_rhocallviz", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr1.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr10.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr11.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr12.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr13.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr14.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr15.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr16.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr17.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr18.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr19.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr2.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr20.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr21.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr22.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr3.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr4.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr5.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr6.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr7.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr8.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chr9.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrM.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrX.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz.bed_chrY.png", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bed", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.bw", - "annotate_snv/genome/slowlycivilbuck_rhocallviz/slowlycivilbuck_rhocallviz.wig", "annotate_snv/mitochondria", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", @@ -672,33 +536,23 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", - "call_sv/earlycasualcaiman.saltshaker.png", - "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", - "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", - "fastqc/earlycasualcaiman_LNUMBER1", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", - "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.zip", - "fastqc/hugelymodelbat_LNUMBER3", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.html", - "fastqc/hugelymodelbat_LNUMBER3/hugelymodelbat_LNUMBER3.zip", - "fastqc/slowlycivilbuck_LNUMBER2", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.html", - "fastqc/slowlycivilbuck_LNUMBER2/slowlycivilbuck_LNUMBER2.zip", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", "multiqc/multiqc_report.html", "ngsbits_samplegender", - "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", - "ngsbits_samplegender/slowlycivilbuck_ngsbits_sex.tsv", "peddy", "peddy/justhusky.het_check.csv", "peddy/justhusky.het_check.png", @@ -715,59 +569,6 @@ "pipeline_info", "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", "qc_bam", - "qc_bam/earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_mosdepth.global.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.per-base.d4", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.region.dist.txt", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "qc_bam/earlycasualcaiman_mosdepth.summary.txt", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz", - "qc_bam/earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/earlycasualcaiman_tidditcov.bed", - "qc_bam/earlycasualcaiman_tidditcov.bw", - "qc_bam/earlycasualcaiman_tidditcov.wig", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr1.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr10.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr11.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr12.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr13.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr14.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr15.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr16.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr17.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr18.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr19.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr2.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr20.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr21.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr22.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr3.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr4.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr5.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr6.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr7.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr8.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chr9.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrM.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrX.png", - "qc_bam/earlycasualcaiman_tidditcov.wig_chrY.png", - "qc_bam/earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/earlycasualcaiman_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", @@ -821,59 +622,6 @@ "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_hsmetrics.CollectHsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_mosdepth.global.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.per-base.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.per-base.d4", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.quantized.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.region.dist.txt", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.regions.bed.gz.csi", - "qc_bam/slowlycivilbuck_mosdepth.summary.txt", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz", - "qc_bam/slowlycivilbuck_mosdepth.thresholds.bed.gz.csi", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "qc_bam/slowlycivilbuck_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "qc_bam/slowlycivilbuck_tidditcov.bed", - "qc_bam/slowlycivilbuck_tidditcov.bw", - "qc_bam/slowlycivilbuck_tidditcov.wig", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr1.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr10.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr11.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr12.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr13.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr14.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr15.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr16.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr17.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr18.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr19.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr2.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr20.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr21.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr22.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr3.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr4.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr5.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr6.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr7.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr8.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chr9.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrM.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrX.png", - "qc_bam/slowlycivilbuck_tidditcov.wig_chrY.png", - "qc_bam/slowlycivilbuck_wgsmetrics.CollectWgsMetrics.coverage_metrics", - "qc_bam/slowlycivilbuck_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", "rank_and_filter", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", @@ -888,47 +636,29 @@ "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", "repeat_expansions", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam", - "repeat_expansions/earlycasualcaiman_exphunter_sorted.bam.bai", - "repeat_expansions/earlycasualcaiman_repeat_expansion.vcf", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam", - "repeat_expansions/slowlycivilbuck_exphunter_sorted.bam.bai", - "repeat_expansions/slowlycivilbuck_repeat_expansion.vcf", "smncopynumbercaller", "smncopynumbercaller/out", "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", "trimming", - "trimming/earlycasualcaiman_LNUMBER1.fastp.html", - "trimming/earlycasualcaiman_LNUMBER1.fastp.json", - "trimming/earlycasualcaiman_LNUMBER1.fastp.log", - "trimming/earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz", - "trimming/earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3.fastp.html", - "trimming/hugelymodelbat_LNUMBER3.fastp.json", - "trimming/hugelymodelbat_LNUMBER3.fastp.log", - "trimming/hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz", - "trimming/hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2.fastp.html", - "trimming/slowlycivilbuck_LNUMBER2.fastp.json", - "trimming/slowlycivilbuck_LNUMBER2.fastp.log", - "trimming/slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz", - "trimming/slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", "vcf2cytosure", - "vcf2cytosure/earlycasualcaiman.cgh", - "vcf2cytosure/hugelymodelbat.cgh", - "vcf2cytosure/slowlycivilbuck.cgh" + "vcf2cytosure/hugelymodelbat.cgh" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T15:22:52.823500658" + "timestamp": "2026-04-30T11:07:32.350854587" } } \ No newline at end of file From f2049b44293320ff7750907254b1db9b9df5974a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 30 Apr 2026 12:07:33 +0200 Subject: [PATCH 656/872] update docs and citations --- .github/CONTRIBUTING.md | 11 +++++++++++ CITATIONS.md | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index aa03cdafc..b68bd5416 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -170,6 +170,17 @@ Devcontainer specs: ### Style +- Sort `include` statements alphabetically by the name inside the braces. Right-pad each name with spaces so all closing `}` align to the same column (the longest name in the block sets the width): + + ```groovy + include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' + include { ALIGN_MT } from '../align_MT' + include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' + include { SAMTOOLS_VIEW as CONVERTTOCRAM_ALTFILTERED } from '../../../modules/nf-core/samtools/view/main' + include { SAMTOOLS_VIEW as CONVERTTOCRAM_UNFILTERED } from '../../../modules/nf-core/samtools/view/main' + include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf-core/samtools/view/main' + ``` + - Both `take:` and `emit:` block entries require an inline type comment. Use `name // type: [mandatory|optional] description` for `take:` and `name = value // channel: [type description]` for `emit:`. Always include the comment — never leave an entry uncommented. ```groovy diff --git a/CITATIONS.md b/CITATIONS.md index c55cbf4e1..854af10d4 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -108,7 +108,7 @@ > John G. Cleary, Ross Braithwaite, Kurt Gaastra, Brian S. Hilbush, Stuart Inglis, Sean A. Irvine, Alan Jackson, Richard Littin, Mehul Rathod, David Ware, Justin M. Zook, Len Trigg, and Francisco M. De La Vega. "Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines." bioRxiv, 2015. doi:10.1101/023754. -- [saltshaker](https://pypi.org/project/saltshaker/) +- [saltshaker](https://gitlab.com/genomedx/annotation/saltshaker) - [Sambamba](https://academic.oup.com/bioinformatics/article/31/12/2032/213831) From e542158b5c1620fcbfc0aff8b421243b72027061 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 30 Apr 2026 13:39:39 +0200 Subject: [PATCH 657/872] collect mitosalt prep so it runs on all --- subworkflows/local/call_sv_MT/main.nf | 4 +++- tests/default.nf.test.snap | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 90c420d98..77e4d479d 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -83,9 +83,11 @@ workflow CALL_SV_MT { val_mitochondria_name ) + ch_prep_mitosalt = PREP_MITOSALT.out.msconfig.collect() + MITOSALT( SEQTK_SAMPLE.out.reads, - PREP_MITOSALT.out.msconfig, + ch_prep_mitosalt, ch_genome_chrsizes, ch_genome_fai, ch_genome_hisat2index, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2f0b2b959..92d477556 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -671,6 +671,7 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", + "call_sv/earlycasualcaiman.saltshaker.png", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", @@ -678,6 +679,7 @@ "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck.saltshaker.png", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -928,6 +930,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-29T15:18:41.727506862" + "timestamp": "2026-04-30T13:22:59.360128566" } } \ No newline at end of file From 8b454ccff3385b8f8fb4f504ae9c146c1754802b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 30 Apr 2026 14:23:34 +0200 Subject: [PATCH 658/872] switch out for nf-core concat module --- modules.json | 5 + modules/local/concat_saltshaker/main.nf | 15 -- .../nf-core/find/concatenate/environment.yml | 8 + modules/nf-core/find/concatenate/main.nf | 70 ++++++ modules/nf-core/find/concatenate/meta.yml | 112 ++++++++++ .../find/concatenate/tests/main.nf.test | 154 +++++++++++++ .../find/concatenate/tests/main.nf.test.snap | 207 ++++++++++++++++++ .../tests/nextflow_unzipped_zipped.config | 5 + .../tests/nextflow_zipped_unzipped.config | 6 + subworkflows/local/call_sv_MT/main.nf | 6 +- 10 files changed, 570 insertions(+), 18 deletions(-) delete mode 100644 modules/local/concat_saltshaker/main.nf create mode 100644 modules/nf-core/find/concatenate/environment.yml create mode 100644 modules/nf-core/find/concatenate/main.nf create mode 100644 modules/nf-core/find/concatenate/meta.yml create mode 100644 modules/nf-core/find/concatenate/tests/main.nf.test create mode 100644 modules/nf-core/find/concatenate/tests/main.nf.test.snap create mode 100644 modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config create mode 100644 modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config diff --git a/modules.json b/modules.json index 1b505b1e1..312c859b6 100644 --- a/modules.json +++ b/modules.json @@ -166,6 +166,11 @@ "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", "installed_by": ["modules"] }, + "find/concatenate": { + "branch": "master", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", + "installed_by": ["modules"] + }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", diff --git a/modules/local/concat_saltshaker/main.nf b/modules/local/concat_saltshaker/main.nf deleted file mode 100644 index 004b83dcb..000000000 --- a/modules/local/concat_saltshaker/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -process CONCAT_SALTSHAKER { - tag "$meta.id" - label "process_low" - - input: - tuple val(meta), path(txts) - - output: - tuple val(meta), path("*.txt"), emit: txt - - script: - """ - cat ${txts.join(' ')} > ${meta.id}.saltshaker_classify.txt - """ -} diff --git a/modules/nf-core/find/concatenate/environment.yml b/modules/nf-core/find/concatenate/environment.yml new file mode 100644 index 000000000..874a4bd0d --- /dev/null +++ b/modules/nf-core/find/concatenate/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - coreutils==9.4 + - findutils==4.6.0 + - pigz==2.8 diff --git a/modules/nf-core/find/concatenate/main.nf b/modules/nf-core/find/concatenate/main.nf new file mode 100644 index 000000000..9fc8915f6 --- /dev/null +++ b/modules/nf-core/find/concatenate/main.nf @@ -0,0 +1,70 @@ +process FIND_CONCATENATE { + tag "${meta.id}" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7f/7fd226561e12b32bcacdf4f5ff74577e76233adf52ae5cbc499a2cdfe0e27d82/data' + : 'community.wave.seqera.io/library/findutils_pigz:c4dd5edc44402661'}" + + input: + tuple val(meta), path(files_in, stageAs: 'to_concatenate/*', arity: '1..*') + + output: + tuple val(meta), path("${prefix}"), emit: file_out + tuple val("${task.process}"), val("find"), eval("find --version | sed '1!d; s/.* //'"), topic: versions, emit: versions_find + tuple val("${task.process}"), val("pigz"), eval("pigz --version 2>&1 | sed 's/pigz //g'"), topic: versions, emit: versions_pigz + tuple val("${task.process}"), val("coreutils"), eval("cat --version | sed '1!d; s/.* //'"), topic: versions, emit: versions_coreutils + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: "" + + // | input | output | command1 | command2 | + // |-----------|------------|----------|----------| + // | gzipped | gzipped | cat | | + // | ungzipped | ungzipped | cat | | + // | gzipped | ungzipped | pigz | | + // | ungzipped | gzipped | cat | pigz | + + // Use input file ending as default + // get file extensions, if extension is .gz then get the second to last extension as well + file_extensions = files_in.collect { in_file -> in_file.name - in_file.getBaseName(in_file.name.endsWith('.gz') ? 2 : 1) } + + // Use input file ending as default for output file + prefix = task.ext.prefix ?: "${meta.id}${file_extensions[0]}" + + if (files_in.any{ file -> file.toString().endsWith('.gz')} && !files_in.every{ file -> file.toString().endsWith('.gz') }) { + error("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") + } + + in_zip = files_in[0].toString().endsWith('.gz') + out_zip = task.ext.prefix ? task.ext.prefix.endsWith('.gz') : file_extensions[0].endsWith('.gz') + + out_fname = in_zip && out_zip ? prefix : prefix.endsWith('.gz') ? prefix.replace('.gz', '') : prefix + + cmd1 = in_zip && !out_zip ? "pigz -cd -p ${task.cpus}" : "cat" + cmd2 = !in_zip && out_zip ? "pigz -p ${task.cpus} ${args} ${out_fname}" : "" + + """ + while IFS= read -r -d \$'\\0' file; do + ${cmd1} \$file \\ + >> ${out_fname} + done < <( find to_concatenate/ -mindepth 1 -print0 | sort -z ) + + ${cmd2} + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + + if (files_in.any{ file -> file.toString().endsWith('.gz')} && !files_in.every{ file -> file.toString().endsWith('.gz') }) { + error("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") + } + + """ + touch ${prefix} + """ +} diff --git a/modules/nf-core/find/concatenate/meta.yml b/modules/nf-core/find/concatenate/meta.yml new file mode 100644 index 000000000..046acb691 --- /dev/null +++ b/modules/nf-core/find/concatenate/meta.yml @@ -0,0 +1,112 @@ +name: "find_concatenate" +description: A module for concatenation of gzipped or uncompressed files getting around + UNIX terminal argument size +keywords: + - concatenate + - gzip + - cat + - find + - pigz +tools: + - find: + description: GNU find searches the directory tree rooted at each given starting-point + by evaluating the given expression + documentation: https://man7.org/linux/man-pages/man1/find.1.html + licence: + - "GPL-3.0-or-later" + identifier: "" + - pigz: + description: pigz, which stands for Parallel Implementation of GZip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. + documentation: https://zlib.net/pigz/pigz.pdf + licence: + - "other" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - files_in: + type: file + description: List of either compressed or uncompressed files + pattern: "*" + ontologies: [] +output: + file_out: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${prefix}: + type: file + description: Concatenated file. Will be gzipped if ${prefix} ends with ".gz" + or inputs are gzipped, will be uncompressed otherwise. + pattern: "${file_out}" + ontologies: [] + versions_find: + - - ${task.process}: + type: string + description: The name of the process + - find: + type: string + description: The name of the tool + - find --version | sed '1!d; s/.* //': + type: eval + description: The expression to obtain the version of the tool + versions_pigz: + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - pigz --version 2>&1 | sed 's/pigz //g': + type: eval + description: The expression to obtain the version of the tool + versions_coreutils: + - - ${task.process}: + type: string + description: The name of the process + - coreutils: + type: string + description: The name of the tool + - cat --version | sed '1!d; s/.* //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - find: + type: string + description: The name of the tool + - find --version | sed '1!d; s/.* //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - pigz: + type: string + description: The name of the tool + - pigz --version 2>&1 | sed 's/pigz //g': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - coreutils: + type: string + description: The name of the tool + - cat --version | sed '1!d; s/.* //': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@BioWilko" +maintainers: + - "@BioWilko" diff --git a/modules/nf-core/find/concatenate/tests/main.nf.test b/modules/nf-core/find/concatenate/tests/main.nf.test new file mode 100644 index 000000000..c96f9e48d --- /dev/null +++ b/modules/nf-core/find/concatenate/tests/main.nf.test @@ -0,0 +1,154 @@ +nextflow_process { + + name "Test Process FIND_CONCATENATE" + script "../main.nf" + process "FIND_CONCATENATE" + tag "modules" + tag "modules_nfcore" + tag "find" + tag "find/concatenate" + + test("test_mixed_input") { + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") }, + ) + } + } + + test("test_cat_unzipped_unzipped") { + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() }, + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() }, + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() }, + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() }, + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(sanitizeOutput(process.out)).match() }, + ) + } + } +} diff --git a/modules/nf-core/find/concatenate/tests/main.nf.test.snap b/modules/nf-core/find/concatenate/tests/main.nf.test.snap new file mode 100644 index 000000000..56494eacd --- /dev/null +++ b/modules/nf-core/find/concatenate/tests/main.nf.test.snap @@ -0,0 +1,207 @@ +{ + "test_cat_unzipped_unzipped": { + "content": [ + { + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions_coreutils": [ + [ + "FIND_CONCATENATE", + "coreutils", + "9.4" + ] + ], + "versions_find": [ + [ + "FIND_CONCATENATE", + "find", + "4.6.0" + ] + ], + "versions_pigz": [ + [ + "FIND_CONCATENATE", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-11T11:55:56.090740487" + }, + "test_cat_zipped_zipped": { + "content": [ + { + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.gff3.gz:md5,1a983f97a01107efe42c8c3e7728b4c1" + ] + ], + "versions_coreutils": [ + [ + "FIND_CONCATENATE", + "coreutils", + "9.4" + ] + ], + "versions_find": [ + [ + "FIND_CONCATENATE", + "find", + "4.6.0" + ] + ], + "versions_pigz": [ + [ + "FIND_CONCATENATE", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-11T11:56:03.72242729" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,1a983f97a01107efe42c8c3e7728b4c1" + ] + ], + "versions_coreutils": [ + [ + "FIND_CONCATENATE", + "coreutils", + "9.4" + ] + ], + "versions_find": [ + [ + "FIND_CONCATENATE", + "find", + "4.6.0" + ] + ], + "versions_pigz": [ + [ + "FIND_CONCATENATE", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-11T11:56:11.488401849" + }, + "test_cat_one_file_unzipped_zipped": { + "content": [ + { + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,6e9fe4042a72f2345f644f239272b7e6" + ] + ], + "versions_coreutils": [ + [ + "FIND_CONCATENATE", + "coreutils", + "9.4" + ] + ], + "versions_find": [ + [ + "FIND_CONCATENATE", + "find", + "4.6.0" + ] + ], + "versions_pigz": [ + [ + "FIND_CONCATENATE", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-11T11:56:26.254644609" + }, + "test_cat_unzipped_zipped": { + "content": [ + { + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions_coreutils": [ + [ + "FIND_CONCATENATE", + "coreutils", + "9.4" + ] + ], + "versions_find": [ + [ + "FIND_CONCATENATE", + "find", + "4.6.0" + ] + ], + "versions_pigz": [ + [ + "FIND_CONCATENATE", + "pigz", + "2.8" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.2" + }, + "timestamp": "2026-03-11T11:56:18.76821511" + } +} \ No newline at end of file diff --git a/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config b/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config new file mode 100644 index 000000000..aec380fd8 --- /dev/null +++ b/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,5 @@ +process { + withName: FIND_CONCATENATE { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config b/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config new file mode 100644 index 000000000..5e10af2bb --- /dev/null +++ b/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,6 @@ +process { + + withName: FIND_CONCATENATE { + ext.prefix = 'cat.txt' + } +} diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 77e4d479d..b09d5a8fb 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -9,7 +9,7 @@ include { MITOSALT } from '../../../modules/local/mitosalt/main' include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' -include { CONCAT_SALTSHAKER } from '../../../modules/local/concat_saltshaker/main' +include { FIND_CONCATENATE } from '../../../modules/nf-core/find/concatenate/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' @@ -133,10 +133,10 @@ workflow CALL_SV_MT { .combine(ch_saltshaker_files) .set { ch_saltshaker_txts } - CONCAT_SALTSHAKER( + FIND_CONCATENATE( ch_saltshaker_txts ) - ch_saltshaker_txt = CONCAT_SALTSHAKER.out.txt + ch_saltshaker_txt = FIND_CONCATENATE.out.file_out SALTSHAKER_TO_HTML( ch_saltshaker_txt, From 6bd4bf5e73bba66d494152ff5f7cb2a7dbd69489 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 30 Apr 2026 13:33:26 +0000 Subject: [PATCH 659/872] Template update for nf-core/tools version 4.0.2 --- .github/workflows/download_pipeline.yml | 8 +++++--- .github/workflows/fix_linting.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 2 +- README.md | 2 +- nextflow_schema.json | 1 - ro-crate-metadata.json | 18 +++++++++--------- 8 files changed, 19 insertions(+), 18 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 5b6592c1e..a7bf4fc21 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -38,6 +38,9 @@ jobs: runs-on: ubuntu-latest needs: configure steps: + - name: Check out pipeline code + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 + - name: Install Nextflow uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 @@ -55,10 +58,9 @@ jobs: apptainer-version: 1.3.4 - name: Read .nf-core.yml - uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml - with: - config: ${{ github.workspace }}/.nf-core.yml + run: | + echo "nf_core_version=$(yq '.nf_core_version' ${{ github.workspace }}/.nf-core.yml)" >> "$GITHUB_OUTPUT" - name: Install dependencies run: | diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml index 1e256aebb..bbacef323 100644 --- a/.github/workflows/fix_linting.yml +++ b/.github/workflows/fix_linting.yml @@ -37,7 +37,7 @@ jobs: # Install and run prek - name: Run prek id: prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 continue-on-error: true # indication that the linting has finished diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfe46c98f..8738ffc99 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -17,7 +17,7 @@ jobs: uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 - name: Run prek - uses: j178/prek-action@cbc2f23eb5539cf20d82d1aabd0d0ecbcc56f4e3 # v2 + uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2 nf-core: runs-on: ubuntu-latest diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 2bc3c07fd..5b0c24f75 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@8305c0f1062bb0d184d09ef4493ecb9288447732 # v20 + uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index 4b01d75e6..7bbfd55e3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -8,7 +8,7 @@ lint: - docs/images/nf-core-raredisease_logo_light.png - assets/nf-core-raredisease_logo_light.png modules_config: false -nf_core_version: 4.0.0 +nf_core_version: 4.0.2 repository_type: pipeline template: author: Clinical Genomics Stockholm diff --git a/README.md b/README.md index d7dace8d4..5a71f59d9 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) -[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/nextflow_schema.json b/nextflow_schema.json index 4f86ae951..bf48a0f82 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -74,7 +74,6 @@ }, "igenomes_base": { "type": "string", - "format": "directory-path", "description": "The base path to the igenomes reference files", "fa_icon": "fas fa-ban", "hidden": true, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 828d8a6e6..f477c09df 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2026-04-28T11:20:55+00:00", - "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-04-30T13:33:17+00:00", + "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#9ef09118-0930-47d1-ad79-681897eb2572" + "@id": "#99193e7c-c95c-40dd-abcc-388a9812e2dc" } ], "name": "nf-core/raredisease" @@ -124,11 +124,11 @@ "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "contributor": [ { - "@id": "#43cd2794-2544-43e3-bff1-c22b2c4e90af" + "@id": "#7f7d72e3-cddf-4a0e-8c7e-2fb2556c7173" } ], "dateCreated": "", - "dateModified": "2026-04-28T11:20:55Z", + "dateModified": "2026-04-30T13:33:17Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -166,11 +166,11 @@ "version": "!>=25.10.4" }, { - "@id": "#9ef09118-0930-47d1-ad79-681897eb2572", + "@id": "#99193e7c-c95c-40dd-abcc-388a9812e2dc", "@type": "TestSuite", "instance": [ { - "@id": "#9d02ecc1-065e-4b66-a104-c2d4d511429e" + "@id": "#1bfa89ef-b072-475f-80dc-442d25bb83c8" } ], "mainEntity": { @@ -179,7 +179,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#9d02ecc1-065e-4b66-a104-c2d4d511429e", + "@id": "#1bfa89ef-b072-475f-80dc-442d25bb83c8", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -308,7 +308,7 @@ "url": "https://nf-co.re/" }, { - "@id": "#43cd2794-2544-43e3-bff1-c22b2c4e90af", + "@id": "#7f7d72e3-cddf-4a0e-8c7e-2fb2556c7173", "@type": "Person", "name": "Clinical Genomics Stockholm" } From 551bdc11f2cbe1dcd7a9af249991c849a773f0e4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 4 May 2026 10:58:41 +0200 Subject: [PATCH 660/872] only concat if files exist --- subworkflows/local/call_sv_MT/main.nf | 1 + tests/default.nf.test.snap | 9 +++++++-- tests/test_bam.nf.test.snap | 5 ++--- tests/test_singleton.nf.test.snap | 9 +++++++-- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index b09d5a8fb..15a6aabaa 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -131,6 +131,7 @@ workflow CALL_SV_MT { ch_case_info .combine(ch_saltshaker_files) + .filter { _meta, files -> files.size() > 0 } .set { ch_saltshaker_txts } FIND_CONCATENATE( diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 92d477556..c26a4c2b8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -165,6 +165,11 @@ "FASTQC": { "fastqc": "0.12.1" }, + "FIND_CONCATENATE": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -675,7 +680,7 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -930,6 +935,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-30T13:22:59.360128566" + "timestamp": "2026-04-30T14:28:57.614342021" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 16290e3be..379140f52 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 775, + 773, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -622,7 +622,6 @@ "call_sv", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", @@ -849,6 +848,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-30T11:05:32.425390809" + "timestamp": "2026-05-04T10:55:14.853068641" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index d0201c8d5..0cd2b7e17 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -157,6 +157,11 @@ "FASTQC": { "fastqc": "0.12.1" }, + "FIND_CONCATENATE": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -538,7 +543,7 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -659,6 +664,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-30T11:07:32.350854587" + "timestamp": "2026-04-30T14:31:58.593909358" } } \ No newline at end of file From b961f6b48ff33c7361003433d6c826df3f97ffe3 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 4 May 2026 11:12:00 +0200 Subject: [PATCH 661/872] update report name and documents --- CHANGELOG.md | 1 + docs/output.md | 4 ++-- modules/local/saltshaker_to_html/main.nf | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 882750e44..314c11f9d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) +- Add find/concatenate step to concatenate saltshaker classification files before creating the html report, so the final report is case-level. [#826](https://github.com/nf-core/raredisease/pull/826) ### `Changed` diff --git a/docs/output.md b/docs/output.md index edbbaa14b..ce3e6aecd 100644 --- a/docs/output.md +++ b/docs/output.md @@ -470,8 +470,8 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen [Saltshaker](https://github.com/aksenia/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. - `call_sv` - - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. - - `.saltshaker.png`: circos plot. + - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. Only created when MitoSAlt finds at least one cluster. + - `.saltshaker.png`: circos plot. Only created when MitoSAlt finds at least one cluster. #### Annotation diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 64c1dfd8e..9213236ef 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -19,7 +19,7 @@ process SALTSHAKER_TO_HTML { return html_content html = saltshaker_txt_to_html("${classify}") - with open("${classify.baseName}.html", 'w') as f: + with open("${classify.baseName}.saltshaker_classify.html", 'w') as f: f.write('') f.write(f'
    {html}
    ') f.write('') From 0e635f88d56bd122524dca7ebb5a8271133d5fc4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 4 May 2026 11:21:35 +0200 Subject: [PATCH 662/872] new snaps --- tests/default.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c26a4c2b8..2ae47bd47 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -680,7 +680,7 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.html", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -935,6 +935,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-30T14:28:57.614342021" + "timestamp": "2026-05-04T11:16:28.055158441" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 0cd2b7e17..7ed6802e5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -543,7 +543,7 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.html", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -664,6 +664,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-04-30T14:31:58.593909358" + "timestamp": "2026-05-04T11:21:18.197114243" } } \ No newline at end of file From fbfa69e4216d418ff3a533e179969559a2aeef7b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 4 May 2026 11:45:51 +0200 Subject: [PATCH 663/872] update usage --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index c25bb64ac..4bbe8cce4 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -100,7 +100,7 @@ Running the pipeline involves three steps: A samplesheet is used to provide information about the sample(s) to the pipeline in CSV format, including the path to the FASTQ files and other metadata such as sex and phenotype. -The nf-core/raredisease pipeline accepts FASTQ files, SPRING files, or BAM files as input. Currently, the pipeline does not support single-end data from Illumina. The pedigree information in the samplesheet (sex and phenotype) should be provided in the same format as a [PED file](https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format), with sex indicated as 1 for male, 2 for female, and other for unknown. +The nf-core/raredisease pipeline accepts FASTQ files, SPRING files, or BAM files as input. Currently, the pipeline does not support single-end data from Illumina, and mitochondrial SV calling with MitoSAlt and saltshaker does not run with BAM file input. The pedigree information in the samplesheet (sex and phenotype) should be provided in the same format as a [PED file](https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format), with sex indicated as 1 for male, 2 for female, and other for unknown. | Fields | Description | | ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | From d76e49ff3e8e599351eec3319594cd775c57849c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 4 May 2026 13:20:56 +0200 Subject: [PATCH 664/872] fix alignment --- .github/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index b68bd5416..c75f209ee 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -173,7 +173,7 @@ Devcontainer specs: - Sort `include` statements alphabetically by the name inside the braces. Right-pad each name with spaces so all closing `}` align to the same column (the longest name in the block sets the width): ```groovy - include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' + include { ALIGN_BWA_BWAMEM2_BWAMEME } from '../align_bwa_bwamem2_bwameme' include { ALIGN_MT } from '../align_MT' include { ALIGN_MT as ALIGN_MT_SHIFT } from '../align_MT' include { SAMTOOLS_VIEW as CONVERTTOCRAM_ALTFILTERED } from '../../../modules/nf-core/samtools/view/main' From 98cc300ee827fb445cdb19060648988def3abbd9 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 5 May 2026 09:36:52 +0200 Subject: [PATCH 665/872] Update docs/output.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index ce3e6aecd..841bed06b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -470,7 +470,7 @@ The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sen [Saltshaker](https://github.com/aksenia/saltshaker) allows for downstream clustering and classification of mtDNA strucutral variants. Called variants are combined with structural variants called in the nuclear genome. - `call_sv` - - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. Only created when MitoSAlt finds at least one cluster. + - `.saltshaker_classify.html`: report containing case-level classification of mitochondrial deletions. Only created when MitoSAlt finds at least one cluster. - `.saltshaker.png`: circos plot. Only created when MitoSAlt finds at least one cluster. #### Annotation From 1760a8889fbe34100bd7b4a96128e5b443919a6f Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 5 May 2026 09:43:00 +0200 Subject: [PATCH 666/872] no double list --- subworkflows/local/call_sv_MT/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 15a6aabaa..568776fc0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -126,7 +126,6 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map{ _meta, txt -> txt } .toSortedList{ a, b -> a.name <=> b.name } - .toList() .set{ ch_saltshaker_files } ch_case_info From 47a0a5a435b9ef09a334f7cae2f80363c3366e33 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 5 May 2026 09:43:51 +0200 Subject: [PATCH 667/872] Remove unnecessary toList() --- subworkflows/local/call_sv_MT/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 15a6aabaa..568776fc0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -126,7 +126,6 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map{ _meta, txt -> txt } .toSortedList{ a, b -> a.name <=> b.name } - .toList() .set{ ch_saltshaker_files } ch_case_info From 9a652f86cab70971f268337b476c454d3834189c Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 5 May 2026 09:49:44 +0200 Subject: [PATCH 668/872] remove sorting for concat input --- subworkflows/local/call_sv_MT/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 568776fc0..e02bcc39f 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -125,7 +125,7 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map{ _meta, txt -> txt } - .toSortedList{ a, b -> a.name <=> b.name } + .toList() .set{ ch_saltshaker_files } ch_case_info From c667e692e89f00e23408b8d7aed35668167b68a7 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 5 May 2026 09:52:52 +0200 Subject: [PATCH 669/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 314c11f9d..779f6806a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,6 +75,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) +- Fixed mitosalt channel handling so it runs on all samples in a trio [#826](https://github.com/nf-core/raredisease/pull/826) ### Parameters From 176f1a535f4ed34508e1864e497b16c30669f18b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 5 May 2026 11:29:37 +0200 Subject: [PATCH 670/872] extend vcfanno sanity check --- CHANGELOG.md | 1 + subworkflows/local/annotate_genome_snvs/main.nf | 11 +---------- .../annotate_genome_snvs/tests/main.nf.test | 7 ++----- subworkflows/local/annotate_mt_snvs/main.nf | 4 ++-- workflows/raredisease.nf | 16 +++++++++++++--- 5 files changed, 19 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 882750e44..d3a00469b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameters `save_all_mapped_as_cram` and `save_noalt_mapped_as_cram` to replace `save_mapped_as_cram`, allowing independent control over publishing unfiltered and alt-filtered alignment files as CRAM [#807](https://github.com/nf-core/raredisease/pull/807) - Parameter `run_vcfanno_db_sanity_check` to check vcfanno database files for zero records and remove the corresponding annotation blocks from the TOML config before running vcfanno [#821](https://github.com/nf-core/raredisease/pull/821) - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) +- Extended vcfanno database sanity check to include extra vcfanno resources (`vcfanno_extra`) alongside the main resources, and moved the check upstream to `raredisease.nf` so it covers both genome and mitochondrial SNV annotation subworkflows [#834](https://github.com/nf-core/raredisease/pull/834) ### `Changed` diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 616a82b6d..708baf259 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -16,7 +16,6 @@ include { TABIX_BGZIPTABIX as ZIP_TABIX_ROHCALL } from '../../../modules/nf-core include { GATK4_SELECTVARIANTS } from '../../../modules/nf-core/gatk4/selectvariants/main' include { ANNOTATE_CADD } from '../annotate_cadd' include { ANNOTATE_RHOCALLVIZ } from '../annotate_rhocallviz' -include { SANITY_CHECK_VCFANNO_DATABASES } from '../../../modules/local/sanity_check_vcfanno_databases/main' workflow ANNOTATE_GENOME_SNVS { @@ -33,13 +32,12 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] + ch_vcfanno_toml_final // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] val_analysis_type // string: wgs, wes, or mito val_cadd_resources // string: path to cadd resources file val_genome // string: GRCh37 or GRCh38 - val_run_vcfanno_db_sanity_check // boolean: run sanity check on vcfanno databases val_vep_cache_version // string: vep version ex: 107 main: @@ -99,13 +97,6 @@ workflow ANNOTATE_GENOME_SNVS { .combine(ch_vcfanno_extra) .set { ch_vcfanno_in } - if (val_run_vcfanno_db_sanity_check) { - SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_vcfanno_resources) - ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml - } else { - ch_vcfanno_toml_final = ch_vcfanno_toml - } - VCFANNO (ch_vcfanno_in, ch_vcfanno_toml_final, ch_vcfanno_lua, ch_vcfanno_resources) VCFANNO.out.vcf diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 6a579463c..0b6b95c53 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -19,7 +19,6 @@ nextflow_workflow { tag "ensemblvep/vep" tag "tabix/bgziptabix" tag "gatk4/selectvariants" - tag "sanity_check_vcfanno_databases" config "./nextflow.config" @@ -52,8 +51,7 @@ nextflow_workflow { input[15] = 'wgs' input[16] = null input[17] = 'GRCh37' - input[18] = true - input[19] = 107 + input[18] = 107 """ } } @@ -109,8 +107,7 @@ nextflow_workflow { input[15] = 'wes' input[16] = null input[17] = 'GRCh37' - input[18] = true - input[19] = 107 + input[18] = 107 """ } } diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 975f96f89..a78dd001e 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -19,7 +19,7 @@ workflow ANNOTATE_MT_SNVS { ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] + ch_vcfanno_toml_final // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] val_cadd_resources // string: path to cadd resources file @@ -34,7 +34,7 @@ workflow ANNOTATE_MT_SNVS { .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } - VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) + VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml_final, ch_vcfanno_lua, ch_vcfanno_resources) // Annotating with CADD if (!val_cadd_resources.equals(null)) { diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 400ce17ce..272f22e66 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -34,6 +34,7 @@ include { STRANGER } from '../modules/n include { RENAME_ALIGN_FILES as RENAME_BAM } from '../modules/local/rename_align_files' include { RENAME_ALIGN_FILES as RENAME_BAI } from '../modules/local/rename_align_files' +include { SANITY_CHECK_VCFANNO_DATABASES } from '../modules/local/sanity_check_vcfanno_databases/main' // // SUBWORKFLOWS @@ -441,6 +442,16 @@ workflow RAREDISEASE { ) ch_call_snv_publish = CALL_SNV.out.publish + ch_vcfanno_toml_final = ch_vcfanno_toml + if (val_run_vcfanno_db_sanity_check && (!skip_snv_annotation || (!skip_mt_annotation && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))))) { + ch_vcfanno_resources + .combine(ch_vcfanno_extra) + .map { resources, extra -> [resources, extra].flatten() } + .set { ch_all_vcfanno_dbs } + SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_all_vcfanno_dbs) + ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml + } + // // ANNOTATE GENOME SNVs // @@ -459,13 +470,12 @@ workflow RAREDISEASE { ch_vcfanno_extra, ch_vcfanno_lua, ch_vcfanno_resources, - ch_vcfanno_toml, + ch_vcfanno_toml_final, ch_vep_cache, ch_vep_extra_files, val_analysis_type, val_cadd_resources, val_genome, - val_run_vcfanno_db_sanity_check, val_vep_cache_version ).set { ch_snv_annotate } ch_annotate_genome_snvs_publish = ANNOTATE_GENOME_SNVS.out.publish @@ -531,7 +541,7 @@ workflow RAREDISEASE { ch_vcfanno_extra, ch_vcfanno_lua, ch_vcfanno_resources, - ch_vcfanno_toml, + ch_vcfanno_toml_final, ch_vep_cache, ch_vep_extra_files, val_cadd_resources, From 4b25e223dfed362102fd1a3db937c57e2c5413b7 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 5 May 2026 13:30:26 +0200 Subject: [PATCH 671/872] reinstate double list with explanation --- subworkflows/local/call_sv_MT/main.nf | 2 ++ tests/default.nf.test.snap | 2 +- tests/test_bam.nf.test.snap | 2 +- tests/test_singleton.nf.test.snap | 2 +- 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index e02bcc39f..2dd935740 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -123,9 +123,11 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + // Gather all saltshaker classify txt files in a double list so the full list will be combined with case meta once SALTSHAKER_CLASSIFY.out.txt .map{ _meta, txt -> txt } .toList() + .toList() .set{ ch_saltshaker_files } ch_case_info diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2ae47bd47..fe2137cef 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -935,6 +935,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-05-04T11:16:28.055158441" + "timestamp": "2026-05-05T12:20:20.722620089" } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 379140f52..5e0a0f164 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -848,6 +848,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-05-04T10:55:14.853068641" + "timestamp": "2026-05-05T12:23:18.831109953" } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 7ed6802e5..c9b04ac01 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -664,6 +664,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-05-04T11:21:18.197114243" + "timestamp": "2026-05-05T12:26:57.156579355" } } \ No newline at end of file From 842698c5def084e9b6ab2a8cfb8fc34e57f5a1ec Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 5 May 2026 14:19:57 +0200 Subject: [PATCH 672/872] review suggestion --- subworkflows/local/annotate_genome_snvs/main.nf | 4 ++-- subworkflows/local/annotate_mt_snvs/main.nf | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 708baf259..84b28639a 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -32,7 +32,7 @@ workflow ANNOTATE_GENOME_SNVS { ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml_final // channel: [mandatory] [ path(toml) ] + ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] val_analysis_type // string: wgs, wes, or mito @@ -97,7 +97,7 @@ workflow ANNOTATE_GENOME_SNVS { .combine(ch_vcfanno_extra) .set { ch_vcfanno_in } - VCFANNO (ch_vcfanno_in, ch_vcfanno_toml_final, ch_vcfanno_lua, ch_vcfanno_resources) + VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) VCFANNO.out.vcf .join(VCFANNO.out.tbi, failOnMismatch:true, failOnDuplicate:true) diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index a78dd001e..975f96f89 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -19,7 +19,7 @@ workflow ANNOTATE_MT_SNVS { ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] ch_vcfanno_resources // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ] - ch_vcfanno_toml_final // channel: [mandatory] [ path(toml) ] + ch_vcfanno_toml // channel: [mandatory] [ path(toml) ] ch_vep_cache // channel: [mandatory] [ path(cache) ] ch_vep_extra_files // channel: [mandatory] [ path(files) ] val_cadd_resources // string: path to cadd resources file @@ -34,7 +34,7 @@ workflow ANNOTATE_MT_SNVS { .map { meta, vcf, tbi, resources -> return [meta + [prefix: vcf.simpleName + "_vcfanno"], vcf, tbi, resources]} .set { ch_in_vcfanno } - VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml_final, ch_vcfanno_lua, ch_vcfanno_resources) + VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources) // Annotating with CADD if (!val_cadd_resources.equals(null)) { From 78a4321ae19b062473dea83eb25533a84f812e8f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 5 May 2026 21:02:17 +0200 Subject: [PATCH 673/872] fix bugs in validation --- subworkflows/local/call_sv_MT/main.nf | 5 +++-- workflows/raredisease.nf | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 723d89777..34217b3c2 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -137,10 +137,11 @@ workflow CALL_SV_MT { .set { ch_vcf_file_list } // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs - // exist, combined channel has two elements) to avoid a merge error + // exist) to avoid a merge error. vcf_list is [[vcf1,...]] when populated and [[]] when empty, + // so flatten() gives a non-empty list (truthy) only when VCFs actually exist. ch_case_info .combine(ch_vcf_file_list) - .filter{ it -> it.size() == 2} + .filter{ _case_info, vcf_list -> vcf_list.flatten() } .set { ch_merge_input_vcfs } SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 272f22e66..fcf44b0b8 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -446,7 +446,7 @@ workflow RAREDISEASE { if (val_run_vcfanno_db_sanity_check && (!skip_snv_annotation || (!skip_mt_annotation && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))))) { ch_vcfanno_resources .combine(ch_vcfanno_extra) - .map { resources, extra -> [resources, extra].flatten() } + .map { it -> it.flatten() } .set { ch_all_vcfanno_dbs } SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_all_vcfanno_dbs) ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml From 7f8a68e49b3eba3e9d4d86ebf5fc75653b729d40 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 6 May 2026 10:29:43 +0200 Subject: [PATCH 674/872] fix for saltshaker --- subworkflows/local/call_structural_variants/main.nf | 7 ++++--- subworkflows/local/call_sv_MT/main.nf | 11 ++++++----- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 1a7728a2a..05070ba9c 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -141,9 +141,10 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_merged_tbi = TABIX_TABIX.out.index } else { - // For mito-only analysis, use mitosalt_vcf directly - TABIX_TABIX (ch_saltshaker_vcf) - ch_merged_svs = ch_saltshaker_vcf + // For mito-only analysis, use saltshaker_vcf with meta directly (ch_saltshaker_vcf + // holds collected paths only, ch_sv_mt_out.saltshaker_vcf holds [meta, vcf] tuples) + TABIX_TABIX (ch_sv_mt_out.saltshaker_vcf) + ch_merged_svs = ch_sv_mt_out.saltshaker_vcf ch_merged_tbi = TABIX_TABIX.out.index } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 4330144a1..ad950da8d 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -40,6 +40,7 @@ workflow CALL_SV_MT { val_mitosalt_heteroplasmy_limit // string: [mandatory] mitosalt_heteroplasmy_limit main: + ch_saltshaker_html = channel.empty() ch_saltshaker_txt = channel.empty() ch_saltshaker_vcf = channel.empty() ch_saltshaker_plot = channel.empty() @@ -131,17 +132,17 @@ workflow CALL_SV_MT { ) ch_saltshaker_plot = SALTSHAKER_PLOT.out.plot + // Only merge if Saltshaker produced VCFs; filter on the flat list before wrapping so + // combine never sees an empty-spread issue (combining case_info with [[]] would produce + // a 1-element channel item that breaks 2-param destructuring closures downstream). SALTSHAKER_CLASSIFY.out.vcf .collect{ _meta, vcf -> vcf } - .toList() + .filter{ !it.isEmpty() } + .map{ vcf_list -> [vcf_list] } .set { ch_vcf_file_list } - // Saltshaker only runs if there are mitosalt calls, so we only merge in that case (ie vcfs - // exist) to avoid a merge error. vcf_list is [[vcf1,...]] when populated and [[]] when empty, - // so flatten() gives a non-empty list (truthy) only when VCFs actually exist. ch_case_info .combine(ch_vcf_file_list) - .filter{ _case_info, vcf_list -> vcf_list.flatten() } .set { ch_merge_input_vcfs } SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf From 17b90ff3c9bac1c267efd9a9b1378582e4ebe002 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 6 May 2026 10:57:17 +0200 Subject: [PATCH 675/872] new snaps --- tests/default.nf.test.snap | 940 ++++++++++++++++++++++++++++++ tests/test_bam.nf.test.snap | 853 +++++++++++++++++++++++++++ tests/test_singleton.nf.test.snap | 669 +++++++++++++++++++++ 3 files changed, 2462 insertions(+) create mode 100644 tests/default.nf.test.snap create mode 100644 tests/test_bam.nf.test.snap create mode 100644 tests/test_singleton.nf.test.snap diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 000000000..fafadade0 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,940 @@ +{ + "-profile test": { + "content": [ + { + "ADD_VARCALLER_TO_BED": { + "bgzip": 1.21, + "tabix": 1.21 + }, + "BCFTOOLS_ANNOTATE": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT": { + "bcftools": 1.22 + }, + "BCFTOOLS_CONCAT_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_MERGE_MT": { + "bcftools": 1.22 + }, + "BCFTOOLS_REHEADER_EXP": { + "bcftools": 1.22 + }, + "BCFTOOLS_REHEADER_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_ROH": { + "bcftools": 1.22 + }, + "BCFTOOLS_SORT": { + "bcftools": 1.22 + }, + "BCFTOOLS_SORT_ME": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_CNVNATOR": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_FILTER": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_MANTA": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_RHOCALL": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_TIDDIT": { + "bcftools": 1.22 + }, + "BCFTOOLS_VIEW_UNCOMPRESS": { + "bcftools": 1.22 + }, + "BEDTOOLS_PAD_TARGET_BED": { + "bedtools": "2.31.1" + }, + "BWAMEM2_INDEX_GENOME": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_INDEX_MT": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_INDEX_MT_SHIFT": { + "bwamem2": "2.2.1" + }, + "BWAMEM2_MEM": { + "bwamem2": "2.2.1", + "samtools": "1.22.1" + }, + "BWAMEM2_MEM_MT": { + "bwamem2": "2.2.1", + "samtools": "1.22.1" + }, + "BWA_INDEX_GENOME": { + "bwa": "0.7.19-r1273" + }, + "CAT_CAT_BAIT": { + "pigz": 2.8 + }, + "CAT_FASTQ": { + "cat": 9.5 + }, + "CHROMOGRAPH_AUTOZYG": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_COV": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_REGIONS": { + "chromograph": "1.3.1" + }, + "CHROMOGRAPH_SITES": { + "chromograph": "1.3.1" + }, + "CNVNATOR_CALL": { + "cnvnator": "0.4.1" + }, + "CNVNATOR_CONVERT2VCF": { + "cnvnator": "0.4.1" + }, + "CNVNATOR_HIST": { + "cnvnator": "0.4.1" + }, + "CNVNATOR_PARTITION": { + "cnvnator": "0.4.1" + }, + "CNVNATOR_RD": { + "cnvnator": "0.4.1" + }, + "CNVNATOR_STAT": { + "cnvnator": "0.4.1" + }, + "CREATE_HGNCIDS_FILE": { + "create_hgncids_file": 1.0, + "python": "3.14.3" + }, + "CREATE_PEDIGREE_FILE": { + "coreutils": 9.5 + }, + "CUSTOM_ADDMOSTSEVERECONSEQUENCE": { + "addmostsevereconsequence": "1.2.0", + "bgzip": 1.21 + }, + "CUSTOM_ADDMOSTSEVEREPLI": { + "addmostseverepli": "1.2.0", + "bgzip": 1.21 + }, + "DEEPVARIANT": { + "deepvariant": "1.9.0" + }, + "ENSEMBLVEP_FILTERVEP": { + "ensemblvep": 115.2, + "perl-math-cdf": 0.1 + }, + "ENSEMBLVEP_ME": { + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 + }, + "ENSEMBLVEP_MT": { + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 + }, + "ENSEMBLVEP_SNV": { + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 + }, + "ENSEMBLVEP_SV": { + "ensemblvep": 110.1, + "perl-math-cdf": 0.1, + "tabix": 1.21 + }, + "EXPANSIONHUNTER": { + "bgzip": "1.22.1", + "expansionhunter": "5.0.0" + }, + "FASTP": { + "fastp": "1.0.1" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FIND_CONCATENATE": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, + "GATK4_FILTERMUTECTCALLS_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_MERGEBAMALIGNMENT_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_MERGEVCFS_LIFT_UNLIFT_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_MUTECT2_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_PRINTREADS_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_REVERTSAM_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_SAMTOFASTQ_MT": { + "gatk4": "4.6.2.0" + }, + "GATK4_SELECTVARIANTS": { + "gatk4": "4.6.2.0" + }, + "GATK4_SPLITINTERVALS": { + "gatk4": "4.6.2.0" + }, + "GATK4_VARIANTFILTRATION_MT": { + "gatk4": "4.6.2.0" + }, + "GATK_BILT": { + "gatk4": "4.6.2.0" + }, + "GATK_ILT": { + "gatk4": "4.6.2.0" + }, + "GATK_SD": { + "gatk4": "4.6.2.0" + }, + "GATK_SD_MT": { + "gatk4": "4.6.2.0" + }, + "GATK_SHIFTFASTA": { + "gatk4": "4.6.2.0" + }, + "GAWK": { + "gawk": "5.3.1" + }, + "GENMOD_ANNOTATE": { + "genmod": "3.10.2" + }, + "GENMOD_COMPOUND": { + "genmod": "3.10.2" + }, + "GENMOD_MODELS": { + "genmod": "3.10.2" + }, + "GENMOD_SCORE": { + "genmod": "3.10.2" + }, + "GET_CHROM_SIZES": { + "coreutils": 9.5 + }, + "GLNEXUS": { + "glnexus": "1.4.1" + }, + "HISAT2_INDEX_GENOME": { + "hisat2": "2.2.1" + }, + "INDEX_CNVNATOR": { + "bgzip": 1.21, + "tabix": 1.21 + }, + "INDEX_TIDDIT": { + "bgzip": 1.21, + "tabix": 1.21 + }, + "LAST_INDEX_MT": { + "last": 1611 + }, + "MANTA": { + "manta": "1.6.0" + }, + "MARKDUPLICATES": { + "picard": "3.4.0" + }, + "ME_SPLIT_ALIGNMENT": { + "samtools": "1.22.1" + }, + "MITOSALT": { + "mitosalt": "1.1.1" + }, + "MOSDEPTH": { + "mosdepth": "0.3.11" + }, + "MT_DELETION": { + "mitodel": 1.0, + "samtools": 1.23 + }, + "NGSBITS_SAMPLEGENDER": { + "ngsbits": 202512 + }, + "PEDDY": { + "peddy": "0.4.8" + }, + "PICARD_ADDORREPLACEREADGROUPS_MT": { + "picard": "3.4.0" + }, + "PICARD_COLLECTHSMETRICS": { + "picard": "3.4.0" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.4.0" + }, + "PICARD_COLLECTWGSMETRICS_WG": { + "picard": "3.4.0" + }, + "PICARD_COLLECTWGSMETRICS_Y": { + "picard": "3.4.0" + }, + "PICARD_LIFTOVERVCF": { + "picard": "3.4.0" + }, + "PICARD_MARKDUPLICATES_MT": { + "picard": "3.4.0" + }, + "PICARD_SORTVCF": { + "picard": "3.4.0" + }, + "REMOVE_DUPLICATES_GL": { + "bcftools": 1.22 + }, + "REMOVE_DUPLICATES_MT": { + "bcftools": 1.22 + }, + "RENAMESAMPLE_EXP": { + "picard": "3.4.0" + }, + "RENAME_BAI": { + "coreutils": 9.5 + }, + "RENAME_BAM": { + "coreutils": 9.5 + }, + "RETROSEQ_CALL": { + "retroseq": 1.5 + }, + "RETROSEQ_DISCOVER": { + "retroseq": 1.5 + }, + "RHOCALL_ANNOTATE": { + "rhocall": "0.5.1" + }, + "RHOCALL_VIZ": { + "rhocall": "0.5.1" + }, + "SALTSHAKER_CALL": { + "saltshaker": "1.0.0" + }, + "SALTSHAKER_CLASSIFY": { + "saltshaker": "1.0.1" + }, + "SALTSHAKER_PLOT": { + "saltshaker": "1.0.0" + }, + "SAMTOOLS_COLLATE": { + "samtools": "1.22.1" + }, + "SAMTOOLS_EXTRACT_MT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_FAIDX_MT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_ALIGN": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MARKDUP": { + "samtools": "1.22.1" + }, + "SAMTOOLS_INDEX_MT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_SORT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_SORT_MT": { + "samtools": "1.22.1" + }, + "SAMTOOLS_STATS": { + "samtools": "1.22.1" + }, + "SAMTOOLS_VIEW": { + "samtools": "1.22.1" + }, + "SAM_TO_BAM": { + "samtools": "1.22.1" + }, + "SEQTK_SAMPLE": { + "seqtk": "1.4-r122" + }, + "SMNCOPYNUMBERCALLER": { + "smncopynumbercaller": "1.1.2" + }, + "SPLIT_AND_FILTER_SV_VCF": { + "bcftools": 1.22 + }, + "SPLIT_CHR": { + "bioawk": 1.0 + }, + "SPLIT_MULTIALLELICS_EXP": { + "bcftools": 1.22 + }, + "SPLIT_MULTIALLELICS_GL": { + "bcftools": 1.22 + }, + "SPLIT_MULTIALLELICS_MT": { + "bcftools": 1.22 + }, + 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"annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bed", + "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.bw", + "annotate_snv/genome/hugelymodelbat_rhocallviz/hugelymodelbat_rhocallviz.wig", + "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz", + "annotate_snv/genome/justhusky_rhocall_filter_vep.vcf.gz.tbi", + "annotate_snv/mitochondria", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz", + "annotate_snv/mitochondria/justhusky_mitochondria_vcfanno_vep.vcf.gz.tbi", + "annotate_sv", + "annotate_sv/justhusky_svdbquery_vep.vcf.gz", + "annotate_sv/justhusky_svdbquery_vep.vcf.gz.tbi", + "annotate_sv/justhusky_svdbquery_vep_summary.html", + "call_mobile_elements", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz", + "call_mobile_elements/justhusky_mobile_elements.vcf.gz.tbi", + "call_snv", + "call_snv/genome", + "call_snv/genome/justhusky_snv.vcf.gz", + "call_snv/genome/justhusky_snv.vcf.gz.tbi", + "call_snv/mitochondria", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz", + "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", + "call_sv", + "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_saltshaker.vcf.gz", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", + "fastqc", + "fastqc/hugelymodelbat_LNUMBER1", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", + "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.zip", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/.stub", + "multiqc/multiqc_plots", + "multiqc/multiqc_report.html", + "ngsbits_samplegender", + "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", + "peddy", + "peddy/justhusky.het_check.csv", + "peddy/justhusky.het_check.png", + "peddy/justhusky.html", + "peddy/justhusky.ped_check.csv", + "peddy/justhusky.ped_check.png", + "peddy/justhusky.ped_check.rel-difference.csv", + "peddy/justhusky.peddy.ped", + "peddy/justhusky.sex_check.csv", + "peddy/justhusky.sex_check.png", + "peddy/justhusky.vs.html", + "pedigree", + "pedigree/justhusky.ped", + "pipeline_info", + "pipeline_info/nf_core_raredisease_software_mqc_versions.yml", + "qc_bam", + "qc_bam/hugelymodelbat_hsmetrics.CollectHsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_mosdepth.global.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.per-base.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.per-base.d4", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.quantized.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.region.dist.txt", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.regions.bed.gz.csi", + "qc_bam/hugelymodelbat_mosdepth.summary.txt", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz", + "qc_bam/hugelymodelbat_mosdepth.thresholds.bed.gz.csi", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "qc_bam/hugelymodelbat_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "qc_bam/hugelymodelbat_tidditcov.bed", + "qc_bam/hugelymodelbat_tidditcov.bw", + "qc_bam/hugelymodelbat_tidditcov.wig", + "qc_bam/hugelymodelbat_tidditcov.wig_chr1.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr10.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr11.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr12.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr13.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr14.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr15.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr16.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr17.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr18.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr19.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr2.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr20.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr21.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr22.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr3.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr4.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr5.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr6.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr7.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr8.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chr9.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrM.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrX.png", + "qc_bam/hugelymodelbat_tidditcov.wig_chrY.png", + "qc_bam/hugelymodelbat_wgsmetrics.CollectWgsMetrics.coverage_metrics", + "qc_bam/hugelymodelbat_wgsmetrics_y.CollectWgsMetrics.coverage_metrics", + "rank_and_filter", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz", + "rank_and_filter/justhusky_mt_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_snv_ranked_research.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_clinical.vcf.gz.tbi", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz", + "rank_and_filter/justhusky_sv_ranked_research.vcf.gz.tbi", + "repeat_expansions", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam", + "repeat_expansions/hugelymodelbat_exphunter_sorted.bam.bai", + "repeat_expansions/hugelymodelbat_repeat_expansion.vcf", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz", + "repeat_expansions/justhusky_repeat_expansion_stranger.vcf.gz.tbi", + "smncopynumbercaller", + "smncopynumbercaller/out", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.json", + "smncopynumbercaller/out/justhusky_smncopynumbercaller.tsv", + "trimming", + "trimming/hugelymodelbat_LNUMBER1.fastp.html", + "trimming/hugelymodelbat_LNUMBER1.fastp.json", + "trimming/hugelymodelbat_LNUMBER1.fastp.log", + "trimming/hugelymodelbat_LNUMBER1_R1.fastp.fastq.gz", + "trimming/hugelymodelbat_LNUMBER1_R2.fastp.fastq.gz", + "vcf2cytosure", + "vcf2cytosure/hugelymodelbat.cgh" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-05-06T10:54:12.680904463" + } +} \ No newline at end of file From 35174c869d9421de918f09e98835d010707bb951 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 6 May 2026 13:35:34 +0200 Subject: [PATCH 676/872] mitosalt fix --- CHANGELOG.md | 1 + nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9459b716c..75fd4a8b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,6 +75,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) +- Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#834](https://github.com/nf-core/raredisease/pull/834) ### Parameters diff --git a/nextflow_schema.json b/nextflow_schema.json index c1289e4f3..a5b135431 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -620,7 +620,7 @@ "fa_icon": "fas fa-forward", "description": "Disable specified tools.", "help_text": "Multiple tools can be specified, separated by commas.", - "pattern": "^((fastp|gens|germlinecnvcaller|peddy|smncopynumbercaller|vcf2cytosure|fastqc|ngsbits)?,?)*(? Date: Wed, 6 May 2026 13:41:48 +0200 Subject: [PATCH 677/872] Update raredisease.nf --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index fcf44b0b8..2c1e1b530 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -446,7 +446,7 @@ workflow RAREDISEASE { if (val_run_vcfanno_db_sanity_check && (!skip_snv_annotation || (!skip_mt_annotation && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))))) { ch_vcfanno_resources .combine(ch_vcfanno_extra) - .map { it -> it.flatten() } + .map { files -> files.flatten() } .set { ch_all_vcfanno_dbs } SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_all_vcfanno_dbs) ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml From df5c4d578b3fec86e24175a46a4cb2fbd5e15609 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 6 May 2026 13:46:05 +0200 Subject: [PATCH 678/872] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 75fd4a8b4..5604ad388 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,7 +75,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) -- Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#834](https://github.com/nf-core/raredisease/pull/834) +- Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#837](https://github.com/nf-core/raredisease/pull/837) +- Fixed vcfanno sanity check map closure to handle `ch_vcfanno_resources` emitting a list of paths [#837](https://github.com/nf-core/raredisease/pull/837) ### Parameters From ddada5db29c4084545dfd2a84892c7e863220d47 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 7 May 2026 00:13:17 +0200 Subject: [PATCH 679/872] review comments --- conf/modules/call_repeat_expansions.config | 2 +- docs/usage.md | 2 +- subworkflows/local/align/main.nf | 29 +++++------ .../align_sentieon/tests/nextflow.config | 1 - .../local/annotate_genome_snvs/main.nf | 9 ++-- .../tests/nextflow.config | 2 +- .../local/annotate_mt_snvs/tests/main.nf.test | 3 ++ subworkflows/local/call_snv/main.nf | 52 +++++++++---------- subworkflows/local/call_snv_MT/main.nf | 4 +- .../call_snv_sentieon/tests/nextflow.config | 4 +- .../local/call_structural_variants/main.nf | 2 +- .../local/call_sv_MT/tests/nextflow.config | 2 +- subworkflows/local/prepare_references/main.nf | 14 ++--- workflows/raredisease.nf | 1 + 14 files changed, 65 insertions(+), 62 deletions(-) diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config index 916cff868..88b4320f2 100644 --- a/conf/modules/call_repeat_expansions.config +++ b/conf/modules/call_repeat_expansions.config @@ -27,7 +27,7 @@ process { withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' { ext.args = "--temp-prefix ." - ext.args2 = "-O v" + ext.args2 = "--output-type v" ext.prefix = { "${meta.id}_repeat_expansion" } } diff --git a/docs/usage.md b/docs/usage.md index be1e5cfc0..e5963d4d2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -309,7 +309,7 @@ no header and the following columns: `CHROM POS REF_ALLELE,ALT_ALLELE AF`. Sampl 9Used by GENMOD while modeling the variants. Contains a list of loci that show [reduced penetrance](https://medlineplus.gov/genetics/understanding/inheritance/penetranceexpressivity/) in people. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/reduced_penetrance.tsv).
    10 This file contains a list of candidate genes (with [HGNC](https://www.genenames.org/) IDs) that is used to split the variants into candidate variants and research variants. Research variants contain all the variants, while candidate variants are a subset of research variants and are associated with candidate genes. Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt). Not required if `--skip_subworkflows generate_clinical_set` is set.
    11Path to a folder containing cadd annotations. Equivalent of the data/annotations/ folder described [here](https://github.com/kircherlab/CADD-scripts/#manual-installation), and it is used to calculate CADD scores for small indels.
    -12When set to `true`, each vcfanno database file listed in `vcfanno_resources` is checked for records (non-header lines). Any database with zero records is removed from the vcfanno TOML config before annotation runs. Default: `false`.
    +12When set to `true`, each vcfanno database file listed in `vcfanno_resources` is checked for records (non-header lines). Any database with zero records is removed from the vcfanno TOML config before annotation runs to prevent vcfanno from crashing on default resource files. Default: `false`.
    :::note We use CADD only to annotate small indels. To annotate SNVs with precomputed CADD scores, pass the file containing CADD scores as a resource to vcfanno instead. Files containing the precomputed CADD scores for SNVs can be downloaded from [here](https://cadd.gs.washington.edu/download) (download files listed under the description: "All possible SNVs of GRCh3<7/8>/hg3<7/8>") diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 8faeb99bd..932ace4f8 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -76,21 +76,20 @@ workflow ALIGN { // // If input is bam // - ch_alignments.map { meta, files -> - def new_id = meta.sample - def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') - return [new_meta, files].flatten() - } - .map { meta, bam, _bai -> [meta, bam] } - .set{ch_input_bam} - - ch_alignments.map { meta, files -> - def new_id = meta.sample - def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') - return [new_meta, files].flatten() - } - .map { meta, _bam, bai -> [meta, bai] } - .set{ch_input_bai} + ch_alignments + .map { meta, files -> + def new_id = meta.sample + def new_meta = meta + [id:new_id, read_group:"\'@RG\\tID:" + new_id + "\\tPL:" + val_platform + "\\tSM:" + new_id + "\'"] - meta.subMap('lane') + return [new_meta, files].flatten() + } + .multiMap { meta, bam, bai -> + bam: [meta, bam] + bai: [meta, bai] + } + .set { ch_input_aligned } + + ch_input_bam = ch_input_aligned.bam + ch_input_bai = ch_input_aligned.bai if (val_aligner.matches("bwamem2|bwa|bwameme")) { ALIGN_BWA_BWAMEM2_BWAMEME ( diff --git a/subworkflows/local/align_sentieon/tests/nextflow.config b/subworkflows/local/align_sentieon/tests/nextflow.config index bb4c7f5bc..a5eb17b20 100644 --- a/subworkflows/local/align_sentieon/tests/nextflow.config +++ b/subworkflows/local/align_sentieon/tests/nextflow.config @@ -15,7 +15,6 @@ process { withName: 'EXTRACT_ALIGNMENTS' { ext.prefix = { "${meta.id}_merged_extracted" } - ext.args2 = { params.restrict_to_contigs } } withName: 'SENTIEON_DEDUP' { diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 245701c14..64de7e73a 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -58,6 +58,10 @@ workflow ANNOTATE_GENOME_SNVS { ZIP_TABIX_ROHCALL (RHOCALL_ANNOTATE.out.vcf) + // BCFTOOLS_ROH and RHOCALL_ANNOTATE only run when probands are present (filtered above). + // The remainder:true join pads cases without rohcall output with a single null, giving + // tuples of length 4 (no rohcall) vs 5 (rohcall). After combining with an interval both + // grow by one, so size==6 means this case has probands and a rohcall-annotated VCF. ch_vcf .join(ZIP_TABIX_ROHCALL.out.gz_index, remainder: true) .combine(ch_split_intervals) @@ -160,11 +164,6 @@ workflow ANNOTATE_GENOME_SNVS { ch_vep_vcf_out .join(ch_vep_tbi_out, failOnMismatch:true) .groupTuple() - .map { meta, vcfs, tbis -> - def sortedvcfs = vcfs.sort { vcf -> vcf.baseName } - def sortedtbis = tbis.sort { tbi -> tbi.baseName } - return [ meta, sortedvcfs, sortedtbis ] - } .set { ch_concat_in } BCFTOOLS_CONCAT (ch_concat_in) diff --git a/subworkflows/local/annotate_genome_snvs/tests/nextflow.config b/subworkflows/local/annotate_genome_snvs/tests/nextflow.config index ca73a5c7f..9f051f6a3 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/nextflow.config +++ b/subworkflows/local/annotate_genome_snvs/tests/nextflow.config @@ -68,6 +68,6 @@ process { } withName: 'BCFTOOLS_CONCAT' { - ext.args = { "-Oz" } + ext.args = { "--output-type z" } } } diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 35fd0be24..63910dd93 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -22,6 +22,9 @@ nextflow_workflow { options "-stub" when { + params { + homoplasmy_af_threshold = 0.95 + } workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index b36cc1d7d..7700eaace 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -43,20 +43,20 @@ workflow CALL_SNV { val_variant_caller // string: 'deepvariant' or 'sentieon' main: - ch_concat_publish = channel.empty() - ch_deepvar_vcf = channel.empty() - ch_deepvar_tbi = channel.empty() - ch_deepvar_gvcf = channel.empty() - ch_deepvar_gtbi = channel.empty() - ch_deepvar_publish = channel.empty() - ch_mt_snv_publish = channel.empty() - ch_mt_tabix = channel.empty() - ch_mt_vcf = channel.empty() - ch_mt_vcf_tabix = channel.empty() - ch_sentieon_vcf = channel.empty() - ch_sentieon_tbi = channel.empty() - ch_sentieon_gvcf = channel.empty() - ch_sentieon_gtbi = channel.empty() + ch_concat_publish = channel.empty() + ch_deepvariant_vcf = channel.empty() + ch_deepvariant_tbi = channel.empty() + ch_deepvariant_gvcf = channel.empty() + ch_deepvariant_gtbi = channel.empty() + ch_deepvariant_publish = channel.empty() + ch_mt_snv_publish = channel.empty() + ch_mt_tabix = channel.empty() + ch_mt_vcf = channel.empty() + ch_mt_vcf_tabix = channel.empty() + ch_sentieon_vcf = channel.empty() + ch_sentieon_tbi = channel.empty() + ch_sentieon_gvcf = channel.empty() + ch_sentieon_gtbi = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( @@ -71,11 +71,11 @@ workflow CALL_SNV { val_analysis_type, val_skip_split_multiallelics ) - ch_deepvar_vcf = CALL_SNV_DEEPVARIANT.out.vcf - ch_deepvar_tbi = CALL_SNV_DEEPVARIANT.out.tabix - ch_deepvar_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf - ch_deepvar_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix - ch_deepvar_publish = CALL_SNV_DEEPVARIANT.out.publish + ch_deepvariant_vcf = CALL_SNV_DEEPVARIANT.out.vcf + ch_deepvariant_tbi = CALL_SNV_DEEPVARIANT.out.tabix + ch_deepvariant_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf + ch_deepvariant_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix + ch_deepvariant_publish = CALL_SNV_DEEPVARIANT.out.publish } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, @@ -97,16 +97,16 @@ workflow CALL_SNV { ch_sentieon_gtbi = CALL_SNV_SENTIEON.out.gvcf_tbi } - ch_vcf = channel.empty().mix(ch_deepvar_vcf, ch_sentieon_vcf) - ch_tabix = channel.empty().mix(ch_deepvar_tbi, ch_sentieon_tbi) - ch_gvcf = channel.empty().mix(ch_deepvar_gvcf, ch_sentieon_gvcf) - ch_gtabix = channel.empty().mix(ch_deepvar_gtbi, ch_sentieon_gtbi) + ch_vcf = channel.empty().mix(ch_deepvariant_vcf, ch_sentieon_vcf) + ch_tabix = channel.empty().mix(ch_deepvariant_tbi, ch_sentieon_tbi) + ch_gvcf = channel.empty().mix(ch_deepvariant_gvcf, ch_sentieon_gvcf) + ch_gtabix = channel.empty().mix(ch_deepvariant_gtbi, ch_sentieon_gtbi) ch_vcf .join(ch_tabix, failOnMismatch:true, failOnDuplicate:true) .map { meta, vcf, tbi -> return [meta, vcf, tbi, []]} - .set {ch_selvar_in} - GATK4_SELECTVARIANTS(ch_selvar_in) // remove mitochondrial variants + .set {ch_select_variants_in} + GATK4_SELECTVARIANTS(ch_select_variants_in) // remove mitochondrial variants ch_genome_vcf = GATK4_SELECTVARIANTS.out.vcf ch_genome_tabix = GATK4_SELECTVARIANTS.out.tbi @@ -159,7 +159,7 @@ workflow CALL_SNV { ch_publish = GATK4_SELECTVARIANTS.out.vcf .mix(GATK4_SELECTVARIANTS.out.tbi) - .mix(ch_deepvar_publish) + .mix(ch_deepvariant_publish) .map { meta, value -> ['call_snv/genome/', [meta, value]] } .mix(ch_concat_publish) .mix(ch_mt_snv_publish) diff --git a/subworkflows/local/call_snv_MT/main.nf b/subworkflows/local/call_snv_MT/main.nf index 8c0b2b176..ac479f3be 100644 --- a/subworkflows/local/call_snv_MT/main.nf +++ b/subworkflows/local/call_snv_MT/main.nf @@ -15,9 +15,9 @@ workflow CALL_SNV_MT { main: - ch_bam_bai_int = ch_bam_bai.combine(ch_intervals) + ch_bam_bai_intervals = ch_bam_bai.combine(ch_intervals) - GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) + GATK4_MUTECT2_MT (ch_bam_bai_intervals, ch_fasta, ch_fai.map{meta, fai -> return [meta,fai,[]]}, ch_dict, [], [], [], [], [],[]) // Filter Mutect2 calls ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true) diff --git a/subworkflows/local/call_snv_sentieon/tests/nextflow.config b/subworkflows/local/call_snv_sentieon/tests/nextflow.config index 3cb843d93..f13feedfc 100644 --- a/subworkflows/local/call_snv_sentieon/tests/nextflow.config +++ b/subworkflows/local/call_snv_sentieon/tests/nextflow.config @@ -9,12 +9,12 @@ process { } withName: 'BCF_FILTER_ONE' { - ext.args = "-s 'ML_FAIL' -i 'INFO/ML_PROB <= 0.95' -m x -Oz --write-index=tbi" + ext.args = "-s 'ML_FAIL' -i 'INFO/ML_PROB <= 0.95' -m x --output-type z --write-index=tbi" ext.prefix = { "${meta.id}_mlfiltered_0.95" } } withName: 'BCF_FILTER_TWO' { - ext.args = "-i FILTER='\"PASS\"' -m x -Oz --write-index=tbi" + ext.args = "-i FILTER='\"PASS\"' -m x --output-type z --write-index=tbi" ext.prefix = { "${meta.id}_passed" } } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 05070ba9c..b5407b11e 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -129,7 +129,7 @@ workflow CALL_STRUCTURAL_VARIANTS { .concat(ch_cnvnator_vcf) .concat(ch_saltshaker_vcf) .collect() - .map { vcf_list -> [vcf_list] } // + .map { vcf_list -> [vcf_list] } .set { ch_vcf_paths } ch_case_info .combine(ch_vcf_paths) diff --git a/subworkflows/local/call_sv_MT/tests/nextflow.config b/subworkflows/local/call_sv_MT/tests/nextflow.config index 772073c54..d0a2a2e68 100644 --- a/subworkflows/local/call_sv_MT/tests/nextflow.config +++ b/subworkflows/local/call_sv_MT/tests/nextflow.config @@ -1,7 +1,7 @@ process { withName: 'MT_DELETION' { - ext.args = {"params.mt_del"} + ext.args = { params.mt_del } ext.prefix = { "${meta.id}_mitochondria_deletions" } } diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index 0b180e2b5..b513bb4e6 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -61,7 +61,7 @@ workflow PREPARE_REFERENCES { main: ch_bait_intervals = channel.empty() - ch_bwa = channel.empty() + ch_genome_bwa_index = channel.empty() ch_genome_bwameme_index = channel.empty() ch_genome_bwamem2_index = channel.empty() ch_genome_hisat2_index = channel.empty() @@ -112,13 +112,13 @@ workflow PREPARE_REFERENCES { // if (!val_bwa) { if (!val_aligner.equals("sentieon") || val_mtaligner.equals("bwa")) { - ch_bwa = BWA_INDEX_GENOME(ch_genome_fasta).index.collect() + ch_genome_bwa_index = BWA_INDEX_GENOME(ch_genome_fasta).index.collect() } if (val_aligner.equals("sentieon") || val_mtaligner.equals("sentieon")) { - ch_bwa = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() + ch_genome_bwa_index = SENTIEON_BWAINDEX_GENOME(ch_genome_fasta).index.collect() } } else if (val_bwa) { - ch_bwa = channel.fromPath(val_bwa).map {it -> [[id:it.simpleName], it]}.collect() + ch_genome_bwa_index = channel.fromPath(val_bwa).map {it -> [[id:it.simpleName], it]}.collect() } if (!val_bwamem2 && (val_aligner.equals("bwamem2") || val_mtaligner.equals("bwamem2"))) { @@ -225,6 +225,8 @@ workflow PREPARE_REFERENCES { GATK_ILT.out.interval_list .collect{ _meta, list -> list } .map { list -> + // list is e.g. [/path/mybed_split_0001.interval_list, ...]; strip the _split suffix + // and directory to get the base name (e.g. "mybed"), then build the merged output name def meta = list.toString().split("_split")[0].split("/")[-1] + "_bait.intervals_list" return [[id:meta], list] } @@ -275,7 +277,7 @@ workflow PREPARE_REFERENCES { if (val_save_reference) { ch_publish = ch_dbsnp .mix(ch_dbsnp_tbi) - .mix(ch_bwa) + .mix(ch_genome_bwa_index) .mix(ch_genome_bwamem2_index) .mix(ch_genome_bwameme_index) .mix(ch_genome_fai) @@ -317,7 +319,7 @@ workflow PREPARE_REFERENCES { bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] - genome_bwa_index = ch_bwa // channel:[ val(meta), path(index) ] + genome_bwa_index = ch_genome_bwa_index // channel:[ val(meta), path(index) ] genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2c1e1b530..8936f603d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -442,6 +442,7 @@ workflow RAREDISEASE { ) ch_call_snv_publish = CALL_SNV.out.publish + // Removes vcfanno resource with empty records to keep vcfanno from crashing on those files ch_vcfanno_toml_final = ch_vcfanno_toml if (val_run_vcfanno_db_sanity_check && (!skip_snv_annotation || (!skip_mt_annotation && (val_run_mt_for_wes || val_analysis_type.matches("wgs|mito"))))) { ch_vcfanno_resources From 6349fe7ce7e921686adef584f21397ac8339c571 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 7 May 2026 10:07:04 +0200 Subject: [PATCH 680/872] new classify grouping --- subworkflows/local/call_sv_MT/main.nf | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 159659fb6..2d312e57c 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -124,21 +124,17 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf - // Gather all saltshaker classify txt files in a double list so the full list will be combined with case meta once - SALTSHAKER_CLASSIFY.out.txt - .map{ _meta, txt -> txt } - .toList() - .toList() - .set{ ch_saltshaker_files } + SALTSHAKER_CLASSIFY.out.txt.view() - ch_case_info - .combine(ch_saltshaker_files) - .filter { _meta, files -> files.size() > 0 } + SALTSHAKER_CLASSIFY.out.txt + .map { meta, txt -> meta.id = meta.case_id + return [meta, txt] } + .groupTuple() .set { ch_saltshaker_txts } FIND_CONCATENATE( ch_saltshaker_txts - ) + ) ch_saltshaker_txt = FIND_CONCATENATE.out.file_out SALTSHAKER_TO_HTML( From 30139c23a62426d723522ffd71a0f1cdbecd4bc1 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 7 May 2026 11:05:34 +0200 Subject: [PATCH 681/872] clean up classify grouping --- subworkflows/local/call_sv_MT/main.nf | 29 +++++++++++++-------------- 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 2d312e57c..4aec951e2 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -63,13 +63,13 @@ workflow CALL_SV_MT { [combined_meta, all_reads] } - .set {ch_cat_fastq} + .set { ch_cat_fastq } CAT_FASTQ(ch_cat_fastq) ch_reads_subdepth = CAT_FASTQ.out.reads.combine(ch_subdepth) - SEQTK_SAMPLE (ch_reads_subdepth) + SEQTK_SAMPLE(ch_reads_subdepth) PREP_MITOSALT( ch_genome_chrsizes, @@ -98,12 +98,12 @@ workflow CALL_SV_MT { ) MITOSALT.out.cluster - .filter{ _meta, out -> out.countLines() > 0 } - .set{ ch_cluster } + .filter { _meta, out -> out.countLines() > 0 } + .set { ch_cluster } MITOSALT.out.breakpoint .join(ch_cluster) - .set{ ch_saltshaker_in } + .set { ch_saltshaker_in } // Saltshaker modules will only run if mitosalt called SVs and created a cluster file SALTSHAKER_CALL( @@ -124,21 +124,20 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf - SALTSHAKER_CLASSIFY.out.txt.view() - SALTSHAKER_CLASSIFY.out.txt - .map { meta, txt -> meta.id = meta.case_id - return [meta, txt] } + .map { meta, txt -> + return [['id': meta.case_id], txt] + } .groupTuple() .set { ch_saltshaker_txts } FIND_CONCATENATE( ch_saltshaker_txts - ) + ) ch_saltshaker_txt = FIND_CONCATENATE.out.file_out SALTSHAKER_TO_HTML( - ch_saltshaker_txt, + ch_saltshaker_txt ) ch_saltshaker_html = SALTSHAKER_TO_HTML.out.classify_html @@ -151,16 +150,16 @@ workflow CALL_SV_MT { // combine never sees an empty-spread issue (combining case_info with [[]] would produce // a 1-element channel item that breaks 2-param destructuring closures downstream). SALTSHAKER_CLASSIFY.out.vcf - .collect{ _meta, vcf -> vcf } - .filter{ !it.isEmpty() } - .map{ vcf_list -> [vcf_list] } + .collect { _meta, vcf -> vcf } + .filter { !it.isEmpty() } + .map { vcf_list -> [vcf_list] } .set { ch_vcf_file_list } ch_case_info .combine(ch_vcf_file_list) .set { ch_merge_input_vcfs } - SVDB_MERGE ( ch_merge_input_vcfs, [], true ).vcf + SVDB_MERGE( ch_merge_input_vcfs, [], true ).vcf .set {ch_saltshaker_vcf} // Saltshaker only runs if there are mitosalt calls. We update priority list when the // saltshaker vcf is created so the priority matches the list of vcfs that will be merged later From d9d8e1f17c7c5e9020dd6ffd7a5f09e6006cfdc1 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Thu, 7 May 2026 11:15:35 +0200 Subject: [PATCH 682/872] resolve merge conflicts Resolved merge conflicts and updated changelog entries for various fixes. --- CHANGELOG.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ada98fccb..8467c7b80 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,12 +76,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed CADD annotation to support chr prefix [#745](https://github.com/nf-core/raredisease/pull/745) - Fixed mismatch between VCF and ROH calls when analysing multiple samples [#755](https://github.com/nf-core/raredisease/pull/755) - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) -<<<<<<< concat_saltshaker - Fixed mitosalt channel handling so it runs on all samples in a trio [#826](https://github.com/nf-core/raredisease/pull/826) -======= - Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#837](https://github.com/nf-core/raredisease/pull/837) - Fixed vcfanno sanity check map closure to handle `ch_vcfanno_resources` emitting a list of paths [#837](https://github.com/nf-core/raredisease/pull/837) ->>>>>>> dev ### Parameters From 97d0be71209e73cf244ac373304f60edf6decae4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 00:10:36 +0200 Subject: [PATCH 683/872] Maxime comments --- .../local/mitosalt/resources/usr/bin => bin}/MitoSAlt1.1.1.pl | 0 .../resources/usr/bin => bin}/create_hgncids_file.py | 0 .../resources/usr/bin => bin}/replace_spaces_in_vcfinfo.py | 0 .../resources/usr/bin => bin}/sanity_check_vcfanno_databases.py | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename {modules/local/mitosalt/resources/usr/bin => bin}/MitoSAlt1.1.1.pl (100%) rename {modules/local/create_hgncids_file/resources/usr/bin => bin}/create_hgncids_file.py (100%) rename {modules/local/replace_spaces_in_vcfinfo/resources/usr/bin => bin}/replace_spaces_in_vcfinfo.py (100%) rename {modules/local/sanity_check_vcfanno_databases/resources/usr/bin => bin}/sanity_check_vcfanno_databases.py (100%) diff --git a/modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl b/bin/MitoSAlt1.1.1.pl similarity index 100% rename from modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl rename to bin/MitoSAlt1.1.1.pl diff --git a/modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py b/bin/create_hgncids_file.py similarity index 100% rename from modules/local/create_hgncids_file/resources/usr/bin/create_hgncids_file.py rename to bin/create_hgncids_file.py diff --git a/modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py b/bin/replace_spaces_in_vcfinfo.py similarity index 100% rename from modules/local/replace_spaces_in_vcfinfo/resources/usr/bin/replace_spaces_in_vcfinfo.py rename to bin/replace_spaces_in_vcfinfo.py diff --git a/modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py b/bin/sanity_check_vcfanno_databases.py similarity index 100% rename from modules/local/sanity_check_vcfanno_databases/resources/usr/bin/sanity_check_vcfanno_databases.py rename to bin/sanity_check_vcfanno_databases.py From b6a92bcd4586f889d131d1777209f583aad1a522 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 10:01:42 +0200 Subject: [PATCH 684/872] move nf-core/custom to local --- .../usr/bin => bin}/add_most_severe_consequence.py | 0 .../resources/usr/bin => bin}/add_most_severe_pli.py | 0 modules.json | 10 ---------- .../custom/addmostsevereconsequence/environment.yml | 0 .../custom/addmostsevereconsequence/main.nf | 0 .../custom/addmostsevereconsequence/meta.yml | 0 .../custom/addmostsevereconsequence/tests/main.nf.test | 0 .../addmostsevereconsequence/tests/main.nf.test.snap | 0 .../addmostsevereconsequence/tests/nextflow.config | 0 .../custom/addmostseverepli/environment.yml | 0 .../{nf-core => local}/custom/addmostseverepli/main.nf | 0 .../custom/addmostseverepli/meta.yml | 0 .../custom/addmostseverepli/tests/main.nf.test | 0 .../custom/addmostseverepli/tests/main.nf.test.snap | 0 .../custom/addmostseverepli/tests/nextflow.config | 0 subworkflows/local/annotate_consequence_pli/main.nf | 4 ++-- 16 files changed, 2 insertions(+), 12 deletions(-) rename {modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin => bin}/add_most_severe_consequence.py (100%) rename {modules/nf-core/custom/addmostseverepli/resources/usr/bin => bin}/add_most_severe_pli.py (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/environment.yml (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/main.nf (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/meta.yml (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/tests/main.nf.test (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/tests/main.nf.test.snap (100%) rename modules/{nf-core => local}/custom/addmostsevereconsequence/tests/nextflow.config (100%) rename modules/{nf-core => local}/custom/addmostseverepli/environment.yml (100%) rename modules/{nf-core => local}/custom/addmostseverepli/main.nf (100%) rename modules/{nf-core => local}/custom/addmostseverepli/meta.yml (100%) rename modules/{nf-core => local}/custom/addmostseverepli/tests/main.nf.test (100%) rename modules/{nf-core => local}/custom/addmostseverepli/tests/main.nf.test.snap (100%) rename modules/{nf-core => local}/custom/addmostseverepli/tests/nextflow.config (100%) diff --git a/modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py b/bin/add_most_severe_consequence.py similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/resources/usr/bin/add_most_severe_consequence.py rename to bin/add_most_severe_consequence.py diff --git a/modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py b/bin/add_most_severe_pli.py similarity index 100% rename from modules/nf-core/custom/addmostseverepli/resources/usr/bin/add_most_severe_pli.py rename to bin/add_most_severe_pli.py diff --git a/modules.json b/modules.json index 1b505b1e1..4bb0c67b5 100644 --- a/modules.json +++ b/modules.json @@ -125,16 +125,6 @@ "git_sha": "dfe412ff862fdafd658b0d7beca1e084800ba5b2", "installed_by": ["modules"] }, - "custom/addmostsevereconsequence": { - "branch": "master", - "git_sha": "0e225fbda197093af4d54a88b9a2908c14ce660b", - "installed_by": ["modules"] - }, - "custom/addmostseverepli": { - "branch": "master", - "git_sha": "0e225fbda197093af4d54a88b9a2908c14ce660b", - "installed_by": ["modules"] - }, "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", diff --git a/modules/nf-core/custom/addmostsevereconsequence/environment.yml b/modules/local/custom/addmostsevereconsequence/environment.yml similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/environment.yml rename to modules/local/custom/addmostsevereconsequence/environment.yml diff --git a/modules/nf-core/custom/addmostsevereconsequence/main.nf b/modules/local/custom/addmostsevereconsequence/main.nf similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/main.nf rename to modules/local/custom/addmostsevereconsequence/main.nf diff --git a/modules/nf-core/custom/addmostsevereconsequence/meta.yml b/modules/local/custom/addmostsevereconsequence/meta.yml similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/meta.yml rename to modules/local/custom/addmostsevereconsequence/meta.yml diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test b/modules/local/custom/addmostsevereconsequence/tests/main.nf.test similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test rename to modules/local/custom/addmostsevereconsequence/tests/main.nf.test diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap b/modules/local/custom/addmostsevereconsequence/tests/main.nf.test.snap similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/tests/main.nf.test.snap rename to modules/local/custom/addmostsevereconsequence/tests/main.nf.test.snap diff --git a/modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config b/modules/local/custom/addmostsevereconsequence/tests/nextflow.config similarity index 100% rename from modules/nf-core/custom/addmostsevereconsequence/tests/nextflow.config rename to modules/local/custom/addmostsevereconsequence/tests/nextflow.config diff --git a/modules/nf-core/custom/addmostseverepli/environment.yml b/modules/local/custom/addmostseverepli/environment.yml similarity index 100% rename from modules/nf-core/custom/addmostseverepli/environment.yml rename to modules/local/custom/addmostseverepli/environment.yml diff --git a/modules/nf-core/custom/addmostseverepli/main.nf b/modules/local/custom/addmostseverepli/main.nf similarity index 100% rename from modules/nf-core/custom/addmostseverepli/main.nf rename to modules/local/custom/addmostseverepli/main.nf diff --git a/modules/nf-core/custom/addmostseverepli/meta.yml b/modules/local/custom/addmostseverepli/meta.yml similarity index 100% rename from modules/nf-core/custom/addmostseverepli/meta.yml rename to modules/local/custom/addmostseverepli/meta.yml diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test b/modules/local/custom/addmostseverepli/tests/main.nf.test similarity index 100% rename from modules/nf-core/custom/addmostseverepli/tests/main.nf.test rename to modules/local/custom/addmostseverepli/tests/main.nf.test diff --git a/modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap b/modules/local/custom/addmostseverepli/tests/main.nf.test.snap similarity index 100% rename from modules/nf-core/custom/addmostseverepli/tests/main.nf.test.snap rename to modules/local/custom/addmostseverepli/tests/main.nf.test.snap diff --git a/modules/nf-core/custom/addmostseverepli/tests/nextflow.config b/modules/local/custom/addmostseverepli/tests/nextflow.config similarity index 100% rename from modules/nf-core/custom/addmostseverepli/tests/nextflow.config rename to modules/local/custom/addmostseverepli/tests/nextflow.config diff --git a/subworkflows/local/annotate_consequence_pli/main.nf b/subworkflows/local/annotate_consequence_pli/main.nf index 111d49986..50a2e6ee2 100644 --- a/subworkflows/local/annotate_consequence_pli/main.nf +++ b/subworkflows/local/annotate_consequence_pli/main.nf @@ -2,8 +2,8 @@ // A subworkflow to add most severe consequence and pli to a vep annotated vcf // -include { CUSTOM_ADDMOSTSEVERECONSEQUENCE } from '../../../modules/nf-core/custom/addmostsevereconsequence' -include { CUSTOM_ADDMOSTSEVEREPLI } from '../../../modules/nf-core/custom/addmostseverepli' +include { CUSTOM_ADDMOSTSEVERECONSEQUENCE } from '../../../modules/local/custom/addmostsevereconsequence' +include { CUSTOM_ADDMOSTSEVEREPLI } from '../../../modules/local/custom/addmostseverepli' include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow ANNOTATE_CSQ_PLI { From a13547fec78ce1cafa95dfacbcd78e9b663a0931 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 10:14:02 +0200 Subject: [PATCH 685/872] update config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 0234c8007..4baa3cf23 100644 --- a/nextflow.config +++ b/nextflow.config @@ -316,7 +316,7 @@ profiles { // Set AWS client to anonymous when using the default igenomes_base aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false // Stage locally scoped binary scripts -nextflow.enable.moduleBinaries = true +// nextflow.enable.moduleBinaries = true // Load nf-core custom profiles from different institutions From 5307f31e641cb2d023c8117a38613e5ac6f41aff Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 14:06:08 +0200 Subject: [PATCH 686/872] switch queue to value --- workflows/raredisease.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8936f603d..b3b1c1470 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -450,7 +450,7 @@ workflow RAREDISEASE { .map { files -> files.flatten() } .set { ch_all_vcfanno_dbs } SANITY_CHECK_VCFANNO_DATABASES (ch_vcfanno_toml, ch_all_vcfanno_dbs) - ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml + ch_vcfanno_toml_final = SANITY_CHECK_VCFANNO_DATABASES.out.toml.collect() } // From ce46a48be007e5a13cee4ceb597c85cd1b5a95be Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 16:41:39 +0200 Subject: [PATCH 687/872] convert channel to value --- subworkflows/local/call_sv_MT/main.nf | 3 ++- subworkflows/local/call_sv_MT/tests/main.nf.test.snap | 4 ++-- tests/default.nf.test.snap | 6 +++++- 3 files changed, 9 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index ad950da8d..2c462f72a 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -83,9 +83,10 @@ workflow CALL_SV_MT { val_mitochondria_name ) + ch_prepmitosalt_config = PREP_MITOSALT.out.msconfig.collect() MITOSALT( SEQTK_SAMPLE.out.reads, - PREP_MITOSALT.out.msconfig, + ch_prepmitosalt_config, ch_genome_chrsizes, ch_genome_fai, ch_genome_hisat2index, diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 8d7ae6e46..e4541ada9 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -300,10 +300,10 @@ ] ] ], + "timestamp": "2026-04-14T15:53:31.425509861", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-14T15:53:31.425509861" + } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 938b6899f..ea6fc5d95 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -674,10 +674,14 @@ "call_sv/earlycasualcaiman.saltshaker.png", "call_sv/earlycasualcaiman.saltshaker_classify.html", "call_sv/earlycasualcaiman_mitochondria_deletions.txt", + "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/hugelymodelbat.saltshaker_classify.html", "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", + "call_sv/slowlycivilbuck.saltshaker.png", + "call_sv/slowlycivilbuck.saltshaker_classify.html", "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", @@ -924,7 +928,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-29T22:20:44.976982426", + "timestamp": "2026-05-08T16:30:33.887641119", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 6041bb5764cad932807b24921335cd3440d2ac06 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 8 May 2026 22:39:59 +0200 Subject: [PATCH 688/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5604ad388..4a9fb7879 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -77,6 +77,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed pipeline to run variant calling even with bait_padding set to 0 [#757](https://github.com/nf-core/raredisease/pull/757) - Fixed runtime errors in `call_sv_MT` and `call_structural_variants` when MitoSAlt produces no structural variant calls [#837](https://github.com/nf-core/raredisease/pull/837) - Fixed vcfanno sanity check map closure to handle `ch_vcfanno_resources` emitting a list of paths [#837](https://github.com/nf-core/raredisease/pull/837) +- Fixed `PREP_MITOSALT` msconfig output being consumed as a queue channel by converting it to a value channel with `.collect()` before passing to `MITOSALT` [#837](https://github.com/nf-core/raredisease/pull/843) ### Parameters From 1b18bd1a9aab26865aee79cd1d256d54bd121775 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 11 May 2026 23:44:38 +0200 Subject: [PATCH 689/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a9fb7879..f37c1d751 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 3.0.0 - Mario [xxxx-xx-xx] +## 3.0.0 - Mario [2026-05-12] ### `Added` From 52cbe81717808f2c3ffe62b54aa2e572b6c5eb0f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 13 May 2026 14:57:38 +0200 Subject: [PATCH 690/872] Bump version --- .nf-core.yml | 2 +- CHANGELOG.md | 18 ++++++++++++++++++ assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 22 +++++++++++----------- 5 files changed, 32 insertions(+), 14 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 0b2f130e4..6ac444bf3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 3.0.0 + version: 3.1.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index f37c1d751..29699099a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,24 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 3.1.0 - Luigi [XXXX-XX-XX] + +### `Added` + +### `Changed` + +### `Fixed` + +| Old parameter | New parameter | +| ------------- | ------------- | +| | | + +### Tool updates + +| Tool | Old version | New version | +| ---- | ----------- | ----------- | +| | | | + ## 3.0.0 - Mario [2026-05-12] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 0b6823681..ca317b0d1 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,7 +2,7 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-raredisease-methods-description": diff --git a/nextflow.config b/nextflow.config index 4baa3cf23..13a0d776e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -481,7 +481,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '3.0.0' + version = '3.1.0dev' doi = '10.5281/zenodo.7995798' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 11886e712..0b6c8cdd0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-04-29T08:07:02+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-05-13T12:53:33+00:00", "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**6. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker)\n\n**7. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**8. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**9. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**10. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**11. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**12. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**13. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541" + "@id": "#887a7397-4dcc-4f72-b531-7f9faffbe771" } ], "name": "nf-core/raredisease" @@ -142,7 +142,7 @@ ], "contributor": [ { - "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3" + "@id": "#4e768a30-2f70-4c38-adbb-71ae33643784" }, { "@id": "https://orcid.org/0000-0002-5044-7754" @@ -173,7 +173,7 @@ } ], "dateCreated": "", - "dateModified": "2026-04-29T10:07:02Z", + "dateModified": "2026-05-13T14:53:33Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -209,10 +209,10 @@ }, "url": [ "https://github.com/nf-core/raredisease", - "https://nf-co.re/raredisease/3.0.0/" + "https://nf-co.re/raredisease/dev/" ], "version": [ - "3.0.0" + "3.1.0dev" ] }, { @@ -228,11 +228,11 @@ "version": "!>=25.10.4" }, { - "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541", + "@id": "#887a7397-4dcc-4f72-b531-7f9faffbe771", "@type": "TestSuite", "instance": [ { - "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24" + "@id": "#db536a56-cb03-49ff-aa55-c29a281a564e" } ], "mainEntity": { @@ -241,7 +241,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24", + "@id": "#db536a56-cb03-49ff-aa55-c29a281a564e", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -396,7 +396,7 @@ "url": "https://github.com/jemten" }, { - "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3", + "@id": "#4e768a30-2f70-4c38-adbb-71ae33643784", "@type": "Person", "email": "25568561+projectoriented@users.noreply.github.com", "name": "Mei Wu", From 1840347a4ad7d2e77f20b743f3b0041e01beebda Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 13 May 2026 16:59:49 +0200 Subject: [PATCH 691/872] fix --- main.nf | 7 +++-- .../utils_nfcore_raredisease_pipeline/main.nf | 1 + workflows/raredisease.nf | 27 ++++++++++++------- 3 files changed, 24 insertions(+), 11 deletions(-) diff --git a/main.nf b/main.nf index 2fa3d17d3..b5f388dec 100644 --- a/main.nf +++ b/main.nf @@ -103,6 +103,7 @@ workflow NFCORE_RAREDISEASE { val_multiqc_methods_description val_multiqc_samples val_ngsbits_samplegender_method + val_outdir val_par_bed val_platform val_ploidy_model @@ -214,7 +215,6 @@ workflow NFCORE_RAREDISEASE { ch_vep_cache = ch_references.vep_resources // Using channelFromPath helper (val_x ? channel.fromPath(val_x).collect() : channel.value([])) - ch_multiqc_samples = channelFromPath(val_multiqc_samples, true) ch_reduced_penetrance = channelFromPath(val_reduced_penetrance, true) ch_rtg_truthvcfs = channelFromPath(val_rtg_truthvcfs, true) ch_score_config_mt = channelFromPath(val_score_config_mt, true) @@ -421,7 +421,6 @@ workflow NFCORE_RAREDISEASE { ch_mtshift_fai, ch_mtshift_fasta, ch_mtshift_intervals, - ch_multiqc_samples, ch_ngsbits_method, ch_par_bed, ch_pedfile, @@ -516,6 +515,8 @@ workflow NFCORE_RAREDISEASE { val_multiqc_config, val_multiqc_logo, val_multiqc_methods_description, + val_multiqc_samples, + val_outdir, val_platform, val_run_mt_for_wes, val_run_rtgvcfeval, @@ -557,6 +558,7 @@ workflow { params.input, params.help, params.help_full, + params.monochrome_logs, params.show_hidden ) // @@ -627,6 +629,7 @@ workflow { params.multiqc_methods_description, params.multiqc_samples, params.ngsbits_samplegender_method, + params.outdir, params.par_bed, params.platform, params.ploidy_model, diff --git a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf index 7c94448dc..83f7de8a9 100644 --- a/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf @@ -33,6 +33,7 @@ workflow PIPELINE_INITIALISATION { input // string: Path to input samplesheet help // boolean: Display help message and exit help_full // boolean: Show the full help message + monochrome_logs // boolean: Disable ANSI colour codes in log output show_hidden // boolean: Show hidden parameters in the help message main: diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0d8b4a0e7..6125640cf 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -120,7 +120,6 @@ workflow RAREDISEASE { ch_mtshift_fai ch_mtshift_fasta ch_mtshift_intervals - ch_multiqc_samples ch_ngsbits_method ch_par_bed ch_pedfile @@ -215,6 +214,8 @@ workflow RAREDISEASE { val_multiqc_config val_multiqc_logo val_multiqc_methods_description + val_multiqc_samples + val_outdir val_platform val_run_mt_for_wes val_run_rtgvcfeval @@ -927,7 +928,7 @@ workflow RAREDISEASE { def ch_collated_versions = softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file)) .mix(topic_versions_string) .collectFile( - storeDir: "${outdir}/pipeline_info", + storeDir: "${val_outdir}/pipeline_info", name: 'nf_core_' + 'raredisease_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true @@ -982,14 +983,22 @@ workflow RAREDISEASE { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.sex_check_csv.map{_meta, reports -> reports}.collect().ifEmpty([])) } + // config: custom config if provided, otherwise the default pipeline config + // logo: custom logo if provided, otherwise omitted + // sample_names: optional TSV for MultiQC --sample-names MULTIQC ( - ch_multiqc_files.flatten().collect() - .combine(ch_multiqc_config.mix(ch_multiqc_custom_config).collect().toList()) - .combine(ch_multiqc_logo.toList()) - .combine(ch_multiqc_samples.toList()) - .map { files, configs, logo, sample_names -> - [ [id: 'raredisease'], files, configs, logo, [], sample_names ] - } + ch_multiqc_files.flatten().collect().map { files -> + [ + [id: 'raredisease'], + files, + val_multiqc_config + ? file(val_multiqc_config, checkIfExists: true) + : file("${projectDir}/assets/multiqc_config.yml", checkIfExists: true), + val_multiqc_logo ? file(val_multiqc_logo, checkIfExists: true) : [], + [], + val_multiqc_samples ? file(val_multiqc_samples) : [], + ] + } ) ch_multiqc_publish = MULTIQC.out.report .mix(MULTIQC.out.data) From bcc9a8c5834ade07f371fae4d539edbd46f5f6f4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 13 May 2026 17:23:38 +0200 Subject: [PATCH 692/872] update snaps --- tests/default.nf.test.snap | 4 ++-- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ea6fc5d95..572d85273 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -483,7 +483,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -928,7 +928,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-08T16:30:33.887641119", + "timestamp": "2026-05-13T17:08:05.423400617", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index e26145db1..ef85a04d6 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -441,7 +441,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -844,7 +844,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-29T22:26:48.082490207", + "timestamp": "2026-05-13T17:14:03.036891427", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 66f438cc4..de6c2c335 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -466,7 +466,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -655,7 +655,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-04-29T22:30:32.111448817", + "timestamp": "2026-05-13T17:17:41.421517958", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 1fe71dcb1d4771ced83376ddf24d11025fff2ba1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 18 May 2026 11:11:47 +0200 Subject: [PATCH 693/872] Update snapshots --- tests/default.nf.test.snap | 407 +++++++++++++++++++++++++++++- tests/test_bam.nf.test.snap | 3 +- tests/test_singleton.nf.test.snap | 3 +- 3 files changed, 410 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 572d85273..b956a4033 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -697,6 +697,7 @@ "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", 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"justhusky_mt_ranked_research.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mt_ranked_research.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_snv_ranked_clinical.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv_ranked_clinical.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_snv_ranked_research.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv_ranked_research.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_sv_ranked_clinical.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_sv_ranked_clinical.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_sv_ranked_research.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_sv_ranked_research.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_repeat_expansion_stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_repeat_expansion_stranger.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_smncopynumbercaller.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_smncopynumbercaller.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_LNUMBER1.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_LNUMBER1.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_LNUMBER1.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_LNUMBER1_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman_LNUMBER1_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "hugelymodelbat_LNUMBER3.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_LNUMBER3.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_LNUMBER3.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_LNUMBER3_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "hugelymodelbat_LNUMBER3_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "slowlycivilbuck_LNUMBER2.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_LNUMBER2.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_LNUMBER2.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_LNUMBER2_R1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "slowlycivilbuck_LNUMBER2_R2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "earlycasualcaiman.cgh:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat.cgh:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-13T17:08:05.423400617", + "timestamp": "2026-05-18T09:07:41.312354342", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index ef85a04d6..a1c4e1147 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -629,6 +629,7 @@ "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", + "multiqc/multiqc_plots/.stub", "multiqc/multiqc_report.html", "ngsbits_samplegender", "ngsbits_samplegender/earlycasualcaiman_ngsbits_sex.tsv", @@ -844,7 +845,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-13T17:14:03.036891427", + "timestamp": "2026-05-18T09:13:39.46322688", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index de6c2c335..d62d36b3b 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -550,6 +550,7 @@ "multiqc/multiqc_data", "multiqc/multiqc_data/.stub", "multiqc/multiqc_plots", + "multiqc/multiqc_plots/.stub", "multiqc/multiqc_report.html", "ngsbits_samplegender", "ngsbits_samplegender/hugelymodelbat_ngsbits_sex.tsv", @@ -655,7 +656,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-13T17:17:41.421517958", + "timestamp": "2026-05-18T09:17:23.560290017", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 3c6bab7813e7b0cdb30eaccc13d9e6d123f98bae Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 18 May 2026 11:43:17 +0200 Subject: [PATCH 694/872] Update main.nf.test.snap --- .../tests/main.nf.test.snap | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index ee140eaa3..9e6ff93d1 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -17,7 +17,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" ] ] ], @@ -36,7 +36,7 @@ "11", [ [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -750,7 +750,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], [ @@ -766,7 +766,7 @@ "references/", [ [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -836,7 +836,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" ] ], [ @@ -1057,7 +1057,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" ] ] ], @@ -1096,7 +1096,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" ] ] ], @@ -1188,7 +1188,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" ] ] ], @@ -1216,7 +1216,7 @@ "gnomad_af_idx", [ [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -1632,7 +1632,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], [ @@ -1648,7 +1648,7 @@ "references/", [ [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -1718,7 +1718,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" ] ], [ @@ -2162,9 +2162,9 @@ ] ] ], - "timestamp": "2026-03-18T21:59:15.358100588", + "timestamp": "2026-05-18T11:32:42.39661125", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } From f0748368a6d5d4de05863fac7ebee72c6546f221 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 18 May 2026 13:52:32 +0200 Subject: [PATCH 695/872] Update test-data path --- .../tests/main.nf.test.snap | 26 +++++++++---------- tests/nextflow.config | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 9e6ff93d1..dade19398 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -17,7 +17,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ] ], @@ -36,7 +36,7 @@ "11", [ [ - "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -750,7 +750,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], [ @@ -766,7 +766,7 @@ "references/", [ [ - "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -836,7 +836,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ], [ @@ -1057,7 +1057,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ] ], @@ -1096,7 +1096,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ] ], @@ -1188,7 +1188,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ] ], @@ -1216,7 +1216,7 @@ "gnomad_af_idx", [ [ - "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -1632,7 +1632,7 @@ { "id": "dbsnp_-138-" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/dbsnp_-138-.vcf.gz" + "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" ] ], [ @@ -1648,7 +1648,7 @@ "references/", [ [ - "/nf-core/test-datasets/refs/heads/raredisease/reference/gnomad_reformated.tab.gz", + "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", "gnomad_reformated.tab.gz.tbi:md5,854afcf42d656c3d00a39dd9b69f66f7" ] ] @@ -1718,7 +1718,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/refs/heads/raredisease/reference/reference.fasta" + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ], [ @@ -2162,7 +2162,7 @@ ] ] ], - "timestamp": "2026-05-18T11:32:42.39661125", + "timestamp": "2026-05-18T13:51:28.575024127", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/nextflow.config b/tests/nextflow.config index 1a9c39fc7..1caf522fb 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -14,7 +14,7 @@ process { params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/raredisease/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/' sarscov_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' } From 9bf647efc52daebd5cd5bf4b4c3914098fac1a66 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 18 May 2026 15:09:57 +0200 Subject: [PATCH 696/872] update snap --- tests/default.nf.test.snap | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c6b4ca820..062aef247 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1099,16 +1099,14 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", "slowlycivilbuck_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.html:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.zip:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1336,11 +1334,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-18T09:07:41.312354342", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-05-06T10:50:08.628862072" + "timestamp": "2026-05-18T15:03:40.296274957" } } \ No newline at end of file From 146491f03f2aabbac754efc0bab99c027d3260d2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 19 May 2026 16:04:25 +0200 Subject: [PATCH 697/872] migrate alignment --- main.nf | 32 ++++++++-- subworkflows/local/align/main.nf | 60 +++++++------------ .../local/align_bwa_bwamem2_bwameme/main.nf | 15 ++--- subworkflows/local/align_sentieon/main.nf | 27 ++++----- subworkflows/local/subsample_mt_frac/main.nf | 7 +-- subworkflows/local/subsample_mt_reads/main.nf | 7 +-- workflows/raredisease.nf | 39 ++++++++---- 7 files changed, 98 insertions(+), 89 deletions(-) diff --git a/main.nf b/main.nf index b5f388dec..3c4fd3dd1 100644 --- a/main.nf +++ b/main.nf @@ -532,11 +532,19 @@ workflow NFCORE_RAREDISEASE { val_vep_cache_version ) emit: - multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - publish = RAREDISEASE.out.publish - .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] + align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] + align_genome_marked_bai = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] + align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] + align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] + align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] + multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] + subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] + publish = RAREDISEASE.out.publish + .mix(ch_scatter_genome_publish) + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -688,10 +696,24 @@ workflow { ) publish: + alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai) + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram) + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai) + .mix(NFCORE_RAREDISEASE.out.align_markdup_metrics) + .mix(NFCORE_RAREDISEASE.out.subsample_mt_bam) + .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) + fastp = NFCORE_RAREDISEASE.out.align_fastp_out subworkflow_results = NFCORE_RAREDISEASE.out.publish } output { + alignment { + path { _meta, _file -> "alignment/" } + } + fastp { + path { _meta, _file -> "trimming/" } + } subworkflow_results { path { destination, _value -> destination } } diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 932ace4f8..26a103301 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -49,28 +49,26 @@ workflow ALIGN { ch_bwamem2_bam = channel.empty() ch_bwamem2_bai = channel.empty() ch_fastp_json = channel.empty() - ch_fastp_publish = channel.empty() + ch_fastp_out = channel.empty() + ch_genome_marked_cram = channel.empty() + ch_genome_marked_crai = channel.empty() ch_markdup_metrics = channel.empty() ch_mt_bam_bai = channel.empty() ch_mt_bam_bai_gatksubwf = channel.empty() ch_mtshift_bam_bai_gatksubwf = channel.empty() ch_sentieon_bam = channel.empty() ch_sentieon_bai = channel.empty() - ch_cram_altfiltered = channel.empty() - ch_cram_publish = channel.empty() - ch_cram_unfiltered = channel.empty() if (!skip_fastp) { FASTP (ch_input_reads.map {meta, reads -> return [meta, reads, []] }, false, false, false) - ch_input_reads = FASTP.out.reads - ch_fastp_json = FASTP.out.json - ch_fastp_publish = FASTP.out.json + ch_input_reads = FASTP.out.reads + ch_fastp_json = FASTP.out.json + ch_fastp_out = FASTP.out.json .mix(FASTP.out.html) .mix(FASTP.out.log) .mix(FASTP.out.reads) .mix(FASTP.out.reads_fail) .mix(FASTP.out.reads_merged) - .map { meta, value -> ['trimming/', [meta, value]] } } // @@ -107,7 +105,7 @@ workflow ALIGN { ) ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai - ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.metrics + ch_markdup_metrics = ALIGN_BWA_BWAMEM2_BWAMEME.out.markdup_metrics } else if (val_aligner.equals("sentieon")) { ALIGN_SENTIEON ( ch_genome_bwaindex, @@ -119,6 +117,9 @@ workflow ALIGN { ) ch_sentieon_bam = ALIGN_SENTIEON.out.marked_bam ch_sentieon_bai = ALIGN_SENTIEON.out.marked_bai + ch_markdup_metrics = ALIGN_SENTIEON.out.dedup_metrics + .mix(ALIGN_SENTIEON.out.dedup_metrics_multiqc) + .mix(ALIGN_SENTIEON.out.score) } ch_genome_marked_bam_initial = channel.empty().mix(ch_bwamem2_bam, ch_sentieon_bam, ch_input_bam) @@ -184,41 +185,26 @@ workflow ALIGN { if (val_save_noalt_mapped_as_cram) { CONVERTTOCRAM_ALTFILTERED( ch_genome_marked_bam_bai, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) - ch_cram_altfiltered = CONVERTTOCRAM_ALTFILTERED.out.cram - .mix(CONVERTTOCRAM_ALTFILTERED.out.crai) + ch_genome_marked_cram = ch_genome_marked_cram.mix(CONVERTTOCRAM_ALTFILTERED.out.cram) + ch_genome_marked_crai = ch_genome_marked_crai.mix(CONVERTTOCRAM_ALTFILTERED.out.crai) } if (val_save_all_mapped_as_cram) { CONVERTTOCRAM_UNFILTERED( ch_genome_marked_bam_bai_initial, ch_genome_fasta.map{meta, fasta -> return [meta, fasta, []]}, [], 'crai' ) - ch_cram_unfiltered = CONVERTTOCRAM_UNFILTERED.out.cram - .mix(CONVERTTOCRAM_UNFILTERED.out.crai) + ch_genome_marked_cram = ch_genome_marked_cram.mix(CONVERTTOCRAM_UNFILTERED.out.cram) + ch_genome_marked_crai = ch_genome_marked_crai.mix(CONVERTTOCRAM_UNFILTERED.out.crai) } - ch_cram_publish = ch_cram_altfiltered - .mix(ch_cram_unfiltered) - .map { meta, value -> ['alignment/', [meta, value]] } - - ch_bam_publish = channel.empty() - if (!val_save_noalt_mapped_as_cram && !val_save_all_mapped_as_cram) { - if (val_aligner.matches("bwamem2|bwa|bwameme")) { - ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.publish - } else if (val_aligner.equals("sentieon")) { - ch_bam_publish = ALIGN_SENTIEON.out.publish - } - } - - ch_publish = ch_fastp_publish - .mix(ch_bam_publish) - .mix(ch_cram_publish) - emit: - fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] - genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] - genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] - genome_marked_bam_bai = ch_genome_marked_bam_bai // channel: [ val(meta), path(bam), path(bai) ] - markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(txt) ] - mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + fastp_json = ch_fastp_json // channel: [ val(meta), path(json) ] + fastp_out = ch_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] + genome_marked_cram = ch_genome_marked_cram // channel: [ val(meta), path(cram) ] + genome_marked_crai = ch_genome_marked_crai // channel: [ val(meta), path(crai) ] + genome_marked_bam = ch_genome_marked_bam // channel: [ val(meta), path(bam) ] + genome_marked_bai = ch_genome_marked_bai // channel: [ val(meta), path(bai) ] + genome_marked_bam_bai = ch_genome_marked_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + markdup_metrics = ch_markdup_metrics // channel: [ val(meta), path(metrics) ] + mt_bam_bai = ch_mt_bam_bai // channel: [ val(meta), path(bam), path(bai) ] mt_bam_bai_gatksubwf = ch_mt_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] mtshift_bam_bai_gatksubwf = ch_mtshift_bam_bai_gatksubwf // channel: [ val(meta), path(bam), path(bai) ] - publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 6ea0434de..7884e546c 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -77,16 +77,9 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { MARKDUPLICATES ( prepared_bam , ch_genome_fasta, ch_genome_fai ) SAMTOOLS_INDEX_MARKDUP ( MARKDUPLICATES.out.bam ) - ch_publish = MARKDUPLICATES.out.bam - .mix(MARKDUPLICATES.out.metrics) - .mix(SAMTOOLS_INDEX_MARKDUP.out.bai) - .mix(SAMTOOLS_INDEX_MARKDUP.out.csi) - .map { meta, value -> ['alignment/', [meta, value]] } - emit: - marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] - marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] - metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + marked_bai = SAMTOOLS_INDEX_MARKDUP.out.bai // channel: [ val(meta), path(bai) ] + marked_bam = MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] + markdup_metrics = MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] } diff --git a/subworkflows/local/align_sentieon/main.nf b/subworkflows/local/align_sentieon/main.nf index 5269ccb45..5d7ee89d7 100644 --- a/subworkflows/local/align_sentieon/main.nf +++ b/subworkflows/local/align_sentieon/main.nf @@ -48,21 +48,16 @@ workflow ALIGN_SENTIEON { SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai ) - ch_publish = SENTIEON_DEDUP.out.bam - .mix(SENTIEON_DEDUP.out.bai) - .mix(SENTIEON_DEDUP.out.score) - .mix(SENTIEON_DEDUP.out.metrics) - .mix(SENTIEON_DEDUP.out.metrics_multiqc_tsv) - .map { meta, value -> ['alignment/', [meta, value]] } - emit: - marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] - marked_bai = SENTIEON_DEDUP.out.bai // channel: [ val(meta), path(bai) ] - mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ] - qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ] - gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ] - gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] - aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] - is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + marked_bam = SENTIEON_DEDUP.out.bam // channel: [ val(meta), path(bam) ] + marked_bai = SENTIEON_DEDUP.out.bai // channel: [ val(meta), path(bai) ] + score = SENTIEON_DEDUP.out.score // channel: [ val(meta), path(score) ] + dedup_metrics = SENTIEON_DEDUP.out.metrics // channel: [ val(meta), path(metrics) ] + dedup_metrics_multiqc = SENTIEON_DEDUP.out.metrics_multiqc_tsv // channel: [ val(meta), path(tsv) ] + mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ] + qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ] + gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ] + gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ] + aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ] + is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ] } diff --git a/subworkflows/local/subsample_mt_frac/main.nf b/subworkflows/local/subsample_mt_frac/main.nf index 1ea24dac0..6d07e689b 100644 --- a/subworkflows/local/subsample_mt_frac/main.nf +++ b/subworkflows/local/subsample_mt_frac/main.nf @@ -32,10 +32,7 @@ workflow SUBSAMPLE_MT_FRAC { SAMTOOLS_VIEW(ch_subsample_in, [[:],[],[]], [], 'bai') - ch_publish = SAMTOOLS_VIEW.out.bam - .mix(SAMTOOLS_VIEW.out.bai) - .map { meta, value -> ['alignment/', [meta, value]] } - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] + bam = SAMTOOLS_VIEW.out.bam // channel: [ val(meta), path(bam) ] + bai = SAMTOOLS_VIEW.out.bai // channel: [ val(meta), path(bai) ] } diff --git a/subworkflows/local/subsample_mt_reads/main.nf b/subworkflows/local/subsample_mt_reads/main.nf index cc78d17ee..d6fc4f0b4 100644 --- a/subworkflows/local/subsample_mt_reads/main.nf +++ b/subworkflows/local/subsample_mt_reads/main.nf @@ -26,10 +26,7 @@ workflow SUBSAMPLE_MT_READS { SAMTOOLS_SORT(SAM_TO_BAM.out.bam, [[:],[]], 'bai') - ch_publish = SAMTOOLS_SORT.out.bam - .mix(SAMTOOLS_SORT.out.bai) - .map { meta, value -> ['alignment/', [meta, value]] } - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), path(bam) ] + bai = SAMTOOLS_SORT.out.bai // channel: [ val(meta), path(bai) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 6125640cf..ec4f074c3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -233,13 +233,19 @@ workflow RAREDISEASE { main: ch_multiqc_files = channel.empty() - ch_align_publish = channel.empty() + ch_align_fastp_out = channel.empty() + ch_align_genome_marked_cram = channel.empty() + ch_align_genome_marked_crai = channel.empty() + ch_align_genome_marked_bam = channel.empty() + ch_align_genome_marked_bai = channel.empty() + ch_align_markdup_metrics = channel.empty() + ch_subsample_mt_bam = channel.empty() + ch_subsample_mt_bai = channel.empty() ch_qc_bam_publish = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() - ch_subsample_publish = channel.empty() ch_annotate_genome_snvs_publish = channel.empty() ch_annotate_mt_snvs_publish = channel.empty() ch_annotate_sv_publish = channel.empty() @@ -325,7 +331,12 @@ workflow RAREDISEASE { val_save_noalt_mapped_as_cram ) .set { ch_mapped } - ch_align_publish = ALIGN.out.publish + ch_align_fastp_out = ALIGN.out.fastp_out + ch_align_genome_marked_bam = ALIGN.out.genome_marked_bam + ch_align_genome_marked_bai = ALIGN.out.genome_marked_bai + ch_align_genome_marked_cram = ALIGN.out.genome_marked_cram + ch_align_genome_marked_crai = ALIGN.out.genome_marked_crai + ch_align_markdup_metrics = ALIGN.out.markdup_metrics if (!(skip_mt_subsample) && (val_analysis_type.equals("wgs") || val_run_mt_for_wes)) { if (val_mt_subsample_approach.equals("fraction")) { @@ -334,12 +345,14 @@ workflow RAREDISEASE { val_mt_subsample_rd, val_mt_subsample_seed ) - ch_subsample_publish = SUBSAMPLE_MT_FRAC.out.publish + ch_subsample_mt_bam = SUBSAMPLE_MT_FRAC.out.bam + ch_subsample_mt_bai = SUBSAMPLE_MT_FRAC.out.bai } else { SUBSAMPLE_MT_READS( ch_mapped.mt_bam_bai, ) - ch_subsample_publish = SUBSAMPLE_MT_READS.out.publish + ch_subsample_mt_bam = SUBSAMPLE_MT_READS.out.bam + ch_subsample_mt_bai = SUBSAMPLE_MT_READS.out.bai } } @@ -1006,11 +1019,17 @@ workflow RAREDISEASE { .map { _meta, value -> ['multiqc/', value] } emit: - multiqc_report = MULTIQC.out.report.map { _meta, report -> report }.toList() - versions = ch_versions - publish = ch_align_publish - .mix(ch_qc_bam_publish) - .mix(ch_subsample_publish) + align_fastp_out = ch_align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] + align_genome_marked_bam = ch_align_genome_marked_bam // channel: [ val(meta), path(bam) ] + align_genome_marked_bai = ch_align_genome_marked_bai // channel: [ val(meta), path(bai) ] + align_genome_marked_cram = ch_align_genome_marked_cram // channel: [ val(meta), path(cram) ] + align_genome_marked_crai = ch_align_genome_marked_crai // channel: [ val(meta), path(crai) ] + align_markdup_metrics = ch_align_markdup_metrics // channel: [ val(meta), path(metrics) ] + multiqc_report = MULTIQC.out.report.map { _meta, report -> report }.toList() + subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] + subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] + versions = ch_versions + publish = ch_qc_bam_publish .mix(ch_call_snv_publish) .mix(ch_call_sv_publish) .mix(ch_call_repeat_expansions_publish) From 200b50c1c38dd18329a04f8b9d57343317e3ccee Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 00:30:03 +0200 Subject: [PATCH 698/872] update tests and snaps --- nf-test.config | 2 +- subworkflows/local/align/main.nf | 2 +- subworkflows/local/align/tests/main.nf.test | 30 +- .../local/align/tests/main.nf.test.snap | 662 ++++++++++++++++-- .../tests/main.nf.test | 12 +- .../tests/main.nf.test.snap | 64 +- .../local/align_sentieon/tests/main.nf.test | 7 +- .../subsample_mt_frac/tests/main.nf.test | 14 +- .../subsample_mt_frac/tests/main.nf.test.snap | 136 ++++ .../subsample_mt_reads/tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 130 ++++ 11 files changed, 970 insertions(+), 103 deletions(-) create mode 100644 subworkflows/local/subsample_mt_frac/tests/main.nf.test.snap create mode 100644 subworkflows/local/subsample_mt_reads/tests/main.nf.test.snap diff --git a/nf-test.config b/nf-test.config index dd32a52bb..625be563e 100644 --- a/nf-test.config +++ b/nf-test.config @@ -34,7 +34,7 @@ config { // load the necessary plugins plugins { load "nft-utils@0.0.3" - load "nft-bam@0.6.0" + load "nft-bam@0.6.1" load "nft-vcf@1.0.7" } diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 26a103301..cd4f24db7 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -66,7 +66,7 @@ workflow ALIGN { ch_fastp_out = FASTP.out.json .mix(FASTP.out.html) .mix(FASTP.out.log) - .mix(FASTP.out.reads) + .mix(FASTP.out.reads.transpose()) .mix(FASTP.out.reads_fail) .mix(FASTP.out.reads_merged) } diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 7a8e427ac..58e4860d3 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -130,10 +130,11 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.fastp_json, + workflow.out.genome_marked_cram + .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + workflow.out.genome_marked_crai + .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -237,10 +238,11 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.fastp_json, + workflow.out.genome_marked_cram + .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + workflow.out.genome_marked_crai + .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai @@ -248,7 +250,7 @@ nextflow_workflow { workflow.out.mt_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mtshift_bam_bai_gatksubwf - .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, + .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } ) @@ -335,15 +337,15 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.genome_marked_cram + .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + workflow.out.genome_marked_crai + .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mtshift_bam_bai + workflow.out.mtshift_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index e56d30a3b..1331d96a3 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,33 +2,274 @@ "align bwamem2 - wgs": { "content": [ [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "earlycasualcaiman_sorted_md_primary_contigs.cram", - "earlycasualcaiman_sorted_md_primary_contigs.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "hugelymodelbat_sorted_md_primary_contigs.cram", - "hugelymodelbat_sorted_md_primary_contigs.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai", - "slowlycivilbuck_sorted_md_primary_contigs.cram", - "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d473c195ec66e23d39a02d4566b92d75" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat.fastp.json:md5,364c1702f8e833c70fbd36c2e0634f86" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,7ad34e9e48159c794ce777e4e48c0b96" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d948b0bd18f6f6526f5d8832465e1542" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "bb547b29eca1afded4229826c774fc90" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "2530fd24192b09084f45011703bd4954" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, 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+ ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md_primary_contigs.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": 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"slowlycivilbuck_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" + ] ], [ [ @@ -267,21 +508,125 @@ ] ] ], - "timestamp": "2026-04-14T11:13:27.943707346", + "timestamp": "2026-05-19T23:32:16.647720143", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "align bwameme - wgs": { "content": [ [ - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "9266e8231917cc16ff9845e50ed22801" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "1df3c2e109a79ba4e7b8293aefbad8" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "645db4b1d55d6d42cba2b55eee1a630" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": 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+ "case_id": "justhusky" + } + }, + "9f79604c77dc54d30daff682a50399bf", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "8d810d8acecdeadc5a0e7ea159cb1343", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ] ], - "timestamp": "2026-04-14T09:52:25.609505795", + "timestamp": "2026-05-19T23:39:15.518562527", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "align bwamem2 - wes": { "content": [ [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + }, + "hugelymodelbat.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "lane": 1, + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "slowlycivilbuck.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ] ], [ [ @@ -505,9 +1045,9 @@ ] ], - "timestamp": "2026-04-14T08:57:37.024004334", + "timestamp": "2026-05-19T23:32:53.898811922", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 7e64d0355..740663911 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -66,10 +66,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.markdup_metrics, + workflow.out.stats, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() @@ -126,10 +124,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.markdup_metrics, + workflow.out.stats, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 7632f79b8..03eae7816 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -2,9 +2,31 @@ "align bwamem2": { "content": [ [ - "test_sorted_md.bam", - "test_sorted_md.bam.bai", - "test_sorted_md.metrics.txt" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,4427ebc749ff70c29570353a2e9d1b03" + ] + ], + [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,f0914a56ae73007ebd242cab27861700" + ] ], [ [ @@ -37,18 +59,40 @@ ] ] ], - "timestamp": "2026-03-13T15:04:33.885203481", + "timestamp": "2026-05-19T23:41:11.371852162", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "align bwameme": { "content": [ [ - "test_sorted_md.bam", - "test_sorted_md.bam.bai", - "test_sorted_md.metrics.txt" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_sorted_md.metrics.txt:md5,9f2e6adbb9ac7546a4ee62cf79dcf54d" + ] + ], + [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,f0914a56ae73007ebd242cab27861700" + ] ], [ [ @@ -81,9 +125,9 @@ ] ] ], - "timestamp": "2026-03-13T15:05:20.75721248", + "timestamp": "2026-05-19T23:41:57.243720366", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 63b4b6f97..29e208af4 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -67,10 +67,9 @@ nextflow_workflow { workflow.out.is_metrics, workflow.out.mq_metrics, workflow.out.qd_metrics, - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.dedup_metrics, + workflow.out.dedup_metrics_multiqc, + workflow.out.score, ).match() } diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test b/subworkflows/local/subsample_mt_frac/tests/main.nf.test index 9f2ddf63f..2c6ebe899 100644 --- a/subworkflows/local/subsample_mt_frac/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test @@ -29,7 +29,14 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.bai.collect { meta, baifile -> [ meta, file(baifile).name ] } + ).match() + } + ) } } @@ -52,7 +59,10 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) } } } diff --git a/subworkflows/local/subsample_mt_frac/tests/main.nf.test.snap b/subworkflows/local/subsample_mt_frac/tests/main.nf.test.snap new file mode 100644 index 000000000..585a5abf5 --- /dev/null +++ b/subworkflows/local/subsample_mt_frac/tests/main.nf.test.snap @@ -0,0 +1,136 @@ +{ + "SUBSAMPLE_MT_FRAC": { + "content": [ + [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": "31.339226", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "3738567deb98475ea48267fc25568a6a" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": "31.339226", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai" + ] + ] + ], + "timestamp": "2026-05-20T00:15:22.219541427", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "SUBSAMPLE_MT_FRAC -stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": null, + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": null, + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bai": [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": null, + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "earlycasualcaiman", + "seedfrac": null, + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-05-20T00:15:41.615447408", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/subsample_mt_reads/tests/main.nf.test b/subworkflows/local/subsample_mt_reads/tests/main.nf.test index 21b924311..f4f747ada 100644 --- a/subworkflows/local/subsample_mt_reads/tests/main.nf.test +++ b/subworkflows/local/subsample_mt_reads/tests/main.nf.test @@ -31,7 +31,14 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.bai.collect { meta, baifile -> [ meta, file(baifile).name ] } + ).match() + } + ) } } @@ -55,7 +62,10 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) } } } diff --git a/subworkflows/local/subsample_mt_reads/tests/main.nf.test.snap b/subworkflows/local/subsample_mt_reads/tests/main.nf.test.snap new file mode 100644 index 000000000..d06a6d7c3 --- /dev/null +++ b/subworkflows/local/subsample_mt_reads/tests/main.nf.test.snap @@ -0,0 +1,130 @@ +{ + "SUBSAMPLE_MT_READS": { + "content": [ + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "39e02db7f5cdce7a716cbd0de5352c63" + ] + ], + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai" + ] + ] + ], + "timestamp": "2026-05-20T00:16:23.836648543", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "SUBSAMPLE_MT_READS -stub": { + "content": [ + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bai": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mt_subsample.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "timestamp": "2026-05-20T00:16:46.901941587", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 401564197f072fcb512be779109c8e9d41d70b2a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 01:10:56 +0200 Subject: [PATCH 699/872] update sentieon test --- .../local/align_sentieon/tests/main.nf.test | 31 ++++++++++--------- 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 29e208af4..b6cff9930 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -57,20 +57,23 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot( - workflow.out.marked_bam, - workflow.out.marked_bai, - workflow.out.aln_metrics, - workflow.out.gc_metrics, - workflow.out.gc_summary, - workflow.out.is_metrics, - workflow.out.mq_metrics, - workflow.out.qd_metrics, - workflow.out.dedup_metrics, - workflow.out.dedup_metrics_multiqc, - workflow.out.score, - ).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.marked_bai.collect { meta, baifile -> [ meta, file(baifile).name ] }, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.dedup_metrics, + workflow.out.dedup_metrics_multiqc, + workflow.out.score, + ).match() + } + ) } } From 9d73ac8d299cfa8a845054fb2b6731e7a42f76e4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 01:15:23 +0200 Subject: [PATCH 700/872] Update main.nf.test.snap --- .../align_sentieon/tests/main.nf.test.snap | 54 ++++++++++++++++--- 1 file changed, 46 insertions(+), 8 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index b538612cb..aba84f6fb 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,489a7a6b515bfeb9e22b10732d7586e4" + "2d64e4363d9f3c0e2167fce49d5087cf" ] ], [ @@ -28,7 +28,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,14bc034b61e9f46cc0c0224b8915d7aa" + "test_dedup.bam.bai" ] ], [ @@ -122,14 +122,52 @@ ] ], [ - "test_dedup.bam", - "test_dedup.bam.bai", - "test_dedup.bam.metrics", - "test_dedup.bam.metrics.multiqc.tsv", - "test_dedup.score" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,67c42dfe156b0613d30966768d01b55c" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,107725946bfe75d63c82d4f330872833" + ] ] ], - "timestamp": "2026-03-14T00:02:24.597092362", + "timestamp": "2026-05-20T01:12:45.869407855", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 7bee2c4b280a2fb015d2e48530b411cdeb61f8a4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 02:14:48 +0200 Subject: [PATCH 701/872] update docs --- .github/CONTRIBUTING.md | 17 +++++++---------- CHANGELOG.md | 4 ++++ 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index c75f209ee..265305e8d 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -147,11 +147,12 @@ Devcontainer specs: ### Publishing -- Build a single `ch_publish` channel inside each subworkflow by mixing all publishable outputs into `[destination, value]` tuples. -- The emit name must always be `publish = ch_publish` — never the bare shorthand. -- Group channels that share a destination with `mix` first, then apply **one** `.map` per destination group — never one map per channel. -- If your subworkflow calls inner subworkflows, always mix their `.out.publish` into the outer `ch_publish`. Never discard it. -- Remove the corresponding `publishDir` entry from `conf/modules/` when adding a process to `ch_publish`. +The pipeline uses Nextflow's `publish:` block and `output {}` API for file publishing. Each subworkflow exposes its outputs as named typed channel emits; the top-level `publish:` block in `main.nf` mixes them into destination-named entries. + +- Emit every publishable output as a named typed channel — no `ch_publish` tuple wrapping. +- Group outputs that share the same destination directory under **one** `publish:` entry and **one** `output {}` entry in `main.nf`; mix them together with `.mix()`. + +> **Note:** Some subworkflows still use the legacy `ch_publish`/`subworkflow_results` pattern and are being migrated incrementally. Until a subworkflow is migrated, follow the existing pattern for that subworkflow so it continues to publish correctly via `subworkflow_results`. ### Configuration @@ -191,13 +192,9 @@ Devcontainer specs: process_with_sort // Boolean emit: - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] ``` -- Intermediate publish channels in `workflows/raredisease.nf` follow the `ch__publish` naming convention and are assigned immediately after the subworkflow call, not inline in the emit block. -- Initialize all `ch_*_publish` variables at the top of the `main:` block alongside `ch_multiqc_files`. - ### Adding citations When adding a new tool to the pipeline, update the following three locations: diff --git a/CHANGELOG.md b/CHANGELOG.md index 29699099a..46442f253 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [[#TODO](https://github.com/nf-core/raredisease/pull/TODO)] + ### `Fixed` +### Parameters + | Old parameter | New parameter | | ------------- | ------------- | | | | From 608bb7552dbdcacc9023973c2e17db62e4873c7c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 09:20:26 +0200 Subject: [PATCH 702/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 46442f253..69eaa2d33 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [[#TODO](https://github.com/nf-core/raredisease/pull/TODO)] +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` From 6283c4fd490b1691897726084650035dffe716f3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 10:45:27 +0200 Subject: [PATCH 703/872] Update bwa* subwf tests and snapshots --- .../tests/main.nf.test | 4 +-- .../tests/main.nf.test.snap | 36 ++++--------------- 2 files changed, 8 insertions(+), 32 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 740663911..ec376deef 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -66,7 +66,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.markdup_metrics, + workflow.out.markdup_metrics.collect { meta, metrics -> file(metrics).name }, workflow.out.stats, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } @@ -124,7 +124,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.markdup_metrics, + workflow.out.markdup_metrics.collect { meta, metrics -> file(metrics).name }, workflow.out.stats, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 03eae7816..a60f30bae 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -2,19 +2,7 @@ "align bwamem2": { "content": [ [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,4427ebc749ff70c29570353a2e9d1b03" - ] + "test_sorted_md.metrics.txt" ], [ [ @@ -59,28 +47,16 @@ ] ] ], - "timestamp": "2026-05-19T23:41:11.371852162", + "timestamp": "2026-05-20T10:42:39.715894878", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } }, "align bwameme": { "content": [ [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,9f2e6adbb9ac7546a4ee62cf79dcf54d" - ] + "test_sorted_md.metrics.txt" ], [ [ @@ -125,9 +101,9 @@ ] ] ], - "timestamp": "2026-05-19T23:41:57.243720366", + "timestamp": "2026-05-20T10:43:22.366256053", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } } From d2326f58c0a50e66c1ce91e4fb57640b980ea875 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor=20Bj=C3=B6rgen?= Date: Wed, 20 May 2026 10:41:44 +0200 Subject: [PATCH 704/872] Update docs/CONTRIBUTING.md on forked repos, CI/CD --- docs/CONTRIBUTING.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 66288c96a..9c3133abd 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -34,6 +34,11 @@ To contribute code to any nf-core pipeline: If you are not used to this workflow with Git, see the [GitHub documentation](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or [Git resources](https://try.github.io/) for more information. +#### Forks and CI/CD Tests + +When creating a pull request from a forked repository, it's likely that some tests will fail that are related to nf-core/raredisease private license files (Sentieon etc) +as they are not available in the forked repository. If this is the case, push the branch into raredisease instead and open a PR from the new branch. + ## Use of AI and LLMs The nf-core stance on the use of AI and LLMs is that humans are still ultimately responsible for their submitted code, regardless of the tools they use. From 986e011ffe7f1f1b336234fb376342b1cd34de8c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 16:05:58 +0200 Subject: [PATCH 705/872] update dv snap --- subworkflows/local/call_snv_deepvariant/tests/main.nf.test | 2 +- .../local/call_snv_deepvariant/tests/main.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 5ea64aa2f..53de1dd91 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -46,7 +46,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - path(workflow.out.vcf[0][1]).vcf.variantsMD5, + path(workflow.out.vcf[0][1]).vcf.summary, workflow.out.tabix.collect { meta, tbi -> file(tbi).name }, workflow.out.gvcf.collect { meta, gvcf -> file(gvcf).name } ).match() } diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index 6f17d088b..85701c2d3 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -152,7 +152,7 @@ }, "CALL_SNV_DEEPVARIANT - wgs": { "content": [ - "e4e9e39859d7df52fd955fb32796fdb2", + "VcfFile [chromosomes=[MT, 21], sampleCount=1, variantCount=7601, phased=false, phasedAutodetect=false]", [ "justhusky_split_rmdup_info.vcf.gz.tbi" ], @@ -160,7 +160,7 @@ "earlycasualcaiman_deepvar.g.vcf.gz" ] ], - "timestamp": "2026-03-17T23:21:13.603834111", + "timestamp": "2026-05-20T16:02:09.449313235", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From ec48cdfda63a3c57f55e83866f8557076c590151 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 17:19:55 +0200 Subject: [PATCH 706/872] update test and snaps --- main.nf | 54 +++--- subworkflows/local/qc_bam/main.nf | 23 ++- subworkflows/local/qc_bam/tests/main.nf.test | 71 +++----- subworkflows/local/scatter_genome/main.nf | 12 +- .../scatter_genome/tests/main.nf.test.snap | 156 ++++++++---------- workflows/raredisease.nf | 11 +- 6 files changed, 153 insertions(+), 174 deletions(-) diff --git a/main.nf b/main.nf index 3c4fd3dd1..dbdc327ff 100644 --- a/main.nf +++ b/main.nf @@ -364,8 +364,8 @@ workflow NFCORE_RAREDISEASE { // // Create chromosome bed and intervals for splitting and gathering operations // - ch_scatter_split_intervals = channel.empty() - ch_scatter_genome_publish = channel.empty() + ch_scatter_split_intervals = channel.empty() + ch_scatter_split_intervals_publish = channel.empty() if (!skip_snv_annotation) { SCATTER_GENOME ( ch_genome_dictionary, @@ -373,8 +373,8 @@ workflow NFCORE_RAREDISEASE { ch_genome_fasta, params.save_reference ) - ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals - ch_scatter_genome_publish = SCATTER_GENOME.out.publish + ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals + ch_scatter_split_intervals_publish = SCATTER_GENOME.out.split_intervals_publish } RAREDISEASE ( @@ -532,19 +532,21 @@ workflow NFCORE_RAREDISEASE { val_vep_cache_version ) emit: - align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] - align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] - align_genome_marked_bai = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] - align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] - align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] - align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] - multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] - subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] - publish = RAREDISEASE.out.publish - .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] + align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] + align_genome_marked_bai. = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] + align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] + align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] + align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] + multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + qc_bam_files = RAREDISEASE.out.qc_bam_files // channel: [ val(meta), path(file) ] + qc_sex_check = RAREDISEASE.out.qc_sex_check // channel: [ val(meta), path(tsv) ] + scatter_split_intervals_publish = ch_scatter_split_intervals_publish // channel: [ val(meta), path(intervals) ] + subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] + subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] + publish = RAREDISEASE.out.publish + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -696,15 +698,18 @@ workflow { ) publish: - alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam + alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam .mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai) .mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram) .mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai) .mix(NFCORE_RAREDISEASE.out.align_markdup_metrics) .mix(NFCORE_RAREDISEASE.out.subsample_mt_bam) .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) - fastp = NFCORE_RAREDISEASE.out.align_fastp_out - subworkflow_results = NFCORE_RAREDISEASE.out.publish + fastp = NFCORE_RAREDISEASE.out.align_fastp_out + ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_sex_check + processed_references = NFCORE_RAREDISEASE.out.scatter_split_intervals_publish + qc_bam = NFCORE_RAREDISEASE.out.qc_bam_files + subworkflow_results = NFCORE_RAREDISEASE.out.publish } output { @@ -714,6 +719,15 @@ output { fastp { path { _meta, _file -> "trimming/" } } + ngsbits_samplegender { + path { _meta, _file -> "ngsbits_samplegender/" } + } + processed_references { + path { _meta, _file -> "processed_references/" } + } + qc_bam { + path { _meta, _file -> "qc_bam/" } + } subworkflow_results { path { destination, _value -> destination } } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index fdbca0b2d..507ca87bc 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -89,12 +89,12 @@ workflow QC_BAM { ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) - ch_publish = PICARD_COLLECTMULTIPLEMETRICS.out.metrics - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf) + ch_qc_bam_files = PICARD_COLLECTMULTIPLEMETRICS.out.metrics.transpose() + .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf.transpose()) .mix(TIDDIT_COV.out.wig) .mix(TIDDIT_COV.out.cov) .mix(UCSC_WIGTOBIGWIG.out.bw) - .mix(CHROMOGRAPH_COV.out.plots) + .mix(CHROMOGRAPH_COV.out.plots.transpose()) .mix(MOSDEPTH.out.global_txt) .mix(MOSDEPTH.out.summary_txt) .mix(MOSDEPTH.out.per_base_d4) @@ -117,20 +117,17 @@ workflow QC_BAM { .mix(ch_hsmetrics) .mix(ch_cov) .mix(ch_cov_y) - .map { meta, value -> ['qc_bam/', [meta, value]] } - .mix(ch_ngsbits - .map { meta, tsv -> ['ngsbits_samplegender/', [meta, tsv]] }) emit: - multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] - hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] - tiddit_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] bigwig = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] + cov = ch_cov // channel: [ val(meta), path(metrics) ] + cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] d4 = MOSDEPTH.out.per_base_d4 // channel: [ val(meta), path(d4) ] global_dist = MOSDEPTH.out.global_txt // channel: [ val(meta), path(txt) ] - sex_check = ch_ngsbits // channel: [ val(meta), path(tsv) ] + hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] + multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] + qc_bam_files = ch_qc_bam_files // channel: [ val(meta), path(file) ] self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] - cov = ch_cov // channel: [ val(meta), path(metrics) ] - cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + sex_check = ch_ngsbits // channel: [ val(meta), path(tsv) ] + tiddit_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 522858f9e..5bd8cca3e 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -62,33 +62,24 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), workflow.out.multiple_metrics - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, workflow.out.hs_metrics - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, workflow.out.d4 - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, f -> [meta, file(f).name] }, workflow.out.cov - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), - workflow.out.tiddit_wig, - workflow.out.bigwig, + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.cov_y + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.tiddit_wig + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.bigwig + .collect { meta, f -> [meta, file(f).name] }, workflow.out.global_dist + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.self_sm + .collect { meta, f -> [meta, file(f).name] } ).match() } ) @@ -134,36 +125,26 @@ nextflow_workflow { then { assertAll ( - { assert workflow.success }, { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), workflow.out.multiple_metrics - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, workflow.out.hs_metrics - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, workflow.out.d4 - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), + .collect { meta, f -> [meta, file(f).name] }, workflow.out.cov - .collect {it[1]} - .flatten() - .collect { file(it).name } - .toSorted(), - workflow.out.tiddit_wig, - workflow.out.bigwig, + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.cov_y + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.tiddit_wig + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.bigwig + .collect { meta, f -> [meta, file(f).name] }, workflow.out.global_dist + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.self_sm + .collect { meta, f -> [meta, file(f).name] } ).match() } ) diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index b6a258828..53dfbd862 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -19,14 +19,10 @@ workflow SCATTER_GENOME { GATK4_SPLITINTERVALS(GAWK.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) - ch_publish = channel.empty() - if (val_save_reference) { - ch_publish = GATK4_SPLITINTERVALS.out.split_intervals - .map { meta, value -> ['processed_references/', [meta, value]] } - } + ch_split_intervals_publish = val_save_reference ? GATK4_SPLITINTERVALS.out.split_intervals : channel.empty() emit: - bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] - split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] - publish = ch_publish // channel: [ val(destination), val(value) ] + bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] + split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ path(interval_list) ] + split_intervals_publish = ch_split_intervals_publish // channel: [ val(meta), path(intervals) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 823e91d1a..fade09df3 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -20,15 +20,12 @@ ], "2": [ [ - "processed_references/", + { + "id": "genome" + }, [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -40,20 +37,6 @@ "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "publish": [ - [ - "processed_references/", - [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] - ], "split_intervals": [ [ "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -61,12 +44,23 @@ [ "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "split_intervals_publish": [ + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] } ], - "timestamp": "2026-03-30T10:55:18.112519", + "timestamp": "2026-05-20T17:15:58.636121358", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -145,33 +139,30 @@ ], "2": [ [ - "processed_references/", + { + "id": "genome" + }, [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] ] ], @@ -183,38 +174,6 @@ "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], - "publish": [ - [ - "processed_references/", - [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] - ] - ] - ], "split_intervals": [ [ "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" @@ -276,12 +235,41 @@ [ "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] + ], + "split_intervals_publish": [ + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ] ] } ], - "timestamp": "2026-03-17T00:19:06.789641139", + "timestamp": "2026-05-20T17:15:35.25891204", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ec4f074c3..8f1dfac5d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -241,7 +241,8 @@ workflow RAREDISEASE { ch_align_markdup_metrics = channel.empty() ch_subsample_mt_bam = channel.empty() ch_subsample_mt_bai = channel.empty() - ch_qc_bam_publish = channel.empty() + ch_qc_bam_files = channel.empty() + ch_qc_sex_check = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() @@ -378,7 +379,8 @@ workflow RAREDISEASE { val_target_bed, skip_ngsbits ) - ch_qc_bam_publish = QC_BAM.out.publish + ch_qc_bam_files = QC_BAM.out.qc_bam_files + ch_qc_sex_check = QC_BAM.out.sex_check /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1026,11 +1028,12 @@ workflow RAREDISEASE { align_genome_marked_crai = ch_align_genome_marked_crai // channel: [ val(meta), path(crai) ] align_markdup_metrics = ch_align_markdup_metrics // channel: [ val(meta), path(metrics) ] multiqc_report = MULTIQC.out.report.map { _meta, report -> report }.toList() + qc_bam_files = ch_qc_bam_files // channel: [ val(meta), path(file) ] + qc_sex_check = ch_qc_sex_check // channel: [ val(meta), path(tsv) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions - publish = ch_qc_bam_publish - .mix(ch_call_snv_publish) + publish = ch_call_snv_publish .mix(ch_call_sv_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) From 181511a4d5bb2dd5181e97a3f90c89554764dd55 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 17:35:09 +0200 Subject: [PATCH 707/872] update qc bam test --- subworkflows/local/qc_bam/tests/main.nf.test | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 5bd8cca3e..566f74dac 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -79,7 +79,9 @@ nextflow_workflow { workflow.out.global_dist .collect { meta, f -> [meta, file(f).name] }, workflow.out.self_sm - .collect { meta, f -> [meta, file(f).name] } + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.qc_bam_files + .collect { meta, f -> file(f).name }.sort() ).match() } ) From bd7fcbe3d487d028c1c03c88c4e56490ec04e992 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 17:50:43 +0200 Subject: [PATCH 708/872] Update qc_bam tests and snaps --- subworkflows/local/qc_bam/tests/main.nf.test | 4 +- .../local/qc_bam/tests/main.nf.test.snap | 260 ++++++++++++------ 2 files changed, 186 insertions(+), 78 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 566f74dac..1f9c5552d 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -146,7 +146,9 @@ nextflow_workflow { workflow.out.global_dist .collect { meta, f -> [meta, file(f).name] }, workflow.out.self_sm - .collect { meta, f -> [meta, file(f).name] } + .collect { meta, f -> [meta, file(f).name] }, + workflow.out.qc_bam_files + .collect { meta, f -> file(f).name }.sort() ).match() } ) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 42f458e1c..35ef7f3e9 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,65 +2,70 @@ "QC_BAM - test, bwamem2": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov_1.png", - "earlycasualcaiman_tidditcov_10.png", - "earlycasualcaiman_tidditcov_11.png", - "earlycasualcaiman_tidditcov_12.png", - "earlycasualcaiman_tidditcov_13.png", - "earlycasualcaiman_tidditcov_14.png", - "earlycasualcaiman_tidditcov_15.png", - "earlycasualcaiman_tidditcov_16.png", - "earlycasualcaiman_tidditcov_17.png", - "earlycasualcaiman_tidditcov_18.png", - "earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] ], [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], [ - + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] ], [ - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ], [ [ @@ -77,7 +82,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + "earlycasualcaiman_tidditcov.wig" ] ], [ @@ -95,7 +100,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + "earlycasualcaiman_tidditcov.bw" ] ], [ @@ -113,18 +118,12 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" ] - ] - ], - "timestamp": "2026-03-27T16:45:40.990778813", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "QC_BAM - test, sentieon": { - "content": [ + ], + [ + + ], [ "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", @@ -168,23 +167,82 @@ "earlycasualcaiman_tidditcov_M.png", "earlycasualcaiman_tidditcov_X.png", "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.txt" - ], + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ] + ], + "timestamp": "2026-05-20T17:37:41.846430552", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "QC_BAM - test, sentieon": { + "content": [ [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ] ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ] ], [ ], [ - "earlycasualcaiman_wgsmetrics.txt" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_wgsmetrics.txt" + ] + ], + [ + ], [ [ @@ -201,7 +259,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + "earlycasualcaiman_tidditcov.wig" ] ], [ @@ -219,7 +277,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + "earlycasualcaiman_tidditcov.bw" ] ], [ @@ -237,11 +295,59 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" ] + ], + [ + + ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", + "earlycasualcaiman_mosdepth.mosdepth.summary.txt", + "earlycasualcaiman_mosdepth.per-base.bed.gz", + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", + "earlycasualcaiman_tidditcov.bw", + "earlycasualcaiman_tidditcov.wig", + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png", + "earlycasualcaiman_wgsmetrics.txt" ] ], - "timestamp": "2026-03-27T17:07:36.836738984", + "timestamp": "2026-05-20T17:43:21.933661098", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From aaed091eb6d29575c83b2b8e59773b5ca8b6d48a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 18:08:48 +0200 Subject: [PATCH 709/872] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc2a9e613..9d58bcac5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- Fix intermittent `CALL_SNV_DEEPVARIANT - wgs` test failure caused by non-deterministic GLnexus quality scores by replacing `variantsMD5` with `vcf.summary` [#850](https://github.com/nf-core/raredisease/pull/850) + ### Parameters | Old parameter | New parameter | From e43a8ddf6b060fd62c3acd052d301d4917ee3dbf Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 18:11:20 +0200 Subject: [PATCH 710/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 46442f253..14d25a6fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [[#TODO](https://github.com/nf-core/raredisease/pull/TODO)] +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam and scatter_genome subworkflows [[#852](https://github.com/nf-core/raredisease/pull/852)] ### `Fixed` From 0fa3709753fbfa1ecf9fc2338cb35fc0710fc8f7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 20 May 2026 23:29:58 +0200 Subject: [PATCH 711/872] review suggestions --- subworkflows/local/align/tests/main.nf.test | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 58e4860d3..0c68db7ca 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -132,7 +132,7 @@ nextflow_workflow { { assert snapshot( workflow.out.fastp_json, workflow.out.genome_marked_cram - .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + .collect { meta, cramfile -> [ meta, cram(cramfile, params.pipelines_testdata_base_path + 'reference/reference.fasta').getReadsMD5() ] }, workflow.out.genome_marked_crai .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai @@ -240,7 +240,7 @@ nextflow_workflow { { assert snapshot( workflow.out.fastp_json, workflow.out.genome_marked_cram - .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + .collect { meta, cramfile -> [ meta, cram(cramfile, params.pipelines_testdata_base_path + 'reference/reference.fasta').getReadsMD5() ] }, workflow.out.genome_marked_crai .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai @@ -338,7 +338,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.genome_marked_cram - .collect { meta, cramfile -> [ meta, cram(cramfile, "${params.pipelines_testdata_base_path}reference/reference.fasta").getReadsMD5() ] }, + .collect { meta, cramfile -> [ meta, cram(cramfile, params.pipelines_testdata_base_path + 'reference/reference.fasta').getReadsMD5() ] }, workflow.out.genome_marked_crai .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai From b054363a8b76e810df58a2b1bd315053bdab69d1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 21 May 2026 10:06:59 +0200 Subject: [PATCH 712/872] update snaps --- CHANGELOG.md | 2 +- main.nf | 20 +-- subworkflows/local/scatter_genome/main.nf | 12 +- .../scatter_genome/tests/main.nf.test.snap | 156 ++++++++++-------- 4 files changed, 101 insertions(+), 89 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c0159e9e5..883efe596 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam and scatter_genome subworkflows [[#852](https://github.com/nf-core/raredisease/pull/852)] +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [[#852](https://github.com/nf-core/raredisease/pull/852)] - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` diff --git a/main.nf b/main.nf index dbdc327ff..b3dd62543 100644 --- a/main.nf +++ b/main.nf @@ -364,8 +364,8 @@ workflow NFCORE_RAREDISEASE { // // Create chromosome bed and intervals for splitting and gathering operations // - ch_scatter_split_intervals = channel.empty() - ch_scatter_split_intervals_publish = channel.empty() + ch_scatter_split_intervals = channel.empty() + ch_scatter_genome_publish = channel.empty() if (!skip_snv_annotation) { SCATTER_GENOME ( ch_genome_dictionary, @@ -373,8 +373,8 @@ workflow NFCORE_RAREDISEASE { ch_genome_fasta, params.save_reference ) - ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals - ch_scatter_split_intervals_publish = SCATTER_GENOME.out.split_intervals_publish + ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals + ch_scatter_genome_publish = SCATTER_GENOME.out.publish } RAREDISEASE ( @@ -541,12 +541,12 @@ workflow NFCORE_RAREDISEASE { multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html qc_bam_files = RAREDISEASE.out.qc_bam_files // channel: [ val(meta), path(file) ] qc_sex_check = RAREDISEASE.out.qc_sex_check // channel: [ val(meta), path(tsv) ] - scatter_split_intervals_publish = ch_scatter_split_intervals_publish // channel: [ val(meta), path(intervals) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] - publish = RAREDISEASE.out.publish - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + publish = RAREDISEASE.out.publish + .mix(ch_scatter_genome_publish) + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -707,7 +707,6 @@ workflow { .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) fastp = NFCORE_RAREDISEASE.out.align_fastp_out ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_sex_check - processed_references = NFCORE_RAREDISEASE.out.scatter_split_intervals_publish qc_bam = NFCORE_RAREDISEASE.out.qc_bam_files subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -722,9 +721,6 @@ output { ngsbits_samplegender { path { _meta, _file -> "ngsbits_samplegender/" } } - processed_references { - path { _meta, _file -> "processed_references/" } - } qc_bam { path { _meta, _file -> "qc_bam/" } } diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index 53dfbd862..b6a258828 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -19,10 +19,14 @@ workflow SCATTER_GENOME { GATK4_SPLITINTERVALS(GAWK.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) - ch_split_intervals_publish = val_save_reference ? GATK4_SPLITINTERVALS.out.split_intervals : channel.empty() + ch_publish = channel.empty() + if (val_save_reference) { + ch_publish = GATK4_SPLITINTERVALS.out.split_intervals + .map { meta, value -> ['processed_references/', [meta, value]] } + } emit: - bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] - split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ path(interval_list) ] - split_intervals_publish = ch_split_intervals_publish // channel: [ val(meta), path(intervals) ] + bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] + split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index fade09df3..823e91d1a 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -20,12 +20,15 @@ ], "2": [ [ - { - "id": "genome" - }, + "processed_references/", [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ] ], @@ -37,6 +40,20 @@ "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "publish": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], "split_intervals": [ [ "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -44,23 +61,12 @@ [ "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "split_intervals_publish": [ - [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] ] } ], - "timestamp": "2026-05-20T17:15:58.636121358", + "timestamp": "2026-03-30T10:55:18.112519", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } }, @@ -139,30 +145,33 @@ ], "2": [ [ - { - "id": "genome" - }, + "processed_references/", [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] ] ] ], @@ -174,6 +183,38 @@ "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], + "publish": [ + [ + "processed_references/", + [ + { + "id": "genome" + }, + [ + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + ] + ] + ] + ], "split_intervals": [ [ "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" @@ -235,41 +276,12 @@ [ "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] - ], - "split_intervals_publish": [ - [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] - ] ] } ], - "timestamp": "2026-05-20T17:15:35.25891204", + "timestamp": "2026-03-17T00:19:06.789641139", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } } From 4cf1dddfebd407d9c7fe4cc5be54d7512aa576d6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 21 May 2026 10:09:51 +0200 Subject: [PATCH 713/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 883efe596..0329d2a71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [[#852](https://github.com/nf-core/raredisease/pull/852)] +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [[#853](https://github.com/nf-core/raredisease/pull/853)] - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` From f3d85b44d157e40ca278f04acc94e5ddfee21d80 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 21 May 2026 10:15:15 +0200 Subject: [PATCH 714/872] Remove . --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index b3dd62543..d3492562c 100644 --- a/main.nf +++ b/main.nf @@ -534,7 +534,7 @@ workflow NFCORE_RAREDISEASE { emit: align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] - align_genome_marked_bai. = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] + align_genome_marked_bai = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] From d7829973ae906ed2e95b45cad52c50500425ab7c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 10:17:37 +0200 Subject: [PATCH 715/872] review suggestions --- .github/CONTRIBUTING.md | 21 +++- CHANGELOG.md | 2 +- main.nf | 64 ++++++++++- subworkflows/local/qc_bam/main.nf | 69 +++++------- subworkflows/local/qc_bam/tests/main.nf.test | 108 ++++++++++++------- workflows/raredisease.nf | 50 ++++++--- 6 files changed, 212 insertions(+), 102 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 265305e8d..be1996389 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -149,8 +149,25 @@ Devcontainer specs: The pipeline uses Nextflow's `publish:` block and `output {}` API for file publishing. Each subworkflow exposes its outputs as named typed channel emits; the top-level `publish:` block in `main.nf` mixes them into destination-named entries. -- Emit every publishable output as a named typed channel — no `ch_publish` tuple wrapping. -- Group outputs that share the same destination directory under **one** `publish:` entry and **one** `output {}` entry in `main.nf`; mix them together with `.mix()`. +- Emit every publishable output as its own named typed channel — one emit per file type, no `ch_publish` tuple wrapping and no grouped mix inside the subworkflow. +- In `main.nf`, mix all channels that share a destination into **one** `publish:` entry and **one** `output {}` entry. The mixing belongs at the routing layer, not inside the subworkflow. +- Channels consumed by downstream processes (e.g. MultiQC) and also published are emitted once; the caller wires the same channel to both consumers. + +#### Emit naming convention + +Use `_` (lowercase, underscored) inside the subworkflow's `emit:` block: + +- Use the **alias name** as the prefix when a process is imported with `as` — the alias already encodes the distinction (e.g. `PICARD_COLLECTWGSMETRICS as PICARD_COLLECTWGSMETRICS_WG` → prefix `picard_collectwgsmetrics_wg`). +- Append the **module's emit name** verbatim. +- Drop obvious redundancy when the emit name exactly repeats a word already in the process/alias name (e.g. `sentieon_wgsmetrics_wg_wgs_metrics` → `sentieon_wgsmetrics_wg_metrics`). Do not rename to describe the file format — always use the emit name. +- For `VERIFYBAMID_VERIFYBAMID2`, drop the repetition: use prefix `verifybamid_`. + +| Layer | Convention | Example | +|---|---|---| +| Subworkflow `emit:` | `_` | `mosdepth_global_txt` | +| `raredisease.nf` variable | `ch__` | `ch_qc_bam_mosdepth_global_txt` | +| `NFCORE_RAREDISEASE` emit | `_` | `qc_bam_mosdepth_global_txt` | +| `publish:` entry | one entry per destination, mixing all channels for that destination | `qc_bam = NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt.mix(...)` | > **Note:** Some subworkflows still use the legacy `ch_publish`/`subworkflow_results` pattern and are being migrated incrementally. Until a subworkflow is migrated, follow the existing pattern for that subworkflow so it continues to publish correctly via `subworkflow_results`. diff --git a/CHANGELOG.md b/CHANGELOG.md index 0329d2a71..5e7a8fd5d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [[#853](https://github.com/nf-core/raredisease/pull/853)] +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` diff --git a/main.nf b/main.nf index d3492562c..a803c290d 100644 --- a/main.nf +++ b/main.nf @@ -538,9 +538,36 @@ workflow NFCORE_RAREDISEASE { align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] - multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - qc_bam_files = RAREDISEASE.out.qc_bam_files // channel: [ val(meta), path(file) ] - qc_sex_check = RAREDISEASE.out.qc_sex_check // channel: [ val(meta), path(tsv) ] + multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + qc_bam_chromograph_cov_plots = RAREDISEASE.out.qc_bam_chromograph_cov_plots // channel: [ val(meta), path(png) ] + qc_bam_mosdepth_global_txt = RAREDISEASE.out.qc_bam_mosdepth_global_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_per_base_bed = RAREDISEASE.out.qc_bam_mosdepth_per_base_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_per_base_csi = RAREDISEASE.out.qc_bam_mosdepth_per_base_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_per_base_d4 = RAREDISEASE.out.qc_bam_mosdepth_per_base_d4 // channel: [ val(meta), path(d4) ] + qc_bam_mosdepth_quantized_bed = RAREDISEASE.out.qc_bam_mosdepth_quantized_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_quantized_csi = RAREDISEASE.out.qc_bam_mosdepth_quantized_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_bed = RAREDISEASE.out.qc_bam_mosdepth_regions_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_regions_csi = RAREDISEASE.out.qc_bam_mosdepth_regions_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_txt = RAREDISEASE.out.qc_bam_mosdepth_regions_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_summary_txt = RAREDISEASE.out.qc_bam_mosdepth_summary_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_thresholds_bed = RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_thresholds_csi = RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi // channel: [ val(meta), path(csi) ] + qc_bam_ngsbits_samplegender_tsv = RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv // channel: [ val(meta), path(tsv) ] + qc_bam_picard_collecthsmetrics_metrics = RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_metrics = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_pdf = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf // channel: [ val(meta), path(pdf) ] + qc_bam_sambamba_depth_bed = RAREDISEASE.out.qc_bam_sambamba_depth_bed // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_cov = RAREDISEASE.out.qc_bam_tiddit_cov_cov // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_wig = RAREDISEASE.out.qc_bam_tiddit_cov_wig // channel: [ val(meta), path(wig) ] + qc_bam_ucsc_wigtobigwig_bw = RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + qc_bam_verifybamid_ancestry = RAREDISEASE.out.qc_bam_verifybamid_ancestry // channel: [ val(meta), path(ancestry) ] + qc_bam_verifybamid_bed = RAREDISEASE.out.qc_bam_verifybamid_bed // channel: [ val(meta), path(bed) ] + qc_bam_verifybamid_log = RAREDISEASE.out.qc_bam_verifybamid_log // channel: [ val(meta), path(log) ] + qc_bam_verifybamid_mu = RAREDISEASE.out.qc_bam_verifybamid_mu // channel: [ val(meta), path(mu) ] + qc_bam_verifybamid_self_sm = RAREDISEASE.out.qc_bam_verifybamid_self_sm // channel: [ val(meta), path(selfSM) ] + qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] + qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] + qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish @@ -706,8 +733,35 @@ workflow { .mix(NFCORE_RAREDISEASE.out.subsample_mt_bam) .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) fastp = NFCORE_RAREDISEASE.out.align_fastp_out - ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_sex_check - qc_bam = NFCORE_RAREDISEASE.out.qc_bam_files + ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv + qc_bam = NFCORE_RAREDISEASE.out.qc_bam_chromograph_cov_plots.transpose() + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_d4) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_summary_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics.transpose()) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf.transpose()) + .mix(NFCORE_RAREDISEASE.out.qc_bam_sambamba_depth_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_cov) + .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_wig) + .mix(NFCORE_RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ancestry) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_log) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_mu) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_self_sm) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) + .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) + .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) subworkflow_results = NFCORE_RAREDISEASE.out.publish } diff --git a/subworkflows/local/qc_bam/main.nf b/subworkflows/local/qc_bam/main.nf index 507ca87bc..130a39bc6 100644 --- a/subworkflows/local/qc_bam/main.nf +++ b/subworkflows/local/qc_bam/main.nf @@ -89,45 +89,34 @@ workflow QC_BAM { ch_svd_in = ch_svd_ud.combine(ch_svd_mu).combine(ch_svd_bed).collect() VERIFYBAMID_VERIFYBAMID2(ch_bam_bai, ch_svd_in, [], ch_genome_fasta.map {_meta, fasta-> fasta}) - ch_qc_bam_files = PICARD_COLLECTMULTIPLEMETRICS.out.metrics.transpose() - .mix(PICARD_COLLECTMULTIPLEMETRICS.out.pdf.transpose()) - .mix(TIDDIT_COV.out.wig) - .mix(TIDDIT_COV.out.cov) - .mix(UCSC_WIGTOBIGWIG.out.bw) - .mix(CHROMOGRAPH_COV.out.plots.transpose()) - .mix(MOSDEPTH.out.global_txt) - .mix(MOSDEPTH.out.summary_txt) - .mix(MOSDEPTH.out.per_base_d4) - .mix(MOSDEPTH.out.regions_txt) - .mix(MOSDEPTH.out.per_base_bed) - .mix(MOSDEPTH.out.per_base_csi) - .mix(MOSDEPTH.out.regions_bed) - .mix(MOSDEPTH.out.regions_csi) - .mix(MOSDEPTH.out.quantized_bed) - .mix(MOSDEPTH.out.quantized_csi) - .mix(MOSDEPTH.out.thresholds_bed) - .mix(MOSDEPTH.out.thresholds_csi) - .mix(SAMBAMBA_DEPTH.out.bed) - .mix(VERIFYBAMID_VERIFYBAMID2.out.self_sm) - .mix(VERIFYBAMID_VERIFYBAMID2.out.log) - .mix(VERIFYBAMID_VERIFYBAMID2.out.ud) - .mix(VERIFYBAMID_VERIFYBAMID2.out.bed) - .mix(VERIFYBAMID_VERIFYBAMID2.out.mu) - .mix(VERIFYBAMID_VERIFYBAMID2.out.ancestry) - .mix(ch_hsmetrics) - .mix(ch_cov) - .mix(ch_cov_y) - emit: - bigwig = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] - cov = ch_cov // channel: [ val(meta), path(metrics) ] - cov_y = ch_cov_y // channel: [ val(meta), path(metrics) ] - d4 = MOSDEPTH.out.per_base_d4 // channel: [ val(meta), path(d4) ] - global_dist = MOSDEPTH.out.global_txt // channel: [ val(meta), path(txt) ] - hs_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] - multiple_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] - qc_bam_files = ch_qc_bam_files // channel: [ val(meta), path(file) ] - self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] - sex_check = ch_ngsbits // channel: [ val(meta), path(tsv) ] - tiddit_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] + chromograph_cov_plots = CHROMOGRAPH_COV.out.plots // channel: [ val(meta), path(png) ] + mosdepth_global_txt = MOSDEPTH.out.global_txt // channel: [ val(meta), path(txt) ] + mosdepth_per_base_bed = MOSDEPTH.out.per_base_bed // channel: [ val(meta), path(bed.gz) ] + mosdepth_per_base_csi = MOSDEPTH.out.per_base_csi // channel: [ val(meta), path(csi) ] + mosdepth_per_base_d4 = MOSDEPTH.out.per_base_d4 // channel: [ val(meta), path(d4) ] + mosdepth_quantized_bed = MOSDEPTH.out.quantized_bed // channel: [ val(meta), path(bed.gz) ] + mosdepth_quantized_csi = MOSDEPTH.out.quantized_csi // channel: [ val(meta), path(csi) ] + mosdepth_regions_bed = MOSDEPTH.out.regions_bed // channel: [ val(meta), path(bed.gz) ] + mosdepth_regions_csi = MOSDEPTH.out.regions_csi // channel: [ val(meta), path(csi) ] + mosdepth_regions_txt = MOSDEPTH.out.regions_txt // channel: [ val(meta), path(txt) ] + mosdepth_summary_txt = MOSDEPTH.out.summary_txt // channel: [ val(meta), path(txt) ] + mosdepth_thresholds_bed = MOSDEPTH.out.thresholds_bed // channel: [ val(meta), path(bed.gz) ] + mosdepth_thresholds_csi = MOSDEPTH.out.thresholds_csi // channel: [ val(meta), path(csi) ] + ngsbits_samplegender_tsv = ch_ngsbits // channel: [ val(meta), path(tsv) ] + picard_collecthsmetrics_metrics = ch_hsmetrics // channel: [ val(meta), path(metrics) ] + picard_collectmultiplemetrics_metrics = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), path(metrics) ] + picard_collectmultiplemetrics_pdf = PICARD_COLLECTMULTIPLEMETRICS.out.pdf // channel: [ val(meta), path(pdf) ] + sambamba_depth_bed = SAMBAMBA_DEPTH.out.bed // channel: [ val(meta), path(bed) ] + tiddit_cov_cov = TIDDIT_COV.out.cov // channel: [ val(meta), path(bed) ] + tiddit_cov_wig = TIDDIT_COV.out.wig // channel: [ val(meta), path(wig) ] + ucsc_wigtobigwig_bw = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] + verifybamid_ancestry = VERIFYBAMID_VERIFYBAMID2.out.ancestry // channel: [ val(meta), path(ancestry) ] + verifybamid_bed = VERIFYBAMID_VERIFYBAMID2.out.bed // channel: [ val(meta), path(bed) ] + verifybamid_log = VERIFYBAMID_VERIFYBAMID2.out.log // channel: [ val(meta), path(log) ] + verifybamid_mu = VERIFYBAMID_VERIFYBAMID2.out.mu // channel: [ val(meta), path(mu) ] + verifybamid_self_sm = VERIFYBAMID_VERIFYBAMID2.out.self_sm // channel: [ val(meta), path(selfSM) ] + verifybamid_ud = VERIFYBAMID_VERIFYBAMID2.out.ud // channel: [ val(meta), path(ud) ] + wgsmetrics_wg = ch_cov // channel: [ val(meta), path(metrics) ] + wgsmetrics_y = ch_cov_y // channel: [ val(meta), path(metrics) ] } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 1f9c5552d..6c1f66e09 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -62,26 +62,40 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( - workflow.out.multiple_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, - workflow.out.hs_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, - workflow.out.d4 - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.cov - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.cov_y - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.tiddit_wig - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.bigwig - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.global_dist - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.self_sm - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.qc_bam_files - .collect { meta, f -> file(f).name }.sort() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.picard_collecthsmetrics_metrics + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.mosdepth_global_txt + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_summary_txt + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_bed + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_csi + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_d4 + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.wgsmetrics_wg + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.wgsmetrics_y + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.tiddit_cov_wig + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.tiddit_cov_cov + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.ucsc_wigtobigwig_bw + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.chromograph_cov_plots + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.sambamba_depth_bed + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.verifybamid_self_sm + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.ngsbits_samplegender_tsv + .collect { meta, files -> [meta, file(files).name] } ).match() } ) @@ -129,26 +143,40 @@ nextflow_workflow { assertAll ( { assert workflow.success }, { assert snapshot( - workflow.out.multiple_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, - workflow.out.hs_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file(it).name }.sort() : file(files).name] }, - workflow.out.d4 - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.cov - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.cov_y - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.tiddit_wig - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.bigwig - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.global_dist - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.self_sm - .collect { meta, f -> [meta, file(f).name] }, - workflow.out.qc_bam_files - .collect { meta, f -> file(f).name }.sort() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.picard_collecthsmetrics_metrics + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.mosdepth_global_txt + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_summary_txt + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_bed + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_csi + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.mosdepth_per_base_d4 + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.wgsmetrics_wg + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.wgsmetrics_y + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.tiddit_cov_wig + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.tiddit_cov_cov + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.ucsc_wigtobigwig_bw + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.chromograph_cov_plots + .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + workflow.out.sambamba_depth_bed + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.verifybamid_self_sm + .collect { meta, files -> [meta, file(files).name] }, + workflow.out.ngsbits_samplegender_tsv + .collect { meta, files -> [meta, file(files).name] } ).match() } ) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 8f1dfac5d..0fc7f9728 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -241,8 +241,6 @@ workflow RAREDISEASE { ch_align_markdup_metrics = channel.empty() ch_subsample_mt_bam = channel.empty() ch_subsample_mt_bai = channel.empty() - ch_qc_bam_files = channel.empty() - ch_qc_sex_check = channel.empty() ch_call_snv_publish = channel.empty() ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() @@ -379,9 +377,6 @@ workflow RAREDISEASE { val_target_bed, skip_ngsbits ) - ch_qc_bam_files = QC_BAM.out.qc_bam_files - ch_qc_sex_check = QC_BAM.out.sex_check - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RENAME ALIGNMENT FILES FOR SMNCOPYNUMBERCALLER & REPEATCALLING @@ -984,12 +979,12 @@ workflow RAREDISEASE { } ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{_meta, reports -> reports}.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.markdup_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.global_dist.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.cov.map{_meta, reports -> reports}.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.ngsbits_samplegender_tsv.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.picard_collectmultiplemetrics_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.picard_collecthsmetrics_metrics.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.mosdepth_global_txt.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.wgsmetrics_wg.map{_meta, reports -> reports}.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.verifybamid_self_sm.map{_meta, reports -> reports}.collect().ifEmpty([])) if (!skip_peddy) { ch_multiqc_files = ch_multiqc_files.mix(PEDDY.out.ped.map{_meta, reports -> reports}.collect().ifEmpty([])) @@ -1027,9 +1022,36 @@ workflow RAREDISEASE { align_genome_marked_cram = ch_align_genome_marked_cram // channel: [ val(meta), path(cram) ] align_genome_marked_crai = ch_align_genome_marked_crai // channel: [ val(meta), path(crai) ] align_markdup_metrics = ch_align_markdup_metrics // channel: [ val(meta), path(metrics) ] - multiqc_report = MULTIQC.out.report.map { _meta, report -> report }.toList() - qc_bam_files = ch_qc_bam_files // channel: [ val(meta), path(file) ] - qc_sex_check = ch_qc_sex_check // channel: [ val(meta), path(tsv) ] + multiqc_report = MULTIQC.out.report.map { _meta, report -> report }.toList() + qc_bam_chromograph_cov_plots = QC_BAM.out.chromograph_cov_plots // channel: [ val(meta), path(png) ] + qc_bam_mosdepth_global_txt = QC_BAM.out.mosdepth_global_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_per_base_bed = QC_BAM.out.mosdepth_per_base_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_per_base_csi = QC_BAM.out.mosdepth_per_base_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_per_base_d4 = QC_BAM.out.mosdepth_per_base_d4 // channel: [ val(meta), path(d4) ] + qc_bam_mosdepth_quantized_bed = QC_BAM.out.mosdepth_quantized_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_quantized_csi = QC_BAM.out.mosdepth_quantized_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_bed = QC_BAM.out.mosdepth_regions_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_regions_csi = QC_BAM.out.mosdepth_regions_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_txt = QC_BAM.out.mosdepth_regions_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_summary_txt = QC_BAM.out.mosdepth_summary_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_thresholds_bed = QC_BAM.out.mosdepth_thresholds_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_thresholds_csi = QC_BAM.out.mosdepth_thresholds_csi // channel: [ val(meta), path(csi) ] + qc_bam_ngsbits_samplegender_tsv = QC_BAM.out.ngsbits_samplegender_tsv // channel: [ val(meta), path(tsv) ] + qc_bam_picard_collecthsmetrics_metrics = QC_BAM.out.picard_collecthsmetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_metrics = QC_BAM.out.picard_collectmultiplemetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_pdf = QC_BAM.out.picard_collectmultiplemetrics_pdf // channel: [ val(meta), path(pdf) ] + qc_bam_sambamba_depth_bed = QC_BAM.out.sambamba_depth_bed // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_cov = QC_BAM.out.tiddit_cov_cov // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_wig = QC_BAM.out.tiddit_cov_wig // channel: [ val(meta), path(wig) ] + qc_bam_ucsc_wigtobigwig_bw = QC_BAM.out.ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + qc_bam_verifybamid_ancestry = QC_BAM.out.verifybamid_ancestry // channel: [ val(meta), path(ancestry) ] + qc_bam_verifybamid_bed = QC_BAM.out.verifybamid_bed // channel: [ val(meta), path(bed) ] + qc_bam_verifybamid_log = QC_BAM.out.verifybamid_log // channel: [ val(meta), path(log) ] + qc_bam_verifybamid_mu = QC_BAM.out.verifybamid_mu // channel: [ val(meta), path(mu) ] + qc_bam_verifybamid_self_sm = QC_BAM.out.verifybamid_self_sm // channel: [ val(meta), path(selfSM) ] + qc_bam_verifybamid_ud = QC_BAM.out.verifybamid_ud // channel: [ val(meta), path(ud) ] + qc_bam_wgsmetrics_wg = QC_BAM.out.wgsmetrics_wg // channel: [ val(meta), path(metrics) ] + qc_bam_wgsmetrics_y = QC_BAM.out.wgsmetrics_y // channel: [ val(meta), path(metrics) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions From 8c1b821cf968460f0684307c600e46606ec8342e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 10:34:59 +0200 Subject: [PATCH 716/872] update test --- subworkflows/local/qc_bam/tests/main.nf.test | 68 ++++++++++---------- 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 6c1f66e09..04c62f4be 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -63,39 +63,39 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.picard_collectmultiplemetrics_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.picard_collectmultiplemetrics_pdf - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.picard_collecthsmetrics_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.mosdepth_global_txt - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_summary_txt - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_bed - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_csi - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_d4 - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.wgsmetrics_wg - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.wgsmetrics_y - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.tiddit_cov_wig - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.tiddit_cov_cov - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.ucsc_wigtobigwig_bw - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.chromograph_cov_plots - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.sambamba_depth_bed - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.verifybamid_self_sm - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.ngsbits_samplegender_tsv - .collect { meta, files -> [meta, file(files).name] } + .collect { _meta, files -> file(files).name } ).match() } ) @@ -144,39 +144,39 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( workflow.out.picard_collectmultiplemetrics_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.picard_collectmultiplemetrics_pdf - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.picard_collecthsmetrics_metrics - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.mosdepth_global_txt - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_summary_txt - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_bed - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_csi - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.mosdepth_per_base_d4 - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.wgsmetrics_wg - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.wgsmetrics_y - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.tiddit_cov_wig - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.tiddit_cov_cov - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.ucsc_wigtobigwig_bw - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.chromograph_cov_plots - .collect { meta, files -> [meta, files instanceof List ? files.collect { file_path -> file(file_path).name }.sort() : file(files).name] }, + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, workflow.out.sambamba_depth_bed - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.verifybamid_self_sm - .collect { meta, files -> [meta, file(files).name] }, + .collect { _meta, files -> file(files).name }, workflow.out.ngsbits_samplegender_tsv - .collect { meta, files -> [meta, file(files).name] } + .collect { _meta, files -> file(files).name } ).match() } ) From 8205abbd65356db084b518d69fe59a361e2f6349 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 10:41:21 +0200 Subject: [PATCH 717/872] update snapshots --- .../local/qc_bam/tests/main.nf.test.snap | 402 ++++++------------ 1 file changed, 122 insertions(+), 280 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 35ef7f3e9..befbe1f79 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -3,174 +3,95 @@ "content": [ [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ] ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" ] ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], [ ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" - ] + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig" - ] + "earlycasualcaiman_tidditcov.wig" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw" - ] + + ], + [ + "earlycasualcaiman_tidditcov.bw" ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png" ] ], [ ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov_1.png", - "earlycasualcaiman_tidditcov_10.png", - "earlycasualcaiman_tidditcov_11.png", - "earlycasualcaiman_tidditcov_12.png", - "earlycasualcaiman_tidditcov_13.png", - "earlycasualcaiman_tidditcov_14.png", - "earlycasualcaiman_tidditcov_15.png", - "earlycasualcaiman_tidditcov_16.png", - "earlycasualcaiman_tidditcov_17.png", - "earlycasualcaiman_tidditcov_18.png", - "earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + + ], + [ + ] ], - "timestamp": "2026-05-20T17:37:41.846430552", + "timestamp": "2026-05-25T10:36:52.274714899", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -180,174 +101,95 @@ "content": [ [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" - ] + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ] ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" ] ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], [ ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_wgsmetrics.txt" - ] + "earlycasualcaiman_wgsmetrics.txt" ], [ ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig" - ] + "earlycasualcaiman_tidditcov.wig" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw" - ] + + ], + [ + "earlycasualcaiman_tidditcov.bw" ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png" ] ], [ ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov_1.png", - "earlycasualcaiman_tidditcov_10.png", - "earlycasualcaiman_tidditcov_11.png", - "earlycasualcaiman_tidditcov_12.png", - "earlycasualcaiman_tidditcov_13.png", - "earlycasualcaiman_tidditcov_14.png", - "earlycasualcaiman_tidditcov_15.png", - "earlycasualcaiman_tidditcov_16.png", - "earlycasualcaiman_tidditcov_17.png", - "earlycasualcaiman_tidditcov_18.png", - "earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.txt" + + ], + [ + ] ], - "timestamp": "2026-05-20T17:43:21.933661098", + "timestamp": "2026-05-25T10:37:31.154163467", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 89702f4a55fbfa6de23ed563e0913e728bbb442c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 May 2026 08:44:29 +0000 Subject: [PATCH 718/872] [automated] Fix code linting --- .github/CONTRIBUTING.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index be1996389..6f0b42331 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -162,12 +162,12 @@ Use `_` (lowercase, underscored) inside the subwork - Drop obvious redundancy when the emit name exactly repeats a word already in the process/alias name (e.g. `sentieon_wgsmetrics_wg_wgs_metrics` → `sentieon_wgsmetrics_wg_metrics`). Do not rename to describe the file format — always use the emit name. - For `VERIFYBAMID_VERIFYBAMID2`, drop the repetition: use prefix `verifybamid_`. -| Layer | Convention | Example | -|---|---|---| -| Subworkflow `emit:` | `_` | `mosdepth_global_txt` | -| `raredisease.nf` variable | `ch__` | `ch_qc_bam_mosdepth_global_txt` | -| `NFCORE_RAREDISEASE` emit | `_` | `qc_bam_mosdepth_global_txt` | -| `publish:` entry | one entry per destination, mixing all channels for that destination | `qc_bam = NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt.mix(...)` | +| Layer | Convention | Example | +| ------------------------- | ------------------------------------------------------------------- | --------------------------------------------------------------------- | +| Subworkflow `emit:` | `_` | `mosdepth_global_txt` | +| `raredisease.nf` variable | `ch__` | `ch_qc_bam_mosdepth_global_txt` | +| `NFCORE_RAREDISEASE` emit | `_` | `qc_bam_mosdepth_global_txt` | +| `publish:` entry | one entry per destination, mixing all channels for that destination | `qc_bam = NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt.mix(...)` | > **Note:** Some subworkflows still use the legacy `ch_publish`/`subworkflow_results` pattern and are being migrated incrementally. Until a subworkflow is migrated, follow the existing pattern for that subworkflow so it continues to publish correctly via `subworkflow_results`. From d8495e7405c8933014c9e0cd6e61f964301bf7e4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 12:28:29 +0200 Subject: [PATCH 719/872] fix(postprocess_mt_calls): split multiallelics after bcftools merge --- CHANGELOG.md | 6 ++++++ conf/modules/postprocess_MT_calls.config | 7 ++++++- subworkflows/local/postprocess_MT_calls/main.nf | 8 +++++++- 3 files changed, 19 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f37c1d751..2d049cf01 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 3.0.1 - Mario-patch [2026-05-25] + +### `Fixed` + +- Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#854](https://github.com/nf-core/raredisease/pull/854) + ## 3.0.0 - Mario [2026-05-12] ### `Added` diff --git a/conf/modules/postprocess_MT_calls.config b/conf/modules/postprocess_MT_calls.config index f54c383e6..4bd28abf3 100644 --- a/conf/modules/postprocess_MT_calls.config +++ b/conf/modules/postprocess_MT_calls.config @@ -35,8 +35,13 @@ process { ext.prefix = { "${meta.id}_split_rmdup" } } + withName: '.*POSTPROCESS_MT_CALLS:SPLIT_MULTIALLELICS_POSTMERGE_MT' { + ext.args = '--output-type z --multiallelics -both' + ext.prefix = { "${meta.id}_split_rmdup_merged_split" } + } + withName: '.*POSTPROCESS_MT_CALLS:BCFTOOLS_MERGE_MT' { - ext.args = '--output-type z' + ext.args = '--output-type z --write-index=tbi' ext.prefix = { "${meta.id}_split_rmdup_merged" } } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 758e9ec8d..de88e029a 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -7,6 +7,7 @@ include { BCFTOOLS_ANNOTATE } from '../../.. include { BCFTOOLS_MERGE as BCFTOOLS_MERGE_MT } from '../../../modules/nf-core/bcftools/merge/main' include { BCFTOOLS_NORM as REMOVE_DUPLICATES_MT } from '../../../modules/nf-core/bcftools/norm/main' include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_MT } from '../../../modules/nf-core/bcftools/norm/main' +include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_POSTMERGE_MT } from '../../../modules/nf-core/bcftools/norm/main' include { GATK4_MERGEVCFS as GATK4_MERGEVCFS_LIFT_UNLIFT_MT } from '../../../modules/nf-core/gatk4/mergevcfs/main' include { GATK4_VARIANTFILTRATION as GATK4_VARIANTFILTRATION_MT } from '../../../modules/nf-core/gatk4/variantfiltration/main' include { PICARD_LIFTOVERVCF } from '../../../modules/nf-core/picard/liftovervcf/main' @@ -94,7 +95,12 @@ workflow POSTPROCESS_MT_CALLS { ch_genome_fasta.join(ch_genome_fai, failOnMismatch:true, failOnDuplicate:true).collect() ) - BCFTOOLS_MERGE_MT.out.vcf + SPLIT_MULTIALLELICS_POSTMERGE_MT( + BCFTOOLS_MERGE_MT.out.vcf.join(BCFTOOLS_MERGE_MT.out.index, failOnMismatch:true, failOnDuplicate:true).collect(), + ch_genome_fasta + ) + + SPLIT_MULTIALLELICS_POSTMERGE_MT.out.vcf .mix(ch_case_vcf.single) .set { ch_addfoundintag_in } From 2f59757c88e3ac2ba185d6ff72e16bfba49cedd1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 12:29:56 +0200 Subject: [PATCH 720/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d049cf01..231aa70f1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#854](https://github.com/nf-core/raredisease/pull/854) +- Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#855](https://github.com/nf-core/raredisease/pull/855) ## 3.0.0 - Mario [2026-05-12] From 685dd904594b64a069e329177806b9919351db23 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 25 May 2026 15:55:05 +0200 Subject: [PATCH 721/872] reports as tabs and include customer ID in report --- bin/saltshaker_to_html.py | 95 +++++++++++++++++++ .../local/saltshaker_to_html/environment.yml | 5 + modules/local/saltshaker_to_html/main.nf | 32 +++---- .../local/call_structural_variants/main.nf | 2 + subworkflows/local/call_sv_MT/main.nf | 52 ++++++---- workflows/raredisease.nf | 1 + 6 files changed, 149 insertions(+), 38 deletions(-) create mode 100755 bin/saltshaker_to_html.py create mode 100644 modules/local/saltshaker_to_html/environment.yml diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py new file mode 100755 index 000000000..f65a8e288 --- /dev/null +++ b/bin/saltshaker_to_html.py @@ -0,0 +1,95 @@ +#!/usr/bin/env python3 +import re +import typer +from pathlib import Path +from typing import List, Optional + +CSS = """.tabcontent { display: none; } +.tabcontent.active { display: block; } +.tablinks { padding: 12px 20px; cursor: pointer; background-color: #f1f1f1; border: 1px solid #ccc; } +.tablinks.active { background-color: #4CAF50; color: white; } +.tablinks:hover { background-color: #ddd; } +""" + +JS = """ +function openTab(evt, tabName) { + var i, tabcontent, tablinks; + tabcontent = document.getElementsByClassName("tabcontent"); + for (i = 0; i < tabcontent.length; i++) { + tabcontent[i].classList.remove("active"); + } + tablinks = document.getElementsByClassName("tablinks"); + for (i = 0; i < tablinks.length; i++) { + tablinks[i].classList.remove("active"); + } + document.getElementById(tabName).classList.add("active"); + evt.currentTarget.classList.add("active"); +} +document.getElementsByClassName("tablinks")[0].click(); +""" + +def txt_to_html(txt_file): + with open(txt_file) as tf: + content = tf.read() + html_content = re.sub(r'\\n', '
    ', content) + return html_content + +def create_tab_button(sample_id): + return f'''\n''' + +def create_tab_content(sample_id, txt_file): + html_content = txt_to_html(txt_file) + return f'''
    +\t

    {sample_id}

    +\t
    {html_content}
    +
    +''' + +app = typer.Typer() + +@app.command() +def main( + input: List[Path] = typer.Option( + ..., + "--input", + exists=True, + file_okay=True, + dir_okay=False, + help="Path to input .txt file (can be multiple)" + ), + sample: List[str] = typer.Option( + ..., + "--sample", + help="Sample ID(s) corresponding to the input .txt file(s)" + ), + output: Path = typer.Option( + ..., + "--output", + help="Path to output .html file" + ) +): + tab_buttons = ''.join(create_tab_button(sid) for sid in sample) + tab_contents = ''.join(create_tab_content(sid, inp) for inp, sid in zip(input, sample)) + + html = f""" + + + + +
    +{tab_buttons} +
    +{tab_contents} + + +""" + + with open(output, 'w') as f: + f.write(html) + +if __name__ == "__main__": + app() diff --git a/modules/local/saltshaker_to_html/environment.yml b/modules/local/saltshaker_to_html/environment.yml new file mode 100644 index 000000000..046b3426c --- /dev/null +++ b/modules/local/saltshaker_to_html/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::typer=0.25.1 diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 9213236ef..068eccb1d 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -1,28 +1,26 @@ process SALTSHAKER_TO_HTML { - tag "$meta.id" + tag "$meta.caseid" label "process_low" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a2/a23c958d5a0439419f82069df6217c542f6ab13816f9808ed73307dff1efe227/data': + 'community.wave.seqera.io/library/typer:0.25.1--25ea8a9ce34456a3' }" + input: - tuple val(meta), path(classify) + tuple val(meta), path(files_in, stageAs: 'to_combine/*', arity: '1..*'), val(ids) output: - tuple val(meta), path("*.html"), emit: classify_html + tuple val(meta), path("*.saltshaker_classify.html"), emit: classify_html script: + def prefix = task.ext.prefix ?: "${meta.caseid}" + def args = task.ext.args ?: "" """ - python3 << 'EOF' - import re - def saltshaker_txt_to_html(txt_file): - with open(txt_file) as f: - content = f.read() - html_content = re.sub(r'\\n', '
    ', content) - return html_content - - html = saltshaker_txt_to_html("${classify}") - with open("${classify.baseName}.saltshaker_classify.html", 'w') as f: - f.write('') - f.write(f'
    {html}
    ') - f.write('') - EOF + saltshaker_to_html.py \ + $args \ + --input ${files_in.join(' --input ')} \ + --sample ${ids.join(' --sample ')} \ + --output ${prefix}.saltshaker_classify.html """ } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index b5407b11e..6c357c8ac 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -32,6 +32,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_sample_id_map // channel: [optional] [val(id), val(id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] @@ -97,6 +98,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_mt_fasta, ch_mt_lastdb, ch_reads, + ch_sample_id_map, ch_subdepth, ch_svcaller_priority, ch_mitosalt_config, diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f636788ff..4b8452f9d 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -3,17 +3,17 @@ // Also detects the number of discordant pairs using the mitodel script. // -include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' -include { MITOSALT } from '../../../modules/local/mitosalt/main' -include { MT_DELETION } from '../../../modules/local/mt_deletion_script' -include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' -include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' -include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' -include { FIND_CONCATENATE } from '../../../modules/nf-core/find/concatenate/main' -include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' -include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' -include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' -include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' +include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' +include { MITOSALT } from '../../../modules/local/mitosalt/main' +include { MT_DELETION } from '../../../modules/local/mt_deletion_script' +include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' +include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' +include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' +include { FIND_CONCATENATE } from '../../../modules/nf-core/find/concatenate/main' +include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' +include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' +include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' +include { SVDB_MERGE } from '../../../modules/nf-core/svdb/merge/main' workflow CALL_SV_MT { take: @@ -27,6 +27,7 @@ workflow CALL_SV_MT { ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] + ch_sample_id_map // channel: [optional] [val(id), val(id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] @@ -42,7 +43,6 @@ workflow CALL_SV_MT { main: ch_saltshaker_html = channel.empty() - ch_saltshaker_txt = channel.empty() ch_saltshaker_vcf = channel.empty() ch_saltshaker_plot = channel.empty() @@ -123,20 +123,30 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + // Create case-level channel ch_saltshaker_html_input, consisting of all saltshaker txt reports and all + // customer IDs (or sample ID if no customer ID) so individual reports have identifers in the final HTML. SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> - return [['id': meta.case_id], txt] - } - .groupTuple() - .set { ch_saltshaker_txts } + def sample_meta = ['id':meta.sample] + def case_meta = ['caseid':meta.case_id] + return [sample_meta, case_meta, txt] + } + .join(ch_sample_id_map, remainder: true) + .branch { sample_meta, case_meta, txt, samplemap -> + id: samplemap.equals(null) + return [case_meta, txt, sample_meta.id] + custid: !(samplemap.equals(null)) + return [case_meta, txt, samplemap] + } + .set { ch_for_mix } - FIND_CONCATENATE( - ch_saltshaker_txts - ) - ch_saltshaker_txt = FIND_CONCATENATE.out.file_out + channel.empty() + .mix(ch_for_mix.id, ch_for_mix.custid) + .groupTuple() + .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( - ch_saltshaker_txt + ch_saltshaker_html_input ) ch_saltshaker_html = SALTSHAKER_TO_HTML.out.classify_html diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ec4f074c3..ba9b08a63 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -658,6 +658,7 @@ workflow RAREDISEASE { ch_ploidy_model, ch_readcount_intervals, ch_input_fastqs, + ch_sample_id_map, ch_subdepth, ch_svcaller_priority, ch_target_bed, From 0e41aa09997a6d2a821ffe4d329d8f00fd5167ad Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 25 May 2026 16:22:25 +0200 Subject: [PATCH 722/872] update snaps --- tests/default.nf.test.snap | 13 ++++--------- tests/test_singleton.nf.test.snap | 14 ++++---------- 2 files changed, 8 insertions(+), 19 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 062aef247..9e1a3388e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -165,11 +165,6 @@ "FASTQC": { "fastqc": "0.12.1" }, - "FIND_CONCATENATE": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -1102,7 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", + "justhusky.saltshaker_classify.html:md5,6007a3aa07cc778bf71cb34f054426da", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1334,10 +1329,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "timestamp": "2026-05-25T16:07:46.556250899", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-05-18T15:03:40.296274957" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f2d6a79d5..67a9d4588 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 356, + 355, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -157,11 +157,6 @@ "FASTQC": { "fastqc": "0.12.1" }, - "FIND_CONCATENATE": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -661,11 +656,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-18T09:17:23.560290017", + "timestamp": "2026-05-25T16:21:58.01161601", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-05-06T10:54:12.680904463" + } } } \ No newline at end of file From 1dd4f7ff26513eb537cace2511f7af86e028ceb6 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 25 May 2026 16:27:31 +0200 Subject: [PATCH 723/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9d58bcac5..ff7f756b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## 3.1.0 - Luigi [XXXX-XX-XX] ### `Added` +- Update saltshaker classification reporting by adding customer ID to samples' reports and displaying them as tabs in html [#856](https://github.com/nf-core/raredisease/pull/856) ### `Changed` From afc7740ffec78ee6dbf909fdb062f3110cdc1c10 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 25 May 2026 16:29:00 +0200 Subject: [PATCH 724/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ff7f756b7..ead292470 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## 3.1.0 - Luigi [XXXX-XX-XX] ### `Added` + - Update saltshaker classification reporting by adding customer ID to samples' reports and displaying them as tabs in html [#856](https://github.com/nf-core/raredisease/pull/856) ### `Changed` From fd680bc1690c9ed7e1fe32d3f3bcf2305be0cb1d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 25 May 2026 23:42:55 +0200 Subject: [PATCH 725/872] update scatter genome --- CHANGELOG.md | 1 + conf/modules/scatter_genome.config | 2 +- main.nf | 101 +++--- .../local/annotate_genome_snvs/main.nf | 10 +- subworkflows/local/scatter_genome/main.nf | 20 +- .../local/scatter_genome/tests/main.nf.test | 2 - .../scatter_genome/tests/main.nf.test.snap | 288 +++++------------- workflows/raredisease.nf | 4 +- 8 files changed, 138 insertions(+), 290 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e7a8fd5d..3e33508a0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) +- Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#xxx](https://github.com/nf-core/raredisease/pull/xxx) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` diff --git a/conf/modules/scatter_genome.config b/conf/modules/scatter_genome.config index 32ce0e700..e36924f17 100644 --- a/conf/modules/scatter_genome.config +++ b/conf/modules/scatter_genome.config @@ -17,7 +17,7 @@ process { - withName: '.*SCATTER_GENOME:GAWK' { + withName: '.*SCATTER_GENOME:GENOME_FAI_TO_BED' { ext.args2 = { '\'BEGIN {SEP="\t"}; {print \$1 SEP "0" SEP \$2}\'' } ext.suffix = "bed" } diff --git a/main.nf b/main.nf index a803c290d..209a40e35 100644 --- a/main.nf +++ b/main.nf @@ -364,17 +364,14 @@ workflow NFCORE_RAREDISEASE { // // Create chromosome bed and intervals for splitting and gathering operations // - ch_scatter_split_intervals = channel.empty() - ch_scatter_genome_publish = channel.empty() + ch_scatter_genome_split_intervals = channel.empty() if (!skip_snv_annotation) { SCATTER_GENOME ( ch_genome_dictionary, ch_genome_fai, - ch_genome_fasta, - params.save_reference + ch_genome_fasta ) - ch_scatter_split_intervals = SCATTER_GENOME.out.split_intervals - ch_scatter_genome_publish = SCATTER_GENOME.out.publish + ch_scatter_genome_split_intervals = SCATTER_GENOME.out.gatk4_splitintervals_split_intervals } RAREDISEASE ( @@ -432,7 +429,7 @@ workflow NFCORE_RAREDISEASE { ch_sambamba_bed, ch_sample_id_map, ch_samples, - ch_scatter_split_intervals, + ch_scatter_genome_split_intervals, ch_score_config_mt, ch_score_config_snv, ch_score_config_sv, @@ -532,48 +529,48 @@ workflow NFCORE_RAREDISEASE { val_vep_cache_version ) emit: - align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] - align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] - align_genome_marked_bai = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] - align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] - align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] - align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] - multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - qc_bam_chromograph_cov_plots = RAREDISEASE.out.qc_bam_chromograph_cov_plots // channel: [ val(meta), path(png) ] - qc_bam_mosdepth_global_txt = RAREDISEASE.out.qc_bam_mosdepth_global_txt // channel: [ val(meta), path(txt) ] - qc_bam_mosdepth_per_base_bed = RAREDISEASE.out.qc_bam_mosdepth_per_base_bed // channel: [ val(meta), path(bed.gz) ] - qc_bam_mosdepth_per_base_csi = RAREDISEASE.out.qc_bam_mosdepth_per_base_csi // channel: [ val(meta), path(csi) ] - qc_bam_mosdepth_per_base_d4 = RAREDISEASE.out.qc_bam_mosdepth_per_base_d4 // channel: [ val(meta), path(d4) ] - qc_bam_mosdepth_quantized_bed = RAREDISEASE.out.qc_bam_mosdepth_quantized_bed // channel: [ val(meta), path(bed.gz) ] - qc_bam_mosdepth_quantized_csi = RAREDISEASE.out.qc_bam_mosdepth_quantized_csi // channel: [ val(meta), path(csi) ] - qc_bam_mosdepth_regions_bed = RAREDISEASE.out.qc_bam_mosdepth_regions_bed // channel: [ val(meta), path(bed.gz) ] - qc_bam_mosdepth_regions_csi = RAREDISEASE.out.qc_bam_mosdepth_regions_csi // channel: [ val(meta), path(csi) ] - qc_bam_mosdepth_regions_txt = RAREDISEASE.out.qc_bam_mosdepth_regions_txt // channel: [ val(meta), path(txt) ] - qc_bam_mosdepth_summary_txt = RAREDISEASE.out.qc_bam_mosdepth_summary_txt // channel: [ val(meta), path(txt) ] - qc_bam_mosdepth_thresholds_bed = RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed // channel: [ val(meta), path(bed.gz) ] - qc_bam_mosdepth_thresholds_csi = RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi // channel: [ val(meta), path(csi) ] - qc_bam_ngsbits_samplegender_tsv = RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv // channel: [ val(meta), path(tsv) ] - qc_bam_picard_collecthsmetrics_metrics = RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics // channel: [ val(meta), path(metrics) ] - qc_bam_picard_collectmultiplemetrics_metrics = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics // channel: [ val(meta), path(metrics) ] - qc_bam_picard_collectmultiplemetrics_pdf = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf // channel: [ val(meta), path(pdf) ] - qc_bam_sambamba_depth_bed = RAREDISEASE.out.qc_bam_sambamba_depth_bed // channel: [ val(meta), path(bed) ] - qc_bam_tiddit_cov_cov = RAREDISEASE.out.qc_bam_tiddit_cov_cov // channel: [ val(meta), path(bed) ] - qc_bam_tiddit_cov_wig = RAREDISEASE.out.qc_bam_tiddit_cov_wig // channel: [ val(meta), path(wig) ] - qc_bam_ucsc_wigtobigwig_bw = RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] - qc_bam_verifybamid_ancestry = RAREDISEASE.out.qc_bam_verifybamid_ancestry // channel: [ val(meta), path(ancestry) ] - qc_bam_verifybamid_bed = RAREDISEASE.out.qc_bam_verifybamid_bed // channel: [ val(meta), path(bed) ] - qc_bam_verifybamid_log = RAREDISEASE.out.qc_bam_verifybamid_log // channel: [ val(meta), path(log) ] - qc_bam_verifybamid_mu = RAREDISEASE.out.qc_bam_verifybamid_mu // channel: [ val(meta), path(mu) ] - qc_bam_verifybamid_self_sm = RAREDISEASE.out.qc_bam_verifybamid_self_sm // channel: [ val(meta), path(selfSM) ] - qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] - qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] - qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] - subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] - subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] - publish = RAREDISEASE.out.publish - .mix(ch_scatter_genome_publish) - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] + align_genome_marked_bam = RAREDISEASE.out.align_genome_marked_bam // channel: [ val(meta), path(bam) ] + align_genome_marked_bai = RAREDISEASE.out.align_genome_marked_bai // channel: [ val(meta), path(bai) ] + align_genome_marked_cram = RAREDISEASE.out.align_genome_marked_cram // channel: [ val(meta), path(cram) ] + align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] + align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] + multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html + scatter_genome_gatk4_splitintervals_split_intervals = skip_snv_annotation ? channel.empty() : SCATTER_GENOME.out.gatk4_splitintervals_split_intervals // channel: [ val(meta), path(interval_list) ] + qc_bam_chromograph_cov_plots = RAREDISEASE.out.qc_bam_chromograph_cov_plots // channel: [ val(meta), path(png) ] + qc_bam_mosdepth_global_txt = RAREDISEASE.out.qc_bam_mosdepth_global_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_per_base_bed = RAREDISEASE.out.qc_bam_mosdepth_per_base_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_per_base_csi = RAREDISEASE.out.qc_bam_mosdepth_per_base_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_per_base_d4 = RAREDISEASE.out.qc_bam_mosdepth_per_base_d4 // channel: [ val(meta), path(d4) ] + qc_bam_mosdepth_quantized_bed = RAREDISEASE.out.qc_bam_mosdepth_quantized_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_quantized_csi = RAREDISEASE.out.qc_bam_mosdepth_quantized_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_bed = RAREDISEASE.out.qc_bam_mosdepth_regions_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_regions_csi = RAREDISEASE.out.qc_bam_mosdepth_regions_csi // channel: [ val(meta), path(csi) ] + qc_bam_mosdepth_regions_txt = RAREDISEASE.out.qc_bam_mosdepth_regions_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_summary_txt = RAREDISEASE.out.qc_bam_mosdepth_summary_txt // channel: [ val(meta), path(txt) ] + qc_bam_mosdepth_thresholds_bed = RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed // channel: [ val(meta), path(bed.gz) ] + qc_bam_mosdepth_thresholds_csi = RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi // channel: [ val(meta), path(csi) ] + qc_bam_ngsbits_samplegender_tsv = RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv // channel: [ val(meta), path(tsv) ] + qc_bam_picard_collecthsmetrics_metrics = RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_metrics = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics // channel: [ val(meta), path(metrics) ] + qc_bam_picard_collectmultiplemetrics_pdf = RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf // channel: [ val(meta), path(pdf) ] + qc_bam_sambamba_depth_bed = RAREDISEASE.out.qc_bam_sambamba_depth_bed // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_cov = RAREDISEASE.out.qc_bam_tiddit_cov_cov // channel: [ val(meta), path(bed) ] + qc_bam_tiddit_cov_wig = RAREDISEASE.out.qc_bam_tiddit_cov_wig // channel: [ val(meta), path(wig) ] + qc_bam_ucsc_wigtobigwig_bw = RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + qc_bam_verifybamid_ancestry = RAREDISEASE.out.qc_bam_verifybamid_ancestry // channel: [ val(meta), path(ancestry) ] + qc_bam_verifybamid_bed = RAREDISEASE.out.qc_bam_verifybamid_bed // channel: [ val(meta), path(bed) ] + qc_bam_verifybamid_log = RAREDISEASE.out.qc_bam_verifybamid_log // channel: [ val(meta), path(log) ] + qc_bam_verifybamid_mu = RAREDISEASE.out.qc_bam_verifybamid_mu // channel: [ val(meta), path(mu) ] + qc_bam_verifybamid_self_sm = RAREDISEASE.out.qc_bam_verifybamid_self_sm // channel: [ val(meta), path(selfSM) ] + qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] + qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] + qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] + subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] + subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] + publish = RAREDISEASE.out.publish + .mix(ch_pedfile_publish) + .mix(ch_references.publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -762,6 +759,9 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + processed_references = params.save_reference + ? NFCORE_RAREDISEASE.out.scatter_genome_gatk4_splitintervals_split_intervals + : channel.empty() subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -778,6 +778,9 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + processed_references { + path { _meta, _file -> "processed_references/" } + } subworkflow_results { path { destination, _value -> destination } } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 64de7e73a..91c8ebedd 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -27,7 +27,7 @@ workflow ANNOTATE_GENOME_SNVS { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_gnomad_af // channel: [optional] [ path(tab), path(tbi) ] ch_samples // channel: [mandatory] [ val(sample_meta) ] - ch_split_intervals // channel: [mandatory] [ path(intervals) ] + ch_split_intervals // channel: [mandatory] [ val(meta), path(interval_list) ] ch_vcf // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] @@ -62,9 +62,15 @@ workflow ANNOTATE_GENOME_SNVS { // The remainder:true join pads cases without rohcall output with a single null, giving // tuples of length 4 (no rohcall) vs 5 (rohcall). After combining with an interval both // grow by one, so size==6 means this case has probands and a rohcall-annotated VCF. + ch_split_intervals + .map { _meta, intervals -> intervals } + .flatten() + .collate(1) + .set { ch_split_intervals_flat } + ch_vcf .join(ZIP_TABIX_ROHCALL.out.gz_index, remainder: true) - .combine(ch_split_intervals) + .combine(ch_split_intervals_flat) .map { it -> def meta = it[0] def vcf = it[1] diff --git a/subworkflows/local/scatter_genome/main.nf b/subworkflows/local/scatter_genome/main.nf index b6a258828..6c898ba12 100644 --- a/subworkflows/local/scatter_genome/main.nf +++ b/subworkflows/local/scatter_genome/main.nf @@ -2,8 +2,8 @@ // A subworkflow to create genome interval files necessary for bam/vcf scatter operations. // -include { GATK4_SPLITINTERVALS } from '../../../modules/nf-core/gatk4/splitintervals/main' -include { GAWK } from '../../../modules/nf-core/gawk' +include { GATK4_SPLITINTERVALS } from '../../../modules/nf-core/gatk4/splitintervals/main' +include { GAWK as GENOME_FAI_TO_BED } from '../../../modules/nf-core/gawk' workflow SCATTER_GENOME { @@ -11,22 +11,14 @@ workflow SCATTER_GENOME { ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - val_save_reference // bool main: - GAWK (ch_genome_fai, [], false) + GENOME_FAI_TO_BED (ch_genome_fai, [], false) - GATK4_SPLITINTERVALS(GAWK.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) - - ch_publish = channel.empty() - if (val_save_reference) { - ch_publish = GATK4_SPLITINTERVALS.out.split_intervals - .map { meta, value -> ['processed_references/', [meta, value]] } - } + GATK4_SPLITINTERVALS(GENOME_FAI_TO_BED.out.output, ch_genome_fasta, ch_genome_fai, ch_genome_dictionary) emit: - bed = GAWK.out.output.collect() // channel: [ val(meta), path(bed) ] - split_intervals = GATK4_SPLITINTERVALS.out.split_intervals.map { _meta, it -> it }.flatten().collate(1) // channel: [ val(meta), [ path(interval_lists) ] ] - publish = ch_publish // channel: [ val(destination), val(value) ] + gatk4_splitintervals_split_intervals = GATK4_SPLITINTERVALS.out.split_intervals // channel: [ val(meta), path(interval_list) ] + genome_fai_to_bed_output = GENOME_FAI_TO_BED.out.output.collect() // channel: [ val(meta), path(bed) ] } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test b/subworkflows/local/scatter_genome/tests/main.nf.test index 598c378fc..b110bed7d 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test +++ b/subworkflows/local/scatter_genome/tests/main.nf.test @@ -27,7 +27,6 @@ nextflow_workflow { input[0] = channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() input[1] = channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() input[2] = channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() - input[3] = "processed_references" """ } } @@ -56,7 +55,6 @@ nextflow_workflow { input[0] = channel.of(params.dict).map {it -> [[id:'genome'], it]}.collect() input[1] = channel.of(params.fai).map {it -> [[id:'genome'], it]}.collect() input[2] = channel.of(params.fasta).map {it -> [[id:'genome'], it]}.collect() - input[3] = "processed_references" """ } } diff --git a/subworkflows/local/scatter_genome/tests/main.nf.test.snap b/subworkflows/local/scatter_genome/tests/main.nf.test.snap index 823e91d1a..b7b366817 100644 --- a/subworkflows/local/scatter_genome/tests/main.nf.test.snap +++ b/subworkflows/local/scatter_genome/tests/main.nf.test.snap @@ -7,32 +7,13 @@ { "id": "genome" }, - "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - "processed_references/", [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], - "bed": [ + "1": [ [ { "id": "genome" @@ -40,33 +21,30 @@ "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "publish": [ + "gatk4_splitintervals_split_intervals": [ [ - "processed_references/", + { + "id": "genome" + }, [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], - "split_intervals": [ - [ - "0000-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ], + "genome_fai_to_bed_output": [ [ - "0001-scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "id": "genome" + }, + "genome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] } ], - "timestamp": "2026-03-30T10:55:18.112519", + "timestamp": "2026-05-25T23:14:53.489816823", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -78,104 +56,31 @@ { "id": "genome" }, - "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" - ] - ], - "1": [ - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" - ], - [ - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73" - ], - [ - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646" - ], - [ - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2" - ], - [ - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319" - ], - [ - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4" - ], - [ - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91" - ], - [ - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0" - ], - [ - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac" - ], - [ - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e" - ], - [ - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88" - ], - [ - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe" - ], - [ - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0" - ], - [ - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4" - ], - [ - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003" - ], - [ - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760" - ], - [ - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e" - ], - [ - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411" - ], - [ - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03" - ], - [ - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] - ], - "2": [ - [ - "processed_references/", [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] ] ], - "bed": [ + "1": [ [ { "id": "genome" @@ -183,105 +88,48 @@ "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ], - "publish": [ + "gatk4_splitintervals_split_intervals": [ [ - "processed_references/", + { + "id": "genome" + }, [ - { - "id": "genome" - }, - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" - ] + "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68", + "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73", + "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646", + "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2", + "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319", + "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4", + "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91", + "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0", + "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac", + "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e", + "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88", + "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe", + "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0", + "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4", + "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003", + "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760", + "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e", + "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411", + "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03", + "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" ] ] ], - "split_intervals": [ - [ - "0000-scattered.interval_list:md5,91c71c99e1a0777d96ed2ed35977fe68" - ], - [ - "0001-scattered.interval_list:md5,8084a75ace330aaa6b5baedcbc408e73" - ], - [ - "0002-scattered.interval_list:md5,61a7e1852764653287dfcca76b177646" - ], - [ - "0003-scattered.interval_list:md5,9f817fda35d09c8d449d7d91bc57d5a2" - ], - [ - "0004-scattered.interval_list:md5,6f023cded659d4cfc8edb96706c3b319" - ], + "genome_fai_to_bed_output": [ [ - "0005-scattered.interval_list:md5,91c3bca4311e2cc9bf55d4ef22281dd4" - ], - [ - "0006-scattered.interval_list:md5,8f2a2f98ac6994859350580a8161cd91" - ], - [ - "0007-scattered.interval_list:md5,5541b78eee72200b98be6af5e4544ed0" - ], - [ - "0008-scattered.interval_list:md5,9f7f7b6f58ec47a73317e3fd64f53bac" - ], - [ - "0009-scattered.interval_list:md5,0bd63474d5fb5284cb8bbb0a202f2e1e" - ], - [ - "0010-scattered.interval_list:md5,c2ff40fe4d17059d38cf40b9b031cb88" - ], - [ - "0011-scattered.interval_list:md5,dd86a813319aa10ca2694505799b8fbe" - ], - [ - "0012-scattered.interval_list:md5,b9424bc405dac67b220e212a749844e0" - ], - [ - "0013-scattered.interval_list:md5,60eee5b05fa8e3d4ff7f026071c4d0e4" - ], - [ - "0014-scattered.interval_list:md5,8c35fb4f332a8bfe56a5d12269def003" - ], - [ - "0015-scattered.interval_list:md5,3fff10ccee5d170b92804ed116f41760" - ], - [ - "0016-scattered.interval_list:md5,c36e542cad7d5b534bde590ce26f356e" - ], - [ - "0017-scattered.interval_list:md5,40c5de97da683709819f0c7404ea6411" - ], - [ - "0018-scattered.interval_list:md5,81820b1a9b029868c58e1abc41c3dc03" - ], - [ - "0019-scattered.interval_list:md5,c4e27e8be0b085a4fa4980d756e21c7f" + { + "id": "genome" + }, + "genome.bed:md5,77b5bd8a06d9f25356c233413bf0318d" ] ] } ], - "timestamp": "2026-03-17T00:19:06.789641139", + "timestamp": "2026-05-25T23:14:30.264088588", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 0fc7f9728..4f68fbb66 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -131,7 +131,7 @@ workflow RAREDISEASE { ch_sambamba_bed ch_sample_id_map ch_samples - ch_scatter_split_intervals + ch_scatter_genome_split_intervals ch_score_config_mt ch_score_config_snv ch_score_config_sv @@ -480,7 +480,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_gnomad_af, ch_samples, - ch_scatter_split_intervals, + ch_scatter_genome_split_intervals, CALL_SNV.out.genome_vcf_tabix, ch_vcfanno_extra, ch_vcfanno_lua, From 829fc237548862b3026dbf3fbc17c788bc0b0da2 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 08:30:45 +0200 Subject: [PATCH 726/872] update tests --- .../tests/main.nf.test | 31 ++++++++++--------- .../local/call_sv_MT/tests/main.nf.test | 25 ++++++++------- 2 files changed, 29 insertions(+), 27 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index f2d69db9d..ecd1482af 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -60,21 +60,22 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[19] = channel.value(10000000) - input[20] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[21] = channel.of([[id:'target'], [], []]) - input[22] = true - input[23] = false - input[24] = 'wgs' - input[25] = 407 - input[26] = 16081 - input[27] = 5763 - input[28] = 5730 - input[29] = 16569 - input[30] = 'MT' - input[31] = 15 - input[32] = 0.01 - input[33] = true + input[19] = channel.empty() + input[20] = channel.value(10000000) + input[21] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[22] = channel.of([[id:'target'], [], []]) + input[23] = true + input[24] = false + input[25] = 'wgs' + input[26] = 407 + input[27] = 16081 + input[28] = 5763 + input[29] = 5730 + input[30] = 16569 + input[31] = 'MT' + input[32] = 15 + input[33] = 0.01 + input[34] = true """ } } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index e49287de5..9318370f3 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -44,18 +44,19 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[10] = channel.value(10000000) - input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[13] = false - input[14] = 16081 - input[15] = 407 - input[16] = 5730 - input[17] = 5763 - input[18] = 16569 - input[19] = 'chrM' - input[20] = 15 - input[21] = 0.01 + input[10] = channel.empty() + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 """ } } From e709053b87b30d64b85ce97ba40f3c2b9eb0c56c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 08:45:23 +0200 Subject: [PATCH 727/872] update snaps --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 9e1a3388e..74f401276 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1097,7 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,6007a3aa07cc778bf71cb34f054426da", + "justhusky.saltshaker_classify.html:md5,0135a6f3a07d456beb3496534dc8bcf1", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1329,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-25T16:07:46.556250899", + "timestamp": "2026-05-26T08:36:11.269628572", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 968bc03e4aa4622ce27e446f18c2241ac02f4563 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 08:59:16 +0200 Subject: [PATCH 728/872] change ID scheme --- modules/local/saltshaker_to_html/main.nf | 4 ++-- subworkflows/local/call_sv_MT/main.nf | 9 ++++----- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 068eccb1d..6149f2cbf 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -1,5 +1,5 @@ process SALTSHAKER_TO_HTML { - tag "$meta.caseid" + tag "$meta.id" label "process_low" conda "${moduleDir}/environment.yml" @@ -14,7 +14,7 @@ process SALTSHAKER_TO_HTML { tuple val(meta), path("*.saltshaker_classify.html"), emit: classify_html script: - def prefix = task.ext.prefix ?: "${meta.caseid}" + def prefix = task.ext.prefix ?: "${meta.id}" def args = task.ext.args ?: "" """ saltshaker_to_html.py \ diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 4b8452f9d..f0d4329d0 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -128,15 +128,14 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> def sample_meta = ['id':meta.sample] - def case_meta = ['caseid':meta.case_id] - return [sample_meta, case_meta, txt] + return [sample_meta, meta.case_id, txt] } .join(ch_sample_id_map, remainder: true) - .branch { sample_meta, case_meta, txt, samplemap -> + .branch { sample_meta, caseid, txt, samplemap -> id: samplemap.equals(null) - return [case_meta, txt, sample_meta.id] + return [['id':caseid], txt, sample_meta.id] custid: !(samplemap.equals(null)) - return [case_meta, txt, samplemap] + return [['id':caseid], txt, samplemap] } .set { ch_for_mix } From d2e3282e1ce1622c66099d18af003673d1fe6de5 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 09:15:17 +0200 Subject: [PATCH 729/872] remove find/concatenate module --- modules.json | 5 - .../nf-core/find/concatenate/environment.yml | 8 - modules/nf-core/find/concatenate/main.nf | 70 ------ modules/nf-core/find/concatenate/meta.yml | 112 ---------- .../find/concatenate/tests/main.nf.test | 154 ------------- .../find/concatenate/tests/main.nf.test.snap | 207 ------------------ .../tests/nextflow_unzipped_zipped.config | 5 - .../tests/nextflow_zipped_unzipped.config | 6 - tests/default.nf.test.snap | 4 +- 9 files changed, 2 insertions(+), 569 deletions(-) delete mode 100644 modules/nf-core/find/concatenate/environment.yml delete mode 100644 modules/nf-core/find/concatenate/main.nf delete mode 100644 modules/nf-core/find/concatenate/meta.yml delete mode 100644 modules/nf-core/find/concatenate/tests/main.nf.test delete mode 100644 modules/nf-core/find/concatenate/tests/main.nf.test.snap delete mode 100644 modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config delete mode 100644 modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config diff --git a/modules.json b/modules.json index f72f65a4f..968c064a6 100644 --- a/modules.json +++ b/modules.json @@ -156,11 +156,6 @@ "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, - "find/concatenate": { - "branch": "master", - "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", - "installed_by": ["modules"] - }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "a89928b3f8b4fa91e4c783e769dbc10f91c89b32", diff --git a/modules/nf-core/find/concatenate/environment.yml b/modules/nf-core/find/concatenate/environment.yml deleted file mode 100644 index 874a4bd0d..000000000 --- a/modules/nf-core/find/concatenate/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ -channels: - - conda-forge - - bioconda - -dependencies: - - coreutils==9.4 - - findutils==4.6.0 - - pigz==2.8 diff --git a/modules/nf-core/find/concatenate/main.nf b/modules/nf-core/find/concatenate/main.nf deleted file mode 100644 index 9fc8915f6..000000000 --- a/modules/nf-core/find/concatenate/main.nf +++ /dev/null @@ -1,70 +0,0 @@ -process FIND_CONCATENATE { - tag "${meta.id}" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7f/7fd226561e12b32bcacdf4f5ff74577e76233adf52ae5cbc499a2cdfe0e27d82/data' - : 'community.wave.seqera.io/library/findutils_pigz:c4dd5edc44402661'}" - - input: - tuple val(meta), path(files_in, stageAs: 'to_concatenate/*', arity: '1..*') - - output: - tuple val(meta), path("${prefix}"), emit: file_out - tuple val("${task.process}"), val("find"), eval("find --version | sed '1!d; s/.* //'"), topic: versions, emit: versions_find - tuple val("${task.process}"), val("pigz"), eval("pigz --version 2>&1 | sed 's/pigz //g'"), topic: versions, emit: versions_pigz - tuple val("${task.process}"), val("coreutils"), eval("cat --version | sed '1!d; s/.* //'"), topic: versions, emit: versions_coreutils - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: "" - - // | input | output | command1 | command2 | - // |-----------|------------|----------|----------| - // | gzipped | gzipped | cat | | - // | ungzipped | ungzipped | cat | | - // | gzipped | ungzipped | pigz | | - // | ungzipped | gzipped | cat | pigz | - - // Use input file ending as default - // get file extensions, if extension is .gz then get the second to last extension as well - file_extensions = files_in.collect { in_file -> in_file.name - in_file.getBaseName(in_file.name.endsWith('.gz') ? 2 : 1) } - - // Use input file ending as default for output file - prefix = task.ext.prefix ?: "${meta.id}${file_extensions[0]}" - - if (files_in.any{ file -> file.toString().endsWith('.gz')} && !files_in.every{ file -> file.toString().endsWith('.gz') }) { - error("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") - } - - in_zip = files_in[0].toString().endsWith('.gz') - out_zip = task.ext.prefix ? task.ext.prefix.endsWith('.gz') : file_extensions[0].endsWith('.gz') - - out_fname = in_zip && out_zip ? prefix : prefix.endsWith('.gz') ? prefix.replace('.gz', '') : prefix - - cmd1 = in_zip && !out_zip ? "pigz -cd -p ${task.cpus}" : "cat" - cmd2 = !in_zip && out_zip ? "pigz -p ${task.cpus} ${args} ${out_fname}" : "" - - """ - while IFS= read -r -d \$'\\0' file; do - ${cmd1} \$file \\ - >> ${out_fname} - done < <( find to_concatenate/ -mindepth 1 -print0 | sort -z ) - - ${cmd2} - """ - - stub: - prefix = task.ext.prefix ?: "${meta.id}" - - if (files_in.any{ file -> file.toString().endsWith('.gz')} && !files_in.every{ file -> file.toString().endsWith('.gz') }) { - error("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") - } - - """ - touch ${prefix} - """ -} diff --git a/modules/nf-core/find/concatenate/meta.yml b/modules/nf-core/find/concatenate/meta.yml deleted file mode 100644 index 046acb691..000000000 --- a/modules/nf-core/find/concatenate/meta.yml +++ /dev/null @@ -1,112 +0,0 @@ -name: "find_concatenate" -description: A module for concatenation of gzipped or uncompressed files getting around - UNIX terminal argument size -keywords: - - concatenate - - gzip - - cat - - find - - pigz -tools: - - find: - description: GNU find searches the directory tree rooted at each given starting-point - by evaluating the given expression - documentation: https://man7.org/linux/man-pages/man1/find.1.html - licence: - - "GPL-3.0-or-later" - identifier: "" - - pigz: - description: pigz, which stands for Parallel Implementation of GZip, is a fully - functional replacement for gzip that exploits multiple processors and multiple - cores to the hilt when compressing data. - documentation: https://zlib.net/pigz/pigz.pdf - licence: - - "other" - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - files_in: - type: file - description: List of either compressed or uncompressed files - pattern: "*" - ontologies: [] -output: - file_out: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - ${prefix}: - type: file - description: Concatenated file. Will be gzipped if ${prefix} ends with ".gz" - or inputs are gzipped, will be uncompressed otherwise. - pattern: "${file_out}" - ontologies: [] - versions_find: - - - ${task.process}: - type: string - description: The name of the process - - find: - type: string - description: The name of the tool - - find --version | sed '1!d; s/.* //': - type: eval - description: The expression to obtain the version of the tool - versions_pigz: - - - ${task.process}: - type: string - description: The name of the process - - pigz: - type: string - description: The name of the tool - - pigz --version 2>&1 | sed 's/pigz //g': - type: eval - description: The expression to obtain the version of the tool - versions_coreutils: - - - ${task.process}: - type: string - description: The name of the process - - coreutils: - type: string - description: The name of the tool - - cat --version | sed '1!d; s/.* //': - type: eval - description: The expression to obtain the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The name of the process - - find: - type: string - description: The name of the tool - - find --version | sed '1!d; s/.* //': - type: eval - description: The expression to obtain the version of the tool - - - ${task.process}: - type: string - description: The name of the process - - pigz: - type: string - description: The name of the tool - - pigz --version 2>&1 | sed 's/pigz //g': - type: eval - description: The expression to obtain the version of the tool - - - ${task.process}: - type: string - description: The name of the process - - coreutils: - type: string - description: The name of the tool - - cat --version | sed '1!d; s/.* //': - type: eval - description: The expression to obtain the version of the tool -authors: - - "@BioWilko" -maintainers: - - "@BioWilko" diff --git a/modules/nf-core/find/concatenate/tests/main.nf.test b/modules/nf-core/find/concatenate/tests/main.nf.test deleted file mode 100644 index c96f9e48d..000000000 --- a/modules/nf-core/find/concatenate/tests/main.nf.test +++ /dev/null @@ -1,154 +0,0 @@ -nextflow_process { - - name "Test Process FIND_CONCATENATE" - script "../main.nf" - process "FIND_CONCATENATE" - tag "modules" - tag "modules_nfcore" - tag "find" - tag "find/concatenate" - - test("test_mixed_input") { - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) - ] - ] - """ - } - } - then { - assertAll( - { assert !process.success }, - { assert process.stdout.toString().contains("All files provided to this module must either be gzipped (and have the .gz extension) or unzipped (and not have the .gz extension). A mix of both is not allowed.") }, - ) - } - } - - test("test_cat_unzipped_unzipped") { - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) - ] - ] - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() }, - ) - } - } - - - test("test_cat_zipped_zipped") { - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) - ] - ] - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() }, - ) - } - } - - test("test_cat_zipped_unzipped") { - config './nextflow_zipped_unzipped.config' - - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) - ] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() }, - ) - } - - } - - test("test_cat_unzipped_zipped") { - config './nextflow_unzipped_zipped.config' - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) - ] - ] - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() }, - ) - } - } - - test("test_cat_one_file_unzipped_zipped") { - config './nextflow_unzipped_zipped.config' - when { - process { - """ - input[0] = - [ - [ id:'test', single_end:true ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - ] - """ - } - } - then { - assertAll( - { assert process.success }, - { assert snapshot(sanitizeOutput(process.out)).match() }, - ) - } - } -} diff --git a/modules/nf-core/find/concatenate/tests/main.nf.test.snap b/modules/nf-core/find/concatenate/tests/main.nf.test.snap deleted file mode 100644 index 56494eacd..000000000 --- a/modules/nf-core/find/concatenate/tests/main.nf.test.snap +++ /dev/null @@ -1,207 +0,0 @@ -{ - "test_cat_unzipped_unzipped": { - "content": [ - { - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" - ] - ], - "versions_coreutils": [ - [ - "FIND_CONCATENATE", - "coreutils", - "9.4" - ] - ], - "versions_find": [ - [ - "FIND_CONCATENATE", - "find", - "4.6.0" - ] - ], - "versions_pigz": [ - [ - "FIND_CONCATENATE", - "pigz", - "2.8" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T11:55:56.090740487" - }, - "test_cat_zipped_zipped": { - "content": [ - { - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "test.gff3.gz:md5,1a983f97a01107efe42c8c3e7728b4c1" - ] - ], - "versions_coreutils": [ - [ - "FIND_CONCATENATE", - "coreutils", - "9.4" - ] - ], - "versions_find": [ - [ - "FIND_CONCATENATE", - "find", - "4.6.0" - ] - ], - "versions_pigz": [ - [ - "FIND_CONCATENATE", - "pigz", - "2.8" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T11:56:03.72242729" - }, - "test_cat_zipped_unzipped": { - "content": [ - { - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "cat.txt:md5,1a983f97a01107efe42c8c3e7728b4c1" - ] - ], - "versions_coreutils": [ - [ - "FIND_CONCATENATE", - "coreutils", - "9.4" - ] - ], - "versions_find": [ - [ - "FIND_CONCATENATE", - "find", - "4.6.0" - ] - ], - "versions_pigz": [ - [ - "FIND_CONCATENATE", - "pigz", - "2.8" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T11:56:11.488401849" - }, - "test_cat_one_file_unzipped_zipped": { - "content": [ - { - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "cat.txt.gz:md5,6e9fe4042a72f2345f644f239272b7e6" - ] - ], - "versions_coreutils": [ - [ - "FIND_CONCATENATE", - "coreutils", - "9.4" - ] - ], - "versions_find": [ - [ - "FIND_CONCATENATE", - "find", - "4.6.0" - ] - ], - "versions_pigz": [ - [ - "FIND_CONCATENATE", - "pigz", - "2.8" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T11:56:26.254644609" - }, - "test_cat_unzipped_zipped": { - "content": [ - { - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" - ] - ], - "versions_coreutils": [ - [ - "FIND_CONCATENATE", - "coreutils", - "9.4" - ] - ], - "versions_find": [ - [ - "FIND_CONCATENATE", - "find", - "4.6.0" - ] - ], - "versions_pigz": [ - [ - "FIND_CONCATENATE", - "pigz", - "2.8" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.2" - }, - "timestamp": "2026-03-11T11:56:18.76821511" - } -} \ No newline at end of file diff --git a/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config b/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config deleted file mode 100644 index aec380fd8..000000000 --- a/modules/nf-core/find/concatenate/tests/nextflow_unzipped_zipped.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: FIND_CONCATENATE { - ext.prefix = 'cat.txt.gz' - } -} diff --git a/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config b/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config deleted file mode 100644 index 5e10af2bb..000000000 --- a/modules/nf-core/find/concatenate/tests/nextflow_zipped_unzipped.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - withName: FIND_CONCATENATE { - ext.prefix = 'cat.txt' - } -} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 74f401276..1e4cae80d 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1097,7 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,0135a6f3a07d456beb3496534dc8bcf1", + "justhusky.saltshaker_classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1329,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-26T08:36:11.269628572", + "timestamp": "2026-05-26T09:05:02.351229625", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 46056a48243158a3e8359c030aa2bbe9568f5672 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 09:25:13 +0200 Subject: [PATCH 730/872] finish removing find/concat stuff --- subworkflows/local/call_sv_MT/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f0d4329d0..98e56681e 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -9,7 +9,6 @@ include { MT_DELETION } from '../../../modules/local/mt_deletion_script include { PREP_MITOSALT } from '../../../modules/local/prep_mitosalt/main' include { SALTSHAKER_CALL } from '../../../modules/nf-core/saltshaker/call/main' include { SALTSHAKER_CLASSIFY } from '../../../modules/nf-core/saltshaker/classify/main' -include { FIND_CONCATENATE } from '../../../modules/nf-core/find/concatenate/main' include { SALTSHAKER_PLOT } from '../../../modules/nf-core/saltshaker/plot/main' include { SALTSHAKER_TO_HTML } from '../../../modules/local/saltshaker_to_html/main' include { SEQTK_SAMPLE } from '../../../modules/nf-core/seqtk/sample/main' From b3cebdd6ea5d1d78846d905ddd5c54e2cb034b2c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 10:09:31 +0200 Subject: [PATCH 731/872] update subworkflow snap --- .../local/call_sv_MT/tests/main.nf.test.snap | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index f86f56e63..fe420658f 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -20,7 +20,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" ] ] ], @@ -120,7 +120,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" ] ], [ @@ -200,7 +200,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" ] ], [ @@ -221,7 +221,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" ] ] ], @@ -268,9 +268,9 @@ ] ] ], - "timestamp": "2026-04-14T15:53:31.425509861", + "timestamp": "2026-05-26T10:03:44.531497043", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } From b86d81aa2cd325dc0a4fe51cf66a48dc05b7296e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 26 May 2026 12:20:29 +0200 Subject: [PATCH 732/872] update annotate_rhocallviz and annotate_genome_snvs --- CHANGELOG.md | 2 + main.nf | 104 +- .../local/annotate_genome_snvs/main.nf | 30 +- .../annotate_genome_snvs/tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 1120 ++++++++--------- .../local/annotate_rhocallviz/main.nf | 12 +- .../annotate_rhocallviz/tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 57 + workflows/raredisease.nf | 33 +- 9 files changed, 697 insertions(+), 679 deletions(-) create mode 100644 subworkflows/local/annotate_rhocallviz/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e33508a0..7860b9fb1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#xxx](https://github.com/nf-core/raredisease/pull/xxx) +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#xxx](https://github.com/nf-core/raredisease/pull/xxx) +- Expand annotate_rhocallviz test with snapshot assertions [#xxx](https://github.com/nf-core/raredisease/pull/xxx) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` diff --git a/main.nf b/main.nf index 209a40e35..b648b61c7 100644 --- a/main.nf +++ b/main.nf @@ -566,6 +566,14 @@ workflow NFCORE_RAREDISEASE { qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] + annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_regions_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_sites_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_rhocall_viz_bed = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] + annotate_genome_snvs_rhocall_viz_wig = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] + annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish @@ -722,47 +730,55 @@ workflow { ) publish: - alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam - .mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai) - .mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram) - .mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai) - .mix(NFCORE_RAREDISEASE.out.align_markdup_metrics) - .mix(NFCORE_RAREDISEASE.out.subsample_mt_bam) - .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) - fastp = NFCORE_RAREDISEASE.out.align_fastp_out - ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv - qc_bam = NFCORE_RAREDISEASE.out.qc_bam_chromograph_cov_plots.transpose() - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_csi) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_d4) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_csi) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_csi) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_txt) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_summary_txt) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi) - .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics) - .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics.transpose()) - .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf.transpose()) - .mix(NFCORE_RAREDISEASE.out.qc_bam_sambamba_depth_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_cov) - .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_wig) - .mix(NFCORE_RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ancestry) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_bed) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_log) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_mu) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_self_sm) - .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) - .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) - .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) - processed_references = params.save_reference - ? NFCORE_RAREDISEASE.out.scatter_genome_gatk4_splitintervals_split_intervals - : channel.empty() - subworkflow_results = NFCORE_RAREDISEASE.out.publish + alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai) + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram) + .mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai) + .mix(NFCORE_RAREDISEASE.out.align_markdup_metrics) + .mix(NFCORE_RAREDISEASE.out.subsample_mt_bam) + .mix(NFCORE_RAREDISEASE.out.subsample_mt_bai) + fastp = NFCORE_RAREDISEASE.out.align_fastp_out + ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv + qc_bam = NFCORE_RAREDISEASE.out.qc_bam_chromograph_cov_plots.transpose() + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_d4) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_summary_txt) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics.transpose()) + .mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf.transpose()) + .mix(NFCORE_RAREDISEASE.out.qc_bam_sambamba_depth_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_cov) + .mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_wig) + .mix(NFCORE_RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ancestry) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_bed) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_log) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_mu) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_self_sm) + .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) + .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) + .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots.transpose()) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots.transpose()) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots.transpose()) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig) + annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw + processed_references = params.save_reference + ? NFCORE_RAREDISEASE.out.scatter_genome_gatk4_splitintervals_split_intervals + : channel.empty() + subworkflow_results = NFCORE_RAREDISEASE.out.publish } output { @@ -778,6 +794,12 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + annotate_snv_genome { + path { _meta, _file -> "annotate_snv/genome/" } + } + annotate_snv_genome_rhocallviz_bw { + path { meta, _file -> "annotate_snv/genome/${meta.sample}_rhocallviz/" } + } processed_references { path { _meta, _file -> "processed_references/" } } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 91c8ebedd..815fc5360 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -41,10 +41,11 @@ workflow ANNOTATE_GENOME_SNVS { val_vep_cache_version // string: vep version ex: 107 main: - ch_cadd_vcf = channel.empty() - ch_vcf_scatter_in = channel.empty() - ch_vep_in = channel.empty() - ch_chromograph_publish = channel.empty() + ch_cadd_vcf = channel.empty() + ch_chromograph_regions_plots = channel.empty() + ch_chromograph_sites_plots = channel.empty() + ch_vcf_scatter_in = channel.empty() + ch_vep_in = channel.empty() ch_vcf .filter { meta, _vcf, _tbi -> @@ -188,8 +189,8 @@ workflow ANNOTATE_GENOME_SNVS { UPD_REGIONS(ch_upd_in) CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed) CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]]) - ch_chromograph_publish = CHROMOGRAPH_SITES.out.plots - .mix(CHROMOGRAPH_REGIONS.out.plots) + ch_chromograph_sites_plots = CHROMOGRAPH_SITES.out.plots + ch_chromograph_regions_plots = CHROMOGRAPH_REGIONS.out.plots } BCFTOOLS_CONCAT.out.vcf @@ -204,14 +205,13 @@ workflow ANNOTATE_GENOME_SNVS { //rhocall_viz ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index ) - ch_publish = ch_chromograph_publish - .mix(ch_concat_vcf_out) - .mix(ch_concat_tbi_out) - .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } - .mix(ANNOTATE_RHOCALLVIZ.out.publish) - emit: - tbi = ch_concat_tbi_out // channel: [ val(meta), path(tbi) ] - vcf_ann = ch_concat_vcf_out // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + bcftools_concat_tbi = ch_concat_tbi_out // channel: [ val(meta), path(tbi) ] + bcftools_concat_vcf = ch_concat_vcf_out // channel: [ val(meta), path(vcf) ] + chromograph_autozyg_plots = ANNOTATE_RHOCALLVIZ.out.chromograph_autozyg_plots // channel: [ val(meta), path(png) ] + chromograph_regions_plots = ch_chromograph_regions_plots // channel: [ val(meta), path(png) ] + chromograph_sites_plots = ch_chromograph_sites_plots // channel: [ val(meta), path(png) ] + rhocall_viz_bed = ANNOTATE_RHOCALLVIZ.out.rhocall_viz_bed // channel: [ val(meta), path(bed) ] + rhocall_viz_wig = ANNOTATE_RHOCALLVIZ.out.rhocall_viz_wig // channel: [ val(meta), path(wig) ] + ucsc_wigtobigwig_bw = ANNOTATE_RHOCALLVIZ.out.ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 0b6b95c53..eb12d86ae 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -36,7 +36,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -92,7 +92,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index bbcbf5aa3..b849754fb 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -44,254 +44,110 @@ "2", [ [ - "annotate_snv/genome/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "annotate_snv/genome/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "sex": 1, - "phenotype": 2, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - [ - "earlycasualcaiman_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", - 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"earlycasualcaiman_upd_sites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_upd_sites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + [ + "rhocall_viz_bed", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "rhocall_viz_wig", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "ucsc_wigtobigwig_bw", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "sex": 1, + "phenotype": 2, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_rhocallviz.bw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] ] ] ], - "timestamp": "2026-04-13T12:04:20.194067577", + "timestamp": "2026-05-26T10:49:33.095592057", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/annotate_rhocallviz/main.nf b/subworkflows/local/annotate_rhocallviz/main.nf index d7f50cbe8..3aafcd11d 100644 --- a/subworkflows/local/annotate_rhocallviz/main.nf +++ b/subworkflows/local/annotate_rhocallviz/main.nf @@ -49,13 +49,9 @@ workflow ANNOTATE_RHOCALLVIZ { UCSC_WIGTOBIGWIG(RHOCALL_VIZ.out.wig, ch_genome_chrsizes) - ch_publish = RHOCALL_VIZ.out.bed - .mix(RHOCALL_VIZ.out.wig) - .mix(CHROMOGRAPH_AUTOZYG.out.plots) - .map { meta, value -> ['annotate_snv/genome/', [meta, value]] } - .mix(UCSC_WIGTOBIGWIG.out.bw - .map { meta, bw -> ["annotate_snv/genome/${meta.sample}_rhocallviz/", [meta, bw]] }) - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] + chromograph_autozyg_plots = CHROMOGRAPH_AUTOZYG.out.plots // channel: [ val(meta), path(png) ] + rhocall_viz_bed = RHOCALL_VIZ.out.bed // channel: [ val(meta), path(bed) ] + rhocall_viz_wig = RHOCALL_VIZ.out.wig // channel: [ val(meta), path(wig) ] + ucsc_wigtobigwig_bw = UCSC_WIGTOBIGWIG.out.bw // channel: [ val(meta), path(bw) ] } diff --git a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test index 291fba0ab..7da8f7204 100644 --- a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test +++ b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test @@ -42,7 +42,19 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.rhocall_viz_bed + .collect { meta, bedfile -> [file(bedfile)] }, + workflow.out.rhocall_viz_wig + .collect { meta, wigfile -> [file(wigfile)] }, + workflow.out.ucsc_wigtobigwig_bw + .collect { meta, bwfile -> [file(bwfile)] }, + workflow.out.chromograph_autozyg_plots + .collect { meta, plots -> [plots.collect { png -> file(png) }.sort()] } + ).match() } + ) } } } diff --git a/subworkflows/local/annotate_rhocallviz/tests/main.nf.test.snap b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test.snap new file mode 100644 index 000000000..e6c4f4c5f --- /dev/null +++ b/subworkflows/local/annotate_rhocallviz/tests/main.nf.test.snap @@ -0,0 +1,57 @@ +{ + "ANNOTATE_RHOCALLVIZ - stub": { + "content": [ + [ + [ + "test_sample_rhocallviz.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + "test_sample_rhocallviz.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + "test_sample_rhocallviz.bw:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + [ + "test_sample_rhocallviz.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_sample_rhocallviz.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "timestamp": "2026-05-26T11:46:37.479912106", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 4f68fbb66..689858a3b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -245,7 +245,14 @@ workflow RAREDISEASE { ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() - ch_annotate_genome_snvs_publish = channel.empty() + ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() + ch_annotate_genome_snvs_bcftools_concat_vcf = channel.empty() + ch_annotate_genome_snvs_chromograph_autozyg_plots = channel.empty() + ch_annotate_genome_snvs_chromograph_regions_plots = channel.empty() + ch_annotate_genome_snvs_chromograph_sites_plots = channel.empty() + ch_annotate_genome_snvs_rhocall_viz_bed = channel.empty() + ch_annotate_genome_snvs_rhocall_viz_wig = channel.empty() + ch_annotate_genome_snvs_ucsc_wigtobigwig_bw = channel.empty() ch_annotate_mt_snvs_publish = channel.empty() ch_annotate_sv_publish = channel.empty() ch_generate_cytosure_files_publish = channel.empty() @@ -492,10 +499,17 @@ workflow RAREDISEASE { val_cadd_resources, val_genome, val_vep_cache_version - ).set { ch_snv_annotate } - ch_annotate_genome_snvs_publish = ANNOTATE_GENOME_SNVS.out.publish - - ch_snv_annotate.vcf_ann + ) + ch_annotate_genome_snvs_bcftools_concat_tbi = ANNOTATE_GENOME_SNVS.out.bcftools_concat_tbi + ch_annotate_genome_snvs_bcftools_concat_vcf = ANNOTATE_GENOME_SNVS.out.bcftools_concat_vcf + ch_annotate_genome_snvs_chromograph_autozyg_plots = ANNOTATE_GENOME_SNVS.out.chromograph_autozyg_plots + ch_annotate_genome_snvs_chromograph_regions_plots = ANNOTATE_GENOME_SNVS.out.chromograph_regions_plots + ch_annotate_genome_snvs_chromograph_sites_plots = ANNOTATE_GENOME_SNVS.out.chromograph_sites_plots + ch_annotate_genome_snvs_rhocall_viz_bed = ANNOTATE_GENOME_SNVS.out.rhocall_viz_bed + ch_annotate_genome_snvs_rhocall_viz_wig = ANNOTATE_GENOME_SNVS.out.rhocall_viz_wig + ch_annotate_genome_snvs_ucsc_wigtobigwig_bw = ANNOTATE_GENOME_SNVS.out.ucsc_wigtobigwig_bw + + ch_annotate_genome_snvs_bcftools_concat_vcf .multiMap { meta, vcf -> clinical: [ meta + [ set: "clinical" ], vcf ] research: [ meta + [ set: "research" ], vcf ] @@ -1052,6 +1066,14 @@ workflow RAREDISEASE { qc_bam_verifybamid_ud = QC_BAM.out.verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = QC_BAM.out.wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = QC_BAM.out.wgsmetrics_y // channel: [ val(meta), path(metrics) ] + annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_regions_plots = ch_annotate_genome_snvs_chromograph_regions_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_sites_plots = ch_annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] + annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] + annotate_genome_snvs_ucsc_wigtobigwig_bw = ch_annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions @@ -1059,7 +1081,6 @@ workflow RAREDISEASE { .mix(ch_call_sv_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) - .mix(ch_annotate_genome_snvs_publish) .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) .mix(ch_generate_cytosure_files_publish) From 6aa9bf5f67985419bc36a095ec83410faa2a9bec Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 26 May 2026 13:21:08 +0200 Subject: [PATCH 733/872] Update CHANGELOG.md --- CHANGELOG.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e33508a0..c56d99c4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,9 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` ### `Changed` - +- Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) -- Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#xxx](https://github.com/nf-core/raredisease/pull/xxx) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) ### `Fixed` From e6c03975ae4e5f40de510c3084c5c35f7ff4320c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 14:00:53 +0200 Subject: [PATCH 734/872] sort html inputs --- modules/local/saltshaker_to_html/main.nf | 2 +- subworkflows/local/call_sv_MT/main.nf | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 6149f2cbf..e26e12734 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -8,7 +8,7 @@ process SALTSHAKER_TO_HTML { 'community.wave.seqera.io/library/typer:0.25.1--25ea8a9ce34456a3' }" input: - tuple val(meta), path(files_in, stageAs: 'to_combine/*', arity: '1..*'), val(ids) + tuple val(meta), path(files_in), val(ids) output: tuple val(meta), path("*.saltshaker_classify.html"), emit: classify_html diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 98e56681e..f3a820692 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -141,6 +141,12 @@ workflow CALL_SV_MT { channel.empty() .mix(ch_for_mix.id, ch_for_mix.custid) .groupTuple() + .map { meta, paths, ids -> + def sorted_paths = paths.sort { a, b -> a.getName() <=> b.getName() } + def sorted_ids = ids.sort() + return [meta, sorted_paths, sorted_ids] + } + .dump('tag': 'saltshaker_html_input') .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( From 4b4bc8a041c97afcf3e40d5352297d3bcd00466b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 26 May 2026 14:19:25 +0200 Subject: [PATCH 735/872] update snaps --- tests/default.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1e4cae80d..b67ed722f 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1329,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-26T09:05:02.351229625", + "timestamp": "2026-05-26T14:06:41.515920144", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From c8b23b0d8e47ff7631ecf31f2b7d9f52df156baf Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 08:50:02 +0200 Subject: [PATCH 736/872] suggestions from review --- conf/modules/call_sv_MT.config | 4 ++ modules/local/saltshaker_to_html/main.nf | 10 +-- .../local/call_structural_variants/main.nf | 2 +- subworkflows/local/call_sv_MT/main.nf | 15 ++--- .../local/call_sv_MT/tests/main.nf.test | 66 +++++++++++++++++++ 5 files changed, 80 insertions(+), 17 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index 1c56b31f7..dd9b72241 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -37,6 +37,10 @@ process { ].join(' ') } } + withName: '.*CALL_SV_MT:SALTSHAKER_TO_HTML' { + ext.prefix = { "${meta.id}_saltshaker.classify" } + } + withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { ext.args = '--blacklist --genes' } diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index e26e12734..96f2cbf2c 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -8,10 +8,10 @@ process SALTSHAKER_TO_HTML { 'community.wave.seqera.io/library/typer:0.25.1--25ea8a9ce34456a3' }" input: - tuple val(meta), path(files_in), val(ids) + tuple val(meta), path(saltshaker_classify_reports), val(sample_ids) output: - tuple val(meta), path("*.saltshaker_classify.html"), emit: classify_html + tuple val(meta), path("*.html"), emit: classify_html script: def prefix = task.ext.prefix ?: "${meta.id}" @@ -19,8 +19,8 @@ process SALTSHAKER_TO_HTML { """ saltshaker_to_html.py \ $args \ - --input ${files_in.join(' --input ')} \ - --sample ${ids.join(' --sample ')} \ - --output ${prefix}.saltshaker_classify.html + --input ${saltshaker_classify_reports.join(' --input ')} \ + --sample ${sample_ids.join(' --sample ')} \ + --output ${prefix}.html """ } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 6c357c8ac..2b4d84da1 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -32,7 +32,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [val(id), val(id)] + ch_sample_id_map // channel: [optional] [val(sample_id), val(customer_id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f3a820692..6d2d4b191 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -26,7 +26,7 @@ workflow CALL_SV_MT { ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [val(id), val(id)] + ch_sample_id_map // channel: [optional] [val(sample_id), val(customer_id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] @@ -130,23 +130,16 @@ workflow CALL_SV_MT { return [sample_meta, meta.case_id, txt] } .join(ch_sample_id_map, remainder: true) - .branch { sample_meta, caseid, txt, samplemap -> - id: samplemap.equals(null) - return [['id':caseid], txt, sample_meta.id] - custid: !(samplemap.equals(null)) - return [['id':caseid], txt, samplemap] + .map { sample_meta, case_id, txt, customer_id -> + def report_identifier = customer_id ?: sample_meta.id + return [['id':case_id], txt, report_identifier] } - .set { ch_for_mix } - - channel.empty() - .mix(ch_for_mix.id, ch_for_mix.custid) .groupTuple() .map { meta, paths, ids -> def sorted_paths = paths.sort { a, b -> a.getName() <=> b.getName() } def sorted_ids = ids.sort() return [meta, sorted_paths, sorted_ids] } - .dump('tag': 'saltshaker_html_input') .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 9318370f3..444ad5e0e 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -18,6 +18,72 @@ nextflow_workflow { options "-stub" + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[9] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[10] = channel.of(['cust_ecc', 'earlycasualcaiman']) + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } + ) + } + } + + test("CALL_SV_MT - no_sample_map - stub") { + + options "-stub" + when { params { mt_del = "-s --insert-size 16000" From 8365268d8318f658cfee42e4c9e5423b95d9c993 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 09:12:00 +0200 Subject: [PATCH 737/872] update snaps --- tests/default.nf.test.snap | 6 +++--- tests/test_singleton.nf.test.snap | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b67ed722f..37245f049 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -675,7 +675,7 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -1097,7 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", + "justhusky_saltshaker.classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1329,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-26T14:06:41.515920144", + "timestamp": "2026-05-27T08:57:21.010542925", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 67a9d4588..165445a09 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -538,7 +538,7 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -656,7 +656,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-25T16:21:58.01161601", + "timestamp": "2026-05-27T09:02:58.186687221", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From c0d06084d504d3141a0ea6481119ddc59d59c1fa Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 10:01:36 +0200 Subject: [PATCH 738/872] Review comments --- .github/CONTRIBUTING.md | 9 ++++++++- main.nf | 7 +++---- subworkflows/local/annotate_genome_snvs/main.nf | 4 +--- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 6f0b42331..de05c17e5 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -165,10 +165,17 @@ Use `_` (lowercase, underscored) inside the subwork | Layer | Convention | Example | | ------------------------- | ------------------------------------------------------------------- | --------------------------------------------------------------------- | | Subworkflow `emit:` | `_` | `mosdepth_global_txt` | -| `raredisease.nf` variable | `ch__` | `ch_qc_bam_mosdepth_global_txt` | +| `raredisease.nf` variable | `ch__` | `ch_qc_bam_mosdepth_global_txt` | | `NFCORE_RAREDISEASE` emit | `_` | `qc_bam_mosdepth_global_txt` | | `publish:` entry | one entry per destination, mixing all channels for that destination | `qc_bam = NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt.mix(...)` | +The **semantic suffix** is the part of the emit name that describes what the data is, not which tool produced it. When the subworkflow emit name starts with a process/module name, drop that prefix in the `raredisease.nf` variable if the remainder is unambiguous within the subworkflow's outputs: + +- `scatter_genome` emits `gatk4_splitintervals_split_intervals` → variable is `ch_scatter_genome_split_intervals` (drop `gatk4_splitintervals_`) +- `qc_bam` emits `mosdepth_global_txt` → variable stays `ch_qc_bam_mosdepth_global_txt` (`global_txt` alone would be ambiguous among the many txt outputs in that subworkflow) + +When in doubt, keep enough of the process name to remain unambiguous. + > **Note:** Some subworkflows still use the legacy `ch_publish`/`subworkflow_results` pattern and are being migrated incrementally. Until a subworkflow is migrated, follow the existing pattern for that subworkflow so it continues to publish correctly via `subworkflow_results`. ### Configuration diff --git a/main.nf b/main.nf index 209a40e35..93ff30633 100644 --- a/main.nf +++ b/main.nf @@ -536,7 +536,7 @@ workflow NFCORE_RAREDISEASE { align_genome_marked_crai = RAREDISEASE.out.align_genome_marked_crai // channel: [ val(meta), path(crai) ] align_markdup_metrics = RAREDISEASE.out.align_markdup_metrics // channel: [ val(meta), path(metrics) ] multiqc_report = RAREDISEASE.out.multiqc_report // channel: /path/to/multiqc_report.html - scatter_genome_gatk4_splitintervals_split_intervals = skip_snv_annotation ? channel.empty() : SCATTER_GENOME.out.gatk4_splitintervals_split_intervals // channel: [ val(meta), path(interval_list) ] + scatter_genome_split_intervals = ch_scatter_genome_split_intervals // channel: [ val(meta), path(interval_list) ] qc_bam_chromograph_cov_plots = RAREDISEASE.out.qc_bam_chromograph_cov_plots // channel: [ val(meta), path(png) ] qc_bam_mosdepth_global_txt = RAREDISEASE.out.qc_bam_mosdepth_global_txt // channel: [ val(meta), path(txt) ] qc_bam_mosdepth_per_base_bed = RAREDISEASE.out.qc_bam_mosdepth_per_base_bed // channel: [ val(meta), path(bed.gz) ] @@ -759,9 +759,7 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) - processed_references = params.save_reference - ? NFCORE_RAREDISEASE.out.scatter_genome_gatk4_splitintervals_split_intervals - : channel.empty() + processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -780,6 +778,7 @@ output { } processed_references { path { _meta, _file -> "processed_references/" } + enabled params.save_reference } subworkflow_results { path { destination, _value -> destination } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 91c8ebedd..4463f8839 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -63,9 +63,7 @@ workflow ANNOTATE_GENOME_SNVS { // tuples of length 4 (no rohcall) vs 5 (rohcall). After combining with an interval both // grow by one, so size==6 means this case has probands and a rohcall-annotated VCF. ch_split_intervals - .map { _meta, intervals -> intervals } - .flatten() - .collate(1) + .flatMap { _meta, intervals -> intervals.collect{ interval -> [interval] } } .set { ch_split_intervals_flat } ch_vcf From 5d971847f4f9cfa5cc35ca393eae2ed51931b6b8 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 10:26:37 +0200 Subject: [PATCH 739/872] update test --- subworkflows/local/annotate_genome_snvs/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 0b6b95c53..eb12d86ae 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -36,7 +36,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -92,7 +92,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), From fa9e974419dae26123eeeb7a725d14fded25426c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 11:09:51 +0200 Subject: [PATCH 740/872] update test --- subworkflows/local/annotate_genome_snvs/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index eb12d86ae..7c6e9b3f5 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -36,7 +36,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) + input[7] = channel.of([[id:'split_intervals'], [file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -92,7 +92,7 @@ nextflow_workflow { input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[5] = channel.value([[],[]]) input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of([[id:'split_intervals'], file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]) + input[7] = channel.of([[id:'split_intervals'], [file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]]) input[8] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), From a35b4ead9d45a843f2c8b2fa54d60a539891aeb5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 11:12:06 +0200 Subject: [PATCH 741/872] fix linting --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c56d99c4f..268000afc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` ### `Changed` + - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) From cdde88ea695366a406c1ebaf67e1f037f8c2cf20 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 13:00:51 +0200 Subject: [PATCH 742/872] add sample to test --- .../local/call_sv_MT/tests/main.nf.test | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 444ad5e0e..655cfd498 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -28,6 +28,10 @@ nextflow_workflow { [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) ]) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() @@ -43,8 +47,14 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] + ], + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + ] ]) - input[10] = channel.of(['cust_ecc', 'earlycasualcaiman']) + input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbath']]) input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) @@ -94,6 +104,10 @@ nextflow_workflow { [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true ]) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() @@ -109,6 +123,12 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] + ], + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + ] ]) input[10] = channel.empty() input[11] = channel.value(10000000) From 485fac336f59ac6277be8035be0ab357472b49cd Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 14:01:52 +0200 Subject: [PATCH 743/872] add real tests --- .../local/call_sv_MT/tests/main.nf.test | 158 +++++++++++++++++- 1 file changed, 157 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 655cfd498..025911513 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -14,6 +14,158 @@ nextflow_workflow { config "./nextflow.config" + test("CALL_SV_MT - stub") { + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[9] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbath']]) + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } + ) + } + } + + test("CALL_SV_MT - no_sample_map") { + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[9] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[10] = channel.empty() + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } + ) + } + } + test("CALL_SV_MT - stub") { options "-stub" @@ -29,6 +181,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ], + [ [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) @@ -48,6 +201,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ], + [ [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), @@ -105,9 +259,10 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ], + [ [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) ]) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() @@ -124,6 +279,7 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ], + [ [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), From c94630963397bd03f026d9077cd78594839c87b9 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 14:04:26 +0200 Subject: [PATCH 744/872] change sample map for proper joining --- subworkflows/local/call_sv_MT/main.nf | 13 +- .../local/call_sv_MT/tests/main.nf.test | 90 ++-- .../local/call_sv_MT/tests/main.nf.test.snap | 411 +++++++++++++++++- tests/default.nf.test.snap | 4 +- tests/test_singleton.nf.test.snap | 5 +- 5 files changed, 459 insertions(+), 64 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 6d2d4b191..7e242eb18 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -26,7 +26,7 @@ workflow CALL_SV_MT { ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [val(sample_id), val(customer_id)] + ch_sample_id_map // channel: [optional] [ val(customer_id), val(sample_id) ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] @@ -122,6 +122,10 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf + ch_sample_id_map + .map { customer_id, sample_id -> [sample_id, customer_id] } + .set { ch_sample_id_map_for_join } + // Create case-level channel ch_saltshaker_html_input, consisting of all saltshaker txt reports and all // customer IDs (or sample ID if no customer ID) so individual reports have identifers in the final HTML. SALTSHAKER_CLASSIFY.out.txt @@ -129,17 +133,12 @@ workflow CALL_SV_MT { def sample_meta = ['id':meta.sample] return [sample_meta, meta.case_id, txt] } - .join(ch_sample_id_map, remainder: true) + .join(ch_sample_id_map_for_join) .map { sample_meta, case_id, txt, customer_id -> def report_identifier = customer_id ?: sample_meta.id return [['id':case_id], txt, report_identifier] } .groupTuple() - .map { meta, paths, ids -> - def sorted_paths = paths.sort { a, b -> a.getName() <=> b.getName() } - def sorted_ids = ids.sort() - return [meta, sorted_paths, sorted_ids] - } .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 655cfd498..a780ba6ad 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -24,15 +24,18 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ], - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) - ]) + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true) + ] + ) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() @@ -41,20 +44,23 @@ nextflow_workflow { input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[9] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + input[9] = channel.of( [ - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) - ] - ], - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], [ - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true) + ] ] - ]) - input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbath']]) + ) + input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbat']]) input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) @@ -100,15 +106,18 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ], - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true - ]) + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true) + ] + ) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() @@ -117,19 +126,22 @@ nextflow_workflow { input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[9] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + input[9] = channel.of( [ - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) - ] - ], - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], [ - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true) + ] ] - ]) + ) input[10] = channel.empty() input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index fe420658f..ca5188e89 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -20,10 +20,350 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" + "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" ] ] ], + [ + "2", + [ + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "3", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "mt_del_result", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "saltshaker_html", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ] + ] + ], + "timestamp": "2026-05-27T13:41:36.494759677", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "CALL_SV_MT - no_sample_map - stub": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "1", + [ + + ] + ], [ "2", [ @@ -61,6 +401,22 @@ "case_id": "justhusky" }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -118,9 +474,19 @@ "call_sv/", [ { - "id": "justhusky" + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -152,6 +518,22 @@ "case_id": "justhusky" }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -198,9 +580,19 @@ "call_sv/", [ { - "id": "justhusky" + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -217,12 +609,7 @@ [ "saltshaker_html", [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] + ] ], [ @@ -268,7 +655,7 @@ ] ] ], - "timestamp": "2026-05-26T10:03:44.531497043", + "timestamp": "2026-05-27T13:41:55.991013268", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 37245f049..aed2c28ea 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -675,7 +675,6 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -1097,7 +1096,6 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky_saltshaker.classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1329,7 +1327,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-27T08:57:21.010542925", + "timestamp": "2026-05-27T13:49:36.404619751", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 165445a09..80411cef2 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 355, + 354, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -538,7 +538,6 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -656,7 +655,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-27T09:02:58.186687221", + "timestamp": "2026-05-27T13:57:45.391553212", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From c274f5b4e0041afcfaddcdc1612df55bbae73449 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 27 May 2026 14:56:49 +0200 Subject: [PATCH 745/872] remove real tests --- .../local/call_sv_MT/tests/main.nf.test | 152 ------------------ .../local/call_sv_MT/tests/main.nf.test.snap | 40 ++--- 2 files changed, 20 insertions(+), 172 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 25dc5fc60..a780ba6ad 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -14,158 +14,6 @@ nextflow_workflow { config "./nextflow.config" - test("CALL_SV_MT - stub") { - - when { - params { - mt_del = "-s --insert-size 16000" - } - workflow { - """ - input[0] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ], - [ - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) - ]) - input[1] = channel.of([id:'justhusky']) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[9] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [ - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) - ] - ], - [ - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [ - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) - ] - ]) - input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbath']]) - input[11] = channel.value(10000000) - input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[14] = false - input[15] = 16081 - input[16] = 407 - input[17] = 5730 - input[18] = 5763 - input[19] = 16569 - input[20] = 'chrM' - input[21] = 15 - input[22] = 0.01 - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name - ).match() } - ) - } - } - - test("CALL_SV_MT - no_sample_map") { - - when { - params { - mt_del = "-s --insert-size 16000" - } - workflow { - """ - input[0] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ], - [ - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_sorted_md.bam.bai', checkIfExists: true) - ]) - input[1] = channel.of([id:'justhusky']) - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[9] = channel.of([ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [ - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) - ] - ], - [ - [id:'hugelymodelbath', sample:'hugelymodelbath', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbath\\\\tPL:illumina\\\\tSM:hugelymodelbath'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [ - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbath_mt_2.fastq.gz', checkIfExists: true) - ] - ]) - input[10] = channel.empty() - input[11] = channel.value(10000000) - input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[14] = false - input[15] = 16081 - input[16] = 407 - input[17] = 5730 - input[18] = 5763 - input[19] = 16569 - input[20] = 'chrM' - input[21] = 15 - input[22] = 0.01 - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name - ).match() } - ) - } - } - test("CALL_SV_MT - stub") { options "-stub" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index ca5188e89..077234556 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -338,7 +338,7 @@ ] ] ], - "timestamp": "2026-05-27T13:41:36.494759677", + "timestamp": "2026-05-27T14:54:56.327412606", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -369,8 +369,8 @@ [ [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, "sex": 1, @@ -379,7 +379,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -442,32 +442,32 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ "call_sv/", [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -548,32 +548,32 @@ "sample": "earlycasualcaiman", "single_end": false, "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ "call_sv/", [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, "sex": 1, "phenotype": 1, "paternal": 0, "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -617,8 +617,8 @@ [ [ { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", + "id": "hugelymodelbat", + "sample": "hugelymodelbat", "single_end": false, "num_lanes": 1, "sex": 1, @@ -627,7 +627,7 @@ "maternal": 0, "case_id": "justhusky" }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -655,7 +655,7 @@ ] ] ], - "timestamp": "2026-05-27T13:41:55.991013268", + "timestamp": "2026-05-27T14:55:13.561636052", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 5f5e47b429677ceacf193f4b69650c019e1ab0f0 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 15:36:35 +0200 Subject: [PATCH 746/872] update snap --- tests/default.nf.test.snap | 9 ++++++--- tests/test_bam.nf.test.snap | 10 ++++++---- tests/test_singleton.nf.test.snap | 10 ++++++---- 3 files changed, 18 insertions(+), 11 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 062aef247..ecf1bbf8a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -230,6 +230,9 @@ "GENMOD_SCORE": { "genmod": "3.10.2" }, + "GENOME_FAI_TO_BED": { + "gawk": "5.3.1" + }, "GET_CHROM_SIZES": { "coreutils": 9.5 }, @@ -1334,10 +1337,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "timestamp": "2026-05-27T15:36:04.165275268", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-05-18T15:03:40.296274957" + } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index a710f1bd3..c9f2157aa 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -213,6 +213,9 @@ "GENMOD_SCORE": { "genmod": "3.10.2" }, + "GENOME_FAI_TO_BED": { + "gawk": "5.3.1" + }, "GET_CHROM_SIZES": { "coreutils": 9.5 }, @@ -845,11 +848,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-18T09:13:39.46322688", + "timestamp": "2026-05-27T15:22:23.152275002", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-05-06T10:52:22.394678076" + } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f2d6a79d5..13ab39400 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -222,6 +222,9 @@ "GENMOD_SCORE": { "genmod": "3.10.2" }, + "GENOME_FAI_TO_BED": { + "gawk": "5.3.1" + }, "GET_CHROM_SIZES": { "coreutils": 9.5 }, @@ -661,11 +664,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-18T09:17:23.560290017", + "timestamp": "2026-05-27T15:26:36.71307935", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.5", "nextflow": "25.10.4" - }, - "timestamp": "2026-05-06T10:54:12.680904463" + } } } \ No newline at end of file From 8c021f8fd156549657d3bdf708b74449ff845c4c Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 27 May 2026 22:24:54 +0200 Subject: [PATCH 747/872] fix test --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 2a4a61f2f..1ad072e60 100644 --- a/main.nf +++ b/main.nf @@ -769,9 +769,9 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) - .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots.transpose()) - .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots.transpose()) - .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots.transpose()) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots) + .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig) annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw From c4411d234940d2d2f0c498a1fec137eb1e6043ae Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 28 May 2026 08:40:07 +0200 Subject: [PATCH 748/872] fix sample map join logic --- subworkflows/local/call_sv_MT/main.nf | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 7e242eb18..4b23d823d 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -122,10 +122,6 @@ workflow CALL_SV_MT { ) ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf - ch_sample_id_map - .map { customer_id, sample_id -> [sample_id, customer_id] } - .set { ch_sample_id_map_for_join } - // Create case-level channel ch_saltshaker_html_input, consisting of all saltshaker txt reports and all // customer IDs (or sample ID if no customer ID) so individual reports have identifers in the final HTML. SALTSHAKER_CLASSIFY.out.txt @@ -133,10 +129,22 @@ workflow CALL_SV_MT { def sample_meta = ['id':meta.sample] return [sample_meta, meta.case_id, txt] } + .set { ch_saltshaker_txt } + + ch_sample_id_map + .map { customer_id, sample_id -> [sample_id, customer_id] } + .set { ch_sample_id_map_for_join } + + ch_saltshaker_txt .join(ch_sample_id_map_for_join) .map { sample_meta, case_id, txt, customer_id -> - def report_identifier = customer_id ?: sample_meta.id - return [['id':case_id], txt, report_identifier] + return [['id':case_id], txt, customer_id] + } + .groupTuple() + .set { ch_saltshaker_html_input } ?: + ch_saltshaker_txt + .map { sample_meta, case_id, txt -> + return [['id':case_id], txt, sample_meta.id] } .groupTuple() .set { ch_saltshaker_html_input } From 603725b2405fc71b1d560e1792e5769f80fe72d5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 28 May 2026 09:06:50 +0200 Subject: [PATCH 749/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4926f4932..ebfea8b95 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#xxx](https://github.com/nf-core/raredisease/pull/xxx) +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) - Expand annotate_rhocallviz test with snapshot assertions [#xxx](https://github.com/nf-core/raredisease/pull/xxx) - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) From bb3160c355ba756db032b71d9262a4c9e3498d9a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 28 May 2026 09:07:19 +0200 Subject: [PATCH 750/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ebfea8b95..84e6081f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) -- Expand annotate_rhocallviz test with snapshot assertions [#xxx](https://github.com/nf-core/raredisease/pull/xxx) +- Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858) - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) From 0a27ea24f7c7ddb198698616e3e4aa567577c774 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 28 May 2026 09:25:15 +0200 Subject: [PATCH 751/872] updated snaps --- .../local/call_sv_MT/tests/main.nf.test.snap | 44 +++++++++++++++---- tests/default.nf.test.snap | 4 +- tests/test_singleton.nf.test.snap | 5 ++- 3 files changed, 42 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 077234556..69f0ccf65 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -20,7 +20,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -155,7 +155,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -270,7 +270,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -291,7 +291,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,4bf48ea2b072462c9e4416eda94ffd4c" + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -338,7 +338,7 @@ ] ] ], - "timestamp": "2026-05-27T14:54:56.327412606", + "timestamp": "2026-05-28T08:43:45.522212667", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -361,7 +361,12 @@ [ "1", [ - + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + ] ] ], [ @@ -489,6 +494,15 @@ "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + ] + ], [ "call_sv/", [ @@ -595,6 +609,15 @@ "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + ] + ], [ "call_sv/", [ @@ -609,7 +632,12 @@ [ "saltshaker_html", [ - + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + ] ] ], [ @@ -655,7 +683,7 @@ ] ] ], - "timestamp": "2026-05-27T14:55:13.561636052", + "timestamp": "2026-05-28T08:44:01.668006334", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index aed2c28ea..4797c1cbc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -675,6 +675,7 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -1096,6 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "justhusky_saltshaker.classify.html:md5,8cfd6d90ee9aa97d6b4106ace4752df6", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1327,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-27T13:49:36.404619751", + "timestamp": "2026-05-28T09:15:38.521885471", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 80411cef2..64b62c9c8 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 354, + 355, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -538,6 +538,7 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", + "call_sv/justhusky_saltshaker.classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -655,7 +656,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-27T13:57:45.391553212", + "timestamp": "2026-05-28T09:22:26.143096694", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From 1e78d9b6ba2853d01062f2b43dbd434c3c8419a4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 28 May 2026 09:52:19 +0200 Subject: [PATCH 752/872] fix report prefix name --- conf/modules/call_sv_MT.config | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 20 +++++++++---------- tests/default.nf.test.snap | 6 +++--- tests/test_singleton.nf.test.snap | 4 ++-- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/conf/modules/call_sv_MT.config b/conf/modules/call_sv_MT.config index dd9b72241..2f72115f6 100644 --- a/conf/modules/call_sv_MT.config +++ b/conf/modules/call_sv_MT.config @@ -38,7 +38,7 @@ process { } withName: '.*CALL_SV_MT:SALTSHAKER_TO_HTML' { - ext.prefix = { "${meta.id}_saltshaker.classify" } + ext.prefix = { "${meta.id}.saltshaker_classify" } } withName: '.*CALL_SV_MT:SALTSHAKER_PLOT' { diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 69f0ccf65..751790efb 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -20,7 +20,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -155,7 +155,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -270,7 +270,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -291,7 +291,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -338,7 +338,7 @@ ] ] ], - "timestamp": "2026-05-28T08:43:45.522212667", + "timestamp": "2026-05-28T09:49:15.142259116", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -365,7 +365,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -500,7 +500,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -615,7 +615,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ], [ @@ -636,7 +636,7 @@ { "id": "justhusky" }, - "justhusky_saltshaker.classify.html:md5,17f591b6b334aadda58f3efef7fe9125" + "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" ] ] ], @@ -683,7 +683,7 @@ ] ] ], - "timestamp": "2026-05-28T08:44:01.668006334", + "timestamp": "2026-05-28T09:49:32.527998006", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4797c1cbc..bad1fda58 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -675,7 +675,7 @@ "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky_saltshaker.classify.html", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -1097,7 +1097,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky_saltshaker.classify.html:md5,8cfd6d90ee9aa97d6b4106ace4752df6", + "justhusky.saltshaker_classify.html:md5,79a8e7d32a6842a6637ce88e67f28ea4", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1329,7 +1329,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-28T09:15:38.521885471", + "timestamp": "2026-05-28T09:40:48.240598924", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 64b62c9c8..dd6c5f713 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -538,7 +538,7 @@ "call_sv", "call_sv/hugelymodelbat.saltshaker.png", "call_sv/hugelymodelbat_mitochondria_deletions.txt", - "call_sv/justhusky_saltshaker.classify.html", + "call_sv/justhusky.saltshaker_classify.html", "call_sv/justhusky_saltshaker.vcf.gz", "call_sv/justhusky_sv.vcf.gz", "call_sv/justhusky_sv.vcf.gz.tbi", @@ -656,7 +656,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-28T09:22:26.143096694", + "timestamp": "2026-05-28T09:45:42.467577075", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From dc4b2ecb01a52bfb3e34c76ebb11d14b4a9fd32b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 29 May 2026 12:20:01 +0200 Subject: [PATCH 753/872] fix join logic and sample map order --- .../local/call_structural_variants/main.nf | 2 +- subworkflows/local/call_sv_MT/main.nf | 31 +++++++------------ .../local/call_sv_MT/tests/main.nf.test | 2 +- 3 files changed, 13 insertions(+), 22 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 2b4d84da1..073d84218 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -32,7 +32,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [val(sample_id), val(customer_id)] + ch_sample_id_map // channel: [optional] [val(customer_id), val(sample_id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 4b23d823d..25442948d 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -26,7 +26,7 @@ workflow CALL_SV_MT { ch_mt_fasta // channel: [mandatory] [ val(meta), path(mtfasta) ] ch_mt_lastdb // channel: [mandatory] [ val(meta), path(lastindex) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [ val(customer_id), val(sample_id) ] + ch_sample_id_map // channel: [optional] [ val(sample_id), val(customer_id) ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] @@ -125,28 +125,19 @@ workflow CALL_SV_MT { // Create case-level channel ch_saltshaker_html_input, consisting of all saltshaker txt reports and all // customer IDs (or sample ID if no customer ID) so individual reports have identifers in the final HTML. SALTSHAKER_CLASSIFY.out.txt - .map { meta, txt -> - def sample_meta = ['id':meta.sample] - return [sample_meta, meta.case_id, txt] - } - .set { ch_saltshaker_txt } - - ch_sample_id_map - .map { customer_id, sample_id -> [sample_id, customer_id] } - .set { ch_sample_id_map_for_join } - - ch_saltshaker_txt - .join(ch_sample_id_map_for_join) - .map { sample_meta, case_id, txt, customer_id -> - return [['id':case_id], txt, customer_id] + .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } + .join(ch_sample_id_map, remainder: true) + .map { sample_meta, case_id, txt, cust_id -> + cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] } .groupTuple() - .set { ch_saltshaker_html_input } ?: - ch_saltshaker_txt - .map { sample_meta, case_id, txt -> - return [['id':case_id], txt, sample_meta.id] + .map { meta, paths, ids -> + def zipped = [paths, ids].transpose() + def sorted = zipped.sort { a, b -> a[0].getName() <=> b[0].getName() } + def sorted_paths = sorted.collect { it[0] } + def sorted_ids = sorted.collect { it[1] } + return [meta, sorted_paths, sorted_ids] } - .groupTuple() .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index a780ba6ad..dc8a4f047 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -60,7 +60,7 @@ nextflow_workflow { ] ] ) - input[10] = channel.of(['cust_ecc', ['id':'earlycasualcaiman']], ['cust_hmb', ['id':'hugelymodelbat']]) + input[10] = channel.of([['id':'earlycasualcaiman'], 'cust_ecc'], [['id':'hugelymodelbat'], 'cust_hmb']) input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) From ffbde767fd43f4db011eda6bc3f48c29086d487d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 May 2026 20:35:45 +0200 Subject: [PATCH 754/872] update call_snv --- main.nf | 25 ++++++ subworkflows/local/call_snv/main.nf | 81 +++++++++---------- .../local/call_snv_deepvariant/main.nf | 14 ++-- .../call_snv_deepvariant/tests/main.nf.test | 1 + .../tests/main.nf.test.snap | 37 +++++---- .../local/postprocess_MT_calls/main.nf | 9 +-- .../tests/main.nf.test.snap | 44 +--------- workflows/raredisease.nf | 45 ++++++++--- 8 files changed, 126 insertions(+), 130 deletions(-) diff --git a/main.nf b/main.nf index 1ad072e60..6d0269f48 100644 --- a/main.nf +++ b/main.nf @@ -566,6 +566,14 @@ workflow NFCORE_RAREDISEASE { qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] + call_snv_bcftools_concat_csi = RAREDISEASE.out.call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] + call_snv_bcftools_concat_tbi = RAREDISEASE.out.call_snv_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + call_snv_bcftools_concat_vcf = RAREDISEASE.out.call_snv_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + call_snv_deepvariant_report = RAREDISEASE.out.call_snv_deepvariant_report // channel: [ val(meta), path(html) ] + call_snv_genome_tabix = RAREDISEASE.out.call_snv_genome_tabix // channel: [ val(meta), path(tbi) ] + call_snv_genome_vcf = RAREDISEASE.out.call_snv_genome_vcf // channel: [ val(meta), path(vcf) ] + call_snv_mt_tabix = RAREDISEASE.out.call_snv_mt_tabix // channel: [ val(meta), path(tbi) ] + call_snv_mt_vcf = RAREDISEASE.out.call_snv_mt_vcf. // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] @@ -767,6 +775,14 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + call_snv_genome = NFCORE_RAREDISEASE.out.call_snv_genome_vcf + .mix(NFCORE_RAREDISEASE.out.call_snv_genome_tabix) + .mix(NFCORE_RAREDISEASE.out.call_snv_deepvariant_report) + call_snv_mt = NFCORE_RAREDISEASE.out.call_snv_mt_vcf + .mix(NFCORE_RAREDISEASE.out.call_snv_mt_tabix) + call_snv_concatenated = NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_vcf + .mix(NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_tbi) + .mix(NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_csi) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots) @@ -792,6 +808,15 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + call_snv_genome { + path { _meta, _file -> "call_snv/genome/" } + } + call_snv_mt { + path { _meta, _file -> "call_snv/mitochondria/" } + } + call_snv_concatenated { + path { _meta, _file -> "call_snv/concatenated_calls/" } + } annotate_snv_genome { path { _meta, _file -> "annotate_snv/genome/" } } diff --git a/subworkflows/local/call_snv/main.nf b/subworkflows/local/call_snv/main.nf index 7700eaace..7ce27b358 100644 --- a/subworkflows/local/call_snv/main.nf +++ b/subworkflows/local/call_snv/main.nf @@ -43,20 +43,21 @@ workflow CALL_SNV { val_variant_caller // string: 'deepvariant' or 'sentieon' main: - ch_concat_publish = channel.empty() - ch_deepvariant_vcf = channel.empty() - ch_deepvariant_tbi = channel.empty() - ch_deepvariant_gvcf = channel.empty() - ch_deepvariant_gtbi = channel.empty() - ch_deepvariant_publish = channel.empty() - ch_mt_snv_publish = channel.empty() - ch_mt_tabix = channel.empty() - ch_mt_vcf = channel.empty() - ch_mt_vcf_tabix = channel.empty() - ch_sentieon_vcf = channel.empty() - ch_sentieon_tbi = channel.empty() - ch_sentieon_gvcf = channel.empty() - ch_sentieon_gtbi = channel.empty() + ch_bcftools_concat_csi = channel.empty() + ch_bcftools_concat_tbi = channel.empty() + ch_bcftools_concat_vcf = channel.empty() + ch_deepvariant_gvcf = channel.empty() + ch_deepvariant_gtbi = channel.empty() + ch_deepvariant_report = channel.empty() + ch_deepvariant_tbi = channel.empty() + ch_deepvariant_vcf = channel.empty() + ch_mt_tabix = channel.empty() + ch_mt_vcf = channel.empty() + ch_mt_vcf_tabix = channel.empty() + ch_sentieon_gvcf = channel.empty() + ch_sentieon_gtbi = channel.empty() + ch_sentieon_tbi = channel.empty() + ch_sentieon_vcf = channel.empty() if (val_variant_caller.equals("deepvariant") && !val_analysis_type.equals("mito")) { CALL_SNV_DEEPVARIANT ( @@ -71,11 +72,11 @@ workflow CALL_SNV { val_analysis_type, val_skip_split_multiallelics ) - ch_deepvariant_vcf = CALL_SNV_DEEPVARIANT.out.vcf - ch_deepvariant_tbi = CALL_SNV_DEEPVARIANT.out.tabix - ch_deepvariant_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf - ch_deepvariant_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix - ch_deepvariant_publish = CALL_SNV_DEEPVARIANT.out.publish + ch_deepvariant_vcf = CALL_SNV_DEEPVARIANT.out.vcf + ch_deepvariant_tbi = CALL_SNV_DEEPVARIANT.out.tabix + ch_deepvariant_gvcf = CALL_SNV_DEEPVARIANT.out.gvcf + ch_deepvariant_gtbi = CALL_SNV_DEEPVARIANT.out.gvcf_tabix + ch_deepvariant_report = CALL_SNV_DEEPVARIANT.out.deepvariant_report } else if (val_variant_caller.equals("sentieon")) { CALL_SNV_SENTIEON( ch_genome_bam_bai, @@ -140,10 +141,9 @@ workflow CALL_SNV { ch_mtshift_backchain, CALL_SNV_MT_SHIFT.out.vcf ) - ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf - ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi - ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) - ch_mt_snv_publish = POSTPROCESS_MT_CALLS.out.publish + ch_mt_vcf = POSTPROCESS_MT_CALLS.out.vcf + ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi + ch_mt_vcf_tabix = ch_mt_vcf.join(ch_mt_tabix, failOnMismatch:true, failOnDuplicate:true) } if (val_concatenate_snv_calls) { @@ -151,27 +151,22 @@ workflow CALL_SNV { BCFTOOLS_CONCAT ( ch_concat_vcf_in ) - ch_concat_publish = BCFTOOLS_CONCAT.out.vcf - .mix(BCFTOOLS_CONCAT.out.tbi) - .mix(BCFTOOLS_CONCAT.out.csi) - .map { meta, value -> ['call_snv/concatenated_calls/', [meta, value]] } + ch_bcftools_concat_vcf = BCFTOOLS_CONCAT.out.vcf + ch_bcftools_concat_tbi = BCFTOOLS_CONCAT.out.tbi + ch_bcftools_concat_csi = BCFTOOLS_CONCAT.out.csi } - ch_publish = GATK4_SELECTVARIANTS.out.vcf - .mix(GATK4_SELECTVARIANTS.out.tbi) - .mix(ch_deepvariant_publish) - .map { meta, value -> ['call_snv/genome/', [meta, value]] } - .mix(ch_concat_publish) - .mix(ch_mt_snv_publish) - emit: - genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] - genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] - genome_tabix = ch_genome_tabix // channel: [ val(meta), path(tbi) ] - genome_vcf = ch_genome_vcf // channel: [ val(meta), path(vcf) ] - genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] - mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] - mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] - mt_vcf_tbi = ch_mt_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + bcftools_concat_csi = ch_bcftools_concat_csi // channel: [ val(meta), path(csi) ] + bcftools_concat_tbi = ch_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + bcftools_concat_vcf = ch_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + deepvariant_report = ch_deepvariant_report // channel: [ val(meta), path(html) ] + genome_gtabix = ch_gtabix // channel: [ val(meta), path(gtbi) ] + genome_gvcf = ch_gvcf // channel: [ val(meta), path(gvcf) ] + genome_tabix = ch_genome_tabix // channel: [ val(meta), path(tbi) ] + genome_vcf = ch_genome_vcf // channel: [ val(meta), path(vcf) ] + genome_vcf_tabix = ch_genome_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi) ] + mt_tabix = ch_mt_tabix // channel: [ val(meta), path(tbi) ] + mt_vcf = ch_mt_vcf // channel: [ val(meta), path(vcf) ] + mt_vcf_tbi = ch_mt_vcf_tabix // channel: [ val(meta), path(vcf), path(tbi)] } diff --git a/subworkflows/local/call_snv_deepvariant/main.nf b/subworkflows/local/call_snv_deepvariant/main.nf index 0ac9d70fa..5faeb6641 100644 --- a/subworkflows/local/call_snv_deepvariant/main.nf +++ b/subworkflows/local/call_snv_deepvariant/main.nf @@ -25,8 +25,6 @@ workflow CALL_SNV_DEEPVARIANT { main: - ch_publish = channel.empty() - if (val_analysis_type.equals("wes")) { TABIX_BGZIP(ch_target_bed.map{meta, gzbed, _index -> return [meta, gzbed]}) ch_bam_bai @@ -85,12 +83,10 @@ workflow CALL_SNV_DEEPVARIANT { BCFTOOLS_ANNOTATE(ch_annotate_in) - ch_publish = DEEPVARIANT.out.report - emit: - gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] - gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] - publish = ch_publish // channel: [ val(meta), path(report) ] - tabix = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] + deepvariant_report = DEEPVARIANT.out.report // channel: [ val(meta), path(html) ] + gvcf = DEEPVARIANT.out.gvcf // channel: [ val(meta), path(gvcf)] + gvcf_tabix = DEEPVARIANT.out.gvcf_tbi // channel: [ val(meta), path(gvcf_tbi)] + tabix = BCFTOOLS_ANNOTATE.out.tbi // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test index 53de1dd91..f87da44b3 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test @@ -47,6 +47,7 @@ nextflow_workflow { { assert workflow.success }, { assert snapshot( path(workflow.out.vcf[0][1]).vcf.summary, + workflow.out.deepvariant_report.collect { meta, report -> file(report).name }, workflow.out.tabix.collect { meta, tbi -> file(tbi).name }, workflow.out.gvcf.collect { meta, gvcf -> file(gvcf).name } ).match() } diff --git a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap index 85701c2d3..a67a60a2b 100644 --- a/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv_deepvariant/tests/main.nf.test.snap @@ -4,6 +4,12 @@ [ [ "0", + [ + + ] + ], + [ + "1", [ [ { @@ -24,7 +30,7 @@ ] ], [ - "1", + "2", [ [ { @@ -44,12 +50,6 @@ ] ] ], - [ - "2", - [ - - ] - ], [ "3", [ @@ -72,6 +72,12 @@ ] ] ], + [ + "deepvariant_report", + [ + + ] + ], [ "gvcf", [ @@ -114,12 +120,6 @@ ] ] ], - [ - "publish", - [ - - ] - ], [ "tabix", [ @@ -144,15 +144,18 @@ ] ] ], - "timestamp": "2026-04-26T11:35:57.486021267", + "timestamp": "2026-05-29T18:32:43.797748048", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "CALL_SNV_DEEPVARIANT - wgs": { "content": [ "VcfFile [chromosomes=[MT, 21], sampleCount=1, variantCount=7601, phased=false, phasedAutodetect=false]", + [ + "earlycasualcaiman_deepvar.visual_report.html" + ], [ "justhusky_split_rmdup_info.vcf.gz.tbi" ], @@ -160,9 +163,9 @@ "earlycasualcaiman_deepvar.g.vcf.gz" ] ], - "timestamp": "2026-05-20T16:02:09.449313235", + "timestamp": "2026-05-29T20:33:43.828437561", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/postprocess_MT_calls/main.nf b/subworkflows/local/postprocess_MT_calls/main.nf index 758e9ec8d..39da37c68 100644 --- a/subworkflows/local/postprocess_MT_calls/main.nf +++ b/subworkflows/local/postprocess_MT_calls/main.nf @@ -120,12 +120,7 @@ workflow POSTPROCESS_MT_CALLS { TABIX_ANNOTATE(BCFTOOLS_ANNOTATE.out.vcf) - ch_publish = BCFTOOLS_ANNOTATE.out.vcf - .mix(TABIX_ANNOTATE.out.index) - .map { meta, value -> ['call_snv/mitochondria/', [meta, value]] } - emit: - tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] - vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + tbi = TABIX_ANNOTATE.out.index // channel: [ val(meta), path(tbi) ] + vcf = BCFTOOLS_ANNOTATE.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap index 6ddd843ef..373ecda38 100644 --- a/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap +++ b/subworkflows/local/postprocess_MT_calls/tests/main.nf.test.snap @@ -18,46 +18,6 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "2": [ - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "publish": [ - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], "tbi": [ [ { @@ -76,9 +36,9 @@ ] } ], - "timestamp": "2026-03-13T22:07:26.775535698", + "timestamp": "2026-05-29T16:03:50.71832229", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 689858a3b..d3885783d 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -241,7 +241,14 @@ workflow RAREDISEASE { ch_align_markdup_metrics = channel.empty() ch_subsample_mt_bam = channel.empty() ch_subsample_mt_bai = channel.empty() - ch_call_snv_publish = channel.empty() + ch_call_snv_bcftools_concat_csi = channel.empty() + ch_call_snv_bcftools_concat_tbi = channel.empty() + ch_call_snv_bcftools_concat_vcf = channel.empty() + ch_call_snv_deepvariant_report = channel.empty() + ch_call_snv_genome_tabix = channel.empty() + ch_call_snv_genome_vcf = channel.empty() + ch_call_snv_mt_tabix = channel.empty() + ch_call_snv_mt_vcf = channel.empty() ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() @@ -461,7 +468,14 @@ workflow RAREDISEASE { val_run_mt_for_wes, val_variant_caller ) - ch_call_snv_publish = CALL_SNV.out.publish + ch_call_snv_bcftools_concat_csi = CALL_SNV.out.bcftools_concat_csi + ch_call_snv_bcftools_concat_tbi = CALL_SNV.out.bcftools_concat_tbi + ch_call_snv_bcftools_concat_vcf = CALL_SNV.out.bcftools_concat_vcf + ch_call_snv_deepvariant_report = CALL_SNV.out.deepvariant_report + ch_call_snv_genome_tabix = CALL_SNV.out.genome_tabix + ch_call_snv_genome_vcf = CALL_SNV.out.genome_vcf + ch_call_snv_mt_tabix = CALL_SNV.out.mt_tabix + ch_call_snv_mt_vcf = CALL_SNV.out.mt_vcf // Removes vcfanno resource with empty records to keep vcfanno from crashing on those files ch_vcfanno_toml_final = ch_vcfanno_toml @@ -1066,19 +1080,26 @@ workflow RAREDISEASE { qc_bam_verifybamid_ud = QC_BAM.out.verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = QC_BAM.out.wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = QC_BAM.out.wgsmetrics_y // channel: [ val(meta), path(metrics) ] - annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] - annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] - annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] - annotate_genome_snvs_chromograph_regions_plots = ch_annotate_genome_snvs_chromograph_regions_plots // channel: [ val(meta), path(png) ] - annotate_genome_snvs_chromograph_sites_plots = ch_annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ] - annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] - annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] - annotate_genome_snvs_ucsc_wigtobigwig_bw = ch_annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + call_snv_bcftools_concat_csi = ch_call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] + call_snv_bcftools_concat_tbi = ch_call_snv_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + call_snv_bcftools_concat_vcf = ch_call_snv_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + call_snv_deepvariant_report = ch_call_snv_deepvariant_report // channel: [ val(meta), path(html) ] + call_snv_genome_tabix = ch_call_snv_genome_tabix // channel: [ val(meta), path(tbi) ] + call_snv_genome_vcf = ch_call_snv_genome_vcf // channel: [ val(meta), path(vcf) ] + call_snv_mt_tabix = ch_call_snv_mt_tabix // channel: [ val(meta), path(tbi) ] + call_snv_mt_vcf = ch_call_snv_mt_vcf // channel: [ val(meta), path(vcf) ] + annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] + annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] + annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots. // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_regions_plots = ch_annotate_genome_snvs_chromograph_regions_plots. // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_sites_plots = ch_annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] + annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] + annotate_genome_snvs_ucsc_wigtobigwig_bw = ch_annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions - publish = ch_call_snv_publish - .mix(ch_call_sv_publish) + publish = ch_call_sv_publish .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_mt_snvs_publish) From aad335512d16e813c7f8b33c1af500df1c4008db Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 May 2026 21:49:22 +0200 Subject: [PATCH 755/872] Update snap --- .../local/call_snv/tests/main.nf.test | 1 + .../local/call_snv/tests/main.nf.test.snap | 164 +++++++----------- 2 files changed, 66 insertions(+), 99 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 1c0a323c9..1c77541c8 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -75,6 +75,7 @@ nextflow_workflow { .sort(), path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, + workflow.out.deepvariant_report.collect { meta, report -> file(report).name }, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, workflow.out.mt_vcf.collect { meta, vcf -> file(vcf).name } ).match() } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 9991ce273..352b17b91 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -28,6 +28,53 @@ [ [ "0", + [ + + ] + ], + [ + "1", + [ + + ] + ], + [ + "10", + [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "11", + [ + [ + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "2", + [ + + ] + ], + [ + "3", + [ + + ] + ], + [ + "4", [ [ { @@ -48,7 +95,7 @@ ] ], [ - "1", + "5", [ [ { @@ -69,7 +116,7 @@ ] ], [ - "2", + "6", [ [ { @@ -80,7 +127,7 @@ ] ], [ - "3", + "7", [ [ { @@ -91,7 +138,7 @@ ] ], [ - "4", + "8", [ [ { @@ -103,7 +150,7 @@ ] ], [ - "5", + "9", [ [ { @@ -114,67 +161,27 @@ ] ], [ - "6", + "bcftools_concat_csi", [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ] ], [ - "7", + "bcftools_concat_tbi", [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], [ - "8", + "bcftools_concat_vcf", [ - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + + ] + ], + [ + "deepvariant_report", + [ + ] ], [ @@ -286,51 +293,10 @@ "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] - ], - [ - "publish", - [ - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/mitochondria/", - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_snv/genome/", - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ] ] ] ], - "timestamp": "2026-03-17T23:05:05.226361531", + "timestamp": "2026-05-29T20:52:18.39128556", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 9ac980b2eefffcfe941f0e27d0a795629cca0ba9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 May 2026 22:19:02 +0200 Subject: [PATCH 756/872] fix typo --- workflows/raredisease.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d3885783d..9dca43d44 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -1090,8 +1090,8 @@ workflow RAREDISEASE { call_snv_mt_vcf = ch_call_snv_mt_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] - annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots. // channel: [ val(meta), path(png) ] - annotate_genome_snvs_chromograph_regions_plots = ch_annotate_genome_snvs_chromograph_regions_plots. // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] + annotate_genome_snvs_chromograph_regions_plots = ch_annotate_genome_snvs_chromograph_regions_plots // channel: [ val(meta), path(png) ] annotate_genome_snvs_chromograph_sites_plots = ch_annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ] annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] From 728f677f5916682ef0a894f7786a192d1510c745 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 May 2026 23:51:27 +0200 Subject: [PATCH 757/872] fix typo --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 6d0269f48..efd744bd1 100644 --- a/main.nf +++ b/main.nf @@ -573,7 +573,7 @@ workflow NFCORE_RAREDISEASE { call_snv_genome_tabix = RAREDISEASE.out.call_snv_genome_tabix // channel: [ val(meta), path(tbi) ] call_snv_genome_vcf = RAREDISEASE.out.call_snv_genome_vcf // channel: [ val(meta), path(vcf) ] call_snv_mt_tabix = RAREDISEASE.out.call_snv_mt_tabix // channel: [ val(meta), path(tbi) ] - call_snv_mt_vcf = RAREDISEASE.out.call_snv_mt_vcf. // channel: [ val(meta), path(vcf) ] + call_snv_mt_vcf = RAREDISEASE.out.call_snv_mt_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] From f5d1a98499302c867cf64c2897f741b9ac5880b9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 29 May 2026 23:52:10 +0200 Subject: [PATCH 758/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e6081f6..800e163b3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_snv, call_snv_deepvariant, and postprocess_MT_calls subworkflows [#863](https://github.com/nf-core/raredisease/pull/863) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) - Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858) - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) From 0ba89f9d116184570fb98097015566b8a4e5c1f1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 30 May 2026 00:22:52 +0200 Subject: [PATCH 759/872] update snapshot --- subworkflows/local/call_snv/tests/main.nf.test | 7 ++----- .../local/call_snv/tests/main.nf.test.snap | 17 ++++++++--------- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 1c77541c8..17f3c821f 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -69,15 +69,12 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), path(workflow.out.genome_vcf[0][1]).vcf.variantsMD5, path(workflow.out.genome_vcf[0][1]).vcf.summary, workflow.out.deepvariant_report.collect { meta, report -> file(report).name }, workflow.out.genome_tabix.collect { meta, tbi -> file(tbi).name }, - workflow.out.mt_vcf.collect { meta, vcf -> file(vcf).name } + workflow.out.mt_vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.mt_tabix.collect { meta, tbi -> file(tbi).name } ).match() } ) } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index 352b17b91..c4f13d3f7 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -1,25 +1,24 @@ { "CALL_SNV - deepvariant wgs": { "content": [ - [ - "earlycasualcaiman_deepvar.visual_report.html", - "justhusky_mitochondria.vcf.gz", - "justhusky_mitochondria.vcf.gz.tbi", - "justhusky_snv.vcf.gz", - "justhusky_snv.vcf.gz.tbi" - ], "dfc0eeae02f4c1f04034e0fff555bf50", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=7562, phased=false, phasedAutodetect=false]", + [ + "earlycasualcaiman_deepvar.visual_report.html" + ], [ "justhusky_snv.vcf.gz.tbi" ], [ "justhusky_mitochondria.vcf.gz" + ], + [ + "justhusky_mitochondria.vcf.gz.tbi" ] ], - "timestamp": "2026-04-26T11:22:45.301474135", + "timestamp": "2026-05-30T00:18:20.446833954", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, From f9d47f5655822087f9896e5a896e3b1d8d233060 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 1 Jun 2026 09:34:40 +0200 Subject: [PATCH 760/872] add logic for missing saltshaker output --- subworkflows/local/call_sv_MT/main.nf | 2 +- subworkflows/local/call_sv_MT/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 25442948d..7309537ee 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -128,7 +128,7 @@ workflow CALL_SV_MT { .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } .join(ch_sample_id_map, remainder: true) .map { sample_meta, case_id, txt, cust_id -> - cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] + txt ? (cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id]) : [[],[],[]] } .groupTuple() .map { meta, paths, ids -> diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index dc8a4f047..a9e00b314 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -60,7 +60,7 @@ nextflow_workflow { ] ] ) - input[10] = channel.of([['id':'earlycasualcaiman'], 'cust_ecc'], [['id':'hugelymodelbat'], 'cust_hmb']) + input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc'], [[id:'hugelymodelbat'], 'cust_hmb']) input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) From 74c31b01b4936d208e2897a526244649483c7513 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 1 Jun 2026 11:57:41 +0200 Subject: [PATCH 761/872] test new saltshaker version --- modules/nf-core/saltshaker/call/main.nf | 8 ++++---- modules/nf-core/saltshaker/classify/main.nf | 6 +++--- subworkflows/local/call_sv_MT/main.nf | 12 ++++-------- 3 files changed, 11 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/saltshaker/call/main.nf b/modules/nf-core/saltshaker/call/main.nf index 7565ce603..f4567fd00 100644 --- a/modules/nf-core/saltshaker/call/main.nf +++ b/modules/nf-core/saltshaker/call/main.nf @@ -3,9 +3,9 @@ process SALTSHAKER_CALL { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': - 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(breakpoint), path(cluster) @@ -20,7 +20,7 @@ process SALTSHAKER_CALL { output: tuple val(meta), path("*_call_metadata.tsv"), emit: call - tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/saltshaker/classify/main.nf b/modules/nf-core/saltshaker/classify/main.nf index 72fa27c16..7ee84c9d4 100644 --- a/modules/nf-core/saltshaker/classify/main.nf +++ b/modules/nf-core/saltshaker/classify/main.nf @@ -3,9 +3,9 @@ process SALTSHAKER_CLASSIFY { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0c/0c955cc086622ef50876a10e58a1e6711e42b70a0e4cbbc377142b62b0ad4f47/data': - 'community.wave.seqera.io/library/pip_saltshaker:ef543ea5ca09afbe' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(call) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 7309537ee..eb3d726fa 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -95,12 +95,8 @@ workflow CALL_SV_MT { ch_mt_lastdb ) - MITOSALT.out.cluster - .filter { _meta, out -> out.countLines() > 0 } - .set { ch_cluster } - MITOSALT.out.breakpoint - .join(ch_cluster) + .join(MITOSALT.out.cluster) .set { ch_saltshaker_in } // Saltshaker modules will only run if mitosalt called SVs and created a cluster file @@ -128,7 +124,7 @@ workflow CALL_SV_MT { .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } .join(ch_sample_id_map, remainder: true) .map { sample_meta, case_id, txt, cust_id -> - txt ? (cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id]) : [[],[],[]] + cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] } .groupTuple() .map { meta, paths, ids -> @@ -174,8 +170,8 @@ workflow CALL_SV_MT { } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_saltshaker_html - .mix(ch_saltshaker_vcf) + ch_publish = ch_saltshaker_vcf + .mix(ch_saltshaker_html) .mix(ch_saltshaker_plot) .mix(MT_DELETION.out.mt_del_result) .map { meta, value -> ['call_sv/', [meta, value]] } From a5dfbac061b68d6b687aaaae7afdc9639f0c2c60 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 1 Jun 2026 12:05:44 +0200 Subject: [PATCH 762/872] fix config --- conf/test.config | 61 -- .../local/call_sv_MT/tests/main.nf.test.snap | 692 ------------------ 2 files changed, 753 deletions(-) delete mode 100644 conf/test.config delete mode 100644 subworkflows/local/call_sv_MT/tests/main.nf.test.snap diff --git a/conf/test.config b/conf/test.config deleted file mode 100644 index ca8827f4e..000000000 --- a/conf/test.config +++ /dev/null @@ -1,61 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/raredisease -profile test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '2.h' - ] -} - -env { - MPLCONFIGDIR="." -} - -params { - config_profile_name = 'Test profile - default' - config_profile_description = 'Minimal test dataset to check pipeline function' - - igenomes_ignore = true - mito_name = 'MT' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' - - skip_tools = 'fastp,gens,peddy,germlinecnvcaller,ngsbits' - - input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' - fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' - fai = params.pipelines_testdata_base_path + '/reference/reference.fasta.fai' - genome = 'GRCh37' - gnomad_af = params.pipelines_testdata_base_path + '/reference/gnomad_reformated.tab.gz' - intervals_wgs = params.pipelines_testdata_base_path + '/reference/target_wgs.interval_list' - intervals_y = params.pipelines_testdata_base_path + '/reference/targetY.interval_list' - known_dbsnp = params.pipelines_testdata_base_path + '/reference/dbsnp_-138-.vcf.gz' - mobile_element_references = params.pipelines_testdata_base_path + '/reference/mobile_element_references.tsv' - mobile_element_svdb_annotations = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv' - reduced_penetrance = params.pipelines_testdata_base_path + '/reference/reduced_penetrance.tsv' - score_config_mt = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini' - score_config_snv = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini' - score_config_sv = params.pipelines_testdata_base_path + '/reference/rank_model_sv.ini' - svdb_query_dbs = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv' - target_bed = params.pipelines_testdata_base_path + '/reference/target.bed' - variant_catalog = params.pipelines_testdata_base_path + '/reference/variant_catalog.json' - vcfanno_lua = params.pipelines_testdata_base_path + '/reference/vcfanno_functions.lua' - vcfanno_resources = params.pipelines_testdata_base_path + '/reference/vcfanno_resources.txt' - vcfanno_toml = params.pipelines_testdata_base_path + '/reference/vcfanno_config.toml' - variant_consequences_snv = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt' - variant_consequences_sv = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt' - vep_cache = params.pipelines_testdata_base_path + '/reference/vep_cache_and_plugins.tar.gz' - vep_filters = params.pipelines_testdata_base_path + '/reference/hgnc.txt' - vep_cache_version = 107 - vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' -} diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap deleted file mode 100644 index f1bf248d5..000000000 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ /dev/null @@ -1,692 +0,0 @@ -{ - "CALL_SV_MT - stub": { - "content": [ - [ - [ - "0", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "1", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ] - ], - [ - "2", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "3", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "4", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ], - [ - "5", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ] - ], - [ - "mt_del_result", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "publish", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ] - ], - [ - "saltshaker_html", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ] - ], - [ - "saltshaker_plot", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "saltshaker_vcf", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "updated_priority", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ] - ] - ], - "timestamp": "2026-05-28T09:55:09.413526846", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - }, - "CALL_SV_MT - no_sample_map - stub": { - "content": [ - [ - [ - "0", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "1", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" - ] - ] - ], - [ - "2", - [ - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "3", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "4", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ], - [ - "5", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - 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] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ] - ], - [ - "saltshaker_html", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,17f591b6b334aadda58f3efef7fe9125" - ] - ] - ], - [ - "saltshaker_plot", - [ - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "saltshaker_vcf", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "updated_priority", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ] - ] - ], - "timestamp": "2026-05-28T09:49:32.527998006", - "meta": { - "nf-test": "0.9.5", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file From ea69807bc2c46dfd5f23cfad0e923609d66b4a97 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Jun 2026 14:21:53 +0200 Subject: [PATCH 763/872] Add cadd_prescored --- CHANGELOG.md | 4 + main.nf | 4 + nextflow.config | 1 + nextflow_schema.json | 8 ++ subworkflows/local/annotate_cadd/main.nf | 13 ++-- .../local/annotate_cadd/tests/main.nf.test | 18 +++-- .../local/annotate_genome_snvs/main.nf | 4 +- .../annotate_genome_snvs/tests/main.nf.test | 74 ++++++++++--------- subworkflows/local/annotate_mt_snvs/main.nf | 6 +- .../local/annotate_mt_snvs/tests/main.nf.test | 29 ++++---- workflows/raredisease.nf | 3 + 11 files changed, 97 insertions(+), 67 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d049cf01..647f24b5f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## 3.0.1 - Mario-patch [2026-05-25] +### `Added` + +- Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows + ### `Fixed` - Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#854](https://github.com/nf-core/raredisease/pull/854) diff --git a/main.nf b/main.nf index f847e20e6..881cd401b 100644 --- a/main.nf +++ b/main.nf @@ -48,6 +48,7 @@ workflow NFCORE_RAREDISEASE { val_bwa val_bwamem2 val_bwameme + val_cadd_prescored val_cadd_resources val_call_interval val_concatenate_snv_calls @@ -233,6 +234,7 @@ workflow NFCORE_RAREDISEASE { ch_svd_ud = channelFromPath(val_verifybamid_svd_ud) // Using channelFromPathWithMeta helper (with simpleName). If filepath is null, returns, [[:],[]] + ch_cadd_prescored = channelFromPathWithMeta(val_cadd_prescored, true) ch_cadd_resources = channelFromPathWithMeta(val_cadd_resources, true) ch_call_interval = channelFromPathWithMeta(val_call_interval, true) ch_ml_model = channelFromPathWithMeta(val_ml_model, true) @@ -378,6 +380,7 @@ workflow NFCORE_RAREDISEASE { ch_alignments, ch_bait_intervals, ch_cadd_header, + ch_cadd_prescored, ch_cadd_resources, ch_call_interval, ch_case_info, @@ -566,6 +569,7 @@ workflow { params.bwa, params.bwamem2, params.bwameme, + params.cadd_prescored, params.cadd_resources, params.call_interval, params.concatenate_snv_calls, diff --git a/nextflow.config b/nextflow.config index 4baa3cf23..6c6fdb6d4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -53,6 +53,7 @@ params { bwamem2 = null bwameme = null call_interval = null + cadd_prescored = null cadd_resources = null gcnvcaller_model = null gens_interval_list = null diff --git a/nextflow_schema.json b/nextflow_schema.json index a5b135431..e6016072f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -81,6 +81,14 @@ "help_text": "If none provided, will be generated automatically from the FASTA reference.", "fa_icon": "fas fa-folder-open" }, + "cadd_prescored": { + "type": "string", + "exists": true, + "format": "directory-path", + "fa_icon": "fas fa-folder-open", + "description": "Path to the directory containing pre-scored CADD indel annotations.", + "help_text": "This folder contains the pre-scored indel files that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation." + }, "cadd_resources": { "type": "string", "exists": true, diff --git a/subworkflows/local/annotate_cadd/main.nf b/subworkflows/local/annotate_cadd/main.nf index 5b8d3369a..92f0b6d5d 100644 --- a/subworkflows/local/annotate_cadd/main.nf +++ b/subworkflows/local/annotate_cadd/main.nf @@ -13,11 +13,12 @@ include { TABIX_TABIX as TABIX_CADD } from '../../../modules/nf-core/ workflow ANNOTATE_CADD { take: - ch_cadd_resources // channel: [mandatory] [ path(dir) ] - ch_fai // channel: [optional] [ path(fai) ] - ch_header // channel: [mandatory] [ path(txt) ] - ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] - val_genome // string: GRCh37 or GRCh38 + ch_cadd_resources // channel: [mandatory] [ val(meta), path(dir) ] + ch_cadd_prescored // channel: [optional] [ val(meta), path(prescored) ] + ch_fai // channel: [optional] [ val(meta), path(fai) ] + ch_header // channel: [mandatory] [ path(txt) ] + ch_vcf // channel: [mandatory] [ val(meta), path(vcfs), path(idx) ] + val_genome // string: GRCh37 or GRCh38 main: ch_rename_chrs = channel.value([[]]) @@ -45,7 +46,7 @@ workflow ANNOTATE_CADD { BCFTOOLS_VIEW(ch_vcf, [], [], []) - CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, [[:], []]) + CADD(BCFTOOLS_VIEW.out.vcf, ch_cadd_resources, ch_cadd_prescored) TABIX_CADD(CADD.out.tsv) diff --git a/subworkflows/local/annotate_cadd/tests/main.nf.test b/subworkflows/local/annotate_cadd/tests/main.nf.test index de40e5fe4..d5afb3bb3 100644 --- a/subworkflows/local/annotate_cadd/tests/main.nf.test +++ b/subworkflows/local/annotate_cadd/tests/main.nf.test @@ -26,14 +26,15 @@ nextflow_workflow { workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() - input[3] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() + input[4] = channel.of([ [id:'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) - input[4] = 'GRCh37' + input[5] = 'GRCh37' """ } } @@ -57,14 +58,15 @@ nextflow_workflow { workflow { """ input[0] = Channel.from("\$PWD").map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[1] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[2] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() - input[3] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[3] = channel.of(file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)).collect() + input[4] = channel.of([ [id:'test', single_end: false], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) - input[4] = 'GRCh38' + input[5] = 'GRCh38' """ } } diff --git a/subworkflows/local/annotate_genome_snvs/main.nf b/subworkflows/local/annotate_genome_snvs/main.nf index 64de7e73a..f0e3af434 100644 --- a/subworkflows/local/annotate_genome_snvs/main.nf +++ b/subworkflows/local/annotate_genome_snvs/main.nf @@ -21,7 +21,8 @@ workflow ANNOTATE_GENOME_SNVS { take: ch_cadd_header // channel: [mandatory] [ path(txt) ] - ch_cadd_resources // channel: [mandatory] [ path(annotation) ] + ch_cadd_prescored // channel: [optional] [ val(meta), path(prescored) ] + ch_cadd_resources // channel: [mandatory] [ val(meta), path(annotation) ] ch_genome_chrsizes // channel: [mandatory] [ path(sizes) ] ch_genome_fai // channel: [mandatory] [ path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] @@ -121,6 +122,7 @@ workflow ANNOTATE_GENOME_SNVS { ANNOTATE_CADD ( ch_cadd_resources, + ch_cadd_prescored, ch_genome_fai, ch_cadd_header, ch_cadd_in, diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index 0b6b95c53..cdb8ca0e7 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -30,28 +30,29 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = channel.value([[],[]]) - input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) - input[8] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[6] = channel.value([[],[]]) + input[7] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[9] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) - input[9] = channel.value([[]]) - input[10] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() - input[11] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) - input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() - input[14] = channel.value([]) - input[15] = 'wgs' - input[16] = null - input[17] = 'GRCh37' - input[18] = 107 + input[10] = channel.value([[]]) + input[11] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[12] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[14] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[15] = channel.value([]) + input[16] = 'wgs' + input[17] = null + input[18] = 'GRCh37' + input[19] = 107 """ } } @@ -86,28 +87,29 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() - input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() - input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = channel.value([[],[]]) - input[6] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) - input[8] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = Channel.from(env('PWD')).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[3] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[6] = channel.value([[],[]]) + input[7] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[9] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ]) - input[9] = channel.value([[]]) - input[10] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() - input[11] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) - input[12] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() - input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() - input[14] = channel.value([]) - input[15] = 'wes' - input[16] = null - input[17] = 'GRCh37' - input[18] = 107 + input[10] = channel.value([[]]) + input[11] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[12] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[13] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[14] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[15] = channel.value([]) + input[16] = 'wes' + input[17] = null + input[18] = 'GRCh37' + input[19] = 107 """ } } diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index 5b80e5132..c95545993 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -12,9 +12,10 @@ include { VCFANNO as VCFANNO_MT } from '../../../modules/nf-core/vcf workflow ANNOTATE_MT_SNVS { take: ch_cadd_header // channel: [mandatory] [ path(txt) ] - ch_cadd_resources // channel: [mandatory] [ path(annotation) ] + ch_cadd_prescored // channel: [optional] [ val(meta), path(prescored) ] + ch_cadd_resources // channel: [mandatory] [ val(meta), path(annotation) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_fai // channel: [mandatory] [ path(fai) ] + ch_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_mt_vcf_tbi // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] ch_vcfanno_extra // channel: [mandatory] [ [path(vcf),path(index)] ] ch_vcfanno_lua // channel: [mandatory] [ path(lua) ] @@ -40,6 +41,7 @@ workflow ANNOTATE_MT_SNVS { if (!val_cadd_resources.equals(null)) { ANNOTATE_CADD ( ch_cadd_resources, + ch_cadd_prescored, ch_fai, ch_cadd_header, VCFANNO_MT.out.vcf.join(VCFANNO_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true), diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 63910dd93..7935ee805 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -28,24 +28,25 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[2] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[4] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[5] = channel.of([ [id:'justhusky', case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz.tbi', checkIfExists: true), ]) - input[5] = channel.value([[]]) - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() - input[7] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() - input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() - input[10] = channel.value([]) - input[11] = null - input[12] = 'GRCh37' - input[13] = 1.0 - input[14] = 107 + input[6] = channel.value([[]]) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[8] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[10] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() + input[11] = channel.value([]) + input[12] = null + input[13] = 'GRCh37' + input[14] = 1.0 + input[15] = 107 """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b3b1c1470..b514dd6c5 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -80,6 +80,7 @@ workflow RAREDISEASE { ch_alignments ch_bait_intervals ch_cadd_header + ch_cadd_prescored ch_cadd_resources ch_call_interval ch_case_info @@ -460,6 +461,7 @@ workflow RAREDISEASE { ANNOTATE_GENOME_SNVS ( ch_cadd_header, + ch_cadd_prescored, ch_cadd_resources, ch_genome_chrsizes, ch_genome_fai, @@ -535,6 +537,7 @@ workflow RAREDISEASE { ANNOTATE_MT_SNVS ( ch_cadd_header, + ch_cadd_prescored, ch_cadd_resources, ch_genome_fasta, ch_genome_fai, From 842e71f425f45cb55f5b89073bccc494f59d2934 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Jun 2026 14:30:16 +0200 Subject: [PATCH 764/872] add option to specify callregions for manta --- CHANGELOG.md | 1 + main.nf | 6 +++ nextflow.config | 1 + nextflow_schema.json | 9 ++++ .../local/call_structural_variants/main.nf | 3 +- .../tests/main.nf.test | 47 ++++++++++--------- subworkflows/local/call_sv_manta/main.nf | 7 +-- .../local/call_sv_manta/tests/main.nf.test | 6 ++- workflows/raredisease.nf | 2 + 9 files changed, 53 insertions(+), 29 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 647f24b5f..44a0bcd52 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows +- Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers ### `Fixed` diff --git a/main.nf b/main.nf index 881cd401b..49aa40b2e 100644 --- a/main.nf +++ b/main.nf @@ -74,6 +74,7 @@ workflow NFCORE_RAREDISEASE { val_known_dbsnp_tbi val_light_strand_origin_end val_light_strand_origin_start + val_manta_call_regions val_mbuffer_mem val_mito_length val_mito_name @@ -262,6 +263,9 @@ workflow NFCORE_RAREDISEASE { ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() + ch_manta_call_regions = val_manta_call_regions + ? channel.value([file(val_manta_call_regions), file("${val_manta_call_regions}.tbi")]) + : channel.value([[], []]) ch_ngsbits_method = channel.value(val_ngsbits_samplegender_method) ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model) ch_subdepth = channel.value(val_subdepth) @@ -404,6 +408,7 @@ workflow NFCORE_RAREDISEASE { ch_hgnc_ids, ch_intervals_wgs, ch_intervals_y, + ch_manta_call_regions, ch_me_references, ch_me_svdb_resources, ch_ml_model, @@ -595,6 +600,7 @@ workflow { params.known_dbsnp_tbi, params.light_strand_origin_end, params.light_strand_origin_start, + params.manta_call_regions, params.mbuffer_mem, params.mito_length, params.mito_name, diff --git a/nextflow.config b/nextflow.config index 6c6fdb6d4..7aeb5d817 100644 --- a/nextflow.config +++ b/nextflow.config @@ -55,6 +55,7 @@ params { call_interval = null cadd_prescored = null cadd_resources = null + manta_call_regions = null gcnvcaller_model = null gens_interval_list = null gens_pon_female = null diff --git a/nextflow_schema.json b/nextflow_schema.json index e6016072f..87f6db9c4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -243,6 +243,15 @@ "description": "Local directory base for genome references that map to the config.", "help_text": "This folder is a flat structure with file names that map to the config." }, + "manta_call_regions": { + "type": "string", + "exists": true, + "format": "file-path", + "fa_icon": "fas fa-file", + "pattern": "^\\S+\\.bed\\.gz$", + "description": "Path to a bgzipped, tabix-indexed BED file restricting Manta SV calling to specific regions (e.g. primary chromosomes). Only applied for WGS; for WES, Manta always uses target_bed instead.", + "help_text": "A tabix index (.bed.gz.tbi) must exist alongside the file. Only used when analysis_type is wgs — for wes, Manta uses the target_bed supplied via --target_bed and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38." + }, "mito_name": { "type": "string", "description": "Name of the mitochondrial contig in the reference fasta file", diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index b5407b11e..0bcabc350 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -24,6 +24,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] + ch_manta_call_regions // channel: [optional] [ path(bed), path(tbi) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] @@ -59,7 +60,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_tiddit_vcf = channel.empty() if (!val_analysis_type.equals("mito")) { - CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) + CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, ch_manta_call_regions, val_analysis_type) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } .set{ ch_manta_vcf } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index f2d69db9d..b4d429f67 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -42,39 +42,40 @@ nextflow_workflow { input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } - input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[12] = channel.of([ + input[11] = channel.value([[], []]) + input[12] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[13] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) ]) - input[13] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[15] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } - input[16] = channel.of([[id:'ploidy'], []]) - input[17] = channel.of([[]]) - input[18] = channel.of([ + input[14] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[15] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[16] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[17] = channel.of([[id:'ploidy'], []]) + input[18] = channel.of([[]]) + input[19] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[19] = channel.value(10000000) - input[20] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[21] = channel.of([[id:'target'], [], []]) - input[22] = true - input[23] = false - input[24] = 'wgs' - input[25] = 407 - input[26] = 16081 - input[27] = 5763 - input[28] = 5730 - input[29] = 16569 - input[30] = 'MT' - input[31] = 15 - input[32] = 0.01 - input[33] = true + input[20] = channel.value(10000000) + input[21] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[22] = channel.of([[id:'target'], [], []]) + input[23] = true + input[24] = false + input[25] = 'wgs' + input[26] = 407 + input[27] = 16081 + input[28] = 5763 + input[29] = 5730 + input[30] = 16569 + input[31] = 'MT' + input[32] = 15 + input[33] = 0.01 + input[34] = true """ } } diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index 3a514c3ec..b481fd90f 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -12,8 +12,9 @@ workflow CALL_SV_MANTA { ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] - val_analysis_type // string: "wes", "wgs", or "mito" + ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] + ch_manta_call_regions // channel: [optional] [ path(bed), path(tbi) ] + val_analysis_type // string: "wes", "wgs", or "mito" main: ch_bam.map{ _meta, bam -> bam } @@ -34,7 +35,7 @@ workflow CALL_SV_MANTA { if (val_analysis_type.equals("wgs")) { ch_case_info.combine(bam_file_list) .combine(bai_file_list) - .map { meta, input, index -> [meta, input, index] + [ [], [] ] } + .combine(ch_manta_call_regions) .set { manta_input } MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] ) } else { diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test index fd43a3cda..6bf572265 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -37,7 +37,8 @@ nextflow_workflow { input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() input[4] = channel.of([id:'justhusky']) input[5] = channel.of([[id:'target'], [], []]) - input[6] = 'wgs' + input[6] = channel.value([[], []]) + input[7] = 'wgs' """ } } @@ -79,7 +80,8 @@ nextflow_workflow { input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() input[4] = channel.of([id:'justhusky']) input[5] = channel.of([[id:'target'], [], []]) - input[6] = 'wgs' + input[6] = channel.value([[], []]) + input[7] = 'wgs' """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index b514dd6c5..445c1e055 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -104,6 +104,7 @@ workflow RAREDISEASE { ch_hgnc_ids ch_intervals_wgs ch_intervals_y + ch_manta_call_regions ch_me_references ch_me_svdb_resources ch_ml_model @@ -636,6 +637,7 @@ workflow RAREDISEASE { ch_genome_fai, ch_genome_fasta, ch_genome_hisat2index, + ch_manta_call_regions, ch_mitosalt_config, ch_mapped.mt_bam_bai, ch_mt_fai, From 646c6b8e187448295d4f23bead36180e807497be Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Jun 2026 14:31:42 +0200 Subject: [PATCH 765/872] update usage --- docs/usage.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index e5963d4d2..f40ac9114 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -263,10 +263,13 @@ The mandatory and optional parameters for each category are tabulated below. ##### 5. Variant calling - Structural variants -| Mandatory | Optional | -| --------- | ---------- | -| | target_bed | -| | bwa | +| Mandatory | Optional | +| --------- | --------------------------------- | +| | target_bed | +| | bwa | +| | manta_call_regions1 | + +1 A bgzipped, tabix-indexed BED file (`.bed.gz` + `.bed.gz.tbi`) restricting Manta's SV calling to specific regions. Only applied for WGS; for WES, Manta always uses `target_bed` and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38 by limiting analysis to primary chromosomes. ##### 6. Copy number variant calling From 9bcbde83d7a7c2c1f693476ba03c3848648dd0c3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 1 Jun 2026 14:32:05 +0200 Subject: [PATCH 766/872] update snapshot --- tests/default.nf.test.snap | 5 ++++- tests/test_bam.nf.test.snap | 7 +++++-- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ea6fc5d95..736873282 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -384,6 +384,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPLIT_MULTIALLELICS_POSTMERGE_MT": { + "bcftools": 1.22 + }, "SPRING_DECOMPRESS_TO_FQ_PAIR": { "spring": "1.1.1" }, @@ -928,7 +931,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-08T16:30:33.887641119", + "timestamp": "2026-06-01T14:09:20.631591498", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index e26145db1..a9bee2fd8 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_bam": { "content": [ - 773, + 774, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -345,6 +345,9 @@ "SPLIT_MULTIALLELICS_MT": { "bcftools": 1.22 }, + "SPLIT_MULTIALLELICS_POSTMERGE_MT": { + "bcftools": 1.22 + }, "STRANGER": { "stranger": "0.10.0", "tabix": 1.23 @@ -844,7 +847,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-04-29T22:26:48.082490207", + "timestamp": "2026-06-01T14:15:55.418513656", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From c82ad0a760fc06c91879aba5ae67cb0e98dcda5b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 1 Jun 2026 12:47:58 +0000 Subject: [PATCH 767/872] [automated] Fix code linting --- docs/usage.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index f40ac9114..44e8d125f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -263,11 +263,11 @@ The mandatory and optional parameters for each category are tabulated below. ##### 5. Variant calling - Structural variants -| Mandatory | Optional | -| --------- | --------------------------------- | -| | target_bed | -| | bwa | -| | manta_call_regions1 | +| Mandatory | Optional | +| --------- | ------------------------------ | +| | target_bed | +| | bwa | +| | manta_call_regions1 | 1 A bgzipped, tabix-indexed BED file (`.bed.gz` + `.bed.gz.tbi`) restricting Manta's SV calling to specific regions. Only applied for WGS; for WES, Manta always uses `target_bed` and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38 by limiting analysis to primary chromosomes. From 1f645875bcecc2ade9fec5b2e6d261a66625c0f8 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 1 Jun 2026 15:20:52 +0200 Subject: [PATCH 768/872] test update saltshaker plot --- modules/nf-core/saltshaker/plot/main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/saltshaker/plot/main.nf b/modules/nf-core/saltshaker/plot/main.nf index 56e7b9a3e..fc1555635 100644 --- a/modules/nf-core/saltshaker/plot/main.nf +++ b/modules/nf-core/saltshaker/plot/main.nf @@ -3,16 +3,16 @@ process SALTSHAKER_PLOT { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': - 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(classify) output: tuple val(meta), path("*saltshaker.png"), emit: plot - tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when From ef9950131bca9722e5796f55c3f339185c377a2f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 2 Jun 2026 09:04:43 +0200 Subject: [PATCH 769/872] add a separate param for manta call region tbi --- docs/usage.md | 3 ++- main.nf | 4 +++- nextflow.config | 1 + nextflow_schema.json | 12 ++++++++++-- 4 files changed, 16 insertions(+), 4 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index f40ac9114..936d18464 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -268,8 +268,9 @@ The mandatory and optional parameters for each category are tabulated below. | | target_bed | | | bwa | | | manta_call_regions1 | +| | manta_call_regions_tbi1 | -1 A bgzipped, tabix-indexed BED file (`.bed.gz` + `.bed.gz.tbi`) restricting Manta's SV calling to specific regions. Only applied for WGS; for WES, Manta always uses `target_bed` and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38 by limiting analysis to primary chromosomes. +1 A bgzipped BED file (`.bed.gz`) and its tabix index (`.bed.gz.tbi`) restricting Manta's SV calling to specific regions. Both parameters must be supplied together. Only applied for WGS; for WES, Manta always uses `target_bed` and these parameters have no effect. Useful for reducing runtime on references with many short contigs such as GRCh38 by limiting analysis to primary chromosomes. ##### 6. Copy number variant calling diff --git a/main.nf b/main.nf index 49aa40b2e..4052e744b 100644 --- a/main.nf +++ b/main.nf @@ -75,6 +75,7 @@ workflow NFCORE_RAREDISEASE { val_light_strand_origin_end val_light_strand_origin_start val_manta_call_regions + val_manta_call_regions_tbi val_mbuffer_mem val_mito_length val_mito_name @@ -264,7 +265,7 @@ workflow NFCORE_RAREDISEASE { ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() ch_manta_call_regions = val_manta_call_regions - ? channel.value([file(val_manta_call_regions), file("${val_manta_call_regions}.tbi")]) + ? channel.value([file(val_manta_call_regions), file(val_manta_call_regions_tbi)]) : channel.value([[], []]) ch_ngsbits_method = channel.value(val_ngsbits_samplegender_method) ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model) @@ -601,6 +602,7 @@ workflow { params.light_strand_origin_end, params.light_strand_origin_start, params.manta_call_regions, + params.manta_call_regions_tbi, params.mbuffer_mem, params.mito_length, params.mito_name, diff --git a/nextflow.config b/nextflow.config index 7aeb5d817..858381fdf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -56,6 +56,7 @@ params { cadd_prescored = null cadd_resources = null manta_call_regions = null + manta_call_regions_tbi = null gcnvcaller_model = null gens_interval_list = null gens_pon_female = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 87f6db9c4..5529d2a94 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -249,8 +249,16 @@ "format": "file-path", "fa_icon": "fas fa-file", "pattern": "^\\S+\\.bed\\.gz$", - "description": "Path to a bgzipped, tabix-indexed BED file restricting Manta SV calling to specific regions (e.g. primary chromosomes). Only applied for WGS; for WES, Manta always uses target_bed instead.", - "help_text": "A tabix index (.bed.gz.tbi) must exist alongside the file. Only used when analysis_type is wgs — for wes, Manta uses the target_bed supplied via --target_bed and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38." + "description": "Path to a bgzipped BED file restricting Manta SV calling to specific regions (e.g. primary chromosomes). Only applied for WGS; for WES, Manta always uses target_bed instead.", + "help_text": "Must be supplied together with --manta_call_regions_tbi. Only used when analysis_type is wgs — for wes, Manta uses the target_bed supplied via --target_bed and this parameter has no effect. Useful for reducing runtime on references with many short contigs such as GRCh38." + }, + "manta_call_regions_tbi": { + "type": "string", + "exists": true, + "format": "file-path", + "fa_icon": "fas fa-file", + "pattern": "^\\S+\\.bed\\.gz\\.tbi$", + "description": "Tabix index for the file supplied via --manta_call_regions." }, "mito_name": { "type": "string", From 8a635850afb241dcdfce04e8fa6e0f946cbf8e67 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 2 Jun 2026 09:08:41 +0200 Subject: [PATCH 770/872] update changelog --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 399e303ab..a2af31746 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#855](https://github.com/nf-core/raredisease/pull/855) +### Parameters + +| Old parameter | New parameter | +| ------------- | ---------------------- | +| | cadd_prescored | +| | manta_call_regions | +| | manta_call_regions_tbi | + ## 3.0.0 - Mario [2026-05-12] ### `Added` From aa58f164edfbf1880b5ffe8e6a79e85b3549a5e3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 3 Jun 2026 11:48:47 +0200 Subject: [PATCH 771/872] move logic upstream --- main.nf | 10 +++-- .../local/call_structural_variants/main.nf | 5 +-- .../tests/main.nf.test | 25 ++++++------- .../tests/main.nf.test.snap | 4 +- subworkflows/local/call_sv_manta/main.nf | 37 ++++++------------- .../local/call_sv_manta/tests/main.nf.test | 12 ++---- .../call_sv_manta/tests/main.nf.test.snap | 12 +++--- workflows/raredisease.nf | 5 +-- 8 files changed, 45 insertions(+), 65 deletions(-) diff --git a/main.nf b/main.nf index 4052e744b..ab4402c72 100644 --- a/main.nf +++ b/main.nf @@ -264,9 +264,11 @@ workflow NFCORE_RAREDISEASE { ch_cadd_header = channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect() ch_foundin_header = channel.fromPath("$projectDir/assets/foundin.hdr", checkIfExists: true).collect() - ch_manta_call_regions = val_manta_call_regions - ? channel.value([file(val_manta_call_regions), file(val_manta_call_regions_tbi)]) - : channel.value([[], []]) + ch_manta_regions = val_analysis_type.equals("wgs") + ? (val_manta_call_regions + ? channel.value([file(val_manta_call_regions), file(val_manta_call_regions_tbi)]) + : channel.value([[], []])) + : ch_target_bed.map { _meta, bed, tbi -> [bed, tbi] } ch_ngsbits_method = channel.value(val_ngsbits_samplegender_method) ch_sentieon_pcr_indel_model = channel.value(val_sentieon_dnascope_pcr_indel_model) ch_subdepth = channel.value(val_subdepth) @@ -409,7 +411,7 @@ workflow NFCORE_RAREDISEASE { ch_hgnc_ids, ch_intervals_wgs, ch_intervals_y, - ch_manta_call_regions, + ch_manta_regions, ch_me_references, ch_me_svdb_resources, ch_ml_model, diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 0bcabc350..871914722 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -24,7 +24,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_genome_hisat2index // channel: [mandatory] [ val(meta), path(hisat2index) ] - ch_manta_call_regions // channel: [optional] [ path(bed), path(tbi) ] + ch_manta_regions // channel: [mandatory] [ path(bed), path(tbi) ] ch_mitosalt_config // channel: [mandatory] [val(mitosalt_breakspan),val(mitosalt_breakthreshold),...,val(mitosalt_split_length)] ch_mt_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ] ch_mt_fai // channel: [mandatory] [ val(meta), path(mtfai) ] @@ -35,7 +35,6 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] - ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] skip_germlinecnvcaller // boolean skip_mitosalt // boolean val_analysis_type // string: "wes", "wgs", or "mito" @@ -60,7 +59,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_tiddit_vcf = channel.empty() if (!val_analysis_type.equals("mito")) { - CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, ch_manta_call_regions, val_analysis_type) + CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_manta_regions) .filtered_diploid_sv_vcf .collect{ _meta, vcf -> vcf } .set{ ch_manta_vcf } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index b4d429f67..f4287b53b 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -63,19 +63,18 @@ nextflow_workflow { ]) input[20] = channel.value(10000000) input[21] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[22] = channel.of([[id:'target'], [], []]) - input[23] = true - input[24] = false - input[25] = 'wgs' - input[26] = 407 - input[27] = 16081 - input[28] = 5763 - input[29] = 5730 - input[30] = 16569 - input[31] = 'MT' - input[32] = 15 - input[33] = 0.01 - input[34] = true + input[22] = true + input[23] = false + input[24] = 'wgs' + input[25] = 407 + input[26] = 16081 + input[27] = 5763 + input[28] = 5730 + input[29] = 16569 + input[30] = 'MT' + input[31] = 15 + input[32] = 0.01 + input[33] = true """ } } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index d3b9e9234..3b8a5f36c 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -16,10 +16,10 @@ "justhusky_sv.vcf.gz.tbi" ] ], + "timestamp": "2026-04-14T15:51:47.077800376", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" - }, - "timestamp": "2026-04-14T15:51:47.077800376" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf index b481fd90f..2c01d251f 100644 --- a/subworkflows/local/call_sv_manta/main.nf +++ b/subworkflows/local/call_sv_manta/main.nf @@ -7,14 +7,12 @@ include { MANTA_GERMLINE as MANTA } from '../../../modules/nf-core/ workflow CALL_SV_MANTA { take: - ch_bam // channel: [mandatory] [ val(meta), path(bam) ] - ch_bai // channel: [mandatory] [ val(meta), path(bai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_case_info // channel: [mandatory] [ val(case_info) ] - ch_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] - ch_manta_call_regions // channel: [optional] [ path(bed), path(tbi) ] - val_analysis_type // string: "wes", "wgs", or "mito" + ch_bam // channel: [mandatory] [ val(meta), path(bam) ] + ch_bai // channel: [mandatory] [ val(meta), path(bai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_case_info // channel: [mandatory] [ val(case_info) ] + ch_regions // channel: [mandatory] [ path(bed), path(tbi) ] main: ch_bam.map{ _meta, bam -> bam } @@ -27,24 +25,11 @@ workflow CALL_SV_MANTA { .toList() .set { bai_file_list } - ch_bed.map { - _id, bed_file, index -> - return [bed_file, index]} - .set { bed_input } - - if (val_analysis_type.equals("wgs")) { - ch_case_info.combine(bam_file_list) - .combine(bai_file_list) - .combine(ch_manta_call_regions) - .set { manta_input } - MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] ) - } else { - ch_case_info.combine(bam_file_list) - .combine(bai_file_list) - .combine(bed_input) - .set { manta_input } - MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] ) - } + ch_case_info.combine(bam_file_list) + .combine(bai_file_list) + .combine(ch_regions) + .set { manta_input } + MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] ) MANTA.out.diploid_sv_vcf .join(MANTA.out.diploid_sv_vcf_tbi) diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test b/subworkflows/local/call_sv_manta/tests/main.nf.test index 6bf572265..1757244d9 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test @@ -12,7 +12,7 @@ nextflow_workflow { config "./nextflow.config" - test("CALL_SV_MANTA - wgs") { + test("CALL_SV_MANTA") { when { workflow { @@ -36,9 +36,7 @@ nextflow_workflow { input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() input[4] = channel.of([id:'justhusky']) - input[5] = channel.of([[id:'target'], [], []]) - input[6] = channel.value([[], []]) - input[7] = 'wgs' + input[5] = channel.value([[], []]) """ } } @@ -53,7 +51,7 @@ nextflow_workflow { ) } } - test("CALL_SV_MANTA - wgs, stub") { + test("CALL_SV_MANTA - stub") { options "-stub" @@ -79,9 +77,7 @@ nextflow_workflow { input[2] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() input[3] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() input[4] = channel.of([id:'justhusky']) - input[5] = channel.of([[id:'target'], [], []]) - input[6] = channel.value([[], []]) - input[7] = 'wgs' + input[5] = channel.value([[], []]) """ } } diff --git a/subworkflows/local/call_sv_manta/tests/main.nf.test.snap b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap index cbc481726..b2b600081 100644 --- a/subworkflows/local/call_sv_manta/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_manta/tests/main.nf.test.snap @@ -1,16 +1,16 @@ { - "CALL_SV_MANTA - wgs": { + "CALL_SV_MANTA": { "content": [ "9f37331609347a1685ba4862d8583b2f", "2111e88e54fdd01f0492901606bcea6f" ], - "timestamp": "2026-03-01T20:55:33.556714847", + "timestamp": "2026-06-03T11:38:41.791162924", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, - "CALL_SV_MANTA - wgs, stub": { + "CALL_SV_MANTA - stub": { "content": [ { "0": [ @@ -127,9 +127,9 @@ ] } ], - "timestamp": "2026-03-05T12:58:54.578278212", + "timestamp": "2026-06-03T11:39:05.440330127", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 445c1e055..420c43c7f 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -104,7 +104,7 @@ workflow RAREDISEASE { ch_hgnc_ids ch_intervals_wgs ch_intervals_y - ch_manta_call_regions + ch_manta_regions ch_me_references ch_me_svdb_resources ch_ml_model @@ -637,7 +637,7 @@ workflow RAREDISEASE { ch_genome_fai, ch_genome_fasta, ch_genome_hisat2index, - ch_manta_call_regions, + ch_manta_regions, ch_mitosalt_config, ch_mapped.mt_bam_bai, ch_mt_fai, @@ -648,7 +648,6 @@ workflow RAREDISEASE { ch_input_fastqs, ch_subdepth, ch_svcaller_priority, - ch_target_bed, skip_germlinecnvcaller, skip_mitosalt, val_analysis_type, From d2672d87cc7dd427dff01f8b548699b3ed1c23ee Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 5 Jun 2026 10:18:40 +0200 Subject: [PATCH 772/872] update saltshaker modules for real --- modules.json | 6 +- .../nf-core/saltshaker/call/environment.yml | 2 +- modules/nf-core/saltshaker/call/meta.yml | 29 ++-- .../saltshaker/call/tests/main.nf.test.snap | 18 +-- .../saltshaker/classify/environment.yml | 2 +- modules/nf-core/saltshaker/classify/main.nf | 3 +- modules/nf-core/saltshaker/classify/meta.yml | 8 +- .../classify/tests/main.nf.test.snap | 44 +++--- .../nf-core/saltshaker/plot/environment.yml | 2 +- modules/nf-core/saltshaker/plot/main.nf | 1 + modules/nf-core/saltshaker/plot/meta.yml | 19 ++- .../saltshaker/plot/tests/main.nf.test | 6 +- .../saltshaker/plot/tests/main.nf.test.snap | 29 ++-- .../local/call_sv_MT/tests/main.nf.test | 4 +- .../local/call_sv_MT/tests/main.nf.test.snap | 142 ++---------------- 15 files changed, 99 insertions(+), 216 deletions(-) diff --git a/modules.json b/modules.json index 968c064a6..5acb964f3 100644 --- a/modules.json +++ b/modules.json @@ -383,17 +383,17 @@ }, "saltshaker/call": { "branch": "master", - "git_sha": "9d051963759dda1a424374e23f4f22aaa2b0bd60", + "git_sha": "0932567705843eb10831d31cb200ea3f69a2322e", "installed_by": ["modules"] }, "saltshaker/classify": { "branch": "master", - "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", + "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830", "installed_by": ["modules"] }, "saltshaker/plot": { "branch": "master", - "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", + "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830", "installed_by": ["modules"] }, "sambamba/depth": { diff --git a/modules/nf-core/saltshaker/call/environment.yml b/modules/nf-core/saltshaker/call/environment.yml index f76c4bf5a..ba1172042 100644 --- a/modules/nf-core/saltshaker/call/environment.yml +++ b/modules/nf-core/saltshaker/call/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.0 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/call/meta.yml b/modules/nf-core/saltshaker/call/meta.yml index 51be6c452..773034b7b 100644 --- a/modules/nf-core/saltshaker/call/meta.yml +++ b/modules/nf-core/saltshaker/call/meta.yml @@ -7,10 +7,11 @@ keywords: - structural-variant calling tools: - "saltshaker": - description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - + description: "A Python package for classifying and visualizing mitochondrial structural + variants from MitoSAlt pipeline output." + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker/" + identifier: "" input: - - meta: type: map @@ -58,7 +59,6 @@ input: - light_strand_origin_end: type: integer description: End position of the light strand origin of replication - output: call: - - meta: @@ -68,20 +68,21 @@ output: e.g. `[ id:'sample1' ]` - "*_call_metadata.tsv": type: file - description: tsv with variant call metadata to be used in saltshaker_classify + description: tsv with variant call metadata to be used in + saltshaker_classify pattern: "*_call_metadata.tsv" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_3475 versions_saltshaker: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "saltshaker": + - saltshaker: type: string description: The name of the tool - - "1.0.0": + - 1.1.1: type: string - description: Hardcoded version of saltshaker used in the module - + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -90,9 +91,9 @@ topics: - saltshaker: type: string description: The name of the tool - - 1.0.0: + - 1.1.1: type: string - description: Hardcoded version of saltshaker used in the module + description: The expression to obtain the version of the tool authors: - "@ieduba" maintainers: diff --git a/modules/nf-core/saltshaker/call/tests/main.nf.test.snap b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap index d377c6626..fa9ff6b47 100644 --- a/modules/nf-core/saltshaker/call/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap @@ -7,22 +7,22 @@ { "id": "test" }, - "test.saltshaker_call_metadata.tsv:md5,f0e21ea8c12afecbae37cd9b55f8f8c2" + "test.saltshaker_call_metadata.tsv:md5,5d0d87c5e2a29a07afa0b60cdb9c72d2" ] ], "versions_saltshaker": [ [ "SALTSHAKER_CALL", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-06T15:18:19.555305", + "timestamp": "2026-06-01T13:42:19.667355", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "call - tsv - stub": { @@ -40,15 +40,15 @@ [ "SALTSHAKER_CALL", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-05T09:54:13.739643", + "timestamp": "2026-06-01T13:41:08.005824", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/saltshaker/classify/environment.yml b/modules/nf-core/saltshaker/classify/environment.yml index 3672c7873..ba1172042 100644 --- a/modules/nf-core/saltshaker/classify/environment.yml +++ b/modules/nf-core/saltshaker/classify/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.1 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/classify/main.nf b/modules/nf-core/saltshaker/classify/main.nf index 7ee84c9d4..4a685c5b6 100644 --- a/modules/nf-core/saltshaker/classify/main.nf +++ b/modules/nf-core/saltshaker/classify/main.nf @@ -2,6 +2,7 @@ process SALTSHAKER_CLASSIFY { tag "$meta.id" label 'process_single' + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': @@ -15,7 +16,7 @@ process SALTSHAKER_CLASSIFY { tuple val(meta), path("*_classify_metadata.tsv"), emit: classify tuple val(meta), path("*_classify.txt") , emit: txt tuple val(meta), path("*saltshaker.vcf") , emit: vcf, optional: true - tuple val("${task.process}"), val('saltshaker'), val("1.0.1"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/saltshaker/classify/meta.yml b/modules/nf-core/saltshaker/classify/meta.yml index be07a8946..c02c10c59 100644 --- a/modules/nf-core/saltshaker/classify/meta.yml +++ b/modules/nf-core/saltshaker/classify/meta.yml @@ -8,8 +8,8 @@ keywords: tools: - "saltshaker": description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker" input: - - meta: @@ -74,7 +74,7 @@ output: - saltshaker: type: string description: The name of the tool - - 1.0.1: + - 1.1.1: type: string description: Hardcoded version of saltshaker used in the module topics: @@ -85,7 +85,7 @@ topics: - saltshaker: type: string description: The name of the tool - - 1.0.1: + - 1.1.1: type: string description: Hardcoded version of saltshaker used in the module authors: diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap index 507105e8c..c7e9d7868 100644 --- a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap @@ -25,15 +25,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T12:29:31.591954", + "timestamp": "2026-06-01T13:52:59.878729", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - defaults": { @@ -44,7 +44,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,2ed89e393a16ab2b7602ed06e807e187" ] ], "txt": [ @@ -52,7 +52,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,21b5114cd8e2d1cd720de1bfa18abd3e" ] ], "vcf": [ @@ -62,15 +62,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T12:29:26.57794", + "timestamp": "2026-06-01T15:59:15.738107", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - vcf - stub": { @@ -104,15 +104,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T11:05:52.842015", + "timestamp": "2026-06-01T13:52:46.708731", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - vcf": { @@ -123,7 +123,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,2ed89e393a16ab2b7602ed06e807e187" ] ], "txt": [ @@ -131,7 +131,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,21b5114cd8e2d1cd720de1bfa18abd3e" ] ], "vcf": [ @@ -139,22 +139,24 @@ { "id": "test" }, - "test.saltshaker.vcf:md5,0c59728289ee8bcb19d44aea4d3155ab" + + "test.saltshaker.vcf:md5,e8e3c00ef62888bb217983a4bf5559a5" ] ], "versions_saltshaker": [ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T11:05:45.058275", + + "timestamp": "2026-06-05T09:21:05.922028", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/saltshaker/plot/environment.yml b/modules/nf-core/saltshaker/plot/environment.yml index f76c4bf5a..ba1172042 100644 --- a/modules/nf-core/saltshaker/plot/environment.yml +++ b/modules/nf-core/saltshaker/plot/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.0 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/plot/main.nf b/modules/nf-core/saltshaker/plot/main.nf index fc1555635..75679dfde 100644 --- a/modules/nf-core/saltshaker/plot/main.nf +++ b/modules/nf-core/saltshaker/plot/main.nf @@ -2,6 +2,7 @@ process SALTSHAKER_PLOT { tag "$meta.id" label 'process_single' + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': diff --git a/modules/nf-core/saltshaker/plot/meta.yml b/modules/nf-core/saltshaker/plot/meta.yml index b95deb3f5..200700538 100644 --- a/modules/nf-core/saltshaker/plot/meta.yml +++ b/modules/nf-core/saltshaker/plot/meta.yml @@ -7,10 +7,11 @@ keywords: - structural-variant calling tools: - "saltshaker": - description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - + description: "A Python package for classifying and visualizing mitochondrial structural + variants from MitoSAlt pipeline output." + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker" + identifier: "" input: - - meta: type: map @@ -24,7 +25,6 @@ input: ontologies: - edam: http://edamontology.org/operation_3225 #classification - edam: http://edamontology.org/format_3475 #tsv - output: plot: - - meta: @@ -46,19 +46,18 @@ output: - "saltshaker": type: string description: The name of the tool - - "1.0.0": + - "1.1.1": type: string description: Hardcoded version of saltshaker used in the module - topics: versions: - - - ${task.process}: + - - "${task.process}": type: string description: The name of the process - - saltshaker: + - "saltshaker": type: string description: The name of the tool - - 1.0.0: + - "1.1.1": type: string description: Hardcoded version of saltshaker used in the module authors: diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test b/modules/nf-core/saltshaker/plot/tests/main.nf.test index ec18cc241..f40353dcb 100644 --- a/modules/nf-core/saltshaker/plot/tests/main.nf.test +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test @@ -68,8 +68,10 @@ nextflow_process { assert process.success assertAll( { assert snapshot( - sanitizeOutput(process.out), - ).match() } + process.out.findAll { key, val -> key.startsWith('versions') }, + process.out.plot.collect { meta, plot -> file(plot).name } + ).match() + } ) } diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap index ea7f4d94c..ebde03458 100644 --- a/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap @@ -14,41 +14,36 @@ [ "SALTSHAKER_PLOT", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-17T14:57:52.937691", + "timestamp": "2026-06-03T10:34:26.252966", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "plot - png": { "content": [ { - "plot": [ - [ - { - "id": "test" - }, - "test.saltshaker.png:md5,c5c8f7b96daab112b53dfe42194855af" - ] - ], "versions_saltshaker": [ [ "SALTSHAKER_PLOT", "saltshaker", - "1.0.0" + "1.1.1" ] ] - } + }, + [ + "test.saltshaker.png" + ] ], - "timestamp": "2026-03-17T14:57:46.77575", + "timestamp": "2026-06-05T09:43:08.53978", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index a9e00b314..b02ac76f6 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -40,7 +40,7 @@ nextflow_workflow { input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } @@ -122,7 +122,7 @@ nextflow_workflow { input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index f1bf248d5..56dde4d40 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -5,42 +5,19 @@ [ "0", [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ] ], [ "1", [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] + ] ], [ "2", [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], [ @@ -86,31 +63,13 @@ [ "manta", "tiddit", - "cnvnator", - "mitosalt" + "cnvnator" ] ] ], [ "5", [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], [ "call_sv/", [ @@ -148,24 +107,6 @@ }, "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] ] ] ], @@ -209,23 +150,6 @@ [ "publish", [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], [ "call_sv/", [ @@ -263,66 +187,25 @@ }, "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] ] ] ], [ "saltshaker_html", [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,85aa1a57cce1f14f6494585d4f18e416" - ] + ] ], [ "saltshaker_plot", [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], [ "saltshaker_vcf", [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ] ], [ @@ -331,17 +214,16 @@ [ "manta", "tiddit", - "cnvnator", - "mitosalt" + "cnvnator" ] ] ] ] ], - "timestamp": "2026-05-28T09:55:09.413526846", + "timestamp": "2026-06-05T10:15:17.776703", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } }, "CALL_SV_MT - no_sample_map - stub": { @@ -683,10 +565,10 @@ ] ] ], - "timestamp": "2026-05-28T09:49:32.527998006", + "timestamp": "2026-06-05T10:16:00.612219", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file From 40218d7701a0917057d6edaac909164ccbcbe01f Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 5 Jun 2026 10:26:02 +0200 Subject: [PATCH 773/872] fix some comments --- subworkflows/local/call_structural_variants/main.nf | 2 +- subworkflows/local/call_sv_MT/main.nf | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 073d84218..2b4d84da1 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -32,7 +32,7 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_ploidy_model // channel: [optional; used by mandatory for GATK's cnvcaller][ path(ploidy_model) ] ch_readcount_intervals // channel: [optional; used by mandatory for GATK's cnvcaller][ path(intervals) ] ch_reads // channel: [mandatory] [ val(meta), [path(reads)] ] - ch_sample_id_map // channel: [optional] [val(customer_id), val(sample_id)] + ch_sample_id_map // channel: [optional] [val(sample_id), val(customer_id)] ch_subdepth // channel: [mandatory] [ val(mitosalt_depth) ] ch_svcaller_priority // channel: [mandatory] [ val(["var caller tag 1", ...]) ] ch_target_bed // channel: [mandatory for WES] [ val(meta), path(bed), path(tbi) ] diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index eb3d726fa..9403b2759 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -99,7 +99,6 @@ workflow CALL_SV_MT { .join(MITOSALT.out.cluster) .set { ch_saltshaker_in } - // Saltshaker modules will only run if mitosalt called SVs and created a cluster file SALTSHAKER_CALL( ch_saltshaker_in, ch_mt_fasta, From f5386612737e771e66ed2a6e4dc12c2dca8733a0 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 5 Jun 2026 10:27:59 +0200 Subject: [PATCH 774/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7b5861214..c6866828c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) +- Update saltshaker modules to version 1.1.1 so they can run on empty mitosalt output [#856](https://github.com/nf-core/raredisease/pull/856) ### `Fixed` From f8e019369cd3e4bad34a827faa527265c3e81553 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 5 Jun 2026 11:06:08 +0200 Subject: [PATCH 775/872] update pipeline snapshots --- tests/default.nf.test.snap | 12 ++++++------ tests/test_singleton.nf.test.snap | 10 +++++----- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index d9d92e594..2e1693617 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -325,13 +325,13 @@ "rhocall": "0.5.1" }, "SALTSHAKER_CALL": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.1" + "saltshaker": "1.1.1" }, "SALTSHAKER_PLOT": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -1100,7 +1100,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,79a8e7d32a6842a6637ce88e67f28ea4", + "justhusky.saltshaker_classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1332,10 +1332,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-28T09:40:48.240598924", + "timestamp": "2026-06-05T11:02:01.458054473", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index e413b1f8b..c33f1909a 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -317,13 +317,13 @@ "rhocall": "0.5.1" }, "SALTSHAKER_CALL": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.1" + "saltshaker": "1.1.1" }, "SALTSHAKER_PLOT": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -659,10 +659,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-28T09:45:42.467577075", + "timestamp": "2026-06-05T10:57:12.012973983", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file From 9f887655f10ca29898f623bc5373a5038362806c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 5 Jun 2026 11:50:36 +0200 Subject: [PATCH 776/872] add back test config --- conf/test.config | 61 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 conf/test.config diff --git a/conf/test.config b/conf/test.config new file mode 100644 index 000000000..6c1cf3049 --- /dev/null +++ b/conf/test.config @@ -0,0 +1,61 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/raredisease -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '2.h' + ] +} + +env { + MPLCONFIGDIR="." +} + +params { + config_profile_name = 'Test profile - default' + config_profile_description = 'Minimal test dataset to check pipeline function' + + igenomes_ignore = true + mito_name = 'MT' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease' + + skip_tools = 'fastp,gens,peddy,germlinecnvcaller,ngsbits' + + input = params.pipelines_testdata_base_path + '/testdata/samplesheet_fq_spring.csv' + fasta = params.pipelines_testdata_base_path + '/reference/reference.fasta' + fai = params.pipelines_testdata_base_path + '/reference/reference.fasta.fai' + genome = 'GRCh37' + gnomad_af = params.pipelines_testdata_base_path + '/reference/gnomad_reformated.tab.gz' + intervals_wgs = params.pipelines_testdata_base_path + '/reference/target_wgs.interval_list' + intervals_y = params.pipelines_testdata_base_path + '/reference/targetY.interval_list' + known_dbsnp = params.pipelines_testdata_base_path + '/reference/dbsnp_-138-.vcf.gz' + mobile_element_references = params.pipelines_testdata_base_path + '/reference/mobile_element_references.tsv' + mobile_element_svdb_annotations = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv' + reduced_penetrance = params.pipelines_testdata_base_path + '/reference/reduced_penetrance.tsv' + score_config_mt = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini' + score_config_snv = params.pipelines_testdata_base_path + '/reference/rank_model_snv.ini' + score_config_sv = params.pipelines_testdata_base_path + '/reference/rank_model_sv.ini' + svdb_query_dbs = params.pipelines_testdata_base_path + '/reference/svdb_querydb_files.csv' + target_bed = params.pipelines_testdata_base_path + '/reference/target.bed' + variant_catalog = params.pipelines_testdata_base_path + '/reference/variant_catalog.json' + vcfanno_lua = params.pipelines_testdata_base_path + '/reference/vcfanno_functions.lua' + vcfanno_resources = params.pipelines_testdata_base_path + '/reference/vcfanno_resources.txt' + vcfanno_toml = params.pipelines_testdata_base_path + '/reference/vcfanno_config.toml' + variant_consequences_snv = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt' + variant_consequences_sv = params.pipelines_testdata_base_path + '/reference/variant_consequences_v2.txt' + vep_cache = params.pipelines_testdata_base_path + '/reference/vep_cache_and_plugins.tar.gz' + vep_filters = params.pipelines_testdata_base_path + '/reference/hgnc.txt' + vep_cache_version = 107 + vep_plugin_files = params.pipelines_testdata_base_path + '/reference/vep_files.csv' +} From 5f75e168dfbc1704fd27a3ea5b0fb668cedeeac9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 5 Jun 2026 14:41:52 +0200 Subject: [PATCH 777/872] switch out ensemblvep's filtervep for a custom script --- CHANGELOG.md | 5 + bin/filtervep.py | 862 ++++++++++++++++++ ...g => vcf_filter_bcftools_filtervep.config} | 6 +- modules.json | 10 - modules/local/filtervep/environment.yml | 5 + modules/local/filtervep/main.nf | 40 + .../ensemblvep/filtervep/environment.yml | 8 - modules/nf-core/ensemblvep/filtervep/main.nf | 40 - modules/nf-core/ensemblvep/filtervep/meta.yml | 92 -- .../ensemblvep/filtervep/tests/main.nf.test | 109 --- .../filtervep/tests/main.nf.test.snap | 52 -- .../filtervep/tests/nextflow.config | 10 - .../ensemblvep/filtervep/tests/tab.gz.config | 18 - .../ensemblvep/filtervep/tests/vcf.config | 17 - nextflow.config | 2 +- .../vcf_filter_bcftools_filtervep}/main.nf | 26 +- .../vcf_filter_bcftools_filtervep}/meta.yml | 0 .../nextflow.config | 0 .../tests/main.nf.test | 10 +- .../tests/main.nf.test.snap | 16 +- .../tests/nextflow.config | 2 +- tests/default.nf.test.snap | 9 +- tests/test_bam.nf.test.snap | 9 +- tests/test_singleton.nf.test.snap | 9 +- workflows/raredisease.nf | 8 +- 25 files changed, 959 insertions(+), 406 deletions(-) create mode 100755 bin/filtervep.py rename conf/modules/{vcf_filter_bcftools_ensemblvep.config => vcf_filter_bcftools_filtervep.config} (90%) create mode 100644 modules/local/filtervep/environment.yml create mode 100644 modules/local/filtervep/main.nf delete mode 100644 modules/nf-core/ensemblvep/filtervep/environment.yml delete mode 100644 modules/nf-core/ensemblvep/filtervep/main.nf delete mode 100644 modules/nf-core/ensemblvep/filtervep/meta.yml delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/main.nf.test delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/nextflow.config delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config delete mode 100644 modules/nf-core/ensemblvep/filtervep/tests/vcf.config rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/main.nf (55%) rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/meta.yml (100%) rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/nextflow.config (100%) rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/tests/main.nf.test (94%) rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/tests/main.nf.test.snap (90%) rename subworkflows/{nf-core/vcf_filter_bcftools_ensemblvep => local/vcf_filter_bcftools_filtervep}/tests/nextflow.config (86%) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2af31746..dbcbe35ca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows - Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers +- Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative + +### `Changed` + +- Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` ### `Fixed` diff --git a/bin/filtervep.py b/bin/filtervep.py new file mode 100755 index 000000000..0d02b6a7c --- /dev/null +++ b/bin/filtervep.py @@ -0,0 +1,862 @@ +#!/usr/bin/env python3 +""" +filter_vep_fast - Fast Python reimplementation of Ensembl's filter_vep. + +Replicates all features of the original Perl script. +Uses cyvcf2 for VCF parsing when available (significant speedup for large +VCF / bgzipped files via htslib). +""" + +import sys +import re +import gzip +import argparse +import os + +try: + import cyvcf2 + HAS_CYVCF2 = True +except ImportError: + HAS_CYVCF2 = False + + +# --------------------------------------------------------------------------- +# Filter expression parser / evaluator +# --------------------------------------------------------------------------- + +class FilterSet: + """Parse and evaluate VEP filter expressions. + + Multiple filter strings are ANDed (all must pass). + Within a string: 'and' / 'or' / 'not' and parentheses are supported. + + Operators (with documented synonyms): + is / = / eq case-insensitive equality + is not / != / ne inequality + > / gt greater than + < / lt less than + >= / gte greater than or equal + <= / lte less than or equal + match / matches / re / regex regex search (case-insensitive) + in list or file membership + exists / ex / defined field has a non-null value + is_child SO ontology child (falls back to exact match) + + Special value syntax: + #FieldName compare against another field's value + bare field name equivalent to 'exists' + + Numeric extraction: + Mixed-content values like "deleterious(0.05)" have the number + extracted automatically when a numeric operator is used. + + Source-prefix stripping: + "HGNC:28706" matches "28706" for is/in comparisons. + """ + + # Canonical operator names after synonym normalisation + _OP_SYNONYMS = { + 'eq': 'is', + 'ne': '!=', + 'lt': '<', + 'gt': '>', + 'lte': '<=', + 'gte': '>=', + 'matches': 'match', + 're': 'match', + 'regex': 'match', + 'ex': 'exists', + 'defined': 'exists', + } + # Words that should be tokenised as OP rather than field names + _OP_WORDS = frozenset( + ['is', 'match', 'in', 'exists', 'is_child'] + + list(_OP_SYNONYMS.keys()) + ) + + _file_cache: dict = {} # shared across all instances + + def __init__(self, *filter_strings): + self._parsed = [self._parse(f) for f in filter_strings] + + # -- tokeniser ----------------------------------------------------------- + + def _tokenize(self, expr): + toks = [] + i = 0 + n = len(expr) + while i < n: + c = expr[i] + if c.isspace(): + i += 1 + continue + if c == '(': + toks.append(('LP', None)); i += 1; continue + if c == ')': + toks.append(('RP', None)); i += 1; continue + if c in ('>', '<', '!', '='): + two = expr[i:i+2] + if two in ('>=', '<=', '!='): + toks.append(('OP', two)); i += 2 + else: + toks.append(('OP', c)); i += 1 + continue + m = re.match(r'[^\s()]+', expr[i:]) + if m: + w = m.group(); lo = w.lower() + if lo == 'and': toks.append(('AND', None)) + elif lo == 'or': toks.append(('OR', None)) + elif lo == 'not': toks.append(('NOT', None)) + elif lo in self._OP_WORDS: + # Normalise synonyms to canonical op + toks.append(('OP', self._OP_SYNONYMS.get(lo, lo))) + else: + toks.append(('W', w)) + i += len(w) + continue + i += 1 + toks.append(('EOF', None)) + return toks + + # -- recursive-descent parser -> AST ------------------------------------- + + def _parse(self, expr): + toks = self._tokenize(expr) + pos = [0] + + def peek(): return toks[pos[0]] + def eat(): + t = toks[pos[0]]; pos[0] += 1; return t + + def or_(): + l = and_() + while peek()[0] == 'OR': + eat(); r = and_(); l = ('or', l, r) + return l + + def and_(): + l = not_() + while peek()[0] == 'AND': + eat(); r = not_(); l = ('and', l, r) + return l + + def not_(): + if peek()[0] == 'NOT': + eat(); return ('not', atom()) + return atom() + + def atom(): + if peek()[0] == 'LP': + eat(); node = or_() + if peek()[0] == 'RP': eat() + return node + if peek()[0] != 'W': + raise SyntaxError(f"Expected field name, got {peek()!r} in: {expr!r}") + field = eat()[1] + t = peek() + if t[0] in ('EOF', 'RP', 'AND', 'OR'): + return ('exists', field, None) + if t[0] != 'OP': + return ('exists', field, None) + op = eat()[1].lower() + if op == 'is' and peek()[0] == 'NOT': + eat(); op = 'is not' + if op == 'exists': + return ('exists', field, None) + if peek()[0] in ('EOF', 'AND', 'OR', 'RP'): + val = None + else: + val = eat()[1] + return (op, field, val) + + return or_() + + # -- evaluator ----------------------------------------------------------- + + def evaluate(self, data): + return all(self._eval(ast, data) for ast in self._parsed) + + def _fv(self, data, field): + """Fetch field value with case-insensitive fallback.""" + v = data.get(field) + if v is not None: + return v + fl = field.lower() + for k, val in data.items(): + if k is not None and k.lower() == fl: + return val + return None + + @staticmethod + def _norm(field, val): + """Treat '' and '-' (except for Allele) as missing.""" + if val is None or val == '': + return None + if field != 'Allele' and val == '-': + return None + return val + + # Regex for VEP mixed-type field values: e.g. "HGNC:28706", "deleterious(0.05)" + _MIXED_RE = re.compile(r'^([\w.\-]+)?:?\(?([-\d.e]*)\)?', re.IGNORECASE) + _NUM_RE = re.compile(r'^-?\d+\.?\d*(e-?\d+)?$', re.IGNORECASE) + _PURE_NUM = re.compile(r'^[-\d.e]+$', re.IGNORECASE) + + def _get_input(self, fval, rep_value): + """Replicate VEP 115 FilterSet.get_input() value-extraction logic. + + Given a raw field value and a representative comparison value, + returns the part of fval that should be compared. + + - If fval has the form TEXT:NUM or TEXT(NUM): + - and rep_value is purely numeric → return the NUM part + - otherwise → return fval unchanged + - If fval is plain (no numeric part) → return fval unchanged + """ + if fval is None: + return None + s = str(fval) + m = self._MIXED_RE.match(s) + if not m: + return s + text = m.group(1) or '' + num = m.group(2) or '' + if not num: + return s # no numeric part; unchanged + # Determine whether the comparison side is purely numeric + rep = str(rep_value) if rep_value is not None else '' + if self._PURE_NUM.match(rep): + # comparison is numeric → use num part unless text is already numeric + if not self._NUM_RE.match(text): + return num + return text + # comparison is not purely numeric → return value unchanged + return s + + def _resolve_value(self, value, data): + """If value starts with '#', resolve it to the named field's value.""" + if value and value.startswith('#'): + return self._norm(value[1:], self._fv(data, value[1:])) + return value + + def _eval(self, node, data): + op = node[0] + if op == 'and': return self._eval(node[1], data) and self._eval(node[2], data) + if op == 'or': return self._eval(node[1], data) or self._eval(node[2], data) + if op == 'not': return not self._eval(node[1], data) + + field = node[1] + value = self._resolve_value(node[2] if len(node) > 2 else None, data) + fval = self._norm(field, self._fv(data, field)) + + if op == 'exists': + return fval is not None + + if op in ('is', '='): + if value is None: return fval is None + if fval is None: return False + inp = self._get_input(fval, value) + return inp.lower() == str(value).lower() + + if op in ('is not', '!='): + if value is None: return fval is not None + if fval is None: return True + inp = self._get_input(fval, value) + return inp.lower() != str(value).lower() + + if fval is None: + return False + + if op == 'match': + return bool(re.search(str(value or ''), str(fval), re.IGNORECASE)) + + if op == 'in': + if value is None: return False + in_set = self._in_set(value) + # Pick a representative value to determine numeric vs string mode + rep = next(iter(in_set), None) + inp = self._get_input(fval, rep).lower() + return inp in in_set + + if op == 'is_child': + # Ontology lookup not supported; exact match fallback + inp = self._get_input(fval, value) + return inp.lower() == str(value or '').lower() + + # Ordered comparisons — use _get_input for numeric extraction + inp = self._get_input(fval, value) + sv = inp + tv = str(value or '') + try: + fn, tn = float(sv), float(tv) + if op == '>': return fn > tn + if op == '<': return fn < tn + if op == '>=': return fn >= tn + if op == '<=': return fn <= tn + except (ValueError, TypeError): + pass + if op == '>': return sv > tv + if op == '<': return sv < tv + if op == '>=': return sv >= tv + if op == '<=': return sv <= tv + return False + + def limit_synonym_search(self, _val=True): + """No-op shim (kept for API parity with the Perl module).""" + + def _in_set(self, value): + """Return a set of lowercase values for the 'in' operator. + If value looks like a readable file path, read one value per line. + Otherwise split on commas. + """ + if value in self._file_cache: + return self._file_cache[value] + if os.path.isfile(value): + with open(value) as fh: + s = {line.strip().lower() for line in fh if line.strip()} + self._file_cache[value] = s + return s + s = {v.strip().lower() for v in value.split(',')} + return s + + +# --------------------------------------------------------------------------- +# Parsing helpers +# --------------------------------------------------------------------------- + +def parse_headers(raw_headers, vcf_info_field='CSQ'): + """Return (vep_headers, col_headers, allowed_fields_dict).""" + vep_headers = None + col_headers = None + allowed = {} + for raw in raw_headers: + hashes = len(raw) - len(raw.lstrip('#')) + line = raw.lstrip('#') + if hashes >= 2: + if re.match(r'INFO== 5 + and re.match(r'(chr)?\w+', p[0]) + and re.match(r'^\d+$', p[1]) + and p[3] and re.match(r'^[ACGTN\-.]+$', p[3], re.IGNORECASE) + and p[4]): + return 'vcf' + return 'tab' + + +def open_input(path, force_gz=False): + if path is None: + return sys.stdin + if path.endswith('.gz') or force_gz: + return gzip.open(path, 'rt') + with open(path, 'rb') as f: + magic = f.read(2) + if magic == b'\x1f\x8b': + return gzip.open(path, 'rt') + return open(path, 'r') + + +# --------------------------------------------------------------------------- +# cyvcf2 fast path (VCF only) +# --------------------------------------------------------------------------- + +def process_cyvcf2(args, out_fh): + vcf_info_field = args.vcf_info_field + filter_set = args.filter_set + + vcf = cyvcf2.VCF(args.input_file or '-') + + raw_hdr_lines = vcf.raw_header.rstrip('\n').split('\n') + + vep_headers = None + for h in raw_hdr_lines: + m = re.search(r'ID=' + re.escape(vcf_info_field) + r'.*?Format: (.+?)"', h) + if m: + vep_headers = m.group(1).split('|') + break + + col_headers = None + for h in reversed(raw_hdr_lines): + if h.startswith('#') and not h.startswith('##'): + col_headers = h.lstrip('#').split('\t') + break + + all_fields = set() + if vep_headers: all_fields.update(vep_headers) + if col_headers: all_fields.update(col_headers) + for h in raw_hdr_lines: + m = re.match(r'##INFO=') + hdr_lines.insert(i, '##FILTER=') + break + + if not args.count: + out_fh.write('\n'.join(hdr_lines) + '\n') + + col_names = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] + count = 0 + line_number = 0 + missing_csq = 0 + + for var in vcf: + line_number += 1 + if args.test and line_number > args.test: + break + + vcf_line = str(var) + parts = vcf_line.split('\t') + + main_data = {col_names[i]: (parts[i] if i < len(parts) else None) + for i in range(len(col_names))} + if len(parts) > 7: + for ifield in parts[7].split(';'): + if '=' in ifield: + k, v = ifield.split('=', 1) + if k != vcf_info_field: + main_data[k] = v + elif ifield: + main_data[ifield] = None # Flag: Perl sets to undef, so exists-check fails + + csq_val = var.INFO.get(vcf_info_field) + chunks = [] + data_list = [] + + if csq_val: + chunks = csq_val.split(',') + data_list = [parse_csq_chunk(c, vep_headers or [], main_data) for c in chunks] + else: + missing_csq += 1 + data_list = [main_data] + + line_pass = 0 + new_chunks = [] + for i, parsed in enumerate(data_list): + if filter_set.evaluate(parsed): + line_pass += 1 + if i < len(chunks): + new_chunks.append(chunks[i]) + + count += bool(line_pass) + + if not args.soft_filter and count < args.start: + continue + + if args.soft_filter: + tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' + cur = parts[6] if len(parts) > 6 else '.' + parts[6] = f"{cur};{tag}" if cur and cur != '.' else tag + out_fh.write('\t'.join(parts) + '\n') + elif line_pass and not args.count: + out_line = vcf_line + if args.only_matched and new_chunks and len(new_chunks) != len(chunks): + new_csq = ','.join(new_chunks) + p = out_line.split('\t') + p[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', + vcf_info_field + '=' + new_csq, p[7], count=1) + out_line = '\t'.join(p) + out_fh.write(out_line + '\n') + + if not args.soft_filter and count >= args.limit + args.start - 1: + break + + vcf.close() + + if line_number == 0 and not args.count: + out_fh.write('\n'.join(hdr_lines) + '\n') + + if args.count: + out_fh.write(f"{count}\n") + + if missing_csq: + sys.stderr.write( + f"WARNING: filter_vep couldn't find VEP annotations field " + f"{vcf_info_field} in {missing_csq} line(s) of the input file\n" + ) + + +# --------------------------------------------------------------------------- +# Generic path (tab or VCF without cyvcf2) +# --------------------------------------------------------------------------- + +def process_generic(args, out_fh): + vcf_info_field = args.vcf_info_field + filter_set = args.filter_set + + in_fh = open_input(args.input_file, args.gz) + + raw_headers = [] + vep_headers = None + col_headers = None + fmt = args.format + count = 0 + line_number = 0 + missing_csq = 0 + headers_initialised = False + + csq_re = re.compile(re.escape(vcf_info_field) + r'=(.+?)(?:;|\s|$)') + + for raw_line in in_fh: + line = raw_line.rstrip('\n') + + if line.startswith('#'): + raw_headers.append(line) + continue + + line_number += 1 + if args.test and line_number > args.test: + break + + # -- initialise on first data line -- + if not headers_initialised: + if not raw_headers: + sys.exit("ERROR: No headers found in input file") + + if args.soft_filter: + chrom_hdr = raw_headers.pop() + raw_headers.append('##FILTER=') + raw_headers.append('##FILTER=') + raw_headers.append(chrom_hdr) + + if not args.count and not args.list: + out_fh.write('\n'.join(raw_headers) + '\n') + + vep_headers, col_headers, extra_allowed = parse_headers(raw_headers, vcf_info_field) + + all_fields = set() + if vep_headers: all_fields.update(vep_headers) + if col_headers: all_fields.update(col_headers) + all_fields.update(extra_allowed) + + if args.list: + print("Available fields:\n") + for f in sorted(all_fields): + print(f) + if in_fh is not sys.stdin: + in_fh.close() + return + + headers_initialised = True + + # -- format detection -- + if not fmt: + fmt = detect_format(line) + if fmt not in ('vcf', 'tab'): + sys.exit(f"ERROR: Unable to parse data in format {fmt}") + if fmt != 'vcf' and args.only_matched: + sys.exit("ERROR: --only_matched is compatible only with VCF files") + if fmt != 'vcf' and args.soft_filter: + sys.exit("ERROR: --soft_filter is compatible only with VCF files") + + if args.soft_filter: + args.start = 0 + + chunks = [] + data_list = [] + + if fmt == 'tab': + hdrs = col_headers or vep_headers or [] + data_list.append(parse_tab_line(line, hdrs)) + chunks.append(line) + if not any(h == 'Extra' for h in hdrs): + filter_set.limit_synonym_search(True) + + else: # vcf + parts = line.split('\t') + ch = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] + main_data = {ch[i]: (parts[i] if i < len(parts) else None) + for i in range(len(ch))} + + if len(parts) > 7: + for ifield in parts[7].split(';'): + if '=' in ifield: + k, v = ifield.split('=', 1) + if k != vcf_info_field: + main_data[k] = v + elif ifield: + main_data[ifield] = None # Flag: Perl sets to undef, so exists-check fails + + m = csq_re.search(line) + if m: + raw_csq = m.group(1) + chunks = raw_csq.split(',') + data_list = [parse_csq_chunk(c, vep_headers or [], main_data) for c in chunks] + else: + missing_csq += 1 + data_list = [main_data] + + filter_set.limit_synonym_search(True) + + # -- evaluate -- + line_pass = 0 + new_chunks = [] + for i, parsed in enumerate(data_list): + if filter_set.evaluate(parsed): + line_pass += 1 + if i < len(chunks): + new_chunks.append(chunks[i]) + + count += bool(line_pass) + + if not args.soft_filter and count < args.start: + continue + + # -- output -- + if args.soft_filter: + sp = line.split('\t') + tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' + cur = sp[6] if len(sp) > 6 else '.' + sp[6] = f"{cur};{tag}" if cur and cur != '.' else tag + out_fh.write('\t'.join(sp) + '\n') + + elif line_pass and not args.count: + out_line = line + if args.only_matched and new_chunks and len(new_chunks) != len(chunks): + new_csq = ','.join(new_chunks) + p = out_line.split('\t') + p[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', + vcf_info_field + '=' + new_csq, p[7], count=1) + out_line = '\t'.join(p) + out_fh.write(out_line + '\n') + + if not args.soft_filter and count >= args.limit + args.start - 1: + break + + # -- empty file -- + if not line_number: + if not args.count and not args.list: + out_fh.write('\n'.join(raw_headers) + '\n') + if args.list: + v, c, a = parse_headers(raw_headers, vcf_info_field) + af = set() + if v: af.update(v) + if c: af.update(c) + af.update(a) + print("Available fields:\n") + for f in sorted(af): + print(f) + if in_fh is not sys.stdin: + in_fh.close() + return + + if args.count: + out_fh.write(f"{count}\n") + + if missing_csq: + sys.stderr.write( + f"WARNING: filter_vep couldn't find VEP annotations field " + f"{vcf_info_field} in {missing_csq} line(s) of the input file\n" + ) + + if in_fh is not sys.stdin: + in_fh.close() + + +# --------------------------------------------------------------------------- +# CLI +# --------------------------------------------------------------------------- + +USAGE = """\ +#------------# +# filter_vep # +#------------# + +http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html + +Usage: +./filter_vep_fast.py [arguments] + +--help -h Print usage message and exit + +--input_file [file] -i Input file (VEP results). Reads from STDIN if + not specified. Supports gzip (auto-detected or + force with --gz). +--format [vcf|tab] Input format (tab = any tab-delimited format, + including default VEP output format) + +--output_file [file] -o Output file. Defaults to STDOUT. +--force_overwrite Overwrite existing output file. + +--filter [filters] -f Filter expression. Multiple --filter flags are + treated as logical ANDs, e.g.: + -f "Consequence is missense_variant" + -f "AF < 0.01 or not AF" + -f "HGNC_ID in gene_panels.txt" + -f "(AFR_AF gt #EUR_AF) and SIFT lt 0.05" + + Operators: + is / = / eq case-insensitive equality + != / ne inequality + > / gt greater than + < / lt less than + >= / gte greater than or equal + <= / lte less than or equal + match/matches/re/regex regex (case-insensitive) + in list or file (one value/line) + exists/ex/defined field is present and non-null + is_child SO ontology child term + Logical: and or not ( ) + Value can be #Field to compare two fields. + Mixed content (e.g. "deleterious(0.05)") has its + number extracted for numeric comparisons. + Source prefixes (e.g. "HGNC:34") are stripped + automatically in is/in comparisons. + +--list -l List available fields from the input file. +--count -c Print only a count of matched lines. + +--only_matched In VCF files, rewrite the CSQ field to contain + only annotation blobs that passed the filters. + +--vcf_info_field [key] VCF INFO key for VEP annotations (default: CSQ). + +--soft_filter Add filter_vep_pass / filter_vep_fail to the VCF + FILTER column instead of excluding variants. + +--ontology -y Use Sequence Ontology to match consequence terms + (requires Ensembl API; is_child falls back to + exact match in this implementation). +--host / --user / --pass / --port / --version / --registry + Database connection options for --ontology. + +--start [N] -s Skip first N passing results (1-based, default 1) +--limit [N] Return at most N passing results. +--test [N] Process only the first N non-header lines. +""" + + +def main(): + ap = argparse.ArgumentParser(add_help=False) + ap.add_argument('--help', '-h', action='store_true') + ap.add_argument('--test', type=int) + ap.add_argument('--count', '-c', action='store_true') + ap.add_argument('--list', '-l', action='store_true') + ap.add_argument('--input_file', '-i') + ap.add_argument('--output_file', '-o', default='stdout') + ap.add_argument('--force_overwrite', action='store_true') + ap.add_argument('--format', choices=['vcf', 'tab']) + ap.add_argument('--gz', action='store_true') + ap.add_argument('--only_matched', action='store_true') + ap.add_argument('--vcf_info_field', default='CSQ') + ap.add_argument('--soft_filter', action='store_true') + ap.add_argument('--ontology', '-y', action='store_true') + ap.add_argument('--host', default='ensembldb.ensembl.org') + ap.add_argument('--user', default='anonymous') + ap.add_argument('--pass', dest='password', default=None) + ap.add_argument('--port', type=int, default=3306) + ap.add_argument('--version', type=int) + ap.add_argument('--registry') + ap.add_argument('--start', '-s', type=int, default=1) + ap.add_argument('--limit', type=int, default=int(1e12)) + ap.add_argument('--filter', '-f', action='append') + + args = ap.parse_args() + + if args.help or (not args.filter and not args.list): + print(USAGE) + if not args.help: + sys.exit("ERROR: No valid filters given") + sys.exit(0) + + if args.ontology: + sys.stderr.write( + "WARNING: --ontology requires Ensembl API; " + "is_child will fall back to exact match in this implementation\n" + ) + + args.filter_set = FilterSet(*(args.filter or [])) + + if args.output_file.lower() != 'stdout': + if os.path.exists(args.output_file) and not args.force_overwrite: + sys.exit( + f"ERROR: Output file {args.output_file} already exists. " + "Use --force_overwrite to overwrite." + ) + out_fh = open(args.output_file, 'w') + else: + out_fh = sys.stdout + + try: + use_cyvcf2 = ( + HAS_CYVCF2 + and args.format != 'tab' + and (args.format == 'vcf' + or (args.input_file and + re.search(r'\.vcf(\.gz)?$|\.bcf$', args.input_file, re.IGNORECASE))) + ) + if use_cyvcf2: + process_cyvcf2(args, out_fh) + else: + process_generic(args, out_fh) + finally: + if out_fh is not sys.stdout: + out_fh.close() + + +if __name__ == '__main__': + main() diff --git a/conf/modules/vcf_filter_bcftools_ensemblvep.config b/conf/modules/vcf_filter_bcftools_filtervep.config similarity index 90% rename from conf/modules/vcf_filter_bcftools_ensemblvep.config rename to conf/modules/vcf_filter_bcftools_filtervep.config index 83b282b21..6a4a927af 100644 --- a/conf/modules/vcf_filter_bcftools_ensemblvep.config +++ b/conf/modules/vcf_filter_bcftools_filtervep.config @@ -18,7 +18,7 @@ // SNVs process { - withName: '.*:GENERATE_CLINICAL_SET_SNV:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_SNV:FILTERVEP' { ext.prefix = { "${meta.id}_snv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } @@ -31,7 +31,7 @@ process { // SVs process { - withName: '.*:GENERATE_CLINICAL_SET_SV:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_SV:FILTERVEP' { ext.prefix = { "${meta.id}_sv_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } @@ -52,7 +52,7 @@ process { // ME variants process { - withName: '.*:GENERATE_CLINICAL_SET_ME:ENSEMBLVEP_FILTERVEP' { + withName: '.*:GENERATE_CLINICAL_SET_ME:FILTERVEP' { ext.prefix = { "${meta.id}_me_${meta.set}" } ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } diff --git a/modules.json b/modules.json index 4bb0c67b5..1cb5d52ed 100644 --- a/modules.json +++ b/modules.json @@ -130,11 +130,6 @@ "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", "installed_by": ["modules"] }, - "ensemblvep/filtervep": { - "branch": "master", - "git_sha": "2e751c119b5e6e9c7ecda7a682e157aabb57a812", - "installed_by": ["modules", "vcf_filter_bcftools_ensemblvep"] - }, "ensemblvep/vep": { "branch": "master", "git_sha": "34505e1fc5e9f4fd641210ca440acff6bd33b842", @@ -579,11 +574,6 @@ "branch": "master", "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", "installed_by": ["subworkflows"] - }, - "vcf_filter_bcftools_ensemblvep": { - "branch": "master", - "git_sha": "95518d261ec0561b3dffb332944bebc5ef85efcf", - "installed_by": ["subworkflows"] } } } diff --git a/modules/local/filtervep/environment.yml b/modules/local/filtervep/environment.yml new file mode 100644 index 000000000..0ffb35d7c --- /dev/null +++ b/modules/local/filtervep/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::cyvcf2=0.32.1 diff --git a/modules/local/filtervep/main.nf b/modules/local/filtervep/main.nf new file mode 100644 index 000000000..d25f7def2 --- /dev/null +++ b/modules/local/filtervep/main.nf @@ -0,0 +1,40 @@ +process FILTERVEP { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/48/481e0a88c723eb6abe5a6c36e50bc2119b460f3c6f71aff2111a22e8b704c5d9/data' : + 'community.wave.seqera.io/library/cyvcf2:0.32.1--569b36b775b7f1e5' }" + + input: + tuple val(meta), path(input) + path feature_file + + output: + tuple val(meta), path("*.${extension}"), emit: output + tuple val("${task.process}"), val('filtervep'), val('1.0.0'), topic: versions, emit: versions_filtervep + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--format tab") ? "txt" : "vcf" + """ + filtervep.py \\ + ${args} \\ + --input_file ${input} \\ + --output_file ${prefix}.${extension} \\ + --only_matched + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--format tab") ? "txt" : "vcf" + """ + touch ${prefix}.${extension} + """ +} diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml deleted file mode 100644 index 7e60f7f95..000000000 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::ensembl-vep=115.2 - - bioconda::perl-math-cdf=0.1 diff --git a/modules/nf-core/ensemblvep/filtervep/main.nf b/modules/nf-core/ensemblvep/filtervep/main.nf deleted file mode 100644 index d9deff488..000000000 --- a/modules/nf-core/ensemblvep/filtervep/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -process ENSEMBLVEP_FILTERVEP { - tag "${meta.id}" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3d/3da6e21cbf9803529421d7e136d1ebec5ff71ec50e0d996eda2ce11ec2c19bf9/data' - : 'community.wave.seqera.io/library/ensembl-vep_perl-math-cdf:1e13f65f931a6954'}" - - input: - tuple val(meta), path(input) - path feature_file - - output: - tuple val(meta), path("*.${extension}"), emit: output - tuple val("${task.process}"), val('ensemblvep'), eval("vep --help | sed -n '/ensembl-vep/s/.*: //p'"), topic: versions, emit: versions_ensemblvep - tuple val("${task.process}"), val('perl-math-cdf'), eval("perl -MMath::CDF -e 'print \\\$Math::CDF::VERSION'"), topic: versions, emit: versions_perlmathcdf - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" - """ - filter_vep \\ - ${args} \\ - --input_file ${input} \\ - --output_file ${prefix}.${extension} \\ - --only_matched - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - extension = task.ext.suffix ?: "vcf" - """ - touch ${prefix}.${extension} - """ -} diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml deleted file mode 100644 index 20239ba91..000000000 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ /dev/null @@ -1,92 +0,0 @@ -name: ensemblvep_filtervep -description: Filter variants based on Ensembl Variant Effect Predictor (VEP) - annotations. -keywords: - - annotation - - vcf - - tab - - filter -tools: - - ensemblvep: - description: | - VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs - or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. - homepage: https://www.ensembl.org/info/docs/tools/vep/index.html - documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html - licence: - - "Apache-2.0" - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input: - type: file - description: VCF/TAB file annotated with vep - pattern: "*.{vcf,tab,tsv,txt}" - ontologies: - - edam: http://edamontology.org/format_3475 - - feature_file: - type: file - description: File containing features on separate lines. To be used with - --filter option. - ontologies: [] -output: - output: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - "*.${extension}": - type: file - description: VCF/TAB file - pattern: "*.{vcf,tab,txt,tsv}" - ontologies: - - edam: http://edamontology.org/format_3475 - versions_ensemblvep: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: eval - description: The command used to generate the version of the tool - versions_perlmathcdf: - - - ${task.process}: - type: string - description: The process the versions were collected from - - perl-math-cdf: - type: string - description: The tool name - - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': - type: eval - description: The expression to obtain the version of the tool -topics: - versions: - - - ${task.process}: - type: string - description: The process the versions were collected from - - ensemblvep: - type: string - description: The tool name - - "vep --help | sed -n '/ensembl-vep/s/.*: //p'": - type: eval - description: The command used to generate the version of the tool - - - ${task.process}: - type: string - description: The process the versions were collected from - - perl-math-cdf: - type: string - description: The tool name - - perl -MMath::CDF -e 'print \\$Math::CDF::VERSION': - type: eval - description: The expression to obtain the version of the tool -authors: - - "@ramprasadn" -maintainers: - - "@ramprasadn" diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test deleted file mode 100644 index 044934579..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test +++ /dev/null @@ -1,109 +0,0 @@ -nextflow_process { - - name "Test Process ENSEMBLVEP_FILTERVEP" - script "../main.nf" - process "ENSEMBLVEP_FILTERVEP" - config "./nextflow.config" - - tag "modules" - tag "modules_nfcore" - tag "ensemblvep" - tag "ensemblvep/vep" - tag "ensemblvep/filtervep" - - test("test_ensemblvep_filtervep_vcf") { - config "./vcf.config" - - setup { - run("ENSEMBLVEP_VEP") { - script "../../vep/main.nf" - - process { - """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - [] - ]) - input[1] = params.vep_genome - input[2] = params.vep_species - input[3] = params.vep_cache_version - input[4] = vep_cache - input[5] = Channel.value([ - [id:"fasta"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[6] = [] - """ - } - } - } - - when { - process { - """ - input[0] = ENSEMBLVEP_VEP.out.vcf - input[1] = [] - """ - } - } - - then { - assert process.success - assertAll( - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("##fileformat=VCFv4.2") } - ) - } - } - - test("test_ensemblvep_filtervep_tab_gz") { - config "./tab.gz.config" - - setup { - run("ENSEMBLVEP_VEP") { - script "../../vep/main.nf" - - process { - """ - vep_cache = Channel.of(file('s3://annotation-cache/vep_cache/115_WBcel235/')).collect() - - input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - [] - ]) - input[1] = params.vep_genome - input[2] = params.vep_species - input[3] = params.vep_cache_version - input[4] = vep_cache - input[5] = Channel.value([ - [id:"fasta"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[6] = [] - """ - } - } - } - - when { - process { - """ - input[0] = ENSEMBLVEP_VEP.out.tab - input[1] = [] - """ - } - } - - then { - assert process.success - assertAll( - { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }, - { assert path(process.out.output.get(0).get(1)).readLines().first().contains("## ENSEMBL VARIANT EFFECT PREDICTOR v115.2") } - ) - } - } -} diff --git a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap deleted file mode 100644 index 6ed6da27b..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/main.nf.test.snap +++ /dev/null @@ -1,52 +0,0 @@ -{ - "test_ensemblvep_filtervep_vcf": { - "content": [ - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_FILTERVEP", - "ensemblvep", - "115.2" - ] - ], - "versions_perlmathcdf": [ - [ - "ENSEMBLVEP_FILTERVEP", - "perl-math-cdf", - "0.1" - ] - ] - } - ], - "timestamp": "2026-02-25T10:48:08.943902", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "test_ensemblvep_filtervep_tab_gz": { - "content": [ - { - "versions_ensemblvep": [ - [ - "ENSEMBLVEP_FILTERVEP", - "ensemblvep", - "115.2" - ] - ], - "versions_perlmathcdf": [ - [ - "ENSEMBLVEP_FILTERVEP", - "perl-math-cdf", - "0.1" - ] - ] - } - ], - "timestamp": "2026-02-25T10:48:20.24913", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - } -} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config deleted file mode 100644 index 32ff2cb6f..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ -params { - vep_cache_version = "115" - vep_genome = "WBcel235" - vep_species = "caenorhabditis_elegans" -} diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config deleted file mode 100644 index ace089baa..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ /dev/null @@ -1,18 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -process { - - withName: ENSEMBLVEP_VEP { - ext.args = '--tab --offline' - ext.prefix = { "${meta.id}_vep" } - } - - withName: ENSEMBLVEP_FILTERVEP { - ext.args = '--filter "Feature_type is Transcript"' - ext.suffix = "tab" - } -} diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config deleted file mode 100644 index 9f34e2a90..000000000 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ /dev/null @@ -1,17 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -process { - - withName: ENSEMBLVEP_VEP { - ext.args = '--vcf --offline' - ext.prefix = { "${meta.id}_vep" } - } - - withName: ENSEMBLVEP_FILTERVEP { - ext.args = '--filter "Feature_type is Transcript"' - } -} diff --git a/nextflow.config b/nextflow.config index 858381fdf..5038dec67 100644 --- a/nextflow.config +++ b/nextflow.config @@ -521,7 +521,7 @@ includeConfig 'conf/modules/call_sv_tiddit.config' includeConfig 'conf/modules/postprocess_MT_calls.config' includeConfig 'conf/modules/call_mobile_elements.config' includeConfig 'conf/modules/annotate_mobile_elements.config' -includeConfig 'conf/modules/vcf_filter_bcftools_ensemblvep.config' +includeConfig 'conf/modules/vcf_filter_bcftools_filtervep.config' includeConfig 'conf/modules/variant_evaluation.config' includeConfig 'conf/modules/subsample_mt_frac.config' includeConfig 'conf/modules/subsample_mt_reads.config' diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf similarity index 55% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf rename to subworkflows/local/vcf_filter_bcftools_filtervep/main.nf index 00c752502..e589f7850 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf +++ b/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf @@ -1,20 +1,20 @@ -include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view' -include { ENSEMBLVEP_FILTERVEP } from '../../../modules/nf-core/ensemblvep/filtervep' -include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix' +include { BCFTOOLS_VIEW } from '../../../modules/nf-core/bcftools/view' +include { FILTERVEP } from '../../../modules/local/filtervep' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix' // Please note this subworkflow requires the options for bcftools_view that are included in the nextflow.config -workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { +workflow VCF_FILTER_BCFTOOLS_FILTERVEP { take: - ch_vcf // channel: [ val(meta), path(vcf) ] + ch_vcf // channel: [ val(meta), path(vcf) ] ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] - filter_with_bcftools // bool: should bcftools view be run - filter_with_filter_vep // bool: should filter_vep be run + filter_with_bcftools // bool: should bcftools view be run + filter_with_filter_vep // bool: should filtervep be run main: ch_tbi = channel.empty() - // Since bcftools is likely much faster than filter_vep, - // we run it first to reduce the number of variants that filter_vep has to process. + // Since bcftools is likely much faster than filtervep, + // we run it first to reduce the number of variants that filtervep has to process. if (filter_with_bcftools) { BCFTOOLS_VIEW( @@ -30,13 +30,13 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { if (filter_with_filter_vep) { - ENSEMBLVEP_FILTERVEP( + FILTERVEP( ch_vcf, ch_filter_vep_feature_file.map { _meta, file -> file }, ) TABIX_BGZIPTABIX( - ENSEMBLVEP_FILTERVEP.out.output + FILTERVEP.out.output ) ch_vcf = TABIX_BGZIPTABIX.out.gz_index.map { meta, vcf, _tbi -> [meta, vcf] } @@ -44,6 +44,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP { } emit: - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] - tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] } diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml b/subworkflows/local/vcf_filter_bcftools_filtervep/meta.yml similarity index 100% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/meta.yml rename to subworkflows/local/vcf_filter_bcftools_filtervep/meta.yml diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config b/subworkflows/local/vcf_filter_bcftools_filtervep/nextflow.config similarity index 100% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/nextflow.config rename to subworkflows/local/vcf_filter_bcftools_filtervep/nextflow.config diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test similarity index 94% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test rename to subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test index fb000d16a..622d385d8 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test +++ b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test @@ -1,15 +1,15 @@ nextflow_workflow { - name "Test Subworkflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP" + name "Test Subworkflow VCF_FILTER_BCFTOOLS_FILTERVEP" script "../main.nf" - workflow "VCF_FILTER_BCFTOOLS_ENSEMBLVEP" + workflow "VCF_FILTER_BCFTOOLS_FILTERVEP" config "./nextflow.config" tag "subworkflows" - tag "subworkflows_nfcore" - tag "subworkflows/vcf_filter_bcftools_ensemblvep" + tag "subworkflows_local" + tag "subworkflows/vcf_filter_bcftools_filtervep" tag "bcftools/view" - tag "ensemblvep/filtervep" + tag "filtervep" tag "tabix/bgziptabix" test("vcf, hgnc_ids - filter on expression") { diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test.snap similarity index 90% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap rename to subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test.snap index 03ac1e7b0..9954d80cf 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "18e010447bd23a05a202d44daf66bcd2", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" ], + "timestamp": "2026-01-27T19:43:16.754963", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-01-27T19:43:16.754963" + } }, "vcf, hgnc_ids - filter on hgnc ids and expression": { "content": [ @@ -23,11 +23,11 @@ "18e010447bd23a05a202d44daf66bcd2", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=1, phased=false, phasedAutodetect=false]" ], + "timestamp": "2026-01-27T19:43:25.968654", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-01-27T19:43:25.968654" + } }, "vcf, hgnc_ids - filter on expression": { "content": [ @@ -38,11 +38,11 @@ "9236236d782191442193a20355604927", "VcfFile [chromosomes=[1], sampleCount=3, variantCount=37, phased=false, phasedAutodetect=false]" ], + "timestamp": "2026-01-20T12:44:40.698598144", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.2" - }, - "timestamp": "2026-01-20T12:44:40.698598144" + } }, "vcf, hgnc_ids - filter on hgnc ids and expression - stub": { "content": [ @@ -81,10 +81,10 @@ ] } ], + "timestamp": "2026-01-27T19:43:35.16804", "meta": { "nf-test": "0.9.3", "nextflow": "25.10.3" - }, - "timestamp": "2026-01-27T19:43:35.16804" + } } } \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/nextflow.config similarity index 86% rename from subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config rename to subworkflows/local/vcf_filter_bcftools_filtervep/tests/nextflow.config index 49d12aa8f..670e5d97e 100644 --- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/nextflow.config +++ b/subworkflows/local/vcf_filter_bcftools_filtervep/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: 'ENSEMBLVEP_FILTERVEP' { + withName: 'FILTERVEP' { ext.args = { "--filter \"HGNC_ID in ${feature_file}\"" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 736873282..0d6dea7b2 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -131,10 +131,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 115.2, - "perl-math-cdf": 0.1 - }, "ENSEMBLVEP_ME": { "ensemblvep": 110.1, "perl-math-cdf": 0.1, @@ -165,6 +161,9 @@ "FASTQC": { "fastqc": "0.12.1" }, + "FILTERVEP": { + "filtervep": "1.0.0" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -931,7 +930,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-01T14:09:20.631591498", + "timestamp": "2026-06-05T00:19:48.333529235", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index a9bee2fd8..5952f98d0 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -125,10 +125,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 115.2, - "perl-math-cdf": 0.1 - }, "ENSEMBLVEP_ME": { "ensemblvep": 110.1, "perl-math-cdf": 0.1, @@ -153,6 +149,9 @@ "bgzip": "1.22.1", "expansionhunter": "5.0.0" }, + "FILTERVEP": { + "filtervep": "1.0.0" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -847,7 +846,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-01T14:15:55.418513656", + "timestamp": "2026-06-05T00:25:53.862854239", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 66f438cc4..ba280f7c5 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -123,10 +123,6 @@ "DEEPVARIANT": { "deepvariant": "1.9.0" }, - "ENSEMBLVEP_FILTERVEP": { - "ensemblvep": 115.2, - "perl-math-cdf": 0.1 - }, "ENSEMBLVEP_ME": { "ensemblvep": 110.1, "perl-math-cdf": 0.1, @@ -157,6 +153,9 @@ "FASTQC": { "fastqc": "0.12.1" }, + "FILTERVEP": { + "filtervep": "1.0.0" + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -655,7 +654,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-04-29T22:30:32.111448817", + "timestamp": "2026-06-05T00:29:37.176160755", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 420c43c7f..d65743e77 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -63,10 +63,10 @@ include { RANK_VARIANTS as RANK_VARIANTS_SV } from '.. include { SUBSAMPLE_MT_FRAC } from '../subworkflows/local/subsample_mt_frac' include { SUBSAMPLE_MT_READS } from '../subworkflows/local/subsample_mt_reads' include { VARIANT_EVALUATION } from '../subworkflows/local/variant_evaluation' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' -include { VCF_FILTER_BCFTOOLS_ENSEMBLVEP as GENERATE_CLINICAL_SET_SV } from '../subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main' +include { VCF_FILTER_BCFTOOLS_FILTERVEP as GENERATE_CLINICAL_SET_ME } from '../subworkflows/local/vcf_filter_bcftools_filtervep' +include { VCF_FILTER_BCFTOOLS_FILTERVEP as GENERATE_CLINICAL_SET_MT } from '../subworkflows/local/vcf_filter_bcftools_filtervep' +include { VCF_FILTER_BCFTOOLS_FILTERVEP as GENERATE_CLINICAL_SET_SNV } from '../subworkflows/local/vcf_filter_bcftools_filtervep' +include { VCF_FILTER_BCFTOOLS_FILTERVEP as GENERATE_CLINICAL_SET_SV } from '../subworkflows/local/vcf_filter_bcftools_filtervep' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From befc4bf9406e85c5ce3ac15d2909cc06a10ba32b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 5 Jun 2026 16:17:37 +0200 Subject: [PATCH 778/872] strip new line --- bin/filtervep.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/filtervep.py b/bin/filtervep.py index 0d02b6a7c..e8b1fb1f6 100755 --- a/bin/filtervep.py +++ b/bin/filtervep.py @@ -469,7 +469,7 @@ def process_cyvcf2(args, out_fh): if args.test and line_number > args.test: break - vcf_line = str(var) + vcf_line = str(var).rstrip('\n') parts = vcf_line.split('\t') main_data = {col_names[i]: (parts[i] if i < len(parts) else None) From c1d97b9ec9ff6d99896c5e3ac54d3439edff9645 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 8 Jun 2026 13:18:36 +0200 Subject: [PATCH 779/872] filter classify to avoid mismatched joins --- subworkflows/local/call_sv_MT/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 9403b2759..018d632be 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -122,6 +122,7 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } .join(ch_sample_id_map, remainder: true) + .filter { it.size() == 4 } .map { sample_meta, case_id, txt, cust_id -> cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] } From ec8f4f70bc27f5cb58f5189867fe1563399c8a12 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 8 Jun 2026 13:21:27 +0200 Subject: [PATCH 780/872] add stub for local module --- modules/local/saltshaker_to_html/main.nf | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/modules/local/saltshaker_to_html/main.nf b/modules/local/saltshaker_to_html/main.nf index 96f2cbf2c..3d56fdb6b 100644 --- a/modules/local/saltshaker_to_html/main.nf +++ b/modules/local/saltshaker_to_html/main.nf @@ -23,4 +23,12 @@ process SALTSHAKER_TO_HTML { --sample ${sample_ids.join(' --sample ')} \ --output ${prefix}.html """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo $args + touch ${prefix}.html + """ } From ae0e125a2cf805454f4767f28a4c40b52b4ec000 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 8 Jun 2026 14:01:37 +0200 Subject: [PATCH 781/872] update snaps --- .../tests/main.nf.test | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 692 ++++++++++++++++++ tests/default.nf.test.snap | 4 +- 3 files changed, 695 insertions(+), 3 deletions(-) create mode 100644 subworkflows/local/call_sv_MT/tests/main.nf.test.snap diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index ecd1482af..b869de74f 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -41,7 +41,7 @@ nextflow_workflow { input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[10] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) input[12] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap new file mode 100644 index 000000000..63e887769 --- /dev/null +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -0,0 +1,692 @@ +{ + "CALL_SV_MT - stub": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "2", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "3", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "mt_del_result", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "saltshaker_html", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ] + ] + ], + "timestamp": "2026-06-08T13:58:44.211908065", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "CALL_SV_MT - no_sample_map - stub": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "2", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "3", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "mt_del_result", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "saltshaker_html", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ] + ] + ], + "timestamp": "2026-06-08T13:58:59.838677182", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + } +} \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2e1693617..68bc6ffb6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1100,7 +1100,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,ec31b41e2d101dfcc0e49e2064d6c0a1", + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e", "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1332,7 +1332,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-06-05T11:02:01.458054473", + "timestamp": "2026-06-08T13:40:08.040299351", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 2d577e3afe9ba178a95ca41c42dcb89d4b4c0825 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Jun 2026 08:21:02 +0200 Subject: [PATCH 782/872] change subworkflow test --- .../local/call_sv_MT/tests/main.nf.test | 4 +- .../local/call_sv_MT/tests/main.nf.test.snap | 128 +++++++++++++++++- 2 files changed, 128 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index b02ac76f6..152432a2d 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -43,7 +43,7 @@ nextflow_workflow { input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[8] = channel.of([[id:'mt'], file("${projectDir}/subworkflows/local/variant_evaluation/tests")]).collect() input[9] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], @@ -125,7 +125,7 @@ nextflow_workflow { input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[8] = channel.of([[id:'mt'], file("${projectDir}/subworkflows/local/variant_evaluation/tests")]).collect() input[9] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 63e887769..346ce559a 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -40,6 +40,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -130,6 +144,23 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "call_sv/", [ @@ -245,6 +276,23 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "call_sv/", [ @@ -311,6 +359,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -338,7 +400,7 @@ ] ] ], - "timestamp": "2026-06-08T13:58:44.211908065", + "timestamp": "2026-06-09T08:19:19.961474", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" @@ -385,6 +447,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -475,6 +551,23 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "call_sv/", [ @@ -590,6 +683,23 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], [ "call_sv/", [ @@ -656,6 +766,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -683,7 +807,7 @@ ] ] ], - "timestamp": "2026-06-08T13:58:59.838677182", + "timestamp": "2026-06-09T08:19:58.336196", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 62801ffb44af881682bf3a343a4c613465408cb6 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 9 Jun 2026 12:41:42 +0200 Subject: [PATCH 783/872] Update bin/saltshaker_to_html.py Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- bin/saltshaker_to_html.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py index f65a8e288..9df56d4ac 100755 --- a/bin/saltshaker_to_html.py +++ b/bin/saltshaker_to_html.py @@ -68,6 +68,10 @@ def main( help="Path to output .html file" ) ): + if len(input) != len(sample): + raise typer.BadParameter( + "--input and --sample must have the same number of values" + ) tab_buttons = ''.join(create_tab_button(sid) for sid in sample) tab_contents = ''.join(create_tab_content(sid, inp) for inp, sid in zip(input, sample)) From 32cbf9ac0d6f0bbbe65651d34967032d8ab81c87 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 9 Jun 2026 12:48:09 +0200 Subject: [PATCH 784/872] empty lines in python per suggestion --- bin/saltshaker_to_html.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py index 9df56d4ac..2ac2b87ab 100755 --- a/bin/saltshaker_to_html.py +++ b/bin/saltshaker_to_html.py @@ -4,6 +4,7 @@ from pathlib import Path from typing import List, Optional + CSS = """.tabcontent { display: none; } .tabcontent.active { display: block; } .tablinks { padding: 12px 20px; cursor: pointer; background-color: #f1f1f1; border: 1px solid #ccc; } @@ -11,6 +12,7 @@ .tablinks:hover { background-color: #ddd; } """ + JS = """ function openTab(evt, tabName) { var i, tabcontent, tablinks; @@ -28,15 +30,18 @@ document.getElementsByClassName("tablinks")[0].click(); """ + def txt_to_html(txt_file): with open(txt_file) as tf: content = tf.read() html_content = re.sub(r'\\n', '
    ', content) return html_content + def create_tab_button(sample_id): return f'''\n''' + def create_tab_content(sample_id, txt_file): html_content = txt_to_html(txt_file) return f'''
    @@ -45,6 +50,7 @@ def create_tab_content(sample_id, txt_file):
    ''' + app = typer.Typer() @app.command() @@ -94,6 +100,7 @@ def main( with open(output, 'w') as f: f.write(html) + if __name__ == "__main__": app() From 6fe7f953c411d731a0b94f07cafa2e9b75819bc6 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Jun 2026 13:11:38 +0200 Subject: [PATCH 785/872] fix python linting --- bin/saltshaker_to_html.py | 1 - 1 file changed, 1 deletion(-) diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py index 2ac2b87ab..14cecfea8 100755 --- a/bin/saltshaker_to_html.py +++ b/bin/saltshaker_to_html.py @@ -100,7 +100,6 @@ def main( with open(output, 'w') as f: f.write(html) - if __name__ == "__main__": app() From 506da74b88f242453257a80a6c38fec9e3924245 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Jun 2026 13:42:16 +0200 Subject: [PATCH 786/872] suggestions from review --- CHANGELOG.md | 6 +++--- subworkflows/local/call_sv_MT/main.nf | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4afd26e78..079386a15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,9 +30,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| ---- | ----------- | ----------- | -| | | | +| Tool | Old version | New version | +| ---------- | ----------- | ----------- | +| Saltshaker | 1.0.0 | 1.1.1 | ## 3.0.0 - Mario [2026-05-12] diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 018d632be..b6c4c8919 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -121,7 +121,8 @@ workflow CALL_SV_MT { // customer IDs (or sample ID if no customer ID) so individual reports have identifers in the final HTML. SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } - .join(ch_sample_id_map, remainder: true) + .join(ch_sample_id_map, remainder: true, failOnDuplicate: true) + // Only keep entries that have all 4 elements needed by map (for example stub tests without meta fail without this) .filter { it.size() == 4 } .map { sample_meta, case_id, txt, cust_id -> cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] From 596192c96e9463dcca12d6c3e38b2b22deb08bdc Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 9 Jun 2026 13:47:46 +0200 Subject: [PATCH 787/872] move sorting to python script --- bin/saltshaker_to_html.py | 8 ++++++++ subworkflows/local/call_sv_MT/main.nf | 7 ------- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/bin/saltshaker_to_html.py b/bin/saltshaker_to_html.py index 14cecfea8..07d3a6b1d 100755 --- a/bin/saltshaker_to_html.py +++ b/bin/saltshaker_to_html.py @@ -30,6 +30,13 @@ document.getElementsByClassName("tablinks")[0].click(); """ +def sort_inputs(inputs, sample_ids): + zipped = list(zip(inputs, sample_ids)) + sorted_zipped = sorted(zipped, key=lambda x: x[0].name) + sorted_inputs = [x[0] for x in sorted_zipped] + sorted_sample_ids = [x[1] for x in sorted_zipped] + return sorted_inputs, sorted_sample_ids + def txt_to_html(txt_file): with open(txt_file) as tf: @@ -78,6 +85,7 @@ def main( raise typer.BadParameter( "--input and --sample must have the same number of values" ) + input, sample = sort_inputs(input, sample) tab_buttons = ''.join(create_tab_button(sid) for sid in sample) tab_contents = ''.join(create_tab_content(sid, inp) for inp, sid in zip(input, sample)) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index b6c4c8919..db21dff37 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -128,13 +128,6 @@ workflow CALL_SV_MT { cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] } .groupTuple() - .map { meta, paths, ids -> - def zipped = [paths, ids].transpose() - def sorted = zipped.sort { a, b -> a[0].getName() <=> b[0].getName() } - def sorted_paths = sorted.collect { it[0] } - def sorted_ids = sorted.collect { it[1] } - return [meta, sorted_paths, sorted_ids] - } .set { ch_saltshaker_html_input } SALTSHAKER_TO_HTML( From c582c886d27a5191e6549a7b07539d66029fb58e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 09:32:24 +0200 Subject: [PATCH 788/872] review suggestion --- bin/filtervep.py | 737 +++++++++--------- .../vcf_filter_bcftools_filtervep/main.nf | 4 +- 2 files changed, 376 insertions(+), 365 deletions(-) diff --git a/bin/filtervep.py b/bin/filtervep.py index e8b1fb1f6..e99dd0425 100755 --- a/bin/filtervep.py +++ b/bin/filtervep.py @@ -77,230 +77,239 @@ class FilterSet: _file_cache: dict = {} # shared across all instances def __init__(self, *filter_strings): - self._parsed = [self._parse(f) for f in filter_strings] + self._parsed = [self._parse(filter_string) for filter_string in filter_strings] # -- tokeniser ----------------------------------------------------------- def _tokenize(self, expr): - toks = [] - i = 0 - n = len(expr) - while i < n: - c = expr[i] - if c.isspace(): - i += 1 + tokens = [] + char_idx = 0 + expr_length = len(expr) + while char_idx < expr_length: + char = expr[char_idx] + if char.isspace(): + char_idx += 1 continue - if c == '(': - toks.append(('LP', None)); i += 1; continue - if c == ')': - toks.append(('RP', None)); i += 1; continue - if c in ('>', '<', '!', '='): - two = expr[i:i+2] - if two in ('>=', '<=', '!='): - toks.append(('OP', two)); i += 2 + if char == '(': + tokens.append(('LP', None)); char_idx += 1; continue + if char == ')': + tokens.append(('RP', None)); char_idx += 1; continue + if char in ('>', '<', '!', '='): + two_char = expr[char_idx:char_idx+2] + if two_char in ('>=', '<=', '!='): + tokens.append(('OP', two_char)); char_idx += 2 else: - toks.append(('OP', c)); i += 1 + tokens.append(('OP', char)); char_idx += 1 continue - m = re.match(r'[^\s()]+', expr[i:]) - if m: - w = m.group(); lo = w.lower() - if lo == 'and': toks.append(('AND', None)) - elif lo == 'or': toks.append(('OR', None)) - elif lo == 'not': toks.append(('NOT', None)) - elif lo in self._OP_WORDS: - # Normalise synonyms to canonical op - toks.append(('OP', self._OP_SYNONYMS.get(lo, lo))) + word_match = re.match(r'[^\s()]+', expr[char_idx:]) + if word_match: + word = word_match.group() + word_lower = word.lower() + if word_lower == 'and': tokens.append(('AND', None)) + elif word_lower == 'or': tokens.append(('OR', None)) + elif word_lower == 'not': tokens.append(('NOT', None)) + elif word_lower in self._OP_WORDS: + tokens.append(('OP', self._OP_SYNONYMS.get(word_lower, word_lower))) else: - toks.append(('W', w)) - i += len(w) + tokens.append(('W', word)) + char_idx += len(word) continue - i += 1 - toks.append(('EOF', None)) - return toks + char_idx += 1 + tokens.append(('EOF', None)) + return tokens # -- recursive-descent parser -> AST ------------------------------------- def _parse(self, expr): - toks = self._tokenize(expr) - pos = [0] + tokens = self._tokenize(expr) + token_pos = [0] + + def peek(): + return tokens[token_pos[0]] - def peek(): return toks[pos[0]] def eat(): - t = toks[pos[0]]; pos[0] += 1; return t + token = tokens[token_pos[0]] + token_pos[0] += 1 + return token - def or_(): - l = and_() + def parse_or(): + left_node = parse_and() while peek()[0] == 'OR': - eat(); r = and_(); l = ('or', l, r) - return l + eat() + right_node = parse_and() + left_node = ('or', left_node, right_node) + return left_node - def and_(): - l = not_() + def parse_and(): + left_node = parse_not() while peek()[0] == 'AND': - eat(); r = not_(); l = ('and', l, r) - return l + eat() + right_node = parse_not() + left_node = ('and', left_node, right_node) + return left_node - def not_(): + def parse_not(): if peek()[0] == 'NOT': - eat(); return ('not', atom()) - return atom() + eat() + return ('not', parse_atom()) + return parse_atom() - def atom(): + def parse_atom(): if peek()[0] == 'LP': - eat(); node = or_() - if peek()[0] == 'RP': eat() + eat() + node = parse_or() + if peek()[0] == 'RP': + eat() return node if peek()[0] != 'W': raise SyntaxError(f"Expected field name, got {peek()!r} in: {expr!r}") field = eat()[1] - t = peek() - if t[0] in ('EOF', 'RP', 'AND', 'OR'): + next_token = peek() + if next_token[0] in ('EOF', 'RP', 'AND', 'OR'): return ('exists', field, None) - if t[0] != 'OP': + if next_token[0] != 'OP': return ('exists', field, None) - op = eat()[1].lower() - if op == 'is' and peek()[0] == 'NOT': - eat(); op = 'is not' - if op == 'exists': + operator = eat()[1].lower() + if operator == 'is' and peek()[0] == 'NOT': + eat() + operator = 'is not' + if operator == 'exists': return ('exists', field, None) if peek()[0] in ('EOF', 'AND', 'OR', 'RP'): - val = None + value = None else: - val = eat()[1] - return (op, field, val) + value = eat()[1] + return (operator, field, value) - return or_() + return parse_or() # -- evaluator ----------------------------------------------------------- def evaluate(self, data): - return all(self._eval(ast, data) for ast in self._parsed) + return all(self._eval(ast_node, data) for ast_node in self._parsed) - def _fv(self, data, field): + def _fetch_field_value(self, data, field): """Fetch field value with case-insensitive fallback.""" - v = data.get(field) - if v is not None: - return v - fl = field.lower() - for k, val in data.items(): - if k is not None and k.lower() == fl: - return val + value = data.get(field) + if value is not None: + return value + field_lower = field.lower() + for existing_key, existing_value in data.items(): + if existing_key is not None and existing_key.lower() == field_lower: + return existing_value return None @staticmethod - def _norm(field, val): + def _normalize_missing(field, value): """Treat '' and '-' (except for Allele) as missing.""" - if val is None or val == '': + if value is None or value == '': return None - if field != 'Allele' and val == '-': + if field != 'Allele' and value == '-': return None - return val + return value # Regex for VEP mixed-type field values: e.g. "HGNC:28706", "deleterious(0.05)" _MIXED_RE = re.compile(r'^([\w.\-]+)?:?\(?([-\d.e]*)\)?', re.IGNORECASE) - _NUM_RE = re.compile(r'^-?\d+\.?\d*(e-?\d+)?$', re.IGNORECASE) - _PURE_NUM = re.compile(r'^[-\d.e]+$', re.IGNORECASE) + _NUM_RE = re.compile(r'^-?\d+\.?\d*(e-?\d+)?$', re.IGNORECASE) + _PURE_NUM = re.compile(r'^[-\d.e]+$', re.IGNORECASE) - def _get_input(self, fval, rep_value): + def _get_input(self, field_value, representative_value): """Replicate VEP 115 FilterSet.get_input() value-extraction logic. Given a raw field value and a representative comparison value, - returns the part of fval that should be compared. + returns the part of field_value that should be compared. - - If fval has the form TEXT:NUM or TEXT(NUM): - - and rep_value is purely numeric → return the NUM part - - otherwise → return fval unchanged - - If fval is plain (no numeric part) → return fval unchanged + - If field_value has the form TEXT:NUM or TEXT(NUM): + - and representative_value is purely numeric → return the NUM part + - otherwise → return field_value unchanged + - If field_value is plain (no numeric part) → return field_value unchanged """ - if fval is None: + if field_value is None: return None - s = str(fval) - m = self._MIXED_RE.match(s) - if not m: - return s - text = m.group(1) or '' - num = m.group(2) or '' - if not num: - return s # no numeric part; unchanged - # Determine whether the comparison side is purely numeric - rep = str(rep_value) if rep_value is not None else '' - if self._PURE_NUM.match(rep): - # comparison is numeric → use num part unless text is already numeric - if not self._NUM_RE.match(text): - return num - return text - # comparison is not purely numeric → return value unchanged - return s + field_str = str(field_value) + mixed_match = self._MIXED_RE.match(field_str) + if not mixed_match: + return field_str + text_part = mixed_match.group(1) or '' + numeric_part = mixed_match.group(2) or '' + if not numeric_part: + return field_str + representative_str = str(representative_value) if representative_value is not None else '' + if self._PURE_NUM.match(representative_str): + if not self._NUM_RE.match(text_part): + return numeric_part + return text_part + return field_str def _resolve_value(self, value, data): """If value starts with '#', resolve it to the named field's value.""" if value and value.startswith('#'): - return self._norm(value[1:], self._fv(data, value[1:])) + field_name = value[1:] + return self._normalize_missing(field_name, self._fetch_field_value(data, field_name)) return value def _eval(self, node, data): - op = node[0] - if op == 'and': return self._eval(node[1], data) and self._eval(node[2], data) - if op == 'or': return self._eval(node[1], data) or self._eval(node[2], data) - if op == 'not': return not self._eval(node[1], data) - - field = node[1] - value = self._resolve_value(node[2] if len(node) > 2 else None, data) - fval = self._norm(field, self._fv(data, field)) - - if op == 'exists': - return fval is not None - - if op in ('is', '='): - if value is None: return fval is None - if fval is None: return False - inp = self._get_input(fval, value) - return inp.lower() == str(value).lower() - - if op in ('is not', '!='): - if value is None: return fval is not None - if fval is None: return True - inp = self._get_input(fval, value) - return inp.lower() != str(value).lower() - - if fval is None: + operator = node[0] + if operator == 'and': return self._eval(node[1], data) and self._eval(node[2], data) + if operator == 'or': return self._eval(node[1], data) or self._eval(node[2], data) + if operator == 'not': return not self._eval(node[1], data) + + field = node[1] + value = self._resolve_value(node[2] if len(node) > 2 else None, data) + field_value = self._normalize_missing(field, self._fetch_field_value(data, field)) + + if operator == 'exists': + return field_value is not None + + if operator in ('is', '='): + if value is None: return field_value is None + if field_value is None: return False + processed_input = self._get_input(field_value, value) + return processed_input.lower() == str(value).lower() + + if operator in ('is not', '!='): + if value is None: return field_value is not None + if field_value is None: return True + processed_input = self._get_input(field_value, value) + return processed_input.lower() != str(value).lower() + + if field_value is None: return False - if op == 'match': - return bool(re.search(str(value or ''), str(fval), re.IGNORECASE)) + if operator == 'match': + return bool(re.search(str(value or ''), str(field_value), re.IGNORECASE)) - if op == 'in': + if operator == 'in': if value is None: return False - in_set = self._in_set(value) - # Pick a representative value to determine numeric vs string mode - rep = next(iter(in_set), None) - inp = self._get_input(fval, rep).lower() - return inp in in_set + in_set = self._in_set(value) + representative = next(iter(in_set), None) + processed_input = self._get_input(field_value, representative).lower() + return processed_input in in_set - if op == 'is_child': - # Ontology lookup not supported; exact match fallback - inp = self._get_input(fval, value) - return inp.lower() == str(value or '').lower() + if operator == 'is_child': + processed_input = self._get_input(field_value, value) + return processed_input.lower() == str(value or '').lower() # Ordered comparisons — use _get_input for numeric extraction - inp = self._get_input(fval, value) - sv = inp - tv = str(value or '') + processed_input = self._get_input(field_value, value) + str_field_val = processed_input + str_target_val = str(value or '') try: - fn, tn = float(sv), float(tv) - if op == '>': return fn > tn - if op == '<': return fn < tn - if op == '>=': return fn >= tn - if op == '<=': return fn <= tn + field_num = float(str_field_val) + target_num = float(str_target_val) + if operator == '>': return field_num > target_num + if operator == '<': return field_num < target_num + if operator == '>=': return field_num >= target_num + if operator == '<=': return field_num <= target_num except (ValueError, TypeError): pass - if op == '>': return sv > tv - if op == '<': return sv < tv - if op == '>=': return sv >= tv - if op == '<=': return sv <= tv + if operator == '>': return str_field_val > str_target_val + if operator == '<': return str_field_val < str_target_val + if operator == '>=': return str_field_val >= str_target_val + if operator == '<=': return str_field_val <= str_target_val return False - def limit_synonym_search(self, _val=True): + def limit_synonym_search(self, _value=True): """No-op shim (kept for API parity with the Perl module).""" def _in_set(self, value): @@ -311,12 +320,12 @@ def _in_set(self, value): if value in self._file_cache: return self._file_cache[value] if os.path.isfile(value): - with open(value) as fh: - s = {line.strip().lower() for line in fh if line.strip()} - self._file_cache[value] = s - return s - s = {v.strip().lower() for v in value.split(',')} - return s + with open(value) as file_handle: + value_set = {line.strip().lower() for line in file_handle if line.strip()} + self._file_cache[value] = value_set + return value_set + value_set = {item.strip().lower() for item in value.split(',')} + return value_set # --------------------------------------------------------------------------- @@ -325,50 +334,51 @@ def _in_set(self, value): def parse_headers(raw_headers, vcf_info_field='CSQ'): """Return (vep_headers, col_headers, allowed_fields_dict).""" - vep_headers = None - col_headers = None - allowed = {} - for raw in raw_headers: - hashes = len(raw) - len(raw.lstrip('#')) - line = raw.lstrip('#') - if hashes >= 2: - if re.match(r'INFO== 2: + if re.match(r'INFO== 5 - and re.match(r'(chr)?\w+', p[0]) - and re.match(r'^\d+$', p[1]) - and p[3] and re.match(r'^[ACGTN\-.]+$', p[3], re.IGNORECASE) - and p[4]): + fields = line.split('\t') + if (len(fields) >= 5 + and re.match(r'(chr)?\w+', fields[0]) + and re.match(r'^\d+$', fields[1]) + and fields[3] and re.match(r'^[ACGTN\-.]+$', fields[3], re.IGNORECASE) + and fields[4]): return 'vcf' return 'tab' @@ -402,9 +412,9 @@ def open_input(path, force_gz=False): return sys.stdin if path.endswith('.gz') or force_gz: return gzip.open(path, 'rt') - with open(path, 'rb') as f: - magic = f.read(2) - if magic == b'\x1f\x8b': + with open(path, 'rb') as file_handle: + magic_bytes = file_handle.read(2) + if magic_bytes == b'\x1f\x8b': return gzip.open(path, 'rt') return open(path, 'r') @@ -413,94 +423,95 @@ def open_input(path, force_gz=False): # cyvcf2 fast path (VCF only) # --------------------------------------------------------------------------- -def process_cyvcf2(args, out_fh): +def process_cyvcf2(args, output_fh): vcf_info_field = args.vcf_info_field filter_set = args.filter_set vcf = cyvcf2.VCF(args.input_file or '-') - raw_hdr_lines = vcf.raw_header.rstrip('\n').split('\n') + raw_header_lines = vcf.raw_header.rstrip('\n').split('\n') vep_headers = None - for h in raw_hdr_lines: - m = re.search(r'ID=' + re.escape(vcf_info_field) + r'.*?Format: (.+?)"', h) - if m: - vep_headers = m.group(1).split('|') + for header_line in raw_header_lines: + regex_match = re.search(r'ID=' + re.escape(vcf_info_field) + r'.*?Format: (.+?)"', header_line) + if regex_match: + vep_headers = regex_match.group(1).split('|') break col_headers = None - for h in reversed(raw_hdr_lines): - if h.startswith('#') and not h.startswith('##'): - col_headers = h.lstrip('#').split('\t') + for header_line in reversed(raw_header_lines): + if header_line.startswith('#') and not header_line.startswith('##'): + col_headers = header_line.lstrip('#').split('\t') break all_fields = set() if vep_headers: all_fields.update(vep_headers) if col_headers: all_fields.update(col_headers) - for h in raw_hdr_lines: - m = re.match(r'##INFO=') - hdr_lines.insert(i, '##FILTER=') + for idx, header_line in enumerate(output_header_lines): + if header_line.startswith('#') and not header_line.startswith('##'): + output_header_lines.insert(idx, '##FILTER=') + output_header_lines.insert(idx, '##FILTER=') break if not args.count: - out_fh.write('\n'.join(hdr_lines) + '\n') + output_fh.write('\n'.join(output_header_lines) + '\n') - col_names = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] - count = 0 - line_number = 0 - missing_csq = 0 + column_names = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] + count = 0 + line_number = 0 + missing_csq = 0 - for var in vcf: + for variant in vcf: line_number += 1 if args.test and line_number > args.test: break - vcf_line = str(var).rstrip('\n') - parts = vcf_line.split('\t') - - main_data = {col_names[i]: (parts[i] if i < len(parts) else None) - for i in range(len(col_names))} - if len(parts) > 7: - for ifield in parts[7].split(';'): - if '=' in ifield: - k, v = ifield.split('=', 1) - if k != vcf_info_field: - main_data[k] = v - elif ifield: - main_data[ifield] = None # Flag: Perl sets to undef, so exists-check fails - - csq_val = var.INFO.get(vcf_info_field) + vcf_line = str(variant) + vcf_parts = vcf_line.split('\t') + + main_data = {column_names[idx]: (vcf_parts[idx] if idx < len(vcf_parts) else None) + for idx in range(len(column_names))} + if len(vcf_parts) > 7: + for info_field in vcf_parts[7].split(';'): + if '=' in info_field: + info_key, info_value = info_field.split('=', 1) + if info_key != vcf_info_field: + main_data[info_key] = info_value + elif info_field: + main_data[info_field] = None # Flag: Perl sets to undef, so exists-check fails + + csq_value = variant.INFO.get(vcf_info_field) chunks = [] data_list = [] - if csq_val: - chunks = csq_val.split(',') - data_list = [parse_csq_chunk(c, vep_headers or [], main_data) for c in chunks] + if csq_value: + chunks = csq_value.split(',') + data_list = [parse_csq_chunk(chunk, vep_headers or [], main_data) for chunk in chunks] else: missing_csq += 1 data_list = [main_data] line_pass = 0 new_chunks = [] - for i, parsed in enumerate(data_list): - if filter_set.evaluate(parsed): + for blob_index, parsed_blob in enumerate(data_list): + if filter_set.evaluate(parsed_blob): line_pass += 1 - if i < len(chunks): - new_chunks.append(chunks[i]) + if blob_index < len(chunks): + new_chunks.append(chunks[blob_index]) count += bool(line_pass) @@ -508,19 +519,19 @@ def process_cyvcf2(args, out_fh): continue if args.soft_filter: - tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' - cur = parts[6] if len(parts) > 6 else '.' - parts[6] = f"{cur};{tag}" if cur and cur != '.' else tag - out_fh.write('\t'.join(parts) + '\n') + filter_tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' + existing_filter = vcf_parts[6] if len(vcf_parts) > 6 else '.' + vcf_parts[6] = f"{existing_filter};{filter_tag}" if existing_filter and existing_filter != '.' else filter_tag + output_fh.write('\t'.join(vcf_parts) + '\n') elif line_pass and not args.count: out_line = vcf_line if args.only_matched and new_chunks and len(new_chunks) != len(chunks): - new_csq = ','.join(new_chunks) - p = out_line.split('\t') - p[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', - vcf_info_field + '=' + new_csq, p[7], count=1) - out_line = '\t'.join(p) - out_fh.write(out_line + '\n') + new_csq = ','.join(new_chunks) + vcf_parts_rw = out_line.split('\t') + vcf_parts_rw[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', + vcf_info_field + '=' + new_csq, vcf_parts_rw[7], count=1) + out_line = '\t'.join(vcf_parts_rw) + output_fh.write(out_line + '\n') if not args.soft_filter and count >= args.limit + args.start - 1: break @@ -528,10 +539,10 @@ def process_cyvcf2(args, out_fh): vcf.close() if line_number == 0 and not args.count: - out_fh.write('\n'.join(hdr_lines) + '\n') + output_fh.write('\n'.join(output_header_lines) + '\n') if args.count: - out_fh.write(f"{count}\n") + output_fh.write(f"{count}\n") if missing_csq: sys.stderr.write( @@ -544,24 +555,24 @@ def process_cyvcf2(args, out_fh): # Generic path (tab or VCF without cyvcf2) # --------------------------------------------------------------------------- -def process_generic(args, out_fh): +def process_generic(args, output_fh): vcf_info_field = args.vcf_info_field filter_set = args.filter_set - in_fh = open_input(args.input_file, args.gz) + input_fh = open_input(args.input_file, args.gz) - raw_headers = [] - vep_headers = None - col_headers = None - fmt = args.format - count = 0 - line_number = 0 - missing_csq = 0 - headers_initialised = False + raw_headers = [] + vep_headers = None + col_headers = None + file_format = args.format + count = 0 + line_number = 0 + missing_csq = 0 + headers_initialised = False csq_re = re.compile(re.escape(vcf_info_field) + r'=(.+?)(?:;|\s|$)') - for raw_line in in_fh: + for raw_line in input_fh: line = raw_line.rstrip('\n') if line.startswith('#'): @@ -578,13 +589,13 @@ def process_generic(args, out_fh): sys.exit("ERROR: No headers found in input file") if args.soft_filter: - chrom_hdr = raw_headers.pop() + chrom_header = raw_headers.pop() raw_headers.append('##FILTER=') raw_headers.append('##FILTER=') - raw_headers.append(chrom_hdr) + raw_headers.append(chrom_header) if not args.count and not args.list: - out_fh.write('\n'.join(raw_headers) + '\n') + output_fh.write('\n'.join(raw_headers) + '\n') vep_headers, col_headers, extra_allowed = parse_headers(raw_headers, vcf_info_field) @@ -595,22 +606,22 @@ def process_generic(args, out_fh): if args.list: print("Available fields:\n") - for f in sorted(all_fields): - print(f) - if in_fh is not sys.stdin: - in_fh.close() + for field_name in sorted(all_fields): + print(field_name) + if input_fh is not sys.stdin: + input_fh.close() return headers_initialised = True # -- format detection -- - if not fmt: - fmt = detect_format(line) - if fmt not in ('vcf', 'tab'): - sys.exit(f"ERROR: Unable to parse data in format {fmt}") - if fmt != 'vcf' and args.only_matched: + if not file_format: + file_format = detect_format(line) + if file_format not in ('vcf', 'tab'): + sys.exit(f"ERROR: Unable to parse data in format {file_format}") + if file_format != 'vcf' and args.only_matched: sys.exit("ERROR: --only_matched is compatible only with VCF files") - if fmt != 'vcf' and args.soft_filter: + if file_format != 'vcf' and args.soft_filter: sys.exit("ERROR: --soft_filter is compatible only with VCF files") if args.soft_filter: @@ -619,33 +630,33 @@ def process_generic(args, out_fh): chunks = [] data_list = [] - if fmt == 'tab': - hdrs = col_headers or vep_headers or [] - data_list.append(parse_tab_line(line, hdrs)) + if file_format == 'tab': + tab_headers = col_headers or vep_headers or [] + data_list.append(parse_tab_line(line, tab_headers)) chunks.append(line) - if not any(h == 'Extra' for h in hdrs): + if not any(header == 'Extra' for header in tab_headers): filter_set.limit_synonym_search(True) else: # vcf - parts = line.split('\t') - ch = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] - main_data = {ch[i]: (parts[i] if i < len(parts) else None) - for i in range(len(ch))} - - if len(parts) > 7: - for ifield in parts[7].split(';'): - if '=' in ifield: - k, v = ifield.split('=', 1) - if k != vcf_info_field: - main_data[k] = v - elif ifield: - main_data[ifield] = None # Flag: Perl sets to undef, so exists-check fails - - m = csq_re.search(line) - if m: - raw_csq = m.group(1) - chunks = raw_csq.split(',') - data_list = [parse_csq_chunk(c, vep_headers or [], main_data) for c in chunks] + vcf_parts = line.split('\t') + column_headers = col_headers or ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'] + main_data = {column_headers[idx]: (vcf_parts[idx] if idx < len(vcf_parts) else None) + for idx in range(len(column_headers))} + + if len(vcf_parts) > 7: + for info_field in vcf_parts[7].split(';'): + if '=' in info_field: + info_key, info_value = info_field.split('=', 1) + if info_key != vcf_info_field: + main_data[info_key] = info_value + elif info_field: + main_data[info_field] = None # Flag: Perl sets to undef, so exists-check fails + + regex_match = csq_re.search(line) + if regex_match: + raw_csq_value = regex_match.group(1) + chunks = raw_csq_value.split(',') + data_list = [parse_csq_chunk(chunk, vep_headers or [], main_data) for chunk in chunks] else: missing_csq += 1 data_list = [main_data] @@ -655,11 +666,11 @@ def process_generic(args, out_fh): # -- evaluate -- line_pass = 0 new_chunks = [] - for i, parsed in enumerate(data_list): - if filter_set.evaluate(parsed): + for blob_index, parsed_blob in enumerate(data_list): + if filter_set.evaluate(parsed_blob): line_pass += 1 - if i < len(chunks): - new_chunks.append(chunks[i]) + if blob_index < len(chunks): + new_chunks.append(chunks[blob_index]) count += bool(line_pass) @@ -668,21 +679,21 @@ def process_generic(args, out_fh): # -- output -- if args.soft_filter: - sp = line.split('\t') - tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' - cur = sp[6] if len(sp) > 6 else '.' - sp[6] = f"{cur};{tag}" if cur and cur != '.' else tag - out_fh.write('\t'.join(sp) + '\n') + split_parts = line.split('\t') + filter_tag = 'filter_vep_pass' if line_pass else 'filter_vep_fail' + existing_filter = split_parts[6] if len(split_parts) > 6 else '.' + split_parts[6] = f"{existing_filter};{filter_tag}" if existing_filter and existing_filter != '.' else filter_tag + output_fh.write('\t'.join(split_parts) + '\n') elif line_pass and not args.count: out_line = line if args.only_matched and new_chunks and len(new_chunks) != len(chunks): - new_csq = ','.join(new_chunks) - p = out_line.split('\t') - p[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', - vcf_info_field + '=' + new_csq, p[7], count=1) - out_line = '\t'.join(p) - out_fh.write(out_line + '\n') + new_csq = ','.join(new_chunks) + vcf_parts_rw = out_line.split('\t') + vcf_parts_rw[7] = re.sub(re.escape(vcf_info_field) + r'=[^;]*', + vcf_info_field + '=' + new_csq, vcf_parts_rw[7], count=1) + out_line = '\t'.join(vcf_parts_rw) + output_fh.write(out_line + '\n') if not args.soft_filter and count >= args.limit + args.start - 1: break @@ -690,22 +701,22 @@ def process_generic(args, out_fh): # -- empty file -- if not line_number: if not args.count and not args.list: - out_fh.write('\n'.join(raw_headers) + '\n') + output_fh.write('\n'.join(raw_headers) + '\n') if args.list: - v, c, a = parse_headers(raw_headers, vcf_info_field) - af = set() - if v: af.update(v) - if c: af.update(c) - af.update(a) + vep_headers_parsed, col_headers_parsed, allowed_parsed = parse_headers(raw_headers, vcf_info_field) + all_fields = set() + if vep_headers_parsed: all_fields.update(vep_headers_parsed) + if col_headers_parsed: all_fields.update(col_headers_parsed) + all_fields.update(allowed_parsed) print("Available fields:\n") - for f in sorted(af): - print(f) - if in_fh is not sys.stdin: - in_fh.close() + for field_name in sorted(all_fields): + print(field_name) + if input_fh is not sys.stdin: + input_fh.close() return if args.count: - out_fh.write(f"{count}\n") + output_fh.write(f"{count}\n") if missing_csq: sys.stderr.write( @@ -713,8 +724,8 @@ def process_generic(args, out_fh): f"{vcf_info_field} in {missing_csq} line(s) of the input file\n" ) - if in_fh is not sys.stdin: - in_fh.close() + if input_fh is not sys.stdin: + input_fh.close() # --------------------------------------------------------------------------- @@ -791,31 +802,31 @@ def process_generic(args, out_fh): def main(): - ap = argparse.ArgumentParser(add_help=False) - ap.add_argument('--help', '-h', action='store_true') - ap.add_argument('--test', type=int) - ap.add_argument('--count', '-c', action='store_true') - ap.add_argument('--list', '-l', action='store_true') - ap.add_argument('--input_file', '-i') - ap.add_argument('--output_file', '-o', default='stdout') - ap.add_argument('--force_overwrite', action='store_true') - ap.add_argument('--format', choices=['vcf', 'tab']) - ap.add_argument('--gz', action='store_true') - ap.add_argument('--only_matched', action='store_true') - ap.add_argument('--vcf_info_field', default='CSQ') - ap.add_argument('--soft_filter', action='store_true') - ap.add_argument('--ontology', '-y', action='store_true') - ap.add_argument('--host', default='ensembldb.ensembl.org') - ap.add_argument('--user', default='anonymous') - ap.add_argument('--pass', dest='password', default=None) - ap.add_argument('--port', type=int, default=3306) - ap.add_argument('--version', type=int) - ap.add_argument('--registry') - ap.add_argument('--start', '-s', type=int, default=1) - ap.add_argument('--limit', type=int, default=int(1e12)) - ap.add_argument('--filter', '-f', action='append') - - args = ap.parse_args() + arg_parser = argparse.ArgumentParser(add_help=False) + arg_parser.add_argument('--help', '-h', action='store_true') + arg_parser.add_argument('--test', type=int) + arg_parser.add_argument('--count', '-c', action='store_true') + arg_parser.add_argument('--list', '-l', action='store_true') + arg_parser.add_argument('--input_file', '-i') + arg_parser.add_argument('--output_file', '-o', default='stdout') + arg_parser.add_argument('--force_overwrite', action='store_true') + arg_parser.add_argument('--format', choices=['vcf', 'tab']) + arg_parser.add_argument('--gz', action='store_true') + arg_parser.add_argument('--only_matched', action='store_true') + arg_parser.add_argument('--vcf_info_field', default='CSQ') + arg_parser.add_argument('--soft_filter', action='store_true') + arg_parser.add_argument('--ontology', '-y', action='store_true') + arg_parser.add_argument('--host', default='ensembldb.ensembl.org') + arg_parser.add_argument('--user', default='anonymous') + arg_parser.add_argument('--pass', dest='password', default=None) + arg_parser.add_argument('--port', type=int, default=3306) + arg_parser.add_argument('--version', type=int) + arg_parser.add_argument('--registry') + arg_parser.add_argument('--start', '-s', type=int, default=1) + arg_parser.add_argument('--limit', type=int, default=int(1e12)) + arg_parser.add_argument('--filter', '-f', action='append') + + args = arg_parser.parse_args() if args.help or (not args.filter and not args.list): print(USAGE) @@ -837,9 +848,9 @@ def main(): f"ERROR: Output file {args.output_file} already exists. " "Use --force_overwrite to overwrite." ) - out_fh = open(args.output_file, 'w') + output_fh = open(args.output_file, 'w') else: - out_fh = sys.stdout + output_fh = sys.stdout try: use_cyvcf2 = ( @@ -850,12 +861,12 @@ def main(): re.search(r'\.vcf(\.gz)?$|\.bcf$', args.input_file, re.IGNORECASE))) ) if use_cyvcf2: - process_cyvcf2(args, out_fh) + process_cyvcf2(args, output_fh) else: - process_generic(args, out_fh) + process_generic(args, output_fh) finally: - if out_fh is not sys.stdout: - out_fh.close() + if output_fh is not sys.stdout: + output_fh.close() if __name__ == '__main__': diff --git a/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf b/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf index e589f7850..b355fb026 100644 --- a/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf +++ b/subworkflows/local/vcf_filter_bcftools_filtervep/main.nf @@ -7,8 +7,8 @@ workflow VCF_FILTER_BCFTOOLS_FILTERVEP { take: ch_vcf // channel: [ val(meta), path(vcf) ] ch_filter_vep_feature_file // channel: [ val(meta), path(txt) ] - filter_with_bcftools // bool: should bcftools view be run - filter_with_filter_vep // bool: should filtervep be run + filter_with_bcftools // bool: should bcftools view be run + filter_with_filter_vep // bool: should filtervep be run main: ch_tbi = channel.empty() From 5144481d6cbf9e31b2bd45ea37d6daac8c3e944e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 11:23:54 +0200 Subject: [PATCH 789/872] update script description --- bin/filtervep.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bin/filtervep.py b/bin/filtervep.py index e99dd0425..51d31b86f 100755 --- a/bin/filtervep.py +++ b/bin/filtervep.py @@ -2,7 +2,9 @@ """ filter_vep_fast - Fast Python reimplementation of Ensembl's filter_vep. -Replicates all features of the original Perl script. +Replicates all features of the Perl filter_vep script distributed with Ensembl +VEP (EMBL-EBI). Validated against VEP 110 and 115.2, which are functionally +identical for VCF filtering. Uses cyvcf2 for VCF parsing when available (significant speedup for large VCF / bgzipped files via htslib). """ From 7cf8e94c7131bfe6a41f39cd86933f97b45a5e61 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 10 Jun 2026 12:19:35 +0200 Subject: [PATCH 790/872] add call_sv_MT test --- .../local/call_sv_MT/tests/main.nf.test | 107 ++++- .../local/call_sv_MT/tests/main.nf.test.snap | 407 ++++++++++++++++++ 2 files changed, 512 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index e49287de5..122cd9647 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -14,6 +14,109 @@ nextflow_workflow { config "./nextflow.config" + setup { + run("HISAT2_BUILD") { + script "../../../../modules/nf-core/hisat2/build/main.nf" + config "./nextflow.config" + process { + """ + input[0] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]) + input[1] = [[:],[]] + input[2] = [[:],[]] + """ + } + } + + run("LAST_LASTDB") { + script "../../../../modules/nf-core/last/lastdb/main.nf" + config "./nextflow.config" + process { + """ + input[0] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]) + """ + } + } + } + + test("CALL_SV_MT - 2 samples") { + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true) + ] + ) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = HISAT2_BUILD.out.index.collect() + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = LAST_LASTDB.out.index.collect() + input[9] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true) + ] + ] + ) + input[10] = channel.value(10000000) + input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[13] = false + input[14] = 16081 + input[15] = 407 + input[16] = 5730 + input[17] = 5763 + input[18] = 16569 + input[19] = 'chrM' + input[20] = 15 + input[21] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } + ) + } + } + test("CALL_SV_MT - stub") { options "-stub" @@ -33,10 +136,10 @@ nextflow_workflow { input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[5] = HISAT2_BUILD.out.index.collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } + input[8] = LAST_LASTDB.out.index.collect() input[9] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index f86f56e63..35ec75b68 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,4 +1,411 @@ { + "CALL_SV_MT - 2 samples": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + ] + ] + ], + [ + "2", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" + ] + ] + ], + [ + "3", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" + ] + ] + ], + [ + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" + ] + ] + ] + ], + [ + "mt_del_result", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" + ] + ] + ] + ], + [ + "saltshaker_html", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ] + ] + ], + "timestamp": "2026-06-10T12:14:55.329086", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, "CALL_SV_MT - stub": { "content": [ [ From 46de70b3543c3a5dc6af7798c58a91854bc7688b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 10 Jun 2026 13:38:13 +0200 Subject: [PATCH 791/872] fix vcf snapshotting --- .../local/call_sv_MT/tests/main.nf.test | 16 +- .../local/call_sv_MT/tests/main.nf.test.snap | 460 +++--------------- 2 files changed, 78 insertions(+), 398 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 122cd9647..d21606491 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -102,16 +102,12 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + file(workflow.out.saltshaker_vcf.get(0).get(1)).name, // this vcf has a timestamp in it so we just check that the name... + path(workflow.out.saltshaker_vcf.get(0).get(1)).linesGzip.size(), // ...and the number of lines match + workflow.out.saltshaker_html, + workflow.out.saltshaker_plot, + workflow.out.mt_del_result, + workflow.out.updated_priority ).match() } ) } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 35ec75b68..2704f3be5 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,406 +1,90 @@ { "CALL_SV_MT - 2 samples": { "content": [ + "justhusky_saltshaker.vcf.gz", + 50, [ [ - "0", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" - ] - ] - ], - [ - "1", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" - ] - ] - ], - [ - "2", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" - ] - ] - ], - [ - "3", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" - ] - ] - ], - [ - "4", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ], - [ - "5", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" - ] - ] - ] - ], - [ - "mt_del_result", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" - ] - ] - ], + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + ] + ], + [ [ - "publish", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" - ] - ] - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" ], [ - "saltshaker_html", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" - ] - ] - ], + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" + ] + ], + [ [ - "saltshaker_plot", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" - ] - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" ], [ - "saltshaker_vcf", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,d199ff56c7d1d67be11d8e68dbc2ea79" - ] - ] - ], + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,186bf9bc3fc8d20a6e0e6b5207a20673" + ] + ], + [ [ - "updated_priority", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] + "manta", + "tiddit", + "cnvnator", + "mitosalt" ] ] ], - "timestamp": "2026-06-10T12:14:55.329086", + "timestamp": "2026-06-10T13:36:59.253091", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 9ce303af6a4417a63472b88a70dd61de724c43f5 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 10 Jun 2026 13:50:30 +0200 Subject: [PATCH 792/872] fix png snapshotting --- .../local/call_sv_MT/tests/main.nf.test | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 33 ++----------------- 2 files changed, 3 insertions(+), 32 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index d21606491..ae0864a14 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -105,7 +105,7 @@ nextflow_workflow { file(workflow.out.saltshaker_vcf.get(0).get(1)).name, // this vcf has a timestamp in it so we just check that the name... path(workflow.out.saltshaker_vcf.get(0).get(1)).linesGzip.size(), // ...and the number of lines match workflow.out.saltshaker_html, - workflow.out.saltshaker_plot, + file(workflow.out.saltshaker_plot.get(0).get(1)).name, // pngs are unstable so we just check that the name matches workflow.out.mt_del_result, workflow.out.updated_priority ).match() } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 2704f3be5..5d28e0f85 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -11,36 +11,7 @@ "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" ] ], - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,de7f4f2435992aec5857e3a2c0aa531e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,66d05db7d9e779cb8c4462d6cbdea2be" - ] - ], + "earlycasualcaiman.saltshaker.png", [ [ { @@ -84,7 +55,7 @@ ] ] ], - "timestamp": "2026-06-10T13:36:59.253091", + "timestamp": "2026-06-10T13:49:04.643753", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 994f10a4a3aede7625b7e4ffabb9f475b479ba43 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Wed, 10 Jun 2026 14:06:58 +0200 Subject: [PATCH 793/872] capture variant md5 --- subworkflows/local/call_sv_MT/tests/main.nf.test | 3 +-- subworkflows/local/call_sv_MT/tests/main.nf.test.snap | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index ae0864a14..9be1b30ac 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -102,8 +102,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - file(workflow.out.saltshaker_vcf.get(0).get(1)).name, // this vcf has a timestamp in it so we just check that the name... - path(workflow.out.saltshaker_vcf.get(0).get(1)).linesGzip.size(), // ...and the number of lines match + path(workflow.out.saltshaker_vcf.get(0).get(1)).vcf.variantsMD5, workflow.out.saltshaker_html, file(workflow.out.saltshaker_plot.get(0).get(1)).name, // pngs are unstable so we just check that the name matches workflow.out.mt_del_result, diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 5d28e0f85..d47c00d0a 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,8 +1,7 @@ { "CALL_SV_MT - 2 samples": { "content": [ - "justhusky_saltshaker.vcf.gz", - 50, + "3d2eca57b18e5d0180b333d7370a2bfb", [ [ { @@ -55,7 +54,7 @@ ] ] ], - "timestamp": "2026-06-10T13:49:04.643753", + "timestamp": "2026-06-10T14:05:43.387597", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From f916a9a6d7c81ea6be49655db5644dfdc5e1a98f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 15:51:33 +0200 Subject: [PATCH 794/872] review suggestion --- bin/filtervep.py | 36 +++++++++++++++++++++++------------- 1 file changed, 23 insertions(+), 13 deletions(-) diff --git a/bin/filtervep.py b/bin/filtervep.py index 51d31b86f..2e9f9c284 100755 --- a/bin/filtervep.py +++ b/bin/filtervep.py @@ -2,11 +2,16 @@ """ filter_vep_fast - Fast Python reimplementation of Ensembl's filter_vep. -Replicates all features of the Perl filter_vep script distributed with Ensembl -VEP (EMBL-EBI). Validated against VEP 110 and 115.2, which are functionally -identical for VCF filtering. +Fast Python reimplementation of the Perl filter_vep script distributed with +Ensembl VEP (EMBL-EBI). Validated against VEP 110 and 115.2, which are +functionally identical for VCF filtering. Uses cyvcf2 for VCF parsing when available (significant speedup for large VCF / bgzipped files via htslib). + +All filter operators are supported except is_child, which requires a live +Ensembl Ontology DB. Use the original filter_vep --ontology for +ontology-aware filtering, or replace is_child with an explicit 'in' list +of consequence terms. """ import sys @@ -42,7 +47,7 @@ class FilterSet: match / matches / re / regex regex search (case-insensitive) in list or file membership exists / ex / defined field has a non-null value - is_child SO ontology child (falls back to exact match) + is_child SO ontology child (not supported; see --ontology) Special value syntax: #FieldName compare against another field's value @@ -289,8 +294,11 @@ def _eval(self, node, data): return processed_input in in_set if operator == 'is_child': - processed_input = self._get_input(field_value, value) - return processed_input.lower() == str(value or '').lower() + raise NotImplementedError( + "is_child requires a live Ensembl Ontology DB (--ontology). " + "Use the original filter_vep with --ontology, or replace " + "is_child with an explicit 'in' list of the consequence terms you need." + ) # Ordered comparisons — use _get_input for numeric extraction processed_input = self._get_input(field_value, value) @@ -772,7 +780,7 @@ def process_generic(args, output_fh): match/matches/re/regex regex (case-insensitive) in list or file (one value/line) exists/ex/defined field is present and non-null - is_child SO ontology child term + is_child SO ontology child (not supported here) Logical: and or not ( ) Value can be #Field to compare two fields. Mixed content (e.g. "deleterious(0.05)") has its @@ -791,11 +799,12 @@ def process_generic(args, output_fh): --soft_filter Add filter_vep_pass / filter_vep_fail to the VCF FILTER column instead of excluding variants. ---ontology -y Use Sequence Ontology to match consequence terms - (requires Ensembl API; is_child falls back to - exact match in this implementation). +--ontology -y Accepted for compatibility but not implemented. + is_child requires a live Ensembl Ontology DB; use + the original filter_vep --ontology for that feature, + or replace is_child with an explicit 'in' list. --host / --user / --pass / --port / --version / --registry - Database connection options for --ontology. + Database connection options (accepted, not used). --start [N] -s Skip first N passing results (1-based, default 1) --limit [N] Return at most N passing results. @@ -838,8 +847,9 @@ def main(): if args.ontology: sys.stderr.write( - "WARNING: --ontology requires Ensembl API; " - "is_child will fall back to exact match in this implementation\n" + "WARNING: --ontology is accepted for compatibility but is_child is not " + "implemented. Use the original filter_vep --ontology for ontology-aware " + "filtering, or replace is_child with an explicit 'in' list.\n" ) args.filter_set = FilterSet(*(args.filter or [])) From 8dd2abbaca941bcd0bc4b9148a3e1a0c1fe1a2a2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 16:07:02 +0200 Subject: [PATCH 795/872] rename to filter_vep --- bin/{filtervep.py => filter_vep} | 0 modules/local/filtervep/main.nf | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename bin/{filtervep.py => filter_vep} (100%) diff --git a/bin/filtervep.py b/bin/filter_vep similarity index 100% rename from bin/filtervep.py rename to bin/filter_vep diff --git a/modules/local/filtervep/main.nf b/modules/local/filtervep/main.nf index d25f7def2..6e05dace3 100644 --- a/modules/local/filtervep/main.nf +++ b/modules/local/filtervep/main.nf @@ -23,7 +23,7 @@ process FILTERVEP { def prefix = task.ext.prefix ?: "${meta.id}" extension = args.contains("--format tab") ? "txt" : "vcf" """ - filtervep.py \\ + filter_vep \\ ${args} \\ --input_file ${input} \\ --output_file ${prefix}.${extension} \\ From 0069ecd7643ec648ce68b3772c40251dae77820e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 16:17:41 +0200 Subject: [PATCH 796/872] update name --- bin/filter_vep | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/filter_vep b/bin/filter_vep index 2e9f9c284..ccb35c482 100755 --- a/bin/filter_vep +++ b/bin/filter_vep @@ -1,6 +1,6 @@ #!/usr/bin/env python3 """ -filter_vep_fast - Fast Python reimplementation of Ensembl's filter_vep. +filter_vep - Fast Python reimplementation of Ensembl's filter_vep. Fast Python reimplementation of the Perl filter_vep script distributed with Ensembl VEP (EMBL-EBI). Validated against VEP 110 and 115.2, which are @@ -750,7 +750,7 @@ USAGE = """\ http://www.ensembl.org/info/docs/tools/vep/script/vep_filter.html Usage: -./filter_vep_fast.py [arguments] +./filter_vep [arguments] --help -h Print usage message and exit From 8b46f18463ac9eaa0054150fef17ff7f7b745b4a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 17:29:00 +0200 Subject: [PATCH 797/872] Add bwafastalign/index --- main.nf | 3 + modules.json | 5 + .../bwafastalign/index/environment.yml | 9 ++ modules/nf-core/bwafastalign/index/main.nf | 48 +++++++ modules/nf-core/bwafastalign/index/meta.yml | 106 ++++++++++++++ .../bwafastalign/index/tests/main.nf.test | 64 +++++++++ .../index/tests/main.nf.test.snap | 131 ++++++++++++++++++ .../bwafastalign/index/tests/nextflow.config | 5 + nextflow.config | 1 + nextflow_schema.json | 10 +- subworkflows/local/prepare_references/main.nf | 77 +++++----- .../prepare_references/tests/main.nf.test | 28 ++-- 12 files changed, 440 insertions(+), 47 deletions(-) create mode 100644 modules/nf-core/bwafastalign/index/environment.yml create mode 100644 modules/nf-core/bwafastalign/index/main.nf create mode 100644 modules/nf-core/bwafastalign/index/meta.yml create mode 100644 modules/nf-core/bwafastalign/index/tests/main.nf.test create mode 100644 modules/nf-core/bwafastalign/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/bwafastalign/index/tests/nextflow.config diff --git a/main.nf b/main.nf index ab4402c72..01d769b55 100644 --- a/main.nf +++ b/main.nf @@ -46,6 +46,7 @@ workflow NFCORE_RAREDISEASE { val_aligner val_analysis_type val_bwa + val_bwafastalign val_bwamem2 val_bwameme val_cadd_prescored @@ -160,6 +161,7 @@ workflow NFCORE_RAREDISEASE { val_aligner, val_analysis_type, val_bwa, + val_bwafastalign, val_bwamem2, val_bwameme, val_fai, @@ -575,6 +577,7 @@ workflow { params.aligner, params.analysis_type, params.bwa, + params.bwafastalign, params.bwamem2, params.bwameme, params.cadd_prescored, diff --git a/modules.json b/modules.json index 1cb5d52ed..2eca44d85 100644 --- a/modules.json +++ b/modules.json @@ -75,6 +75,11 @@ "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef", "installed_by": ["modules"] }, + "bwafastalign/index": { + "branch": "master", + "git_sha": "4ddd2d28518c7475bc76f0dd0e0451dd0e19df2a", + "installed_by": ["modules"] + }, "bwamem2/index": { "branch": "master", "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", diff --git a/modules/nf-core/bwafastalign/index/environment.yml b/modules/nf-core/bwafastalign/index/environment.yml new file mode 100644 index 000000000..a89afa0a9 --- /dev/null +++ b/modules/nf-core/bwafastalign/index/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bwa-fastalign=1.0.0 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwafastalign/index/main.nf b/modules/nf-core/bwafastalign/index/main.nf new file mode 100644 index 000000000..8bf8d7eb3 --- /dev/null +++ b/modules/nf-core/bwafastalign/index/main.nf @@ -0,0 +1,48 @@ +process BWAFASTALIGN_INDEX { + tag "$fasta" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f8c975324a12014c8a817c2c1ad0cd68b077cf09c4370717589177b262dcd1dc/data': + 'community.wave.seqera.io/library/bwa-fastalign_mbuffer_samtools:35f24ce8addcd26b'}" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("bwafastalign"), emit: index + tuple val("${task.process}"), val('bwafastalign'), val('1.0.0'), topic: versions, emit: versions_bwafastalign + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | sed '1!d;s/.* //'") , topic: versions, emit: versions_samtools + tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer //p'") , topic: versions, emit: versions_mbuffer + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${fasta}" + """ + mkdir bwafastalign + + bwa-fastalign index \\ + $args \\ + -p bwafastalign/$prefix \\ + $fasta + """ + + stub: + def prefix = task.ext.prefix ?: "${fasta}" + """ + mkdir bwafastalign + touch bwafastalign/${prefix}.amb + touch bwafastalign/${prefix}.ann + touch bwafastalign/${prefix}.bwt + touch bwafastalign/${prefix}.bytesa + touch bwafastalign/${prefix}.fmt + touch bwafastalign/${prefix}.kmer + touch bwafastalign/${prefix}.pac + touch bwafastalign/${prefix}.sa + """ +} diff --git a/modules/nf-core/bwafastalign/index/meta.yml b/modules/nf-core/bwafastalign/index/meta.yml new file mode 100644 index 000000000..5c2fdbca4 --- /dev/null +++ b/modules/nf-core/bwafastalign/index/meta.yml @@ -0,0 +1,106 @@ +name: "bwafastalign_index" +description: Create BWA-FASTALIGN index for reference genome +keywords: + - index + - fasta + - genome + - reference +tools: + - "bwafastalign": + description: "Faster and Cheaper Sequence Alignment on Commercial CPUs (A faster + version of bwa-mem with identical outputs)." + homepage: "https://github.com/zzhofict/BWA-FastAlign" + documentation: "https://github.com/zzhofict/BWA-FastAlign" + doi: "10.1145/3774934.3786421" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input genome fasta file + ontologies: [] +output: + index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bwafastalign: + type: string + description: BWA-FASTALIGN genome index files + pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + ontologies: [] + versions_bwafastalign: + - - ${task.process}: + type: string + description: The name of the process + - bwafastalign: + type: string + description: BWA-FASTALIGN genome index files + pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + ontologies: [] + - 1.0.0: + type: string + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version 2>&1 | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + versions_mbuffer: + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer //p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwafastalign: + type: string + description: BWA-FASTALIGN genome index files + pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + ontologies: [] + - 1.0.0: + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: The name of the tool + - samtools --version 2>&1 | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer //p': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@peterpru" +maintainers: + - "@peterpru" diff --git a/modules/nf-core/bwafastalign/index/tests/main.nf.test b/modules/nf-core/bwafastalign/index/tests/main.nf.test new file mode 100644 index 000000000..3173287b8 --- /dev/null +++ b/modules/nf-core/bwafastalign/index/tests/main.nf.test @@ -0,0 +1,64 @@ +nextflow_process { + + name "Test Process BWAFASTALIGN_INDEX" + script "../main.nf" + process "BWAFASTALIGN_INDEX" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bwafastalign" + tag "bwafastalign/index" + + test("BWAFASTALIGN index") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success + assertAll( + // genome.fasta.kmer is a fixed-size ~4.8 GB hash table — snapshot by name only, MD5 all others + { assert snapshot( + new File(process.out.index[0][1].toString()).listFiles() + .sort { it.name } + .collect { f -> f.name.endsWith('.kmer') ? f.name : file(f.absolutePath) }, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + } + + test("BWAFASTALIGN index - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bwafastalign/index/tests/main.nf.test.snap b/modules/nf-core/bwafastalign/index/tests/main.nf.test.snap new file mode 100644 index 000000000..38524381b --- /dev/null +++ b/modules/nf-core/bwafastalign/index/tests/main.nf.test.snap @@ -0,0 +1,131 @@ +{ + "BWAFASTALIGN index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bytesa:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.fmt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.kmer:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + "BWAFASTALIGN_INDEX", + "bwafastalign", + "1.0.0" + ] + ], + "2": [ + [ + "BWAFASTALIGN_INDEX", + "samtools", + "1.21" + ] + ], + "3": [ + [ + "BWAFASTALIGN_INDEX", + "mbuffer", + "version 20160228" + ] + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.bytesa:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.fmt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.kmer:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome.fasta.sa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_INDEX", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_INDEX", + "mbuffer", + "version 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_INDEX", + "samtools", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.0" + }, + "timestamp": "2026-06-08T12:26:53.94075" + }, + "BWAFASTALIGN index": { + "content": [ + [ + "genome.fasta.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e", + "genome.fasta.ann:md5,c32e11f6c859f166c7525a9c1d583567", + "genome.fasta.bwt:md5,0469c30a1e239dd08f68afe66fde99da", + "genome.fasta.bytesa:md5,9e4ae311370960b31268a5ef0bde324a", + "genome.fasta.fmt:md5,f993b15dc5f10271f3fa0a68720219b6", + "genome.fasta.kmer", + "genome.fasta.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66", + "genome.fasta.sa:md5,ab3952cabf026b48cd3eb5bccbb636d1" + ], + { + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_INDEX", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_INDEX", + "mbuffer", + "version 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_INDEX", + "samtools", + "1.21" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.0" + }, + "timestamp": "2026-06-08T12:26:41.54578" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwafastalign/index/tests/nextflow.config b/modules/nf-core/bwafastalign/index/tests/nextflow.config new file mode 100644 index 000000000..ffc65676f --- /dev/null +++ b/modules/nf-core/bwafastalign/index/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BWAFASTALIGN_INDEX { + memory = 15.GB + } +} diff --git a/nextflow.config b/nextflow.config index 5038dec67..f00a9ea74 100644 --- a/nextflow.config +++ b/nextflow.config @@ -50,6 +50,7 @@ params { fasta = null fai = null bwa = null + bwafastalign = null bwamem2 = null bwameme = null call_interval = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 5529d2a94..df75a0729 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,6 +65,14 @@ "help_text": "If none provided, will be generated automatically from the FASTA reference.", "fa_icon": "fas fa-folder-open" }, + "bwafastalign": { + "type": "string", + "exists": true, + "format": "directory-path", + "description": "Directory for pre-built bwa-fastalign index.", + "help_text": "If none provided, will be generated automatically from the FASTA reference.", + "fa_icon": "fas fa-folder-open" + }, "bwamem2": { "type": "string", "exists": true, @@ -660,7 +668,7 @@ "default": "bwamem2", "description": "Specifies the alignment algorithm to use - available options are 'bwamem2', 'bwa', 'bwameme' and 'sentieon'.", "fa_icon": "fas fa-align-center", - "enum": ["bwa", "bwamem2", "bwameme", "sentieon"] + "enum": ["bwa", "bwafastalign", "bwamem2", "bwameme", "sentieon"] }, "mt_aligner": { "type": "string", diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index b513bb4e6..df83b8652 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -4,6 +4,7 @@ // include { BEDTOOLS_SLOP as BEDTOOLS_PAD_TARGET_BED } from '../../../modules/nf-core/bedtools/slop/main' +include { BWAFASTALIGN_INDEX as BWAFASTALIGN_INDEX_GENOME } from '../../../modules/nf-core/bwafastalign/index/main' include { BWAMEM2_INDEX as BWAMEM2_INDEX_GENOME } from '../../../modules/nf-core/bwamem2/index/main' include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT } from '../../../modules/nf-core/bwamem2/index/main' include { BWAMEM2_INDEX as BWAMEM2_INDEX_MT_SHIFT } from '../../../modules/nf-core/bwamem2/index/main' @@ -36,9 +37,10 @@ include { UNTAR as UNTAR_VEP_CACHE } from '../../../mod workflow PREPARE_REFERENCES { take: - val_aligner // String: "bwa", "bwamem2", "sentieon" or "bwameme" + val_aligner // String: "bwa", "bwafastalign", "bwamem2", "sentieon" or "bwameme" val_analysis_type // String: "wgs", "wes", or "mito" val_bwa // String: path to bwa index + val_bwafastalign // String: path to bwafastalign index val_bwamem2 // String: path to bwamem2 index val_bwameme // String: path to bwameme index val_fai // String: path to genome fasta index @@ -62,6 +64,7 @@ workflow PREPARE_REFERENCES { main: ch_bait_intervals = channel.empty() ch_genome_bwa_index = channel.empty() + ch_genome_bwafastalign_index = channel.empty() ch_genome_bwameme_index = channel.empty() ch_genome_bwamem2_index = channel.empty() ch_genome_hisat2_index = channel.empty() @@ -132,6 +135,12 @@ workflow PREPARE_REFERENCES { } else if (val_bwameme) { ch_genome_bwameme_index = channel.fromPath(val_bwameme).map {it -> [[id:it.simpleName], it]}.collect() } + + if (!val_bwafastalign && val_aligner.equals("bwafastalign")) { + ch_genome_bwafastalign_index = BWAFASTALIGN_INDEX_GENOME(ch_genome_fasta).index.collect() + } else if (val_bwafastalign) { + ch_genome_bwafastalign_index = channel.fromPath(val_bwafastalign).map {it -> [[id:it.simpleName], it]}.collect() + } // // MT genome indices // @@ -278,6 +287,7 @@ workflow PREPARE_REFERENCES { ch_publish = ch_dbsnp .mix(ch_dbsnp_tbi) .mix(ch_genome_bwa_index) + .mix(ch_genome_bwafastalign_index) .mix(ch_genome_bwamem2_index) .mix(ch_genome_bwameme_index) .mix(ch_genome_fai) @@ -316,36 +326,37 @@ workflow PREPARE_REFERENCES { } emit: - bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] - dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] - dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] - genome_bwa_index = ch_genome_bwa_index // channel:[ val(meta), path(index) ] - genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] - genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] - genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] - genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] - genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] - genome_hisat2_index = ch_genome_hisat2_index // channel: [ val(meta), path(index) ] - genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] - gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] - mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] - mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] - mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] - mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] - mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] - mt_intervals = ch_shiftfasta_mtintervals // channel:[ path(intervals) ] - mt_last_index = ch_mt_last_index // channel: [ val(meta), path(index) ] - mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] - mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] - mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] - mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] - mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] - mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] - mtshift_intervals = ch_shiftfasta_mtshiftintervals // channel:[ path(intervals) ] - sdf = ch_sdf // channel:[ val (meta), path(sdf) ] - target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] - target_intervals = ch_target_intervals // channel:[ path(interval_list) ] - vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] - vep_resources = ch_vep_resources // channel:[ path(cache) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] + dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] + dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] + genome_bwa_index = ch_genome_bwa_index // channel:[ val(meta), path(index) ] + genome_bwafastalign_index = ch_genome_bwafastalign_index // channel:[ val(meta), path(index) ] + genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] + genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] + genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] + genome_fai = ch_genome_fai // channel:[ val(meta), path(fai) ] + genome_fasta = ch_genome_fasta // channel:[ val(meta), path(fasta) ] + genome_hisat2_index = ch_genome_hisat2_index // channel: [ val(meta), path(index) ] + genome_dict = ch_genome_dict // channel:[ val(meta), path(dict) ] + gnomad_af_idx = ch_gnomad_af_idx // channel:[ val(gnomad), path(idx) ] + mt_bwa_index = ch_mt_bwa_index // channel:[ val(meta), path(index) ] + mt_bwamem2_index = ch_mt_bwamem2_index // channel:[ val(meta), path(index) ] + mt_dict = ch_mt_dict // channel:[ val(meta), path(dict) ] + mt_fai = ch_mt_fai // channel:[ val(meta), path(fai) ] + mt_fasta = ch_mt_fasta // channel:[ val(meta), path(fasta) ] + mt_intervals = ch_shiftfasta_mtintervals // channel:[ path(intervals) ] + mt_last_index = ch_mt_last_index // channel: [ val(meta), path(index) ] + mtshift_backchain = ch_mtshift_backchain // channel:[ val(meta), path(backchain) ] + mtshift_bwa_index = ch_mtshift_bwa_index // channel:[ val(meta), path(index) ] + mtshift_bwamem2_index = ch_mtshift_bwamem2_index // channel:[ val(meta), path(index) ] + mtshift_dict = ch_mtshift_dict // channel:[ val(meta), path(dict) ] + mtshift_fai = ch_mtshift_fai // channel:[ val(meta), path(fai) ] + mtshift_fasta = ch_mtshift_fasta // channel:[ val(meta), path(fasta) ] + mtshift_intervals = ch_shiftfasta_mtshiftintervals // channel:[ path(intervals) ] + sdf = ch_sdf // channel:[ val (meta), path(sdf) ] + target_bed = ch_target_bed_gz_tbi.collect() // channel:[ val(meta), path(bed), path(tbi) ] + target_intervals = ch_target_intervals // channel:[ path(interval_list) ] + vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] + vep_resources = ch_vep_resources // channel:[ path(cache) ] + publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index 56e9d6831..6784060cc 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -9,6 +9,7 @@ nextflow_workflow { tag "bedtools/slop" tag "bwa/index" + tag "bwafastalign/index" tag "bwamem2/index" tag "bwameme/index" tag "cat/cat" @@ -44,21 +45,22 @@ nextflow_workflow { input[3] = null input[4] = null input[5] = null - input[6] = params.pipelines_testdata_base_path + 'reference/reference.fasta' - input[7] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' - input[8] = null - input[9] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' - input[10] = null - input[11] = "bwa" - input[12] = null - input[13] = false + input[6] = null + input[7] = params.pipelines_testdata_base_path + 'reference/reference.fasta' + input[8] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[9] = null + input[10] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[11] = null + input[12] = "bwa" + input[13] = null input[14] = false - input[15] = null + input[15] = false input[16] = null - input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[18] = null - input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' - input[20] = true + input[17] = null + input[18] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[19] = null + input[20] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' + input[21] = true """ } } From 6fe32764bd16df694e65bd340449e857c7bdff8a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 17:32:28 +0200 Subject: [PATCH 798/872] update changelog --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dbcbe35ca..6aad526b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows - Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers - Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative +- `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner ### `Changed` @@ -23,10 +24,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Old parameter | New parameter | | ------------- | ---------------------- | +| | bwafastalign | | | cadd_prescored | | | manta_call_regions | | | manta_call_regions_tbi | +### Tool updates + +| Tool | Old version | New version | +| -------------------- | ----------- | ----------- | +| bwa-fastalign | | 1.0.0 | + ## 3.0.0 - Mario [2026-05-12] ### `Added` From bba36dc8801ce2bde9f77bd22344950cd015860d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 10 Jun 2026 18:51:59 +0000 Subject: [PATCH 799/872] [automated] Fix code linting --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6aad526b1..57246a6e2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,9 +31,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Tool updates -| Tool | Old version | New version | -| -------------------- | ----------- | ----------- | -| bwa-fastalign | | 1.0.0 | +| Tool | Old version | New version | +| ------------- | ----------- | ----------- | +| bwa-fastalign | | 1.0.0 | ## 3.0.0 - Mario [2026-05-12] From 689dfa93d2f578cbcd05de6bb9a6444ea774e6dd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 20:57:38 +0200 Subject: [PATCH 800/872] Update CHANGELOG.md --- CHANGELOG.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 57246a6e2..1f4b89c62 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,14 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows -- Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers -- Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative -- `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner +- Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows [#866](https://github.com/nf-core/raredisease/pull/866) +- Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers [#867](https://github.com/nf-core/raredisease/pull/867) +- Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative [#870](https://github.com/nf-core/raredisease/pull/870) +- `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner [#877](https://github.com/nf-core/raredisease/pull/877) ### `Changed` -- Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` +- Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` [#870](https://github.com/nf-core/raredisease/pull/870) ### `Fixed` From 1adc7557296a0f0928cee0b8e9feaa6ae88e7a81 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 10 Jun 2026 21:33:55 +0200 Subject: [PATCH 801/872] update snap --- .../tests/main.nf.test.snap | 132 ++++++++++-------- 1 file changed, 72 insertions(+), 60 deletions(-) diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index ee140eaa3..74215cf20 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -28,12 +28,32 @@ { "id": "reference" }, - "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + [ + "reference.1.ht2:md5,f1f1779341ba9a0ab7078e358f6efdde", + "reference.2.ht2:md5,09f0021a3a29a0e4aee96083ea4d4020", + "reference.3.ht2:md5,3b641d6168aa70fe864844bb02ef39f2", + "reference.4.ht2:md5,2dd52cfb372404a3619c0f9367fc4012", + "reference.5.ht2:md5,999891dff8303f7c576f5a1ad4be5036", + "reference.6.ht2:md5,e1a25310dabfaeb7f0fa200785bad49f", + "reference.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "reference.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" + ] ] ] ], [ "11", + [ + [ + { + "id": "reference" + }, + "reference.dict:md5,81abd0fc051c084405024e0927f7b436" + ] + ] + ], + [ + "12", [ [ "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", @@ -42,7 +62,7 @@ ] ], [ - "12", + "13", [ [ { @@ -59,13 +79,13 @@ ] ], [ - "13", + "14", [ ] ], [ - "14", + "15", [ [ { @@ -76,7 +96,7 @@ ] ], [ - "15", + "16", [ [ { @@ -87,7 +107,7 @@ ] ], [ - "16", + "17", [ [ { @@ -98,7 +118,7 @@ ] ], [ - "17", + "18", [ [ "reference_mt.intervals:md5,0930dafc5645246542112ae3d62573a3" @@ -106,7 +126,7 @@ ] ], [ - "18", + "19", [ [ { @@ -125,29 +145,29 @@ ] ], [ - "19", + "2", [ [ { - "id": "reference" + "id": "dbsnp_-138-" }, - "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" + "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" ] ] ], [ - "2", + "20", [ [ { - "id": "dbsnp_-138-" + "id": "reference" }, - "dbsnp_-138-.vcf.gz.tbi:md5,6695b71d9819806d50cd908051cf4cc0" + "reference_shift.back_chain:md5,25d682d73a9bae009f4a38b3ede5dbc8" ] ] ], [ - "20", + "21", [ [ { @@ -164,13 +184,13 @@ ] ], [ - "21", + "22", [ ] ], [ - "22", + "23", [ [ { @@ -181,7 +201,7 @@ ] ], [ - "23", + "24", [ [ { @@ -192,7 +212,7 @@ ] ], [ - "24", + "25", [ [ { @@ -203,7 +223,7 @@ ] ], [ - "25", + "26", [ [ "reference_mt.shifted.intervals:md5,083d8f782fd4228dd9f6948ddbc64fd0" @@ -211,13 +231,13 @@ ] ], [ - "26", + "27", [ ] ], [ - "27", + "28", [ [ { @@ -228,21 +248,11 @@ ] ] ], - [ - "28", - [ - [ - "target_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" - ] - ] - ], [ "29", [ [ - [ - - ] + "target_target.interval_list:md5,2959b7b0e1b298fe84ad708f447d6703" ] ] ], @@ -265,6 +275,16 @@ ], [ "30", + [ + [ + [ + + ] + ] + ] + ], + [ + "31", [ [ [ @@ -498,7 +518,7 @@ ] ], [ - "31", + "32", [ [ "references/", @@ -1010,6 +1030,12 @@ ], [ "4", + [ + + ] + ], + [ + "5", [ [ { @@ -1025,28 +1051,17 @@ ] ] ], - [ - "5", - [ - - ] - ], [ "6", [ - [ - "reference.fasta.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" - ] + ] ], [ "7", [ [ - { - "id": "reference" - }, - "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" + "reference.fasta.sizes:md5,b7bb58fb4d5cb50796e722222a13a2e6" ] ] ], @@ -1057,7 +1072,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "reference.fasta.fai:md5,bf4047e05f95deb372eb8ffd601cbc29" ] ] ], @@ -1068,16 +1083,7 @@ { "id": "reference" }, - [ - "reference.1.ht2:md5,f1f1779341ba9a0ab7078e358f6efdde", - "reference.2.ht2:md5,09f0021a3a29a0e4aee96083ea4d4020", - "reference.3.ht2:md5,3b641d6168aa70fe864844bb02ef39f2", - "reference.4.ht2:md5,2dd52cfb372404a3619c0f9367fc4012", - "reference.5.ht2:md5,999891dff8303f7c576f5a1ad4be5036", - "reference.6.ht2:md5,e1a25310dabfaeb7f0fa200785bad49f", - "reference.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "reference.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb" - ] + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ] ], @@ -1128,6 +1134,12 @@ ] ] ], + [ + "genome_bwafastalign_index", + [ + + ] + ], [ "genome_bwamem2_index", [ @@ -2162,9 +2174,9 @@ ] ] ], - "timestamp": "2026-03-18T21:59:15.358100588", + "timestamp": "2026-06-10T17:23:36.97002628", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } From 694593dea0ab5664dcc37d019a1a3eccd67d3d33 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Thu, 11 Jun 2026 08:44:24 +0200 Subject: [PATCH 802/872] Fix indentation --- subworkflows/local/call_sv_MT/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 9be1b30ac..c8004efe7 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -38,7 +38,7 @@ nextflow_workflow { } } - test("CALL_SV_MT - 2 samples") { + test("CALL_SV_MT - 2 samples") { when { params { From 3be2ae3104c0ebda29bf57d19262cafbe94aeb62 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 11 Jun 2026 09:02:00 +0200 Subject: [PATCH 803/872] changelog entry --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e6081f6..c6c260ec9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -62,6 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added `--skip_split_multiallelics` parameter to allow users to skip the `bcftools norm --multiallelics -both` step in SNV calling (DeepVariant and Sentieon), which can cause indel quality degradation in single-interval runs [#823](https://github.com/nf-core/raredisease/pull/823) - Add find/concatenate step to concatenate saltshaker classification files before creating the html report, so the final report is case-level. [#826](https://github.com/nf-core/raredisease/pull/826) - Extended vcfanno database sanity check to include extra vcfanno resources (`vcfanno_extra`) alongside the main resources, and moved the check upstream to `raredisease.nf` so it covers both genome and mitochondrial SNV annotation subworkflows [#834](https://github.com/nf-core/raredisease/pull/834) +- Add full test to call_sv_MT subworkflow [#874](https://github.com/nf-core/raredisease/pull/874) ### `Changed` From 3a9c190f62f8b67c636d30e8180794091a102386 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 11 Jun 2026 10:14:39 +0200 Subject: [PATCH 804/872] update saltshaker modules --- modules.json | 6 +-- .../nf-core/saltshaker/call/environment.yml | 2 +- modules/nf-core/saltshaker/call/main.nf | 9 ++-- modules/nf-core/saltshaker/call/meta.yml | 29 ++++++------ .../saltshaker/call/tests/main.nf.test.snap | 18 ++++---- .../saltshaker/classify/environment.yml | 2 +- modules/nf-core/saltshaker/classify/main.nf | 9 ++-- modules/nf-core/saltshaker/classify/meta.yml | 8 ++-- .../classify/tests/main.nf.test.snap | 44 ++++++++++--------- .../nf-core/saltshaker/plot/environment.yml | 2 +- modules/nf-core/saltshaker/plot/main.nf | 9 ++-- modules/nf-core/saltshaker/plot/meta.yml | 19 ++++---- .../saltshaker/plot/tests/main.nf.test | 6 ++- .../saltshaker/plot/tests/main.nf.test.snap | 29 +++++------- 14 files changed, 97 insertions(+), 95 deletions(-) diff --git a/modules.json b/modules.json index 4bb0c67b5..c04e4edf8 100644 --- a/modules.json +++ b/modules.json @@ -383,17 +383,17 @@ }, "saltshaker/call": { "branch": "master", - "git_sha": "9d051963759dda1a424374e23f4f22aaa2b0bd60", + "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830", "installed_by": ["modules"] }, "saltshaker/classify": { "branch": "master", - "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", + "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830", "installed_by": ["modules"] }, "saltshaker/plot": { "branch": "master", - "git_sha": "ff5f2ad4481a4a1e1769a1fad922681e7f7fd176", + "git_sha": "a61c82ad6d255d555aa6c7f1c3c0e90c3735c830", "installed_by": ["modules"] }, "sambamba/depth": { diff --git a/modules/nf-core/saltshaker/call/environment.yml b/modules/nf-core/saltshaker/call/environment.yml index f76c4bf5a..ba1172042 100644 --- a/modules/nf-core/saltshaker/call/environment.yml +++ b/modules/nf-core/saltshaker/call/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.0 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/call/main.nf b/modules/nf-core/saltshaker/call/main.nf index 7565ce603..4f16b1f4e 100644 --- a/modules/nf-core/saltshaker/call/main.nf +++ b/modules/nf-core/saltshaker/call/main.nf @@ -2,10 +2,11 @@ process SALTSHAKER_CALL { tag "$meta.id" label 'process_single' + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': - 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(breakpoint), path(cluster) @@ -20,7 +21,7 @@ process SALTSHAKER_CALL { output: tuple val(meta), path("*_call_metadata.tsv"), emit: call - tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/saltshaker/call/meta.yml b/modules/nf-core/saltshaker/call/meta.yml index 51be6c452..773034b7b 100644 --- a/modules/nf-core/saltshaker/call/meta.yml +++ b/modules/nf-core/saltshaker/call/meta.yml @@ -7,10 +7,11 @@ keywords: - structural-variant calling tools: - "saltshaker": - description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - + description: "A Python package for classifying and visualizing mitochondrial structural + variants from MitoSAlt pipeline output." + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker/" + identifier: "" input: - - meta: type: map @@ -58,7 +59,6 @@ input: - light_strand_origin_end: type: integer description: End position of the light strand origin of replication - output: call: - - meta: @@ -68,20 +68,21 @@ output: e.g. `[ id:'sample1' ]` - "*_call_metadata.tsv": type: file - description: tsv with variant call metadata to be used in saltshaker_classify + description: tsv with variant call metadata to be used in + saltshaker_classify pattern: "*_call_metadata.tsv" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_3475 versions_saltshaker: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "saltshaker": + - saltshaker: type: string description: The name of the tool - - "1.0.0": + - 1.1.1: type: string - description: Hardcoded version of saltshaker used in the module - + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -90,9 +91,9 @@ topics: - saltshaker: type: string description: The name of the tool - - 1.0.0: + - 1.1.1: type: string - description: Hardcoded version of saltshaker used in the module + description: The expression to obtain the version of the tool authors: - "@ieduba" maintainers: diff --git a/modules/nf-core/saltshaker/call/tests/main.nf.test.snap b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap index d377c6626..fa9ff6b47 100644 --- a/modules/nf-core/saltshaker/call/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/call/tests/main.nf.test.snap @@ -7,22 +7,22 @@ { "id": "test" }, - "test.saltshaker_call_metadata.tsv:md5,f0e21ea8c12afecbae37cd9b55f8f8c2" + "test.saltshaker_call_metadata.tsv:md5,5d0d87c5e2a29a07afa0b60cdb9c72d2" ] ], "versions_saltshaker": [ [ "SALTSHAKER_CALL", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-06T15:18:19.555305", + "timestamp": "2026-06-01T13:42:19.667355", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "call - tsv - stub": { @@ -40,15 +40,15 @@ [ "SALTSHAKER_CALL", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-05T09:54:13.739643", + "timestamp": "2026-06-01T13:41:08.005824", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/saltshaker/classify/environment.yml b/modules/nf-core/saltshaker/classify/environment.yml index 3672c7873..ba1172042 100644 --- a/modules/nf-core/saltshaker/classify/environment.yml +++ b/modules/nf-core/saltshaker/classify/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.1 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/classify/main.nf b/modules/nf-core/saltshaker/classify/main.nf index 72fa27c16..4a685c5b6 100644 --- a/modules/nf-core/saltshaker/classify/main.nf +++ b/modules/nf-core/saltshaker/classify/main.nf @@ -2,10 +2,11 @@ process SALTSHAKER_CLASSIFY { tag "$meta.id" label 'process_single' + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0c/0c955cc086622ef50876a10e58a1e6711e42b70a0e4cbbc377142b62b0ad4f47/data': - 'community.wave.seqera.io/library/pip_saltshaker:ef543ea5ca09afbe' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(call) @@ -15,7 +16,7 @@ process SALTSHAKER_CLASSIFY { tuple val(meta), path("*_classify_metadata.tsv"), emit: classify tuple val(meta), path("*_classify.txt") , emit: txt tuple val(meta), path("*saltshaker.vcf") , emit: vcf, optional: true - tuple val("${task.process}"), val('saltshaker'), val("1.0.1"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/saltshaker/classify/meta.yml b/modules/nf-core/saltshaker/classify/meta.yml index be07a8946..c02c10c59 100644 --- a/modules/nf-core/saltshaker/classify/meta.yml +++ b/modules/nf-core/saltshaker/classify/meta.yml @@ -8,8 +8,8 @@ keywords: tools: - "saltshaker": description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker" input: - - meta: @@ -74,7 +74,7 @@ output: - saltshaker: type: string description: The name of the tool - - 1.0.1: + - 1.1.1: type: string description: Hardcoded version of saltshaker used in the module topics: @@ -85,7 +85,7 @@ topics: - saltshaker: type: string description: The name of the tool - - 1.0.1: + - 1.1.1: type: string description: Hardcoded version of saltshaker used in the module authors: diff --git a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap index 507105e8c..c7e9d7868 100644 --- a/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/classify/tests/main.nf.test.snap @@ -25,15 +25,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T12:29:31.591954", + "timestamp": "2026-06-01T13:52:59.878729", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - defaults": { @@ -44,7 +44,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,2ed89e393a16ab2b7602ed06e807e187" ] ], "txt": [ @@ -52,7 +52,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,21b5114cd8e2d1cd720de1bfa18abd3e" ] ], "vcf": [ @@ -62,15 +62,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T12:29:26.57794", + "timestamp": "2026-06-01T15:59:15.738107", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - vcf - stub": { @@ -104,15 +104,15 @@ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T11:05:52.842015", + "timestamp": "2026-06-01T13:52:46.708731", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "classify - vcf": { @@ -123,7 +123,7 @@ { "id": "test" }, - "test.saltshaker_classify_metadata.tsv:md5,0c86c16ae38a5dc7070ad76e764aee6d" + "test.saltshaker_classify_metadata.tsv:md5,2ed89e393a16ab2b7602ed06e807e187" ] ], "txt": [ @@ -131,7 +131,7 @@ { "id": "test" }, - "test.saltshaker_classify.txt:md5,8e11ad30539d0b5e0ab9a42b4d68b208" + "test.saltshaker_classify.txt:md5,21b5114cd8e2d1cd720de1bfa18abd3e" ] ], "vcf": [ @@ -139,22 +139,24 @@ { "id": "test" }, - "test.saltshaker.vcf:md5,0c59728289ee8bcb19d44aea4d3155ab" + + "test.saltshaker.vcf:md5,e8e3c00ef62888bb217983a4bf5559a5" ] ], "versions_saltshaker": [ [ "SALTSHAKER_CLASSIFY", "saltshaker", - "1.0.1" + "1.1.1" ] ] } ], - "timestamp": "2026-03-20T11:05:45.058275", + + "timestamp": "2026-06-05T09:21:05.922028", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/modules/nf-core/saltshaker/plot/environment.yml b/modules/nf-core/saltshaker/plot/environment.yml index f76c4bf5a..ba1172042 100644 --- a/modules/nf-core/saltshaker/plot/environment.yml +++ b/modules/nf-core/saltshaker/plot/environment.yml @@ -4,4 +4,4 @@ channels: dependencies: - pip==26.0.1 - pip: - - saltshaker==1.0.0 + - saltshaker==1.1.1 diff --git a/modules/nf-core/saltshaker/plot/main.nf b/modules/nf-core/saltshaker/plot/main.nf index 56e7b9a3e..75679dfde 100644 --- a/modules/nf-core/saltshaker/plot/main.nf +++ b/modules/nf-core/saltshaker/plot/main.nf @@ -2,17 +2,18 @@ process SALTSHAKER_PLOT { tag "$meta.id" label 'process_single' + // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e93d703b195dd27cd920cee46669d3f51043216c12fd05168c937e93adf170e8/data': - 'community.wave.seqera.io/library/pip_saltshaker:e08e38a6d45f8f32' }" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5a902cc9f161d602fde9c268a509be2f593cfac7ed4cdc2219f630e02e43b2ec/data': + 'community.wave.seqera.io/library/pip_saltshaker:be40ca61bbf77cf2' }" input: tuple val(meta), path(classify) output: tuple val(meta), path("*saltshaker.png"), emit: plot - tuple val("${task.process}"), val('saltshaker'), val("1.0.0"), topic: versions, emit: versions_saltshaker + tuple val("${task.process}"), val('saltshaker'), val("1.1.1"), topic: versions, emit: versions_saltshaker when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/saltshaker/plot/meta.yml b/modules/nf-core/saltshaker/plot/meta.yml index b95deb3f5..200700538 100644 --- a/modules/nf-core/saltshaker/plot/meta.yml +++ b/modules/nf-core/saltshaker/plot/meta.yml @@ -7,10 +7,11 @@ keywords: - structural-variant calling tools: - "saltshaker": - description: "A Python package for classifying and visualizing mitochondrial structural variants from MitoSAlt pipeline output." - homepage: "https://github.com/aksenia/saltshaker" - documentation: "https://github.com/aksenia/saltshaker/tree/main/saltshaker/docs" - + description: "A Python package for classifying and visualizing mitochondrial structural + variants from MitoSAlt pipeline output." + homepage: "https://pypi.org/project/saltshaker" + documentation: "https://pypi.org/project/saltshaker" + identifier: "" input: - - meta: type: map @@ -24,7 +25,6 @@ input: ontologies: - edam: http://edamontology.org/operation_3225 #classification - edam: http://edamontology.org/format_3475 #tsv - output: plot: - - meta: @@ -46,19 +46,18 @@ output: - "saltshaker": type: string description: The name of the tool - - "1.0.0": + - "1.1.1": type: string description: Hardcoded version of saltshaker used in the module - topics: versions: - - - ${task.process}: + - - "${task.process}": type: string description: The name of the process - - saltshaker: + - "saltshaker": type: string description: The name of the tool - - 1.0.0: + - "1.1.1": type: string description: Hardcoded version of saltshaker used in the module authors: diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test b/modules/nf-core/saltshaker/plot/tests/main.nf.test index ec18cc241..f40353dcb 100644 --- a/modules/nf-core/saltshaker/plot/tests/main.nf.test +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test @@ -68,8 +68,10 @@ nextflow_process { assert process.success assertAll( { assert snapshot( - sanitizeOutput(process.out), - ).match() } + process.out.findAll { key, val -> key.startsWith('versions') }, + process.out.plot.collect { meta, plot -> file(plot).name } + ).match() + } ) } diff --git a/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap index ea7f4d94c..ebde03458 100644 --- a/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap +++ b/modules/nf-core/saltshaker/plot/tests/main.nf.test.snap @@ -14,41 +14,36 @@ [ "SALTSHAKER_PLOT", "saltshaker", - "1.0.0" + "1.1.1" ] ] } ], - "timestamp": "2026-03-17T14:57:52.937691", + "timestamp": "2026-06-03T10:34:26.252966", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "plot - png": { "content": [ { - "plot": [ - [ - { - "id": "test" - }, - "test.saltshaker.png:md5,c5c8f7b96daab112b53dfe42194855af" - ] - ], "versions_saltshaker": [ [ "SALTSHAKER_PLOT", "saltshaker", - "1.0.0" + "1.1.1" ] ] - } + }, + [ + "test.saltshaker.png" + ] ], - "timestamp": "2026-03-17T14:57:46.77575", + "timestamp": "2026-06-05T09:43:08.53978", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.0" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file From 422de4c7a0b3ca7a6095518eff6815f86b9db7d5 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 11 Jun 2026 10:25:49 +0200 Subject: [PATCH 805/872] update snaps --- tests/default.nf.test.snap | 10 +++++----- tests/test_singleton.nf.test.snap | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ea6fc5d95..37f95627a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -322,13 +322,13 @@ "rhocall": "0.5.1" }, "SALTSHAKER_CALL": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.1" + "saltshaker": "1.1.1" }, "SALTSHAKER_PLOT": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -928,10 +928,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-08T16:30:33.887641119", + "timestamp": "2026-06-11T10:20:14.951812109", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 66f438cc4..1e4c85c11 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -314,13 +314,13 @@ "rhocall": "0.5.1" }, "SALTSHAKER_CALL": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SALTSHAKER_CLASSIFY": { - "saltshaker": "1.0.1" + "saltshaker": "1.1.1" }, "SALTSHAKER_PLOT": { - "saltshaker": "1.0.0" + "saltshaker": "1.1.1" }, "SAMTOOLS_COLLATE": { "samtools": "1.22.1" @@ -655,10 +655,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-04-29T22:30:32.111448817", + "timestamp": "2026-06-11T10:25:31.455621104", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file From b0c4e246930d51676688ef4bfc09556e88259d4e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 11 Jun 2026 10:45:48 +0200 Subject: [PATCH 806/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dbcbe35ca..1fbe04055 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -145,6 +145,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | picard | 3.3.0 | 3.4.0 | | pigz | 2.3.4 | 2.8 | | qualimap | 2.3 | | +| saltshaker | 1.0.0 | 1.1.1 | | sambamba | | 1.0.1 | | samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | From 75f02652109f584fd8afacf3ad36816af4602be1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 11 Jun 2026 11:05:37 +0200 Subject: [PATCH 807/872] Update subworkflows/local/prepare_references/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- subworkflows/local/prepare_references/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index df83b8652..fda4f87f8 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -330,7 +330,7 @@ workflow PREPARE_REFERENCES { dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] dbsnp_tbi = ch_dbsnp_tbi // channel:[ val(meta), path(dbsnp_idx) ] genome_bwa_index = ch_genome_bwa_index // channel:[ val(meta), path(index) ] - genome_bwafastalign_index = ch_genome_bwafastalign_index // channel:[ val(meta), path(index) ] + genome_bwafastalign_index = ch_genome_bwafastalign_index // channel:[ val(meta), path(index) ] genome_bwamem2_index = ch_genome_bwamem2_index // channel:[ val(meta), path(index) ] genome_bwameme_index = ch_genome_bwameme_index // channel:[ val(meta), path(index) ] genome_chrom_sizes = ch_chrom_sizes // channel:[ path(sizes) ] From 6318a7d2db8b788f16b3a8321de99a52987e7931 Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Thu, 11 Jun 2026 16:15:49 +0200 Subject: [PATCH 808/872] trying to update snapshot for bwa_bwamem2_bwameme --- .../tests/main.nf.test.snap | 232 ++---------------- 1 file changed, 16 insertions(+), 216 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 15d0cd517..214750497 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -113,57 +113,7 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "4": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "marked_bai": [ + "markdup_metrics": [ [ { "groupSize": 1, @@ -175,10 +125,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "marked_bam": [ + "marked_bai": [ [ { "groupSize": 1, @@ -190,10 +140,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "metrics": [ + "marked_bam": [ [ { "groupSize": 1, @@ -205,57 +155,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "stats": [ @@ -272,9 +172,9 @@ ] } ], - "timestamp": "2026-04-08T14:48:42.172404", + "timestamp": "2026-06-11T16:06:18.512372", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -338,57 +238,7 @@ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "4": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "marked_bai": [ + "markdup_metrics": [ [ { "groupSize": 1, @@ -400,10 +250,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "marked_bam": [ + "marked_bai": [ [ { "groupSize": 1, @@ -415,10 +265,10 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "metrics": [ + "marked_bam": [ [ { "groupSize": 1, @@ -430,57 +280,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "publish": [ - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "alignment/", - [ - { - "groupSize": 1, - "groupTarget": { - "id": "test", - "sample": "test", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" - } - }, - "test_sorted_md.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test_sorted_md.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "stats": [ @@ -497,9 +297,9 @@ ] } ], - "timestamp": "2026-04-08T14:49:01.39982", + "timestamp": "2026-06-11T16:06:37.969441", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, From 76540836e769681d5a350763abef323b24f73f62 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 12 Jun 2026 09:46:08 +0200 Subject: [PATCH 809/872] Add bwafastalign genome aligner support --- CHANGELOG.md | 1 + conf/modules/align_bwa_bwamem2_bwameme.config | 7 + main.nf | 2 + modules.json | 5 + modules/nf-core/bwafastalign/mem/README.md | 51 ++++ .../nf-core/bwafastalign/mem/environment.yml | 9 + modules/nf-core/bwafastalign/mem/main.nf | 73 ++++++ modules/nf-core/bwafastalign/mem/meta.yml | 144 +++++++++++ .../bwafastalign/mem/tests/main.nf.test | 204 ++++++++++++++++ .../bwafastalign/mem/tests/main.nf.test.snap | 227 ++++++++++++++++++ .../bwafastalign/mem/tests/nextflow.config | 9 + nextflow.config | 2 +- nextflow_schema.json | 6 +- subworkflows/local/align/main.nf | 66 ++--- subworkflows/local/align/tests/main.nf.test | 164 +++++++------ .../local/align_bwa_bwamem2_bwameme/main.nf | 7 +- .../tests/main.nf.test | 41 ++-- workflows/raredisease.nf | 2 + 18 files changed, 884 insertions(+), 136 deletions(-) create mode 100644 modules/nf-core/bwafastalign/mem/README.md create mode 100644 modules/nf-core/bwafastalign/mem/environment.yml create mode 100644 modules/nf-core/bwafastalign/mem/main.nf create mode 100644 modules/nf-core/bwafastalign/mem/meta.yml create mode 100644 modules/nf-core/bwafastalign/mem/tests/main.nf.test create mode 100644 modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap create mode 100644 modules/nf-core/bwafastalign/mem/tests/nextflow.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 1f4b89c62..e2db2fd3c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers [#867](https://github.com/nf-core/raredisease/pull/867) - Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative [#870](https://github.com/nf-core/raredisease/pull/870) - `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner [#877](https://github.com/nf-core/raredisease/pull/877) +- `bwafastalign/mem` nf-core module to support genome alignment with bwa-fastalign when `--aligner bwafastalign` is set [#877](https://github.com/nf-core/raredisease/pull/877) ### `Changed` diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index da2cd83ff..a439215c9 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -17,6 +17,13 @@ process { + withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAFASTALIGN_MEM' { + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-m ${params.mbuffer_mem}M" } + ext.args3 = { "-T ./samtools_sort_tmp -@ ${params.samtools_sort_threads} -m ${(params.mbuffer_mem / params.samtools_sort_threads).intValue()}M" } + ext.prefix = { "${meta.id}_sorted" } + } + withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEM2_MEM' { ext.args = { "-M -K 100000000 -R ${meta.read_group}" } ext.args2 = { "-T ./samtools_sort_tmp" } diff --git a/main.nf b/main.nf index 01d769b55..39caa8bcc 100644 --- a/main.nf +++ b/main.nf @@ -186,6 +186,7 @@ workflow NFCORE_RAREDISEASE { ch_bait_intervals = ch_references.bait_intervals ch_dbsnp = ch_references.dbsnp ch_dbsnp_tbi = ch_references.dbsnp_tbi + ch_genome_bwafastalignindex = ch_references.genome_bwafastalign_index ch_genome_bwaindex = ch_references.genome_bwa_index ch_genome_bwamem2index = ch_references.genome_bwamem2_index ch_genome_bwamemeindex = ch_references.genome_bwameme_index @@ -397,6 +398,7 @@ workflow NFCORE_RAREDISEASE { ch_dbsnp_tbi, ch_foundin_header, ch_gcnvcaller_model, + ch_genome_bwafastalignindex, ch_genome_bwaindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, diff --git a/modules.json b/modules.json index 2eca44d85..c63cac481 100644 --- a/modules.json +++ b/modules.json @@ -80,6 +80,11 @@ "git_sha": "4ddd2d28518c7475bc76f0dd0e0451dd0e19df2a", "installed_by": ["modules"] }, + "bwafastalign/mem": { + "branch": "master", + "git_sha": "d6379deecb794ad5cc6234f3208085aaee27b327", + "installed_by": ["modules"] + }, "bwamem2/index": { "branch": "master", "git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d", diff --git a/modules/nf-core/bwafastalign/mem/README.md b/modules/nf-core/bwafastalign/mem/README.md new file mode 100644 index 000000000..f991034a2 --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/README.md @@ -0,0 +1,51 @@ +# bwafastalign/mem options + +bwa-fastalign is a high-throughput aligner that produces alignments faster than samtools can consume them. To prevent bwa-fastalign from stalling while samtools processes data, mbuffer is used as an intermediary to absorb alignments until samtools is ready. The mbuffer and samtools options are configurable via `ext.args2` and `ext.args3` respectively. + +## Configuring mbuffer (`ext.args2`) + +`ext.args2` is passed to mbuffer. The default buffer size is 3GB (`-m 3072M`). If `-m` is not present in `ext.args2`, the default is injected automatically. + +The mbuffer size should match the total memory allocated to `samtools sort` (`-m` × `-@`) so it can absorb bwa-fastalign output while samtools is flushing its sort buffer to disk. + +``` +withName: 'BWAFASTALIGN_MEM' { + ext.args2 = '-m 20480M' // 20GB mbuffer to match samtools sort total (e.g. -m 1024M x -@ 20) +} +``` + +## Configuring samtools (`ext.args3`) + +`ext.args3` is passed to `samtools sort` or `samtools view` depending on the `sort_bam` input. Defaults are injected if not supplied: + +- `-@ 3` (threads) — always injected if `-@` is absent +- `-m 1024M` (memory per thread) — injected if `-m` is absent and `sort_bam` is true + +``` +withName: 'BWAFASTALIGN_MEM' { + ext.args3 = '-@ 20 -m 1024M' // 20 threads, 1GB per thread = 20GB total +} +``` + +## Example: tuning for human genome alignment + +For a large reference (e.g. human genome) on a well-resourced machine, you may want to increase both values. The mbuffer size should equal the total samtools sort memory: + +``` +withName: 'BWAFASTALIGN_MEM' { + ext.args2 = '-m 20480M' // mbuffer = samtools total (20 threads x 1GB) + ext.args3 = '-@ 20 -m 1024M' +} +``` + +## CRAM output + +To produce CRAM output, pass `--output-fmt` via `ext.args3`: + +``` +withName: 'BWAFASTALIGN_MEM' { + ext.args3 = '--output-fmt cram' +} +``` + +A FASTA reference must be provided as `input[2]` when using CRAM output. diff --git a/modules/nf-core/bwafastalign/mem/environment.yml b/modules/nf-core/bwafastalign/mem/environment.yml new file mode 100644 index 000000000..a89afa0a9 --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bwa-fastalign=1.0.0 + - bioconda::mbuffer=20160228 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/bwafastalign/mem/main.nf b/modules/nf-core/bwafastalign/mem/main.nf new file mode 100644 index 000000000..36bca6fed --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/main.nf @@ -0,0 +1,73 @@ +process BWAFASTALIGN_MEM { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f8c975324a12014c8a817c2c1ad0cd68b077cf09c4370717589177b262dcd1dc/data': + 'community.wave.seqera.io/library/bwa-fastalign_mbuffer_samtools:35f24ce8addcd26b'}" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(index) + tuple val(meta3), path(fasta) + val sort_bam + + output: + tuple val(meta), path("${prefix}.{sam,bam,cram}"), emit: output + tuple val(meta), path("${prefix}.{csi,crai}") , emit: index , optional: true + tuple val("${task.process}"), val('bwafastalign'), val('1.0.0'), topic: versions, emit: versions_bwafastalign + tuple val("${task.process}"), val('samtools'), eval("samtools --version 2>&1 | sed '1!d;s/.* //'") , topic: versions, emit: versions_samtools + tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer version//p'") , topic: versions, emit: versions_mbuffer + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + def samtools_command = sort_bam ? 'sort' : 'view' + // ext.args2 controls mbuffer options; inject default -m if not supplied + def mbuffer_args = args2.contains('-m') ? args2 : "-m 3072M ${args2}" + def mbuffer_command = sort_bam ? "| mbuffer ${mbuffer_args}" : "" + // ext.args3 controls samtools options; inject defaults for -@ and -m (sort only) if not supplied + def samtools_threads_arg = args3.contains('-@') ? '' : '-@ 3' + def samtools_mem_arg = (sort_bam && !args3.contains('-m')) ? '-m 1024M' : '' + def samtools_args = "${samtools_mem_arg} ${samtools_threads_arg} ${args3}" + def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ + def extension_matcher = (args3 =~ extension_pattern) + def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" + def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" + if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" + """ + INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'` + + bwa-fastalign \\ + mem \\ + $args \\ + -t $task.cpus \\ + \$INDEX \\ + $reads \\ + $mbuffer_command \\ + | samtools $samtools_command $samtools_args ${reference} -o ${prefix}.${extension} - + """ + + stub: + + def args3 = task.ext.args3 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ + def extension_matcher = (args3 =~ extension_pattern) + def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" + if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" + + def create_index = extension == "cram" ? "touch ${prefix}.crai" : + extension == "bam" ? "touch ${prefix}.csi" : "" + """ + touch ${prefix}.${extension} + ${create_index} + """ +} diff --git a/modules/nf-core/bwafastalign/mem/meta.yml b/modules/nf-core/bwafastalign/mem/meta.yml new file mode 100644 index 000000000..0a6dfe042 --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/meta.yml @@ -0,0 +1,144 @@ +name: "bwafastalign_mem" +description: Performs fastq alignment to a fasta reference using BWA-FastAlign. +keywords: + - mem + - bwa + - bwafastalign + - alignment + - map + - fastq + - bam + - sam + - cram +tools: + - "bwafastalign": + description: "Faster and Cheaper Sequence Alignment on Commercial CPUs (A faster + version of bwa-mem with identical outputs)." + homepage: "https://github.com/zzhofict/BWA-FastAlign" + documentation: "https://github.com/zzhofict/BWA-FastAlign" + doi: "10.1145/3774934.3786421" + licence: + - "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + ontologies: [] + - - meta2: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + ontologies: [] + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta,fna}" + ontologies: [] + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" +output: + output: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.{sam,bam,cram}: + type: file + description: Output alignment file (SAM, BAM, or CRAM) + pattern: "*.{sam,bam,cram}" + ontologies: [] + index: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.{csi,crai}: + type: file + description: Index file for BAM (.csi) or CRAM (.crai) output + pattern: "*.{csi,crai}" + ontologies: [] + versions_bwafastalign: + - - ${task.process}: + type: string + description: The name of the process + - bwafastalign: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: The expression to obtain the version of the tool + versions_samtools: + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: Name of the tool + - samtools --version 2>&1 | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + versions_mbuffer: + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer version//p': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - bwafastalign: + type: string + description: The name of the tool + - 1.0.0: + type: string + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - samtools: + type: string + description: Name of the tool + - samtools --version 2>&1 | sed '1!d;s/.* //': + type: eval + description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer version//p': + type: eval + description: The expression to obtain the version of the tool +authors: + - "@peterpru" +maintainers: + - "@peterpru" diff --git a/modules/nf-core/bwafastalign/mem/tests/main.nf.test b/modules/nf-core/bwafastalign/mem/tests/main.nf.test new file mode 100644 index 000000000..83fef0386 --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/tests/main.nf.test @@ -0,0 +1,204 @@ +nextflow_process { + + name "Test Process BWAFASTALIGN_MEM" + script "../main.nf" + process "BWAFASTALIGN_MEM" + + tag "modules" + tag "modules_nfcore" + tag "bwafastalign" + tag "bwafastalign/mem" + tag "bwafastalign/index" + config "./nextflow.config" + + setup { + run("BWAFASTALIGN_INDEX") { + script "../../index/main.nf" + config "./nextflow.config" + process { + """ + input[0] = Channel.of([ + [:], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + ]) + """ + } + } + } + + test("sarscov2 - fastq, index, fasta, false") { + + when { + params { + module_args2 = "" + module_args3 = "" + } + + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, fasta, true") { + + when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, fasta, false") { + + when { + params { + module_args2 = "" + module_args3 = "" + } + + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, fasta, true") { + + when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") { + + options "-stub" + when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap b/modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap new file mode 100644 index 000000000..c3064b6ff --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/tests/main.nf.test.snap @@ -0,0 +1,227 @@ +{ + "sarscov2 - [fastq1, fastq2], index, fasta, false": { + "content": [ + "49bb35727c1eec2fc59473c0cf26c09c", + "57aeef88ed701a8ebc8e2f0a381b2a6", + { + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:29:18.833924106", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "3": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ], + "4": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "output": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:32:15.456124051", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - [fastq1, fastq2], index, fasta, true": { + "content": [ + "ff9384834da1473da24b9e75718695f8", + "af8628d9df18b2d3d4f6fd47ef2bb872", + { + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:32:05.037964846", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - fastq, index, fasta, false": { + "content": [ + "8f2ce115e2c6aabbd963c5375dc4637a", + "798439cbd7fd81cbcc5078022dc5479d", + { + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:23:56.737918563", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - fastq, index, fasta, true": { + "content": [ + "bf990ba932129f47990a9a9f98c30038", + "94fcf617f5b994584c4e8d4044e16b4f", + { + "versions_bwafastalign": [ + [ + "BWAFASTALIGN_MEM", + "bwafastalign", + "1.0.0" + ] + ], + "versions_mbuffer": [ + [ + "BWAFASTALIGN_MEM", + "mbuffer", + " 20160228" + ] + ], + "versions_samtools": [ + [ + "BWAFASTALIGN_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:26:37.839861629", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/modules/nf-core/bwafastalign/mem/tests/nextflow.config b/modules/nf-core/bwafastalign/mem/tests/nextflow.config new file mode 100644 index 000000000..fc560b4f6 --- /dev/null +++ b/modules/nf-core/bwafastalign/mem/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'BWAFASTALIGN.*' { + memory = 15.GB + } + withName: 'BWAFASTALIGN_MEM' { + ext.args2 = { params.module_args2 } + ext.args3 = { params.module_args3 } + } +} diff --git a/nextflow.config b/nextflow.config index f00a9ea74..e03f5347e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -114,7 +114,7 @@ params { // Alignment aligner = 'bwamem2' mt_aligner = 'bwamem2' - mbuffer_mem = 3072 + mbuffer_mem = 8192 samtools_sort_threads = 4 min_trimmed_length = 40 mt_subsample_rd = 150 diff --git a/nextflow_schema.json b/nextflow_schema.json index df75a0729..e8d3c34c6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -680,14 +680,14 @@ "samtools_sort_threads": { "type": "integer", "default": 4, - "description": "Number of threads allocated for sorting alignment files (used only by bwameme)", + "description": "Number of threads allocated for sorting alignment files (used by bwameme and bwafastalign)", "help_text": "To know more about this parameter check [bwameme](https://github.com/kaist-ina/BWA-MEME?tab=readme-ov-file#building-pipeline-with-samtools) documentation.", "fa_icon": "fas fa-less-than" }, "mbuffer_mem": { "type": "integer", - "default": 3072, - "description": "Memory allocated for mbuffer in megabytes (used only by bwameme)", + "default": 8192, + "description": "Memory allocated for mbuffer in megabytes (MB) (used by bwameme and bwafastalign)", "help_text": "To know more about this parameter check [bwameme](https://github.com/kaist-ina/BWA-MEME?tab=readme-ov-file#building-pipeline-with-samtools) documentation.", "fa_icon": "fas fa-less-than" }, diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index 932ace4f8..f4ce3c71a 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -14,36 +14,37 @@ include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_EXCLUDE_ALT } from '../../../modules/nf workflow ALIGN { take: - ch_alignments // channel: [optional] [ val(meta), [path(bam),path(bai)] ] - ch_genome_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_bwamemeindex // channel: [mandatory] [ val(meta), path(index) ] - ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_input_reads // channel: [optional] [ val(meta), [path(reads)] ] - ch_mt_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_mt_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_mt_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_mt_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mt_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - ch_mtshift_bwaindex // channel: [mandatory] [ val(meta), path(index) ] - ch_mtshift_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] - ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] - ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] - ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] - skip_fastp // boolean - val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' - val_analysis_type // string: 'wgs', 'wes', or 'mito' - val_exclude_alt // boolean - val_extract_alignments // boolean - val_mbuffer_mem // integer: [mandatory] memory in megabytes - val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' - val_platform // string: [mandatory] illumina or a different technology - val_run_mt_for_wes // boolean - val_samtools_sort_threads // integer: [mandatory] number of sorting threads - val_save_all_mapped_as_cram // boolean - val_save_noalt_mapped_as_cram // boolean + ch_alignments // channel: [optional] [ val(meta), [path(bam),path(bai)] ] + ch_genome_bwafastalignindex // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_bwamemeindex // channel: [mandatory] [ val(meta), path(index) ] + ch_genome_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_input_reads // channel: [optional] [ val(meta), [path(reads)] ] + ch_mt_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_mt_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mt_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mt_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_mtshift_bwaindex // channel: [mandatory] [ val(meta), path(index) ] + ch_mtshift_bwamem2index // channel: [mandatory] [ val(meta), path(index) ] + ch_mtshift_dictionary // channel: [mandatory] [ val(meta), path(dict) ] + ch_mtshift_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_mtshift_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + skip_fastp // boolean + val_aligner // string: 'bwa', 'bwafastalign', 'bwamem2', 'bwameme', or 'sentieon' + val_analysis_type // string: 'wgs', 'wes', or 'mito' + val_exclude_alt // boolean + val_extract_alignments // boolean + val_mbuffer_mem // integer: [mandatory] memory in megabytes + val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' + val_platform // string: [mandatory] illumina or a different technology + val_run_mt_for_wes // boolean + val_samtools_sort_threads // integer: [mandatory] number of sorting threads + val_save_all_mapped_as_cram // boolean + val_save_noalt_mapped_as_cram // boolean main: ch_bwamem2_bam = channel.empty() @@ -91,9 +92,10 @@ workflow ALIGN { ch_input_bam = ch_input_aligned.bam ch_input_bai = ch_input_aligned.bai - if (val_aligner.matches("bwamem2|bwa|bwameme")) { + if (val_aligner.matches("bwamem2|bwa|bwameme|bwafastalign")) { ALIGN_BWA_BWAMEM2_BWAMEME ( ch_genome_bwaindex, + ch_genome_bwafastalignindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, ch_genome_fai, @@ -200,7 +202,7 @@ workflow ALIGN { ch_bam_publish = channel.empty() if (!val_save_noalt_mapped_as_cram && !val_save_all_mapped_as_cram) { - if (val_aligner.matches("bwamem2|bwa|bwameme")) { + if (val_aligner.matches("bwamem2|bwa|bwameme|bwafastalign")) { ch_bam_publish = ALIGN_BWA_BWAMEM2_BWAMEME.out.publish } else if (val_aligner.equals("sentieon")) { ch_bam_publish = ALIGN_SENTIEON.out.publish diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 7a8e427ac..a87e52515 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_workflow { tag "subworkflows" tag "align" tag "align_bwa_bwamem2_bwameme" + tag "bwafastalign/mem" tag "align_sentieon" tag "align_MT" tag "convert_mt_bam_to_fastq" @@ -72,12 +73,13 @@ nextflow_workflow { """ input[0] = channel.empty() input[1] = channel.empty() - input[2] = GENOME_MEM2.out.index.collect() - input[3] = channel.empty() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[7] = channel.of( + input[2] = channel.empty() + input[3] = GENOME_MEM2.out.index.collect() + input[4] = channel.empty() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[8] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -100,28 +102,28 @@ nextflow_workflow { ] ] ) - input[8] = channel.empty() - input[9] = MT_MEM2.out.index.collect() - input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = channel.empty() - input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = false - input[19] = "bwamem2" - input[20] = "wgs" - input[21] = true - input[22] = false - input[23] = 3072 - input[24] = "bwamem2" - input[25] = "illumina" - input[26] = false - input[27] = 4 - input[28] = true + input[9] = channel.empty() + input[10] = MT_MEM2.out.index.collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[13] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[14] = channel.empty() + input[15] = SHIFTMT_MEM2.out.index.collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[18] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[19] = false + input[20] = "bwamem2" + input[21] = "wgs" + input[22] = true + input[23] = false + input[24] = 3072 + input[25] = "bwamem2" + input[26] = "illumina" + input[27] = false + input[28] = 4 input[29] = true + input[30] = true """ } } @@ -179,12 +181,13 @@ nextflow_workflow { """ input[0] = channel.empty() input[1] = channel.empty() - input[2] = GENOME_MEM2.out.index.collect() - input[3] = channel.empty() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[7] = channel.of( + input[2] = channel.empty() + input[3] = GENOME_MEM2.out.index.collect() + input[4] = channel.empty() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[8] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -207,28 +210,28 @@ nextflow_workflow { ] ] ) - input[8] = channel.empty() - input[9] = MT_MEM2.out.index.collect() - input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = channel.empty() - input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = false - input[19] = "bwamem2" - input[20] = "wes" - input[21] = false + input[9] = channel.empty() + input[10] = MT_MEM2.out.index.collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[13] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[14] = channel.empty() + input[15] = SHIFTMT_MEM2.out.index.collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[18] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[19] = false + input[20] = "bwamem2" + input[21] = "wes" input[22] = false - input[23] = 3072 - input[24] = "bwamem2" - input[25] = "illumina" - input[26] = false - input[27] = 4 - input[28] = true - input[29] = false + input[23] = false + input[24] = 3072 + input[25] = "bwamem2" + input[26] = "illumina" + input[27] = false + input[28] = 4 + input[29] = true + input[30] = false """ } } @@ -284,11 +287,12 @@ nextflow_workflow { input[0] = channel.empty() input[1] = channel.empty() input[2] = channel.empty() - input[3] = GENOME_MEME.out.index.collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[7] = channel.fromList([ + input[3] = channel.empty() + input[4] = GENOME_MEME.out.index.collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[8] = channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), @@ -305,28 +309,28 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) - input[8] = channel.empty() - input[9] = MT_MEM2.out.index.collect() - input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = channel.empty() - input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = true - input[19] = "bwameme" - input[20] = "wgs" - input[21] = false + input[9] = channel.empty() + input[10] = MT_MEM2.out.index.collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[13] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[14] = channel.empty() + input[15] = SHIFTMT_MEM2.out.index.collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[18] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[19] = true + input[20] = "bwameme" + input[21] = "wgs" input[22] = false - input[23] = 3072 - input[24] = "bwamem2" - input[25] = "illumina" - input[26] = false - input[27] = 4 - input[28] = true - input[29] = false + input[23] = false + input[24] = 3072 + input[25] = "bwamem2" + input[26] = "illumina" + input[27] = false + input[28] = 4 + input[29] = true + input[30] = false """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 6ea0434de..6c13d9d2f 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -2,6 +2,7 @@ // Map to reference, fetch stats for each demultiplexed read pair, merge, mark duplicates, and index. // +include { BWAFASTALIGN_MEM } from '../../../modules/nf-core/bwafastalign/mem/main' include { BWAMEM2_MEM } from '../../../modules/nf-core/bwamem2/mem/main' include { BWAMEME_MEM } from '../../../modules/nf-core/bwameme/mem/main' include { BWA_MEM as BWA } from '../../../modules/nf-core/bwa/mem/main' @@ -17,12 +18,13 @@ include { SAMTOOLS_VIEW as EXTRACT_ALIGNMENTS } from '../../../modules/nf-c workflow ALIGN_BWA_BWAMEM2_BWAMEME { take: ch_bwa_index // channel: [mandatory] [ val(meta), path(bwa_index) ] + ch_bwafastalign_index // channel: [mandatory] [ val(meta), path(bwafastalign_index) ] ch_bwamem2_index // channel: [mandatory] [ val(meta), path(bwamem2_index) ] ch_bwameme_index // channel: [mandatory] [ val(meta), path(bwameme_index) ] ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ] ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ] ch_input_reads // channel: [mandatory] [ val(meta), path(reads_input) ] - val_aligner // string: 'bwa', 'bwamem2', 'bwameme', or 'sentieon' + val_aligner // string: 'bwa', 'bwafastalign', 'bwamem2', or 'bwameme' val_extract_alignments // boolean val_mbuffer_mem // integer: [mandatory] default: 3072 val_platform // string: [mandatory] default: illumina @@ -33,6 +35,9 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { if (val_aligner.equals("bwa")) { BWA ( ch_input_reads, ch_bwa_index, ch_genome_fasta, true ) ch_align = BWA.out.bam + } else if (val_aligner.equals("bwafastalign")) { + BWAFASTALIGN_MEM ( ch_input_reads, ch_bwafastalign_index, ch_genome_fasta, true ) + ch_align = BWAFASTALIGN_MEM.out.output } else if (val_aligner.equals("bwameme")) { BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) ch_align = BWAMEME_MEM.out.bam diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 7e64d0355..187e36d9a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -8,6 +8,7 @@ nextflow_workflow { tag "align_bwa_bwamem2_bwameme" tag "bwa/mem" + tag "bwafastalign/mem" tag "bwamem2/mem" tag "bwameme/mem" tag "samtools/index" @@ -42,22 +43,23 @@ nextflow_workflow { workflow { """ input[0] = [[:],[]] - input[1] = BWAMEM2_INDEX.out.index - input[2] = [[:],[]] - input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([ + input[1] = [[:],[]] + input[2] = BWAMEM2_INDEX.out.index + input[3] = [[:],[]] + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[6] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[6] = "bwamem2" - input[7] = true - input[8] = 3072 - input[9] = "illumina" - input[10] = 4 + input[7] = "bwamem2" + input[8] = true + input[9] = 3072 + input[10] = "illumina" + input[11] = 4 """ } } @@ -103,21 +105,22 @@ nextflow_workflow { """ input[0] = [[:],[]] input[1] = [[:],[]] - input[2] = BWAMEME_INDEX.out.index - input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([ + input[2] = [[:],[]] + input[3] = BWAMEME_INDEX.out.index + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[6] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[6] = "bwameme" - input[7] = true - input[8] = 3072 - input[9] = "illumina" - input[10] = 4 + input[7] = "bwameme" + input[8] = true + input[9] = 3072 + input[10] = "illumina" + input[11] = 4 """ } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index d65743e77..1f9c75fa6 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -88,6 +88,7 @@ workflow RAREDISEASE { ch_dbsnp_tbi ch_foundin_header ch_gcnvcaller_model + ch_genome_bwafastalignindex ch_genome_bwaindex ch_genome_bwamem2index ch_genome_bwamemeindex @@ -292,6 +293,7 @@ workflow RAREDISEASE { ALIGN ( ch_alignments, + ch_genome_bwafastalignindex, ch_genome_bwaindex, ch_genome_bwamem2index, ch_genome_bwamemeindex, From 68efffa1053f5eb7e68d87f20348b524982faf77 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 12 Jun 2026 14:47:57 +0200 Subject: [PATCH 810/872] add test --- .../tests/main.nf.test | 61 +++++++++++++++++++ .../tests/main.nf.test.snap | 44 +++++++++++++ .../tests/nextflow.config | 11 ++++ 3 files changed, 116 insertions(+) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 187e36d9a..fa44ebb11 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -80,6 +80,67 @@ nextflow_workflow { } } + test("align bwafastalign") { + + setup { + run("BWAFASTALIGN_INDEX") { + script "modules/nf-core/bwafastalign/index/main.nf" + process { + """ + input[0] = channel.of([ + [id:'sarscov2'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + sarscov_testdata_base_path= 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + restrict_to_contigs = "MT192765.1" + } + workflow { + """ + input[0] = [[:],[]] + input[1] = BWAFASTALIGN_INDEX.out.index + input[2] = [[:],[]] + input[3] = [[:],[]] + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[6] = channel.of([ + [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map + [ + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[7] = "bwafastalign" + input[8] = true + input[9] = 3072 + input[10] = "illumina" + input[11] = 4 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.publish.flatten() + .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } + .collect { new File(it).name } + .sort(), + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } + ).match() + } + ) + } + } + test("align bwameme") { setup { diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 7632f79b8..561d4dbcd 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -1,4 +1,48 @@ { + "align bwafastalign": { + "content": [ + [ + "test_sorted_md.bam", + "test_sorted_md.bam.bai", + "test_sorted_md.metrics.txt" + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "b88d51cb3010d98935b39ef6a3c58499" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "af8628d9df18b2d3d4f6fd47ef2bb872" + ] + ] + ], + "timestamp": "2026-06-12T14:44:03.681795857", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, "align bwamem2": { "content": [ [ diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config index 4563b2d78..f43ce84c0 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config @@ -1,5 +1,16 @@ process { + withName: 'BWAFASTALIGN_INDEX' { + memory = 15.GB + } + + withName: 'BWAFASTALIGN_MEM' { + memory = 15.GB + ext.args = { "-M -K 100000000 -R ${meta.read_group}" } + ext.args3 = { "-T ./samtools_sort_tmp" } + ext.prefix = { "${meta.id}_sorted" } + } + withName: 'BWAMEME_INDEX' { ext.args = '-a meme' } From 0c95c24cb4e0cc3e8ca98d8a50d3907ffb0b1f5b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 12 Jun 2026 14:48:08 +0200 Subject: [PATCH 811/872] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e2db2fd3c..ab75063fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers [#867](https://github.com/nf-core/raredisease/pull/867) - Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative [#870](https://github.com/nf-core/raredisease/pull/870) - `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner [#877](https://github.com/nf-core/raredisease/pull/877) -- `bwafastalign/mem` nf-core module to support genome alignment with bwa-fastalign when `--aligner bwafastalign` is set [#877](https://github.com/nf-core/raredisease/pull/877) +- `bwafastalign/mem` nf-core module to support genome alignment with bwa-fastalign when `--aligner bwafastalign` is set [#880](https://github.com/nf-core/raredisease/pull/880) ### `Changed` From 08476a3d15c113e4b85589e244f2b4708ec5c043 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 12 Jun 2026 16:26:27 +0200 Subject: [PATCH 812/872] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab75063fe..abc2c4d79 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` [#870](https://github.com/nf-core/raredisease/pull/870) +- Increase default mbuffer memory value from 3GB to 8GB [#880](https://github.com/nf-core/raredisease/pull/880) ### `Fixed` From a883fad977bd9e0874293a929101b466fb3a1df3 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 13 Jun 2026 11:28:27 +0200 Subject: [PATCH 813/872] update bwameme --- conf/modules/align_bwa_bwamem2_bwameme.config | 5 +- main.nf | 6 - modules.json | 2 +- modules/nf-core/bwameme/mem/README.md | 51 ++++ modules/nf-core/bwameme/mem/main.nf | 56 ++--- modules/nf-core/bwameme/mem/meta.yml | 82 +++---- .../nf-core/bwameme/mem/tests/main.nf.test | 69 +++--- .../bwameme/mem/tests/main.nf.test.snap | 228 ++++++++++++------ .../nf-core/bwameme/mem/tests/nextflow.config | 5 +- subworkflows/local/align/main.nf | 6 +- subworkflows/local/align/tests/main.nf.test | 36 ++- .../local/align_bwa_bwamem2_bwameme/main.nf | 6 +- .../tests/main.nf.test | 12 +- .../tests/main.nf.test.snap | 12 +- .../tests/nextflow.config | 5 +- workflows/raredisease.nf | 4 - 16 files changed, 338 insertions(+), 247 deletions(-) create mode 100644 modules/nf-core/bwameme/mem/README.md diff --git a/conf/modules/align_bwa_bwamem2_bwameme.config b/conf/modules/align_bwa_bwamem2_bwameme.config index a439215c9..c2711965e 100644 --- a/conf/modules/align_bwa_bwamem2_bwameme.config +++ b/conf/modules/align_bwa_bwamem2_bwameme.config @@ -37,8 +37,9 @@ process { } withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:BWAMEME_MEM' { - ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } - ext.args2 = { "-T ./samtools_sort_tmp" } + ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } + ext.args2 = { "-m ${params.mbuffer_mem}M" } + ext.args3 = { "-T ./samtools_sort_tmp -@ ${params.samtools_sort_threads} -m ${(params.mbuffer_mem / params.samtools_sort_threads).intValue()}M" } ext.prefix = { "${meta.id}_sorted" } } diff --git a/main.nf b/main.nf index 39caa8bcc..dba61fb61 100644 --- a/main.nf +++ b/main.nf @@ -77,7 +77,6 @@ workflow NFCORE_RAREDISEASE { val_light_strand_origin_start val_manta_call_regions val_manta_call_regions_tbi - val_mbuffer_mem val_mito_length val_mito_name val_mitosalt_breakspan @@ -115,7 +114,6 @@ workflow NFCORE_RAREDISEASE { val_run_vcfanno_db_sanity_check val_sambamba_regions val_sample_id_map - val_samtools_sort_threads val_save_all_mapped_as_cram val_save_noalt_mapped_as_cram val_save_reference @@ -504,7 +502,6 @@ workflow NFCORE_RAREDISEASE { val_homoplasmy_af_threshold, val_light_strand_origin_end, val_light_strand_origin_start, - val_mbuffer_mem, val_mito_length, val_mito_name, val_mitosalt_breakspan, @@ -530,7 +527,6 @@ workflow NFCORE_RAREDISEASE { val_run_rtgvcfeval, val_run_vcfanno_db_sanity_check, val_sample_id_map, - val_samtools_sort_threads, val_save_all_mapped_as_cram, val_save_noalt_mapped_as_cram, val_svdb_query_bedpedbs, @@ -610,7 +606,6 @@ workflow { params.light_strand_origin_start, params.manta_call_regions, params.manta_call_regions_tbi, - params.mbuffer_mem, params.mito_length, params.mito_name, params.mitosalt_breakspan, @@ -648,7 +643,6 @@ workflow { params.run_vcfanno_db_sanity_check, params.sambamba_regions, params.sample_id_map, - params.samtools_sort_threads, params.save_all_mapped_as_cram, params.save_noalt_mapped_as_cram, params.save_reference, diff --git a/modules.json b/modules.json index c63cac481..7339e34d6 100644 --- a/modules.json +++ b/modules.json @@ -102,7 +102,7 @@ }, "bwameme/mem": { "branch": "master", - "git_sha": "7a41710e25fdcdf8e4d5b324f2eb74022ffc77ff", + "git_sha": "ead2c49d7abda0172e1a0abf585b305b690fb8a8", "installed_by": ["modules"] }, "cadd": { diff --git a/modules/nf-core/bwameme/mem/README.md b/modules/nf-core/bwameme/mem/README.md new file mode 100644 index 000000000..b681f9a02 --- /dev/null +++ b/modules/nf-core/bwameme/mem/README.md @@ -0,0 +1,51 @@ +# bwameme/mem options + +bwa-meme is a high-throughput aligner that produces alignments faster than samtools can consume them. To prevent bwa-meme from stalling while samtools processes data, mbuffer is used as an intermediary to absorb alignments until samtools is ready. The mbuffer and samtools options are configurable via `ext.args2` and `ext.args3` respectively. + +## Configuring mbuffer (`ext.args2`) + +`ext.args2` is passed to mbuffer. The default buffer size is 3GB (`-m 3072M`). If `-m` is not present in `ext.args2`, the default is injected automatically. + +The mbuffer size should match the total memory allocated to `samtools sort` (`-m` × `-@`) so it can absorb bwa-meme output while samtools is flushing its sort buffer to disk. + +``` +withName: 'BWAMEME_MEM' { + ext.args2 = '-m 20480M' // 20GB mbuffer to match samtools sort total (e.g. -m 1024M x -@ 20) +} +``` + +## Configuring samtools (`ext.args3`) + +`ext.args3` is passed to `samtools sort` or `samtools view` depending on the `sort_bam` input. Defaults are injected if not supplied: + +- `-@ 3` (threads) — always injected if `-@` is absent +- `-m 1024M` (memory per thread) — injected if `-m` is absent and `sort_bam` is true + +``` +withName: 'BWAMEME_MEM' { + ext.args3 = '-@ 20 -m 1024M' // 20 threads, 1GB per thread = 20GB total +} +``` + +## Example: tuning for human genome alignment + +For a large reference (e.g. human genome) on a well-resourced machine, you may want to increase both values. The mbuffer size should equal the total samtools sort memory: + +``` +withName: 'BWAMEME_MEM' { + ext.args2 = '-m 20480M' // mbuffer = samtools total (20 threads x 1GB) + ext.args3 = '-@ 20 -m 1024M' +} +``` + +## CRAM output + +To produce CRAM output, pass `--output-fmt` via `ext.args3`: + +``` +withName: 'BWAMEME_MEM' { + ext.args3 = '--output-fmt cram' +} +``` + +A FASTA reference must be provided as `input[2]` when using CRAM output. diff --git a/modules/nf-core/bwameme/mem/main.nf b/modules/nf-core/bwameme/mem/main.nf index 14421453b..6b356e302 100644 --- a/modules/nf-core/bwameme/mem/main.nf +++ b/modules/nf-core/bwameme/mem/main.nf @@ -3,7 +3,7 @@ process BWAMEME_MEM { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9ddd41b93c5e182db9d643ca266dd1677e59593a9cb49904b982ff45ad5aa8c3/data': 'community.wave.seqera.io/library/bwa-meme_mbuffer_samtools:03f3f60b6c289776' }" @@ -12,42 +12,32 @@ process BWAMEME_MEM { tuple val(meta2), path(index) tuple val(meta3), path(fasta) val sort_bam - val mbuffer - val samtools_threads output: - tuple val(meta), path("*.sam") , emit: sam , optional:true - tuple val(meta), path("*.bam") , emit: bam , optional:true - tuple val(meta), path("*.cram") , emit: cram, optional:true - tuple val(meta), path("*.crai") , emit: crai, optional:true - tuple val(meta), path("*.csi") , emit: csi , optional:true + tuple val(meta), path("${prefix}.{sam,bam,cram}"), emit: output + tuple val(meta), path("${prefix}.{csi,crai}") , emit: index , optional: true tuple val("${task.process}"), val('bwameme'), val('1.0.6'), topic: versions, emit: versions_bwameme tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), topic: versions, emit: versions_samtools // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. + tuple val("${task.process}"), val('mbuffer'), eval("mbuffer --version 2>&1 | sed -n 's/mbuffer version //p'") , topic: versions, emit: versions_mbuffer when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args3 = task.ext.args3 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" def samtools_command = sort_bam ? 'sort' : 'view' - if (!mbuffer) { - log.info '[bwameme-mbuffer] Memory for mbuffer is not set - defaulting to 3GB for mbuffer.' - mbuffer_mem = 3072 - } else { - mbuffer_mem = mbuffer - } - if (!samtools_threads) { - log.info 'Number of threads for samtools is not set - defaulting to 2 threads.' - threads = 2 - } else { - threads = samtools_threads - } - mbuffer_command = sort_bam ? "| mbuffer -m ${mbuffer_mem}M" : "" - mem_per_thread = sort_bam ? "-m "+ (mbuffer_mem/threads).intValue()+"M" : "" + // ext.args2 controls mbuffer options; inject default -m if not supplied + def mbuffer_args = args2.contains('-m') ? args2 : "-m 3072M ${args2}".trim() + def mbuffer_command = sort_bam ? "| mbuffer ${mbuffer_args}" : "" + // ext.args3 controls samtools options; inject defaults for -@ and -m (sort only) if not supplied + def samtools_threads_arg = args3.contains('-@') ? '' : '-@ 3' + def samtools_mem_arg = (sort_bam && !args3.contains('-m')) ? '-m 1024M' : '' + def samtools_args = "${samtools_mem_arg} ${samtools_threads_arg} ${args3}".trim() def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args3 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" @@ -61,24 +51,20 @@ process BWAMEME_MEM { \$INDEX \\ $reads \\ $mbuffer_command \\ - | samtools $samtools_command $args2 $mem_per_thread -@ $threads ${reference} -o ${prefix}.${extension} - + | samtools $samtools_command $samtools_args ${reference} -o ${prefix}.${extension} - """ stub: - def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args3 = task.ext.args3 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension_matcher = (args2 =~ extension_pattern) + def extension_matcher = (args3 =~ extension_pattern) def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" - def create_index = "" - if (extension == "cram") { - create_index = "touch ${prefix}.crai" - } else if (extension == "bam") { - create_index = "touch ${prefix}.csi" - } + def create_index = extension == "cram" ? "touch ${prefix}.crai" : + extension == "bam" ? "touch ${prefix}.csi" : "" """ touch ${prefix}.${extension} ${create_index} diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml index 324d96245..32620223e 100644 --- a/modules/nf-core/bwameme/mem/meta.yml +++ b/modules/nf-core/bwameme/mem/meta.yml @@ -17,9 +17,9 @@ tools: homepage: https://github.com/kaist-ina/BWA-MEME documentation: https://github.com/kaist-ina/BWA-MEME#getting-started doi: "10.1093/bioinformatics/btac137" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map @@ -56,67 +56,28 @@ input: type: boolean description: use samtools sort (true) or samtools view (false) pattern: "true or false" - - mbuffer: - type: integer - description: memory for mbuffer in megabytes (default 3072) - - samtools_threads: - type: integer - description: number of threads for samtools (default 2) output: - sam: + output: - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.sam": + - ${prefix}.{sam,bam,cram}: type: file - description: Output SAM file containing read alignments - pattern: "*.{sam}" + description: Output alignment file (SAM, BAM, or CRAM) + pattern: "*.{sam,bam,cram}" ontologies: [] - bam: + index: - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.bam": + - ${prefix}.{csi,crai}: type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - ontologies: [] - cram: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.cram": - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" - ontologies: [] - crai: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.crai": - type: file - description: Index file for CRAM file - pattern: "*.{crai}" - ontologies: [] - csi: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.csi": - type: file - description: Index file for BAM file - pattern: "*.{csi}" + description: Index file for BAM (.csi) or CRAM (.crai) output + pattern: "*.{csi,crai}" ontologies: [] versions_bwameme: - - ${task.process}: @@ -131,13 +92,23 @@ output: versions_samtools: - - ${task.process}: type: string - description: Name of the process + description: The name of the process - samtools: type: string description: Name of the tool - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool + versions_mbuffer: + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer version //p': + type: eval + description: The expression to obtain the version of the tool topics: versions: - - ${task.process}: @@ -151,13 +122,22 @@ topics: description: The expression to obtain the version of the tool - - ${task.process}: type: string - description: Name of the process + description: The name of the process - samtools: type: string description: Name of the tool - samtools version | sed "1!d;s/.* //": type: eval description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process + - mbuffer: + type: string + description: The name of the tool + - mbuffer --version 2>&1 | sed -n 's/mbuffer version //p': + type: eval + description: The expression to obtain the version of the tool authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test b/modules/nf-core/bwameme/mem/tests/main.nf.test index fd378c0b3..31911da25 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test @@ -26,9 +26,14 @@ nextflow_process { } } - test("sarscov2 - fastq, index, fasta, false, 0, 4") { + test("sarscov2 - fastq, index, fasta, false") { when { + params { + module_args2 = "" + module_args3 = "" + } + process { """ input[0] = Channel.of([ @@ -38,8 +43,6 @@ nextflow_process { input[1] = BWAMEME_INDEX.out.index input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[3] = false - input[4] = 0 - input[5] = 4 """ } } @@ -48,18 +51,23 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getHeaderMD5(), - bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } } - test("sarscov2 - fastq, index, fasta, true, 2048, 4") { + test("sarscov2 - fastq, index, fasta, true") { when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + process { """ input[0] = Channel.of([ @@ -69,8 +77,6 @@ nextflow_process { input[1] = BWAMEME_INDEX.out.index input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[3] = true - input[4] = 2048 - input[5] = 4 """ } } @@ -79,18 +85,23 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getHeaderMD5(), - bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } } - test("sarscov2 - [fastq1, fastq2], index, fasta, false, 0, 4") { + test("sarscov2 - [fastq1, fastq2], index, fasta, false") { when { + params { + module_args2 = "" + module_args3 = "" + } + process { """ input[0] = Channel.of([ @@ -103,8 +114,6 @@ nextflow_process { input[1] = BWAMEME_INDEX.out.index input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[3] = false - input[4] = 0 - input[5] = 4 """ } } @@ -113,18 +122,23 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getHeaderMD5(), - bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } } - test("sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''") { + test("sarscov2 - [fastq1, fastq2], index, fasta, true") { when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + process { """ input[0] = Channel.of([ @@ -137,8 +151,6 @@ nextflow_process { input[1] = BWAMEME_INDEX.out.index input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[3] = true - input[4] = 2048 - input[5] = "" """ } } @@ -147,20 +159,25 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - bam(process.out.bam[0][1]).getHeaderMD5(), - bam(process.out.bam[0][1]).getReadsMD5(), - process.out.versions + bam(process.out.output[0][1]).getHeaderMD5(), + bam(process.out.output[0][1]).getReadsMD5(), + process.out.findAll { key, val -> key.startsWith("versions")} ).match() } ) } } - test("sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, 4 - stub") { + test("sarscov2 - [fastq1, fastq2], index, fasta, true - stub") { options "-stub" when { + params { + module_args2 = "-m 2048M" + module_args3 = "-@ 4" + } + process { """ input[0] = Channel.of([ @@ -173,8 +190,6 @@ nextflow_process { input[1] = BWAMEME_INDEX.out.index input[2] = Channel.of([[:], [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) input[3] = true - input[4] = 2048 - input[5] = 4 """ } } diff --git a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap index 5c6487e75..5d3180a46 100644 --- a/modules/nf-core/bwameme/mem/tests/main.nf.test.snap +++ b/modules/nf-core/bwameme/mem/tests/main.nf.test.snap @@ -1,59 +1,42 @@ { - "sarscov2 - [fastq1, fastq2], index, fasta, false, 0, 4": { + "sarscov2 - [fastq1, fastq2], index, fasta, false": { "content": [ - "b537f2936bcb8c120127251ab44d917b", + "2dd7c6542f553040eebaa572c10fe035", "57aeef88ed701a8ebc8e2f0a381b2a6", - null - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T19:51:39.510097" - }, - "sarscov2 - fastq, index, fasta, true, 2048, 4": { - "content": [ - "91c0b36a7aa238cca2acbce1997d94e8", - "94fcf617f5b994584c4e8d4044e16b4f", - null - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T19:51:19.196468" - }, - "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, ''": { - "content": [ - "ffc18373a0992612ccb5df41a245947b", - "af8628d9df18b2d3d4f6fd47ef2bb872", - null - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T19:52:00.628046" - }, - "sarscov2 - fastq, index, fasta, false, 0, 4": { - "content": [ - "585cc3d6cdff0dce2e30b6e8c1542669", - "798439cbd7fd81cbcc5078022dc5479d", - null + { + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "versions_mbuffer": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" + ] + ], + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] + ] + } ], + "timestamp": "2026-06-12T08:19:39.496429529", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T19:50:58.198221" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } }, - "sarscov2 - [fastq1, fastq2], index, fasta, true, 2048, 4 - stub": { + "sarscov2 - [fastq1, fastq2], index, fasta, true - stub": { "content": [ { "0": [ - - ], - "1": [ [ { "id": "test", @@ -62,13 +45,7 @@ "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ - - ], - "3": [ - - ], - "4": [ + "1": [ [ { "id": "test", @@ -77,47 +54,113 @@ "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "5": [ + "2": [ [ "BWAMEME_MEM", "bwameme", "1.0.6" ] ], - "6": [ + "3": [ [ "BWAMEME_MEM", "samtools", "1.21" ] ], - "bam": [ + "4": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" + ] + ], + "index": [ [ { "id": "test", "single_end": false }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ + "output": [ [ { "id": "test", "single_end": false }, - "test.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "versions_mbuffer": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" ] ], - "sam": [ - + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:20:13.023631084", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - [fastq1, fastq2], index, fasta, true": { + "content": [ + "8c45fe3cdc7021ffab9c5eea83fc5850", + "af8628d9df18b2d3d4f6fd47ef2bb872", + { + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] ], + "versions_mbuffer": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" + ] + ], + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:20:02.737739229", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - fastq, index, fasta, false": { + "content": [ + "9661f4c03c6b2abdc93204890aa61673", + "798439cbd7fd81cbcc5078022dc5479d", + { "versions_bwameme": [ [ "BWAMEME_MEM", @@ -125,6 +168,47 @@ "1.0.6" ] ], + "versions_mbuffer": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" + ] + ], + "versions_samtools": [ + [ + "BWAMEME_MEM", + "samtools", + "1.21" + ] + ] + } + ], + "timestamp": "2026-06-12T08:18:55.571422607", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "sarscov2 - fastq, index, fasta, true": { + "content": [ + "30aae1770b553c055553c48dcad73384", + "94fcf617f5b994584c4e8d4044e16b4f", + { + "versions_bwameme": [ + [ + "BWAMEME_MEM", + "bwameme", + "1.0.6" + ] + ], + "versions_mbuffer": [ + [ + "BWAMEME_MEM", + "mbuffer", + "20160228" + ] + ], "versions_samtools": [ [ "BWAMEME_MEM", @@ -134,10 +218,10 @@ ] } ], + "timestamp": "2026-06-12T08:19:17.606378245", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-13T19:52:05.913267" + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/bwameme/mem/tests/nextflow.config b/modules/nf-core/bwameme/mem/tests/nextflow.config index e7dd707ea..835b858dc 100644 --- a/modules/nf-core/bwameme/mem/tests/nextflow.config +++ b/modules/nf-core/bwameme/mem/tests/nextflow.config @@ -1,9 +1,10 @@ process { - withName: BWAMEME_INDEX { ext.args = '-a meme' } withName: BWAMEME_MEM { - ext.args = '-7' + ext.args = '-7' + ext.args2 = { params.module_args2 } + ext.args3 = { params.module_args3 } } } diff --git a/subworkflows/local/align/main.nf b/subworkflows/local/align/main.nf index f4ce3c71a..aedfbf0e3 100644 --- a/subworkflows/local/align/main.nf +++ b/subworkflows/local/align/main.nf @@ -38,11 +38,9 @@ workflow ALIGN { val_analysis_type // string: 'wgs', 'wes', or 'mito' val_exclude_alt // boolean val_extract_alignments // boolean - val_mbuffer_mem // integer: [mandatory] memory in megabytes val_mt_aligner // string: 'bwa', 'bwamem2', or 'sentieon' val_platform // string: [mandatory] illumina or a different technology val_run_mt_for_wes // boolean - val_samtools_sort_threads // integer: [mandatory] number of sorting threads val_save_all_mapped_as_cram // boolean val_save_noalt_mapped_as_cram // boolean @@ -103,9 +101,7 @@ workflow ALIGN { ch_input_reads, val_aligner, val_extract_alignments, - val_mbuffer_mem, - val_platform, - val_samtools_sort_threads + val_platform ) ch_bwamem2_bam = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bam ch_bwamem2_bai = ALIGN_BWA_BWAMEM2_BWAMEME.out.marked_bai diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index a87e52515..c7f41cd5b 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -117,13 +117,11 @@ nextflow_workflow { input[21] = "wgs" input[22] = true input[23] = false - input[24] = 3072 - input[25] = "bwamem2" - input[26] = "illumina" - input[27] = false - input[28] = 4 - input[29] = true - input[30] = true + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = true + input[28] = true """ } } @@ -225,13 +223,11 @@ nextflow_workflow { input[21] = "wes" input[22] = false input[23] = false - input[24] = 3072 - input[25] = "bwamem2" - input[26] = "illumina" - input[27] = false - input[28] = 4 - input[29] = true - input[30] = false + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = true + input[28] = false """ } } @@ -324,13 +320,11 @@ nextflow_workflow { input[21] = "wgs" input[22] = false input[23] = false - input[24] = 3072 - input[25] = "bwamem2" - input[26] = "illumina" - input[27] = false - input[28] = 4 - input[29] = true - input[30] = false + input[24] = "bwamem2" + input[25] = "illumina" + input[26] = false + input[27] = true + input[28] = false """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf index 6c13d9d2f..99af7cd75 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/main.nf @@ -26,9 +26,7 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { ch_input_reads // channel: [mandatory] [ val(meta), path(reads_input) ] val_aligner // string: 'bwa', 'bwafastalign', 'bwamem2', or 'bwameme' val_extract_alignments // boolean - val_mbuffer_mem // integer: [mandatory] default: 3072 val_platform // string: [mandatory] default: illumina - val_sort_threads // integer: [mandatory] default: 4 main: // Map, sort, and index @@ -39,8 +37,8 @@ workflow ALIGN_BWA_BWAMEM2_BWAMEME { BWAFASTALIGN_MEM ( ch_input_reads, ch_bwafastalign_index, ch_genome_fasta, true ) ch_align = BWAFASTALIGN_MEM.out.output } else if (val_aligner.equals("bwameme")) { - BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true, val_mbuffer_mem, val_sort_threads ) - ch_align = BWAMEME_MEM.out.bam + BWAMEME_MEM ( ch_input_reads, ch_bwameme_index, ch_genome_fasta, true ) + ch_align = BWAMEME_MEM.out.output } else { BWAMEM2_MEM ( ch_input_reads, ch_bwamem2_index, ch_genome_fasta, true ) ch_align = BWAMEM2_MEM.out.bam diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index fa44ebb11..803c63ff5 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -57,9 +57,7 @@ nextflow_workflow { ]) input[7] = "bwamem2" input[8] = true - input[9] = 3072 - input[10] = "illumina" - input[11] = 4 + input[9] = "illumina" """ } } @@ -118,9 +116,7 @@ nextflow_workflow { ]) input[7] = "bwafastalign" input[8] = true - input[9] = 3072 - input[10] = "illumina" - input[11] = 4 + input[9] = "illumina" """ } } @@ -179,9 +175,7 @@ nextflow_workflow { ]) input[7] = "bwameme" input[8] = true - input[9] = 3072 - input[10] = "illumina" - input[11] = 4 + input[9] = "illumina" """ } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index 561d4dbcd..109453536 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -37,7 +37,7 @@ ] ] ], - "timestamp": "2026-06-12T14:44:03.681795857", + "timestamp": "2026-06-12T15:46:43.756159921", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -81,9 +81,9 @@ ] ] ], - "timestamp": "2026-03-13T15:04:33.885203481", + "timestamp": "2026-06-12T15:43:33.682165862", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -106,7 +106,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "40408ed51d46ab3f1524be98d6b31441" + "11413e81e47d32ac386d29b693693a2e" ] ], [ @@ -125,9 +125,9 @@ ] ] ], - "timestamp": "2026-03-13T15:05:20.75721248", + "timestamp": "2026-06-12T15:47:31.561305633", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config index f43ce84c0..99347febb 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/nextflow.config @@ -16,8 +16,9 @@ process { } withName: 'BWAMEME_MEM' { - ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } - ext.args2 = { "-T ./samtools_sort_tmp" } + memory = 15.GB + ext.args = { "-7 -M -K 100000000 -R ${meta.read_group}" } + ext.args3 = { "-T ./samtools_sort_tmp" } ext.prefix = { "${meta.id}_sorted" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 1f9c75fa6..7835eb454 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -194,7 +194,6 @@ workflow RAREDISEASE { val_homoplasmy_af_threshold val_light_strand_origin_end val_light_strand_origin_start - val_mbuffer_mem val_mito_length val_mito_name val_mitosalt_breakspan @@ -220,7 +219,6 @@ workflow RAREDISEASE { val_run_rtgvcfeval val_run_vcfanno_db_sanity_check val_sample_id_map - val_samtools_sort_threads val_save_all_mapped_as_cram val_save_noalt_mapped_as_cram val_svdb_query_bedpedbs @@ -316,11 +314,9 @@ workflow RAREDISEASE { val_analysis_type, val_exclude_alt, val_extract_alignments, - val_mbuffer_mem, val_mt_aligner, val_platform, val_run_mt_for_wes, - val_samtools_sort_threads, val_save_all_mapped_as_cram, val_save_noalt_mapped_as_cram ) From 131711f572cc9879c477c12407b734500aeefed1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sat, 13 Jun 2026 11:54:10 +0200 Subject: [PATCH 814/872] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab75063fe..a876d9637 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` [#870](https://github.com/nf-core/raredisease/pull/870) +- Update `bwameme/mem` to new nf-core module signature: `val mbuffer` and `val samtools_threads` replaced by `ext.args2` and `ext.args3`; increase `mbuffer_mem` default from 3072 to 8192 MB to prevent buffer saturation stalling alignment [#881](https://github.com/nf-core/raredisease/pull/881) ### `Fixed` From 17a125e41dd3a6281631acca8c5136291bf93e83 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Sun, 14 Jun 2026 20:01:25 +0200 Subject: [PATCH 815/872] fix new line issue in filter_vep --- bin/filter_vep | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/filter_vep b/bin/filter_vep index ccb35c482..32b072399 100755 --- a/bin/filter_vep +++ b/bin/filter_vep @@ -490,7 +490,7 @@ def process_cyvcf2(args, output_fh): if args.test and line_number > args.test: break - vcf_line = str(variant) + vcf_line = str(variant).rstrip('\n') vcf_parts = vcf_line.split('\t') main_data = {column_names[idx]: (vcf_parts[idx] if idx < len(vcf_parts) else None) From 44c7433b8bebbe84cada14565a7c363f1300d083 Mon Sep 17 00:00:00 2001 From: apolitics Date: Mon, 15 Jun 2026 00:10:26 +0300 Subject: [PATCH 816/872] Fix swapped run_mt_for_wes / skip_split_multiallelics args in CALL_SNV call The CALL_SNV() invocation in workflows/raredisease.nf passed val_skip_split_multiallelics and val_run_mt_for_wes in the opposite order to the subworkflow's take: declaration (call_snv/main.nf), so the values were bound to the wrong inputs. With --run_mt_for_wes true this set skip_split_multiallelics to true internally: SPLIT_MULTIALLELICS_GL was dropped from the DAG (multiallelic records then reach genmod, where genmod compound can deadlock), and MT-for-WES was inverted. Reorder the two args to match the take: block. Fixes #854. --- CHANGELOG.md | 1 + workflows/raredisease.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e6081f6..528c2546b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` - Fix intermittent `CALL_SNV_DEEPVARIANT - wgs` test failure caused by non-deterministic GLnexus quality scores by replacing `variantsMD5` with `vcf.summary` [#850](https://github.com/nf-core/raredisease/pull/850) +- Fix swapped `run_mt_for_wes`/`skip_split_multiallelics` arguments in the `CALL_SNV` call, which disabled multiallelic splitting (and inverted MT-for-WES) when `--run_mt_for_wes` was set [#854](https://github.com/nf-core/raredisease/issues/854) ### Parameters diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 689858a3b..b88732291 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -457,8 +457,8 @@ workflow RAREDISEASE { ch_target_bed, val_analysis_type, val_concatenate_snv_calls, - val_skip_split_multiallelics, val_run_mt_for_wes, + val_skip_split_multiallelics, val_variant_caller ) ch_call_snv_publish = CALL_SNV.out.publish From d9ff6607f65902422965b7ca3c8f1e6174b0fd1c Mon Sep 17 00:00:00 2001 From: Emma Dizdarevic Date: Mon, 15 Jun 2026 13:42:25 +0200 Subject: [PATCH 817/872] Modifed test and snapshot for align, and tests for qc_bam --- subworkflows/local/align/tests/main.nf.test | 13 +- .../local/align/tests/main.nf.test.snap | 720 ++++++++++++++++-- subworkflows/local/qc_bam/tests/main.nf.test | 83 +- 3 files changed, 736 insertions(+), 80 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 9d0d083e6..001e6ca7e 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -437,19 +437,20 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + { assert snapshot( + workflow.out.genome_marked_cram + .collect { meta, cramfile -> [ meta, cram(cramfile, params.pipelines_testdata_base_path + 'reference/reference.fasta').getReadsMD5() ] }, + workflow.out.genome_marked_crai + .collect { meta, craifile -> [meta, file(craifile).name] }, workflow.out.genome_marked_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, workflow.out.mt_bam_bai .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] }, - workflow.out.mtshift_bam_bai + workflow.out.mtshift_bam_bai_gatksubwf .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } + ) } } diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 4d12afc3e..1975202c8 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -2,27 +2,166 @@ "align bwamem2 - wes, stub": { "content": [ [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - 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"phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md_primary_contigs.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md_primary_contigs.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md_primary_contigs.cram.crai" + ] ], [ [ @@ -367,7 +747,7 @@ ] ] ], - "timestamp": "2026-04-29T10:48:31.959971", + "timestamp": "2026-06-12T15:07:25.051508", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -606,10 +986,66 @@ ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "c96587f3323ea479aebf0a8ba3ee710b", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "9f79604c77dc54d30daff682a50399bf", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "8d810d8acecdeadc5a0e7ea159cb1343", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ] ], - "timestamp": "2026-04-29T11:06:56.369571", + "timestamp": "2026-06-12T15:26:16.997745", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -771,12 +1207,116 @@ "align bwameme - wes, stub": { "content": [ [ - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "earlycasualcaiman_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "hugelymodelbat_sorted_md.cram.crai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "slowlycivilbuck_sorted_md.cram.crai" + ] ], [ [ @@ -897,12 +1437,68 @@ ] ], [ - + [ + { + "groupSize": 1, + "groupTarget": { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "sex": 1, + "phenotype": 2, + "paternal": "earlycasualcaiman", + "maternal": "slowlycivilbuck", + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" + ], + [ + { + "groupSize": 1, + "groupTarget": { + "id": "slowlycivilbuck", + "sample": "slowlycivilbuck", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", + "sex": 2, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + } + }, + "d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" + ] ] ], - "timestamp": "2026-04-29T11:13:18.312548", + "timestamp": "2026-06-12T15:33:25.667453", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/qc_bam/tests/main.nf.test b/subworkflows/local/qc_bam/tests/main.nf.test index 4a7fa232b..3e50abfa6 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test +++ b/subworkflows/local/qc_bam/tests/main.nf.test @@ -143,13 +143,42 @@ nextflow_workflow { then { assertAll( - { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collecthsmetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.mosdepth_global_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_summary_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_bed + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_csi + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_d4 + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_wg + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_y + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_wig + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_cov + .collect { _meta, files -> file(files).name }, + workflow.out.ucsc_wigtobigwig_bw + .collect { _meta, files -> file(files).name }, + workflow.out.chromograph_cov_plots + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.sambamba_depth_bed + .collect { _meta, files -> file(files).name }, + workflow.out.verifybamid_self_sm + .collect { _meta, files -> file(files).name }, + workflow.out.ngsbits_samplegender_tsv + .collect { _meta, files -> file(files).name } + ).match() } ) } @@ -278,13 +307,43 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + workflow.out.picard_collectmultiplemetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collectmultiplemetrics_pdf + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.picard_collecthsmetrics_metrics + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.mosdepth_global_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_summary_txt + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_bed + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_csi + .collect { _meta, files -> file(files).name }, + workflow.out.mosdepth_per_base_d4 + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_wg + .collect { _meta, files -> file(files).name }, + workflow.out.wgsmetrics_y + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_wig + .collect { _meta, files -> file(files).name }, + workflow.out.tiddit_cov_cov + .collect { _meta, files -> file(files).name }, + workflow.out.ucsc_wigtobigwig_bw + .collect { _meta, files -> file(files).name }, + workflow.out.chromograph_cov_plots + .collect { _meta, files -> files instanceof List ? files.collect { file(it).name }.sort() : file(files).name }, + workflow.out.sambamba_depth_bed + .collect { _meta, files -> file(files).name }, + workflow.out.verifybamid_self_sm + .collect { _meta, files -> file(files).name }, + workflow.out.ngsbits_samplegender_tsv + .collect { _meta, files -> file(files).name } + ).match() } ) } -} + } } From ff23d53dca0f7e5e0e93e79642023128d52dccb1 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 15 Jun 2026 14:19:07 +0200 Subject: [PATCH 818/872] Updated snapshot for qc_bam incl sentieon --- .../local/qc_bam/tests/main.nf.test.snap | 524 +++++++++--------- 1 file changed, 257 insertions(+), 267 deletions(-) diff --git a/subworkflows/local/qc_bam/tests/main.nf.test.snap b/subworkflows/local/qc_bam/tests/main.nf.test.snap index 0fafcc193..c3bab311a 100644 --- a/subworkflows/local/qc_bam/tests/main.nf.test.snap +++ b/subworkflows/local/qc_bam/tests/main.nf.test.snap @@ -2,254 +2,200 @@ "QC_BAM - test, bwamem2, stub": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_mosdepth.per-base.d4", - "earlycasualcaiman_mosdepth.quantized.bed.gz", - "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "earlycasualcaiman_mosdepth.region.dist.txt", - "earlycasualcaiman_mosdepth.regions.bed.gz", - "earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "earlycasualcaiman_mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.thresholds.bed.gz", - "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bed", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov.wig_chr1.png", - "earlycasualcaiman_tidditcov.wig_chr10.png", - "earlycasualcaiman_tidditcov.wig_chr11.png", - "earlycasualcaiman_tidditcov.wig_chr12.png", - "earlycasualcaiman_tidditcov.wig_chr13.png", - "earlycasualcaiman_tidditcov.wig_chr14.png", - "earlycasualcaiman_tidditcov.wig_chr15.png", - "earlycasualcaiman_tidditcov.wig_chr16.png", - "earlycasualcaiman_tidditcov.wig_chr17.png", - "earlycasualcaiman_tidditcov.wig_chr18.png", - "earlycasualcaiman_tidditcov.wig_chr19.png", - "earlycasualcaiman_tidditcov.wig_chr2.png", - "earlycasualcaiman_tidditcov.wig_chr20.png", - "earlycasualcaiman_tidditcov.wig_chr21.png", - "earlycasualcaiman_tidditcov.wig_chr22.png", - "earlycasualcaiman_tidditcov.wig_chr3.png", - "earlycasualcaiman_tidditcov.wig_chr4.png", - "earlycasualcaiman_tidditcov.wig_chr5.png", - "earlycasualcaiman_tidditcov.wig_chr6.png", - "earlycasualcaiman_tidditcov.wig_chr7.png", - "earlycasualcaiman_tidditcov.wig_chr8.png", - "earlycasualcaiman_tidditcov.wig_chr9.png", - "earlycasualcaiman_tidditcov.wig_chrM.png", - "earlycasualcaiman_tidditcov.wig_chrX.png", - "earlycasualcaiman_tidditcov.wig_chrY.png", + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ], + [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" + ] + ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.wig" + ], + [ + "earlycasualcaiman_tidditcov.bed" + ], + [ + "earlycasualcaiman_tidditcov.bw" + ], + [ + [ + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png" + ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:03:53.405773659", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-27T15:31:05.442602988" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "QC_BAM - test, sentieon, stub": { "content": [ [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_mosdepth.per-base.d4", - "earlycasualcaiman_mosdepth.quantized.bed.gz", - "earlycasualcaiman_mosdepth.quantized.bed.gz.csi", - "earlycasualcaiman_mosdepth.region.dist.txt", - "earlycasualcaiman_mosdepth.regions.bed.gz", - "earlycasualcaiman_mosdepth.regions.bed.gz.csi", - "earlycasualcaiman_mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.thresholds.bed.gz", - "earlycasualcaiman_mosdepth.thresholds.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bed", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov.wig_chr1.png", - "earlycasualcaiman_tidditcov.wig_chr10.png", - "earlycasualcaiman_tidditcov.wig_chr11.png", - "earlycasualcaiman_tidditcov.wig_chr12.png", - "earlycasualcaiman_tidditcov.wig_chr13.png", - "earlycasualcaiman_tidditcov.wig_chr14.png", - "earlycasualcaiman_tidditcov.wig_chr15.png", - "earlycasualcaiman_tidditcov.wig_chr16.png", - "earlycasualcaiman_tidditcov.wig_chr17.png", - "earlycasualcaiman_tidditcov.wig_chr18.png", - "earlycasualcaiman_tidditcov.wig_chr19.png", - "earlycasualcaiman_tidditcov.wig_chr2.png", - "earlycasualcaiman_tidditcov.wig_chr20.png", - "earlycasualcaiman_tidditcov.wig_chr21.png", - "earlycasualcaiman_tidditcov.wig_chr22.png", - "earlycasualcaiman_tidditcov.wig_chr3.png", - "earlycasualcaiman_tidditcov.wig_chr4.png", - "earlycasualcaiman_tidditcov.wig_chr5.png", - "earlycasualcaiman_tidditcov.wig_chr6.png", - "earlycasualcaiman_tidditcov.wig_chr7.png", - "earlycasualcaiman_tidditcov.wig_chr8.png", - "earlycasualcaiman_tidditcov.wig_chr9.png", - "earlycasualcaiman_tidditcov.wig_chrM.png", - "earlycasualcaiman_tidditcov.wig_chrX.png", - "earlycasualcaiman_tidditcov.wig_chrY.png", - "earlycasualcaiman_wgsmetrics.txt" - ] - ], - "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-27T15:38:50.479811008" - }, - "QC_BAM - test, bwamem2": { - "content": [ + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + ] + ], [ - "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics", - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt", - "earlycasualcaiman_mosdepth.mosdepth.summary.txt", - "earlycasualcaiman_mosdepth.per-base.bed.gz", - "earlycasualcaiman_mosdepth.per-base.bed.gz.csi", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf", - "earlycasualcaiman_tidditcov.bw", - "earlycasualcaiman_tidditcov.wig", - "earlycasualcaiman_tidditcov_1.png", - "earlycasualcaiman_tidditcov_10.png", - "earlycasualcaiman_tidditcov_11.png", - "earlycasualcaiman_tidditcov_12.png", - "earlycasualcaiman_tidditcov_13.png", - "earlycasualcaiman_tidditcov_14.png", - "earlycasualcaiman_tidditcov_15.png", - "earlycasualcaiman_tidditcov_16.png", - "earlycasualcaiman_tidditcov_17.png", - "earlycasualcaiman_tidditcov_18.png", - "earlycasualcaiman_tidditcov_19.png", - "earlycasualcaiman_tidditcov_2.png", - "earlycasualcaiman_tidditcov_20.png", - "earlycasualcaiman_tidditcov_21.png", - "earlycasualcaiman_tidditcov_22.png", - "earlycasualcaiman_tidditcov_3.png", - "earlycasualcaiman_tidditcov_4.png", - "earlycasualcaiman_tidditcov_5.png", - "earlycasualcaiman_tidditcov_6.png", - "earlycasualcaiman_tidditcov_7.png", - "earlycasualcaiman_tidditcov_8.png", - "earlycasualcaiman_tidditcov_9.png", - "earlycasualcaiman_tidditcov_M.png", - "earlycasualcaiman_tidditcov_X.png", - "earlycasualcaiman_tidditcov_Y.png", - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + [ + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" + ] ], [ - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", - "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" ], [ - + "earlycasualcaiman_mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + "earlycasualcaiman_mosdepth.per-base.d4" + ], + [ + "earlycasualcaiman_wgsmetrics.txt" ], [ ], [ - "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" + "earlycasualcaiman_tidditcov.wig" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" - ] + "earlycasualcaiman_tidditcov.bed" ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" - ] + "earlycasualcaiman_tidditcov.bw" ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_tidditcov.wig_chr1.png", + "earlycasualcaiman_tidditcov.wig_chr10.png", + "earlycasualcaiman_tidditcov.wig_chr11.png", + "earlycasualcaiman_tidditcov.wig_chr12.png", + "earlycasualcaiman_tidditcov.wig_chr13.png", + "earlycasualcaiman_tidditcov.wig_chr14.png", + "earlycasualcaiman_tidditcov.wig_chr15.png", + "earlycasualcaiman_tidditcov.wig_chr16.png", + "earlycasualcaiman_tidditcov.wig_chr17.png", + "earlycasualcaiman_tidditcov.wig_chr18.png", + "earlycasualcaiman_tidditcov.wig_chr19.png", + "earlycasualcaiman_tidditcov.wig_chr2.png", + "earlycasualcaiman_tidditcov.wig_chr20.png", + "earlycasualcaiman_tidditcov.wig_chr21.png", + "earlycasualcaiman_tidditcov.wig_chr22.png", + "earlycasualcaiman_tidditcov.wig_chr3.png", + "earlycasualcaiman_tidditcov.wig_chr4.png", + "earlycasualcaiman_tidditcov.wig_chr5.png", + "earlycasualcaiman_tidditcov.wig_chr6.png", + "earlycasualcaiman_tidditcov.wig_chr7.png", + "earlycasualcaiman_tidditcov.wig_chr8.png", + "earlycasualcaiman_tidditcov.wig_chr9.png", + "earlycasualcaiman_tidditcov.wig_chrM.png", + "earlycasualcaiman_tidditcov.wig_chrX.png", + "earlycasualcaiman_tidditcov.wig_chrY.png" ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:05:39.811825004", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:45:40.990778813" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, - "QC_BAM - test, sentieon": { + "QC_BAM - test, bwamem2": { "content": [ [ [ @@ -288,7 +234,7 @@ ], [ - "earlycasualcaiman_wgsmetrics.txt" + "earlycasualcaiman_wgsmetrics.CollectWgsMetrics.coverage_metrics" ], [ @@ -338,67 +284,111 @@ ], [ - "earlycasualcaiman_wgsmetrics.txt" - ], + + ] + ], + "timestamp": "2026-06-15T14:02:21.833990928", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "QC_BAM - test, sentieon": { + "content": [ [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.wig:md5,84f66c6f6b8692ca691559fe1723f157" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.alignment_summary_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle_metrics", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution_metrics" ] ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_tidditcov.bw:md5,f5bc7ba5241f809f13451fd373405868" + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.base_distribution_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.insert_size_histogram.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_by_cycle.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.quality_distribution.pdf", + "earlycasualcaiman_multiplemetrics.CollectMultipleMetrics.read_length_histogram.pdf" ] ], + [ + "earlycasualcaiman_hsmetrics.CollectHsMetrics.coverage_metrics" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt" + ], + [ + "earlycasualcaiman_mosdepth.mosdepth.summary.txt" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz" + ], + [ + "earlycasualcaiman_mosdepth.per-base.bed.gz.csi" + ], + [ + + ], + [ + "earlycasualcaiman_wgsmetrics.txt" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.wig" + ], + [ + + ], + [ + "earlycasualcaiman_tidditcov.bw" + ], [ [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mosdepth.mosdepth.global.dist.txt:md5,213fcea07264cb7d35829c11e85428f4" + "earlycasualcaiman_tidditcov_1.png", + "earlycasualcaiman_tidditcov_10.png", + "earlycasualcaiman_tidditcov_11.png", + "earlycasualcaiman_tidditcov_12.png", + "earlycasualcaiman_tidditcov_13.png", + "earlycasualcaiman_tidditcov_14.png", + "earlycasualcaiman_tidditcov_15.png", + "earlycasualcaiman_tidditcov_16.png", + "earlycasualcaiman_tidditcov_17.png", + "earlycasualcaiman_tidditcov_18.png", + "earlycasualcaiman_tidditcov_19.png", + "earlycasualcaiman_tidditcov_2.png", + "earlycasualcaiman_tidditcov_20.png", + "earlycasualcaiman_tidditcov_21.png", + "earlycasualcaiman_tidditcov_22.png", + "earlycasualcaiman_tidditcov_3.png", + "earlycasualcaiman_tidditcov_4.png", + "earlycasualcaiman_tidditcov_5.png", + "earlycasualcaiman_tidditcov_6.png", + "earlycasualcaiman_tidditcov_7.png", + "earlycasualcaiman_tidditcov_8.png", + "earlycasualcaiman_tidditcov_9.png", + "earlycasualcaiman_tidditcov_M.png", + "earlycasualcaiman_tidditcov_X.png", + "earlycasualcaiman_tidditcov_Y.png" ] + ], + [ + + ], + [ + + ], + [ + ] ], + "timestamp": "2026-06-15T14:17:24.028920433", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T17:07:36.836738984" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 57bb6fd9cd680d987be51faa4683756396a16ce6 Mon Sep 17 00:00:00 2001 From: Emma Emma Dizdarevic Date: Mon, 15 Jun 2026 14:45:01 +0200 Subject: [PATCH 819/872] Modified test and snapshot for align_sentieon --- .../local/align_sentieon/tests/main.nf.test | 36 +++++----- .../align_sentieon/tests/main.nf.test.snap | 68 +++++++++++++++---- 2 files changed, 71 insertions(+), 33 deletions(-) diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index e776ce73c..13e208411 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -121,23 +121,23 @@ nextflow_workflow { } then { - assert workflow.success - assert snapshot( - workflow.out.marked_bam, - workflow.out.marked_bai, - workflow.out.aln_metrics, - workflow.out.gc_metrics, - workflow.out.gc_summary, - workflow.out.is_metrics, - workflow.out.mq_metrics, - workflow.out.qd_metrics, - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() - ).match() + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.marked_bai.collect { meta, baifile -> [ meta, file(baifile).name ] }, + workflow.out.aln_metrics, + workflow.out.gc_metrics, + workflow.out.gc_summary, + workflow.out.is_metrics, + workflow.out.mq_metrics, + workflow.out.qd_metrics, + workflow.out.dedup_metrics, + workflow.out.dedup_metrics_multiqc, + workflow.out.score, + ).match() + } + ) } - } - -} +} \ No newline at end of file diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test.snap b/subworkflows/local/align_sentieon/tests/main.nf.test.snap index e2dc6927e..261a909f4 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test.snap +++ b/subworkflows/local/align_sentieon/tests/main.nf.test.snap @@ -13,7 +13,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -28,7 +28,7 @@ "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" } }, - "test_dedup.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_dedup.bam.bai" ] ], [ @@ -122,18 +122,56 @@ ] ], [ - "test_dedup.bam", - "test_dedup.bam.bai", - "test_dedup.bam.metrics", - "test_dedup.bam.metrics.multiqc.tsv", - "test_dedup.score" + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.bam.metrics.multiqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + } + }, + "test_dedup.score:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], + "timestamp": "2026-06-15T14:36:45.068348415", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-28T13:54:38.517974195" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } }, "align sentieon": { "content": [ @@ -303,10 +341,10 @@ ] ] ], + "timestamp": "2026-06-15T14:42:21.699949612", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - }, - "timestamp": "2026-03-14T00:02:24.597092362" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file From 4c85951e3f320bcfd9c36961c00c5a3898a7f263 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 15 Jun 2026 13:14:36 +0000 Subject: [PATCH 820/872] Fix pre-commit whitespace and EOF issues in subworkflow tests --- subworkflows/local/align/tests/main.nf.test | 2 +- subworkflows/local/align_sentieon/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 001e6ca7e..522de9632 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -450,7 +450,7 @@ nextflow_workflow { .collect { meta, bamfile, index -> [ meta, bam(bamfile).getReadsMD5(), file(index).name ] } ).match() } - + ) } } diff --git a/subworkflows/local/align_sentieon/tests/main.nf.test b/subworkflows/local/align_sentieon/tests/main.nf.test index 13e208411..e0500aa00 100644 --- a/subworkflows/local/align_sentieon/tests/main.nf.test +++ b/subworkflows/local/align_sentieon/tests/main.nf.test @@ -140,4 +140,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From c8b4bbd28384c45bc387441d055eb5442ed220ec Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Jun 2026 09:49:35 +0200 Subject: [PATCH 821/872] bump-version --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 20 ++++++++++---------- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 0b2f130e4..c172a7673 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 3.0.0 + version: 3.1.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 87dad6ba3..a92807776 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 3.0.1 - Mario-patch [2026-05-25] +## 3.1.0 - Princess Peach [2026-06-16] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 0b6823681..455f20374 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,7 +2,7 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-raredisease-methods-description": diff --git a/nextflow.config b/nextflow.config index e03f5347e..2d81bb274 100644 --- a/nextflow.config +++ b/nextflow.config @@ -485,7 +485,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '3.0.0' + version = '3.1.0' doi = '10.5281/zenodo.7995798' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 11886e712..da7541994 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2026-04-29T08:07:02+00:00", + "datePublished": "2026-06-16T07:45:55+00:00", "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**6. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker)\n\n**7. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**8. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**9. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**10. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**11. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**12. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**13. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541" + "@id": "#b6b7b66d-5ce4-44de-ae44-7684e4d7e2cc" } ], "name": "nf-core/raredisease" @@ -142,7 +142,7 @@ ], "contributor": [ { - "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3" + "@id": "#dda7739c-42eb-464e-bf07-bbffb815b438" }, { "@id": "https://orcid.org/0000-0002-5044-7754" @@ -173,7 +173,7 @@ } ], "dateCreated": "", - "dateModified": "2026-04-29T10:07:02Z", + "dateModified": "2026-06-16T09:45:55Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -209,10 +209,10 @@ }, "url": [ "https://github.com/nf-core/raredisease", - "https://nf-co.re/raredisease/3.0.0/" + "https://nf-co.re/raredisease/3.1.0/" ], "version": [ - "3.0.0" + "3.1.0" ] }, { @@ -228,11 +228,11 @@ "version": "!>=25.10.4" }, { - "@id": "#7eeb5ab8-231b-47da-b868-7f677b8e7541", + "@id": "#b6b7b66d-5ce4-44de-ae44-7684e4d7e2cc", "@type": "TestSuite", "instance": [ { - "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24" + "@id": "#bdffa306-a84f-4a05-95de-7f4a48125adc" } ], "mainEntity": { @@ -241,7 +241,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#6887a5a3-9c4c-4527-9311-756a87363b24", + "@id": "#bdffa306-a84f-4a05-95de-7f4a48125adc", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -396,7 +396,7 @@ "url": "https://github.com/jemten" }, { - "@id": "#d07fdb6d-482e-4227-a60d-06ad935870e3", + "@id": "#dda7739c-42eb-464e-bf07-bbffb815b438", "@type": "Person", "email": "25568561+projectoriented@users.noreply.github.com", "name": "Mei Wu", From 199b192a48cfe5f3ad9fed117a86d434779e6eba Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 16 Jun 2026 10:33:04 +0200 Subject: [PATCH 822/872] review suggestions --- CHANGELOG.md | 2 +- tests/default.nf.test.snap | 8 ++++---- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 8 ++++---- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a92807776..ad6d26bd3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Tool | Old version | New version | | ------------- | ----------- | ----------- | | bwa-fastalign | | 1.0.0 | +| saltshaker | 1.0.0 | 1.1.1 | ## 3.0.0 - Mario [2026-05-12] @@ -156,7 +157,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | picard | 3.3.0 | 3.4.0 | | pigz | 2.3.4 | 2.8 | | qualimap | 2.3 | | -| saltshaker | 1.0.0 | 1.1.1 | | sambamba | | 1.0.1 | | samtools | 1.21 | 1.22.1 | | sentieon | 202503 | 202503.02 | diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1cf8b8e62..e429834ee 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -485,7 +485,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -930,10 +930,10 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-11T10:20:14.951812109", + "timestamp": "2026-06-16T10:21:33.741825577", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index 5952f98d0..c2970c8f3 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -443,7 +443,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -846,7 +846,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-05T00:25:53.862854239", + "timestamp": "2026-06-16T10:27:30.352705529", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 1e7680598..a5793e9e3 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -465,7 +465,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.0.0" + "nf-core/raredisease": "v3.1.0" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -654,10 +654,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-05T00:29:37.176160755", + "timestamp": "2026-06-16T10:31:08.451259711", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nextflow": "25.10.4" } } -} +} \ No newline at end of file From 8b2321b93bcaf5dca96726d9cb9d0c8e55d3ca49 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 10:13:36 +0200 Subject: [PATCH 823/872] add more tests --- .../local/call_sv_MT/tests/main.nf.test | 141 +++++- .../local/call_sv_MT/tests/main.nf.test.snap | 464 +++++++++++++++++- 2 files changed, 598 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index c8004efe7..2a502d760 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -38,6 +38,64 @@ nextflow_workflow { } } + test("CALL_SV_MT - 1 sample") { + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = HISAT2_BUILD.out.index.collect() + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = LAST_LASTDB.out.index.collect() + input[9] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[10] = channel.value(10000000) + input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[13] = false + input[14] = 16081 + input[15] = 407 + input[16] = 5730 + input[17] = 5763 + input[18] = 16569 + input[19] = 'chrM' + input[20] = 15 + input[21] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.saltshaker_vcf.get(0).get(1)).vcf.variantsMD5, + workflow.out.saltshaker_html, + file(workflow.out.saltshaker_plot.get(0).get(1)).name, // pngs are unstable so we just check that the name matches + workflow.out.mt_del_result, + workflow.out.updated_priority + ).match() } + ) + } + } + test("CALL_SV_MT - 2 samples") { when { @@ -112,7 +170,7 @@ nextflow_workflow { } } - test("CALL_SV_MT - stub") { + test("CALL_SV_MT - 1 sample - stub") { options "-stub" @@ -158,6 +216,87 @@ nextflow_workflow { } } + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.collect { name, channel -> + def sorted_channel = channel.toList().sort { item -> + def sortKey = item + while (sortKey instanceof List) { + sortKey = sortKey[-1] + } + sortKey.toString().split(':md5,')[0].tokenize('/')[-1] + } + [name, sorted_channel] + }.sort { it[0] } // Sort by channel name + ).match() } + ) + } + } + + test("CALL_SV_MT - 2 samples - stub") { + + options "-stub" + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true) + ] + ) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = HISAT2_BUILD.out.index.collect() + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = LAST_LASTDB.out.index.collect() + input[9] = channel.of( + [ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ], + [ + [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true) + ] + ] + ) + input[10] = channel.value(10000000) + input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[13] = false + input[14] = 16081 + input[15] = 407 + input[16] = 5730 + input[17] = 5763 + input[18] = 16569 + input[19] = 'chrM' + input[20] = 15 + input[21] = 0.01 + """ + } + } + then { assertAll( { assert workflow.success }, diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index d47c00d0a..27f7b651f 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,7 +1,7 @@ { "CALL_SV_MT - 2 samples": { "content": [ - "3d2eca57b18e5d0180b333d7370a2bfb", + "106998c7742c3eb0abb532d32526015f", [ [ { @@ -54,13 +54,420 @@ ] ] ], - "timestamp": "2026-06-10T14:05:43.387597", + "timestamp": "2026-06-18T10:03:41.39258", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" } }, - "CALL_SV_MT - stub": { + "CALL_SV_MT - 2 samples - stub": { + "content": [ + [ + [ + "0", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "1", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ] + ], + [ + "2", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "3", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "4", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + [ + "5", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "mt_del_result", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "publish", + [ + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + [ + "call_sv/", + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ] + ], + [ + "saltshaker_html", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ] + ], + [ + "saltshaker_plot", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "saltshaker_vcf", + [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + [ + "updated_priority", + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ] + ] + ], + "timestamp": "2026-06-18T10:10:30.017086", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "CALL_SV_MT - 1 sample - stub": { "content": [ [ [ @@ -329,10 +736,55 @@ ] ] ], - "timestamp": "2026-04-14T15:53:31.425509861", + "timestamp": "2026-06-18T10:09:39.238569", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "CALL_SV_MT - 1 sample": { + "content": [ + "e591669a4985c6b4947b042d9461e8b5", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,c3a6eea9dbaf8bcd7a3e90acffb1c24f" + ] + ], + "earlycasualcaiman.saltshaker.png", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ] + ], + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + "timestamp": "2026-06-18T09:55:02.460892", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file From eafddc2850e2ca432caaf8e271ced2545c3ad785 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 12:06:56 +0200 Subject: [PATCH 824/872] remove ch_publish in sv subworkflows --- main.nf | 13 +++++++ .../local/call_structural_variants/main.nf | 34 +++++++++---------- subworkflows/local/call_sv_MT/main.nf | 6 ---- workflows/raredisease.nf | 20 ++++++++--- 4 files changed, 46 insertions(+), 27 deletions(-) diff --git a/main.nf b/main.nf index 1ad072e60..34970b08b 100644 --- a/main.nf +++ b/main.nf @@ -566,6 +566,11 @@ workflow NFCORE_RAREDISEASE { qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ] + call_sv_vcf = RAREDISEASE.out.call_sv_vcf // channel: [ val(meta), path(vcf) ] + call_sv_tbi = RAREDISEASE.out.call_sv_tbi // channel: [ val(meta), path(tbi) ] + saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] + saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] @@ -767,6 +772,11 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + call_sv = NFCORE_RAREDISEASE.out.call_sv_vcf + .mix(NFCORE_RAREDISEASE.out.call_sv_tbi) + .mix(NFCORE_RAREDISEASE.out.saltshaker_html) + .mix(NFCORE_RAREDISEASE.out.saltshaker_plot) + .mix(NFCORE_RAREDISEASE.out.mt_del_result) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots) @@ -792,6 +802,9 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + call_sv { + path { _meta, _file -> "call_sv/" } + } annotate_snv_genome { path { _meta, _file -> "annotate_snv/genome/" } } diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index b5407b11e..962072abc 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -49,14 +49,16 @@ workflow CALL_STRUCTURAL_VARIANTS { val_run_mt_for_wes // boolean: [mandatory] run_mt_for_wes main: - ch_cnvnator_vcf = channel.empty() - ch_gcnvcaller_vcf = channel.empty() - ch_manta_vcf = channel.empty() - ch_merged_svs = channel.empty() - ch_merged_tbi = channel.empty() - ch_publish_mt = channel.empty() - ch_saltshaker_vcf = channel.empty() - ch_tiddit_vcf = channel.empty() + ch_cnvnator_vcf = channel.empty() + ch_gcnvcaller_vcf = channel.empty() + ch_manta_vcf = channel.empty() + ch_merged_svs = channel.empty() + ch_merged_tbi = channel.empty() + ch_mt_del_result = channel.empty() + ch_saltshaker_html = channel.empty() + ch_saltshaker_plot = channel.empty() + ch_saltshaker_vcf = channel.empty() + ch_tiddit_vcf = channel.empty() if (!val_analysis_type.equals("mito")) { CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed, val_analysis_type) @@ -115,7 +117,8 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_sv_mt_out.saltshaker_vcf .collect{ _meta, vcf -> vcf } .set { ch_saltshaker_vcf } - ch_publish_mt = ch_sv_mt_out.publish + ch_saltshaker_html = ch_sv_mt_out.saltshaker_html + ch_saltshaker_plot = ch_sv_mt_out.saltshaker_plot ch_svcaller_priority = ch_sv_mt_out.updated_priority } @@ -148,13 +151,10 @@ workflow CALL_STRUCTURAL_VARIANTS { ch_merged_tbi = TABIX_TABIX.out.index } - ch_publish = ch_merged_svs - .mix(ch_merged_tbi) - .mix(ch_publish_mt) - .map { meta, value -> ['call_sv/', [meta, value]] } - emit: - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] - tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - publish = ch_publish // channel: [ val(destination), val(value) ] + mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] + saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] + saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] } diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index f636788ff..73520c5ca 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -169,11 +169,6 @@ workflow CALL_SV_MT { } MT_DELETION(ch_bam_bai, ch_genome_fasta) - ch_publish = ch_saltshaker_html - .mix(ch_saltshaker_vcf) - .mix(ch_saltshaker_plot) - .mix(MT_DELETION.out.mt_del_result) - .map { meta, value -> ['call_sv/', [meta, value]] } emit: saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] @@ -181,5 +176,4 @@ workflow CALL_SV_MT { saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = MT_DELETION.out.mt_del_result // channel: [ val(meta), path(txt) ] updated_priority = ch_svcaller_priority // channel: [ val(["caller1", "caller2", ...]) ] - includes "mitosalt" if it ran - publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 689858a3b..ccaf460ce 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -242,7 +242,11 @@ workflow RAREDISEASE { ch_subsample_mt_bam = channel.empty() ch_subsample_mt_bai = channel.empty() ch_call_snv_publish = channel.empty() - ch_call_sv_publish = channel.empty() + ch_call_sv_vcf = channel.empty() + ch_call_sv_tbi = channel.empty() + ch_mt_del_result = channel.empty() + ch_saltshaker_html = channel.empty() + ch_saltshaker_plot = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() @@ -685,7 +689,11 @@ workflow RAREDISEASE { val_mitosalt_heteroplasmy_limit, val_run_mt_for_wes ) - ch_call_sv_publish = CALL_STRUCTURAL_VARIANTS.out.publish + ch_call_sv_vcf = CALL_STRUCTURAL_VARIANTS.out.vcf + ch_call_sv_tbi = CALL_STRUCTURAL_VARIANTS.out.tbi + ch_saltshaker_html = CALL_STRUCTURAL_VARIANTS.out.saltshaker_html + ch_saltshaker_plot = CALL_STRUCTURAL_VARIANTS.out.saltshaker_plot + ch_mt_del_result = CALL_STRUCTURAL_VARIANTS.out.mt_del_result // // ANNOTATE STRUCTURAL VARIANTS @@ -696,7 +704,7 @@ workflow RAREDISEASE { ch_genome_fasta, ch_svdb_bedpedbs, ch_svdb_dbs, - CALL_STRUCTURAL_VARIANTS.out.vcf, + ch_call_sv_vcf, ch_vep_cache, ch_vep_extra_files, val_svdb_query_bedpedbs, @@ -1066,6 +1074,11 @@ workflow RAREDISEASE { qc_bam_verifybamid_ud = QC_BAM.out.verifybamid_ud // channel: [ val(meta), path(ud) ] qc_bam_wgsmetrics_wg = QC_BAM.out.wgsmetrics_wg // channel: [ val(meta), path(metrics) ] qc_bam_wgsmetrics_y = QC_BAM.out.wgsmetrics_y // channel: [ val(meta), path(metrics) ] + call_sv_vcf = ch_call_sv_vcf // channel: [ val(meta), path(vcf) ] + call_sv_tbi = ch_call_sv_tbi // channel: [ val(meta), path(tbi) ] + saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] + saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] @@ -1078,7 +1091,6 @@ workflow RAREDISEASE { subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions publish = ch_call_snv_publish - .mix(ch_call_sv_publish) .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_mt_snvs_publish) From b3b0c70ff169ebbac5f4b0a305dac85c0a60c96c Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 12:18:14 +0200 Subject: [PATCH 825/872] update tests --- .../local/call_structural_variants/main.nf | 1 + .../tests/main.nf.test | 9 +- .../tests/main.nf.test.snap | 21 +- .../local/call_sv_MT/tests/main.nf.test | 16 +- .../local/call_sv_MT/tests/main.nf.test.snap | 280 +----------------- 5 files changed, 34 insertions(+), 293 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 962072abc..812eea8e0 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -119,6 +119,7 @@ workflow CALL_STRUCTURAL_VARIANTS { .set { ch_saltshaker_vcf } ch_saltshaker_html = ch_sv_mt_out.saltshaker_html ch_saltshaker_plot = ch_sv_mt_out.saltshaker_plot + ch_mt_del_result = ch_sv_mt_out.mt_del_result ch_svcaller_priority = ch_sv_mt_out.updated_priority } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index f2d69db9d..ab71cbd3d 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -41,7 +41,7 @@ nextflow_workflow { input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[10] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[10] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) input[12] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], @@ -83,10 +83,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.saltshaker_html.collect { meta, html -> file(html).name }, + workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, + workflow.out.mt_del_result.collect { meta, txt -> file(txt).name }, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index e6385f20d..18f937329 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -2,12 +2,13 @@ "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ [ - "earlycasualcaiman.saltshaker.png", - "earlycasualcaiman_mitochondria_deletions.txt", - "justhusky.saltshaker_classify.html", - "justhusky_saltshaker.vcf.gz", - "justhusky_sv.vcf.gz", - "justhusky_sv.vcf.gz.tbi" + "justhusky.saltshaker_classify.html" + ], + [ + "earlycasualcaiman.saltshaker.png" + ], + [ + "earlycasualcaiman_mitochondria_deletions.txt" ], [ "justhusky_sv.vcf.gz" @@ -16,10 +17,10 @@ "justhusky_sv.vcf.gz.tbi" ] ], + "timestamp": "2026-06-18T12:17:56.876719", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" - }, - "timestamp": "2026-04-29T12:10:29.211103134" + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } } } \ No newline at end of file diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index e49287de5..fa9681f0a 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_workflow { input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = Channel.from("\$PWD").map { dir -> [[id:'genome'], file(dir)] } + input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } @@ -64,16 +64,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + workflow.out.saltshaker_html.collect { meta, html -> file(html).name }, + workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, + workflow.out.mt_del_result.collect { meta, txt -> file(txt).name }, + workflow.out.saltshaker_vcf.collect { meta, vcf -> file(vcf).name } ).match() } ) } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index f86f56e63..736e11bab 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -2,276 +2,22 @@ "CALL_SV_MT - stub": { "content": [ [ - [ - "0", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "1", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ] - ], - [ - "2", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "3", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "4", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ], - [ - "5", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ] - ], - [ - "mt_del_result", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "publish", - [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ] - ], - [ - "saltshaker_html", - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ] - ], - [ - "saltshaker_plot", - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "saltshaker_vcf", - [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - [ - "updated_priority", - [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ] + "justhusky.saltshaker_classify.html" + ], + [ + "earlycasualcaiman.saltshaker.png" + ], + [ + "earlycasualcaiman_mitochondria_deletions.txt" + ], + [ + "justhusky_saltshaker.vcf.gz" ] ], - "timestamp": "2026-04-14T15:53:31.425509861", + "timestamp": "2026-06-18T12:13:26.375753", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file From 26dc8dcb6fd212c3508d347e13b1a1d33aa3b928 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 12:42:28 +0200 Subject: [PATCH 826/872] add saltshaker vcf to output --- main.nf | 2 ++ subworkflows/local/call_structural_variants/main.nf | 11 ++++++----- .../local/call_structural_variants/tests/main.nf.test | 1 + workflows/raredisease.nf | 3 +++ 4 files changed, 12 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index 34970b08b..7aa848803 100644 --- a/main.nf +++ b/main.nf @@ -570,6 +570,7 @@ workflow NFCORE_RAREDISEASE { call_sv_tbi = RAREDISEASE.out.call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] + saltshaker_vcf = RAREDISEASE.out.saltshaker_vcf // channel: [ val(meta), path(vcf) ] mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] @@ -776,6 +777,7 @@ workflow { .mix(NFCORE_RAREDISEASE.out.call_sv_tbi) .mix(NFCORE_RAREDISEASE.out.saltshaker_html) .mix(NFCORE_RAREDISEASE.out.saltshaker_plot) + .mix(NFCORE_RAREDISEASE.out.saltshaker_vcf) .mix(NFCORE_RAREDISEASE.out.mt_del_result) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 812eea8e0..dd5add6cd 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -153,9 +153,10 @@ workflow CALL_STRUCTURAL_VARIANTS { } emit: - mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] - saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] - saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] - vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] + mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] + saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] + saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] + vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index ab71cbd3d..954ec6888 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -86,6 +86,7 @@ nextflow_workflow { workflow.out.saltshaker_html.collect { meta, html -> file(html).name }, workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, workflow.out.mt_del_result.collect { meta, txt -> file(txt).name }, + workflow.out.saltshaker_vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ccaf460ce..364dabeec 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -247,6 +247,7 @@ workflow RAREDISEASE { ch_mt_del_result = channel.empty() ch_saltshaker_html = channel.empty() ch_saltshaker_plot = channel.empty() + ch_saltshaker_vcf = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() @@ -693,6 +694,7 @@ workflow RAREDISEASE { ch_call_sv_tbi = CALL_STRUCTURAL_VARIANTS.out.tbi ch_saltshaker_html = CALL_STRUCTURAL_VARIANTS.out.saltshaker_html ch_saltshaker_plot = CALL_STRUCTURAL_VARIANTS.out.saltshaker_plot + ch_saltshaker_vcf = CALL_STRUCTURAL_VARIANTS.out.saltshaker_vcf ch_mt_del_result = CALL_STRUCTURAL_VARIANTS.out.mt_del_result // @@ -1078,6 +1080,7 @@ workflow RAREDISEASE { call_sv_tbi = ch_call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] From 05deabdc5c13d11a3c9ff69bf52d51e62e704f4a Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 13:18:17 +0200 Subject: [PATCH 827/872] better snapshot capturing --- .../local/call_structural_variants/main.nf | 2 +- .../tests/main.nf.test | 6 ++-- .../tests/main.nf.test.snap | 31 +++++++++++++++++-- .../local/call_sv_MT/tests/main.nf.test | 4 +-- .../local/call_sv_MT/tests/main.nf.test.snap | 26 ++++++++++++++-- 5 files changed, 57 insertions(+), 12 deletions(-) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index dd5add6cd..9c1a267e8 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -156,7 +156,7 @@ workflow CALL_STRUCTURAL_VARIANTS { mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] + saltshaker_vcf = ch_saltshaker_vcf // channel: [ path(vcf) ] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 954ec6888..4cf0aba20 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -83,10 +83,10 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.saltshaker_html.collect { meta, html -> file(html).name }, + workflow.out.saltshaker_html, workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, - workflow.out.mt_del_result.collect { meta, txt -> file(txt).name }, - workflow.out.saltshaker_vcf.collect { meta, vcf -> file(vcf).name }, + workflow.out.mt_del_result, + workflow.out.saltshaker_vcf, workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, workflow.out.tbi.collect { meta, tbi -> file(tbi).name } ).match() } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 18f937329..db876d523 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -2,13 +2,38 @@ "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ [ - "justhusky.saltshaker_classify.html" + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] ], [ "earlycasualcaiman.saltshaker.png" ], [ - "earlycasualcaiman_mitochondria_deletions.txt" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], [ "justhusky_sv.vcf.gz" @@ -17,7 +42,7 @@ "justhusky_sv.vcf.gz.tbi" ] ], - "timestamp": "2026-06-18T12:17:56.876719", + "timestamp": "2026-06-18T13:14:02.120295", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index fa9681f0a..bc69a5440 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -64,9 +64,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.saltshaker_html.collect { meta, html -> file(html).name }, + workflow.out.saltshaker_html, workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, - workflow.out.mt_del_result.collect { meta, txt -> file(txt).name }, + workflow.out.mt_del_result, workflow.out.saltshaker_vcf.collect { meta, vcf -> file(vcf).name } ).match() } ) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 736e11bab..13daf7b61 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -2,19 +2,39 @@ "CALL_SV_MT - stub": { "content": [ [ - "justhusky.saltshaker_classify.html" + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] ], [ "earlycasualcaiman.saltshaker.png" ], [ - "earlycasualcaiman_mitochondria_deletions.txt" + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], [ "justhusky_saltshaker.vcf.gz" ] ], - "timestamp": "2026-06-18T12:13:26.375753", + "timestamp": "2026-06-18T13:16:35.904031", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From d99dbdf83f5aaec984f171dabdc83008a25ba9a9 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 13:39:18 +0200 Subject: [PATCH 828/872] update snaps --- tests/default.nf.test.snap | 16 ++-------------- tests/test_singleton.nf.test.snap | 8 ++------ 2 files changed, 4 insertions(+), 20 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ecf1bbf8a..3b621c074 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -680,15 +680,9 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/earlycasualcaiman.saltshaker.png", - "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", - "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", - "call_sv/justhusky_saltshaker.vcf.gz", - "call_sv/justhusky_sv.vcf.gz", - "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck.saltshaker.png", - "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -1102,15 +1096,9 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.html:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.zip:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_LNUMBER3.html:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1337,10 +1325,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-05-27T15:36:04.165275268", + "timestamp": "2026-06-18T13:35:09.306177124", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 13ab39400..21f22f467 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -545,11 +545,7 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/hugelymodelbat.saltshaker.png", - "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", - "call_sv/justhusky_saltshaker.vcf.gz", - "call_sv/justhusky_sv.vcf.gz", - "call_sv/justhusky_sv.vcf.gz.tbi", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -664,10 +660,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-05-27T15:26:36.71307935", + "timestamp": "2026-06-18T13:38:45.854734171", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file From a164ef5e238213722ab3a1f90d9a137e3b11f2b4 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 18 Jun 2026 14:57:20 +0200 Subject: [PATCH 829/872] capture all workflow.out for subworkflow stub tests --- .../tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 168 +++++++++++++----- .../local/call_sv_MT/tests/main.nf.test | 5 +- .../local/call_sv_MT/tests/main.nf.test.snap | 150 ++++++++++++---- 4 files changed, 248 insertions(+), 82 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 4cf0aba20..433e4be59 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -83,12 +83,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.saltshaker_html, - workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, - workflow.out.mt_del_result, - workflow.out.saltshaker_vcf, - workflow.out.vcf.collect { meta, vcf -> file(vcf).name }, - workflow.out.tbi.collect { meta, tbi -> file(tbi).name } + workflow.out ).match() } ) } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index db876d523..b35a54888 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -1,48 +1,136 @@ { "CALL_STRUCTURAL_VARIANTS - wgs, stub": { "content": [ - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "mt_del_result": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_html": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + "saltshaker_plot": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_vcf": [ + [ + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "tbi": [ + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ] - ], - [ - "earlycasualcaiman.saltshaker.png" - ], - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - [ - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "justhusky_sv.vcf.gz" - ], - [ - "justhusky_sv.vcf.gz.tbi" - ] + } ], - "timestamp": "2026-06-18T13:14:02.120295", + "timestamp": "2026-06-18T14:54:00.528652", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index bc69a5440..5c385b2da 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -64,10 +64,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.saltshaker_html, - workflow.out.saltshaker_plot.collect { meta, plot -> file(plot).name }, - workflow.out.mt_del_result, - workflow.out.saltshaker_vcf.collect { meta, vcf -> file(vcf).name } + workflow.out ).match() } ) } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 13daf7b61..5f409ec54 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,40 +1,126 @@ { "CALL_SV_MT - stub": { "content": [ - [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ], + "mt_del_result": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_html": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + ] + ], + "saltshaker_plot": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "updated_priority": [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] ] - ], - [ - "earlycasualcaiman.saltshaker.png" - ], - [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "justhusky_saltshaker.vcf.gz" - ] + } ], - "timestamp": "2026-06-18T13:16:35.904031", + "timestamp": "2026-06-18T14:55:54.079801", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 3b3100e929b57ea29244e030db338cc3e4bf593d Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 22 Jun 2026 12:42:40 +0200 Subject: [PATCH 830/872] fix saltshaker vcf channel handling --- .../tests/main.nf.test.snap | 10 +++------ subworkflows/local/call_sv_MT/main.nf | 5 +++-- .../local/call_sv_MT/tests/main.nf.test.snap | 22 +++++-------------- tests/default.nf.test.snap | 12 +++++++++- tests/test_singleton.nf.test.snap | 7 ++++-- 5 files changed, 27 insertions(+), 29 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index b35a54888..1b6d51cb1 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -45,9 +45,7 @@ ] ], "3": [ - [ - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "4": [ [ @@ -108,9 +106,7 @@ ] ], "saltshaker_vcf": [ - [ - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "tbi": [ [ @@ -130,7 +126,7 @@ ] } ], - "timestamp": "2026-06-18T14:54:00.528652", + "timestamp": "2026-06-22T12:30:29.306790749", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 73520c5ca..b0b545c85 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -121,7 +121,6 @@ workflow CALL_SV_MT { SALTSHAKER_CALL.out.call, val_mitochondria_name ) - ch_saltshaker_vcf = SALTSHAKER_CLASSIFY.out.vcf SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> @@ -149,7 +148,9 @@ workflow CALL_SV_MT { // combine never sees an empty-spread issue (combining case_info with [[]] would produce // a 1-element channel item that breaks 2-param destructuring closures downstream). SALTSHAKER_CLASSIFY.out.vcf - .collect { _meta, vcf -> vcf } + .map { _meta, vcf -> vcf } + .filter { !it.isEmpty() } // .collect{} produces an ArrayBag which .filter can't be used on, so first convert to regular elements with filter, then collect those to filter the whole list + .collect() .filter { !it.isEmpty() } .map { vcf_list -> [vcf_list] } .set { ch_vcf_file_list } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 5f409ec54..59d282159 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -3,12 +3,7 @@ "content": [ { "0": [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "1": [ [ @@ -56,8 +51,7 @@ [ "manta", "tiddit", - "cnvnator", - "mitosalt" + "cnvnator" ] ], "mt_del_result": [ @@ -103,24 +97,18 @@ ] ], "saltshaker_vcf": [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + ], "updated_priority": [ [ "manta", "tiddit", - "cnvnator", - "mitosalt" + "cnvnator" ] ] } ], - "timestamp": "2026-06-18T14:55:54.079801", + "timestamp": "2026-06-22T12:28:28.921338925", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3b621c074..bd3fd4dac 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -680,9 +680,14 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/earlycasualcaiman.saltshaker.png", + "call_sv/earlycasualcaiman_mitochondria_deletions.txt", "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", "call_sv/slowlycivilbuck.saltshaker.png", + "call_sv/slowlycivilbuck_mitochondria_deletions.txt", "fastqc", "fastqc/earlycasualcaiman_LNUMBER1", "fastqc/earlycasualcaiman_LNUMBER1/earlycasualcaiman_LNUMBER1.html", @@ -1096,9 +1101,14 @@ "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", + "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", + "slowlycivilbuck_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.html:md5,d41d8cd98f00b204e9800998ecf8427e", "earlycasualcaiman_LNUMBER1.zip:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_LNUMBER3.html:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1325,7 +1335,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-06-18T13:35:09.306177124", + "timestamp": "2026-06-22T12:15:47.246320185", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 21f22f467..31030f480 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 356, + 355, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -545,7 +545,10 @@ "call_snv/mitochondria/justhusky_mitochondria.vcf.gz.tbi", "call_sv", "call_sv/hugelymodelbat.saltshaker.png", + "call_sv/hugelymodelbat_mitochondria_deletions.txt", "call_sv/justhusky.saltshaker_classify.html", + "call_sv/justhusky_sv.vcf.gz", + "call_sv/justhusky_sv.vcf.gz.tbi", "fastqc", "fastqc/hugelymodelbat_LNUMBER1", "fastqc/hugelymodelbat_LNUMBER1/hugelymodelbat_LNUMBER1.html", @@ -660,7 +663,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-18T13:38:45.854734171", + "timestamp": "2026-06-22T12:03:04.815283726", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 146e30767d4874d6fbfae628f8c3e9cf55991d67 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Jun 2026 12:58:29 +0200 Subject: [PATCH 831/872] update test --- .../local/call_snv/tests/main.nf.test | 13 +- .../local/call_snv/tests/main.nf.test.snap | 364 ++++++++---------- 2 files changed, 158 insertions(+), 219 deletions(-) diff --git a/subworkflows/local/call_snv/tests/main.nf.test b/subworkflows/local/call_snv/tests/main.nf.test index 17f3c821f..20efee6b9 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test +++ b/subworkflows/local/call_snv/tests/main.nf.test @@ -124,7 +124,7 @@ nextflow_workflow { input[22] = channel.of([[id:'model'], []]) input[23] = channel.of([[id:'target'], [], []]) input[24] = 'wgs' - input[25] = false + input[25] = true input[26] = false input[27] = false input[28] = 'deepvariant' @@ -136,16 +136,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + workflow.out ).match() } ) } diff --git a/subworkflows/local/call_snv/tests/main.nf.test.snap b/subworkflows/local/call_snv/tests/main.nf.test.snap index c4f13d3f7..a405628f6 100644 --- a/subworkflows/local/call_snv/tests/main.nf.test.snap +++ b/subworkflows/local/call_snv/tests/main.nf.test.snap @@ -24,280 +24,228 @@ }, "CALL_SNV - deepvariant wgs, stub": { "content": [ - [ - [ - "0", - [ - - ] + { + "0": [ + ], - [ - "1", + "1": [ [ - + { + "id": "justhusky" + }, + "justhusky_mt_and_nuclear_snvs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "10", + "10": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "11", + "11": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "2", + "2": [ [ - + { + "id": "justhusky" + }, + "justhusky_mt_and_nuclear_snvs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "3", - [ - - ] + "3": [ + ], - [ - "4", + "4": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], - [ - "5", + "5": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], - [ - "6", + "6": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "7", + "7": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "8", + "8": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "9", + "9": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "bcftools_concat_csi", - [ - - ] + "bcftools_concat_csi": [ + ], - [ - "bcftools_concat_tbi", + "bcftools_concat_tbi": [ [ - + { + "id": "justhusky" + }, + "justhusky_mt_and_nuclear_snvs.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "bcftools_concat_vcf", + "bcftools_concat_vcf": [ [ - + { + "id": "justhusky" + }, + "justhusky_mt_and_nuclear_snvs.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "deepvariant_report", - [ - - ] + "deepvariant_report": [ + ], - [ - "genome_gtabix", + "genome_gtabix": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz.tbi:md5,1f7f65ca1a1b41bec29194966ca37228" ] ], - [ - "genome_gvcf", + "genome_gvcf": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_deepvar.g.vcf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" ] ], - [ - "genome_tabix", + "genome_tabix": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "genome_vcf", + "genome_vcf": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "genome_vcf_tabix", + "genome_vcf_tabix": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_snv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_snv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "mt_tabix", + "mt_tabix": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "mt_vcf", + "mt_vcf": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "mt_vcf_tbi", + "mt_vcf_tbi": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky_mitochondria.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "justhusky_mitochondria.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] - ] + } ], - "timestamp": "2026-05-29T20:52:18.39128556", + "timestamp": "2026-06-22T12:57:59.006104185", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } From 36fad3c47ff7330d0134d999d9da944b9dc1fc29 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Mon, 22 Jun 2026 16:36:05 +0200 Subject: [PATCH 832/872] remove saltshaker_vcf from publish --- main.nf | 2 -- .../local/call_structural_variants/main.nf | 1 - .../tests/main.nf.test.snap | 10 ++------- subworkflows/local/call_sv_MT/main.nf | 4 +--- .../local/call_sv_MT/tests/main.nf.test.snap | 22 ++++++++++++++----- tests/test_singleton.nf.test.snap | 4 ++-- workflows/raredisease.nf | 3 --- 7 files changed, 22 insertions(+), 24 deletions(-) diff --git a/main.nf b/main.nf index 7aa848803..34970b08b 100644 --- a/main.nf +++ b/main.nf @@ -570,7 +570,6 @@ workflow NFCORE_RAREDISEASE { call_sv_tbi = RAREDISEASE.out.call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] - saltshaker_vcf = RAREDISEASE.out.saltshaker_vcf // channel: [ val(meta), path(vcf) ] mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] @@ -777,7 +776,6 @@ workflow { .mix(NFCORE_RAREDISEASE.out.call_sv_tbi) .mix(NFCORE_RAREDISEASE.out.saltshaker_html) .mix(NFCORE_RAREDISEASE.out.saltshaker_plot) - .mix(NFCORE_RAREDISEASE.out.saltshaker_vcf) .mix(NFCORE_RAREDISEASE.out.mt_del_result) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) diff --git a/subworkflows/local/call_structural_variants/main.nf b/subworkflows/local/call_structural_variants/main.nf index 9c1a267e8..932edc5d2 100644 --- a/subworkflows/local/call_structural_variants/main.nf +++ b/subworkflows/local/call_structural_variants/main.nf @@ -156,7 +156,6 @@ workflow CALL_STRUCTURAL_VARIANTS { mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - saltshaker_vcf = ch_saltshaker_vcf // channel: [ path(vcf) ] tbi = ch_merged_tbi // channel: [ val(meta), path(tbi)] vcf = ch_merged_svs // channel: [ val(meta), path(vcf)] } diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 1b6d51cb1..4cd3f615e 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -45,9 +45,6 @@ ] ], "3": [ - - ], - "4": [ [ { "id": "justhusky" @@ -55,7 +52,7 @@ "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "5": [ + "4": [ [ { "id": "justhusky" @@ -104,9 +101,6 @@ }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "saltshaker_vcf": [ - ], "tbi": [ [ @@ -126,7 +120,7 @@ ] } ], - "timestamp": "2026-06-22T12:30:29.306790749", + "timestamp": "2026-06-22T16:33:34.786105072", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index b0b545c85..bdcfe85de 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -148,9 +148,7 @@ workflow CALL_SV_MT { // combine never sees an empty-spread issue (combining case_info with [[]] would produce // a 1-element channel item that breaks 2-param destructuring closures downstream). SALTSHAKER_CLASSIFY.out.vcf - .map { _meta, vcf -> vcf } - .filter { !it.isEmpty() } // .collect{} produces an ArrayBag which .filter can't be used on, so first convert to regular elements with filter, then collect those to filter the whole list - .collect() + .collect { _meta, vcf -> vcf } .filter { !it.isEmpty() } .map { vcf_list -> [vcf_list] } .set { ch_vcf_file_list } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 59d282159..fe31efa86 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -3,7 +3,12 @@ "content": [ { "0": [ - + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "1": [ [ @@ -51,7 +56,8 @@ [ "manta", "tiddit", - "cnvnator" + "cnvnator", + "mitosalt" ] ], "mt_del_result": [ @@ -97,18 +103,24 @@ ] ], "saltshaker_vcf": [ - + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] ], "updated_priority": [ [ "manta", "tiddit", - "cnvnator" + "cnvnator", + "mitosalt" ] ] } ], - "timestamp": "2026-06-22T12:28:28.921338925", + "timestamp": "2026-06-22T16:31:54.028454982", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 31030f480..95e8c308e 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test_singleton": { "content": [ - 355, + 356, { "ADD_VARCALLER_TO_BED": { "bgzip": 1.21, @@ -663,7 +663,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-22T12:03:04.815283726", + "timestamp": "2026-06-22T16:29:48.340109138", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index a43a38e13..1c8d0e1ce 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -247,7 +247,6 @@ workflow RAREDISEASE { ch_mt_del_result = channel.empty() ch_saltshaker_html = channel.empty() ch_saltshaker_plot = channel.empty() - ch_saltshaker_vcf = channel.empty() ch_call_repeat_expansions_publish = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() @@ -694,7 +693,6 @@ workflow RAREDISEASE { ch_call_sv_tbi = CALL_STRUCTURAL_VARIANTS.out.tbi ch_saltshaker_html = CALL_STRUCTURAL_VARIANTS.out.saltshaker_html ch_saltshaker_plot = CALL_STRUCTURAL_VARIANTS.out.saltshaker_plot - ch_saltshaker_vcf = CALL_STRUCTURAL_VARIANTS.out.saltshaker_vcf ch_mt_del_result = CALL_STRUCTURAL_VARIANTS.out.mt_del_result // @@ -1080,7 +1078,6 @@ workflow RAREDISEASE { call_sv_tbi = ch_call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] - saltshaker_vcf = ch_saltshaker_vcf // channel: [ val(meta), path(vcf) ] mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] From 04333d1594495c296448680bcc6b72119c37d47a Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 22 Jun 2026 17:30:25 +0200 Subject: [PATCH 833/872] patch deepvariant --- CHANGELOG.md | 6 +++++ modules.json | 3 ++- .../deepvariant-rundeepvariant.diff | 24 +++++++++++++++++++ .../deepvariant/rundeepvariant/main.nf | 7 +++++- 4 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff diff --git a/CHANGELOG.md b/CHANGELOG.md index ad6d26bd3..ce84b5a84 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## 3.1.1 - Princess Peach (patch) [2026-06-23] + +### `Fixed` + +- Patch `deepvariant/rundeepvariant` to tee stdout/stderr to a log file and exit non-zero when `queue.Empty` or `BrokenPipeError` is detected, catching silent failures that previously caused the process to appear successful [#XXX](https://github.com/nf-core/raredisease/pull/XXX) + ## 3.1.0 - Princess Peach [2026-06-16] ### `Added` diff --git a/modules.json b/modules.json index bcb716ff7..8b4103657 100644 --- a/modules.json +++ b/modules.json @@ -138,7 +138,8 @@ "deepvariant/rundeepvariant": { "branch": "master", "git_sha": "f2b138ee1d91f67d31c187317d7e83e429bf0309", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff" }, "ensemblvep/vep": { "branch": "master", diff --git a/modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff b/modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff new file mode 100644 index 000000000..46290df51 --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/deepvariant-rundeepvariant.diff @@ -0,0 +1,24 @@ +Changes in component 'nf-core/deepvariant/rundeepvariant' +'modules/nf-core/deepvariant/rundeepvariant/meta.yml' is unchanged +Changes in 'deepvariant/rundeepvariant/main.nf': +--- modules/nf-core/deepvariant/rundeepvariant/main.nf ++++ modules/nf-core/deepvariant/rundeepvariant/main.nf +@@ -46,7 +46,12 @@ + ${regions} \\ + ${par_regions} \\ + --intermediate_results_dir=tmp \\ +- --num_shards=${task.cpus} ++ --num_shards=${task.cpus} 2>&1 | tee deepvariant.log ++ ++ if grep -qi "queue\.Empty" deepvariant.log; then ++ echo "ERROR: Fatal error detected in tool log" >&2 ++ exit 1 ++ fi + """ + + stub: + +'modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap' is unchanged +'modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config' is unchanged +'modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf index 77889e2e8..9a19b1e1d 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/main.nf +++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf @@ -46,7 +46,12 @@ process DEEPVARIANT_RUNDEEPVARIANT { ${regions} \\ ${par_regions} \\ --intermediate_results_dir=tmp \\ - --num_shards=${task.cpus} + --num_shards=${task.cpus} 2>&1 | tee deepvariant.log + + if grep -qi "queue\\.Empty\\|BrokenPipeError" deepvariant.log; then + echo "ERROR: Fatal error detected in tool log" >&2 + exit 1 + fi """ stub: From f5f045d8e7bb46f4f038d0ebef924ca20073a503 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 23 Jun 2026 08:55:38 +0200 Subject: [PATCH 834/872] fix bracket after merge --- main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/main.nf b/main.nf index e5647f219..6e5ad2214 100644 --- a/main.nf +++ b/main.nf @@ -820,6 +820,7 @@ output { } call_sv { path { _meta, _file -> "call_sv/" } + } call_snv_genome { path { _meta, _file -> "call_snv/genome/" } } From c2618f15f547a9a2f0e893628a8531c34d1c9255 Mon Sep 17 00:00:00 2001 From: Irene Duba <75395041+ieduba@users.noreply.github.com> Date: Tue, 23 Jun 2026 10:59:43 +0200 Subject: [PATCH 835/872] Apply suggestions from code review Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> --- subworkflows/local/call_structural_variants/tests/main.nf.test | 2 +- subworkflows/local/call_sv_MT/tests/main.nf.test | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 433e4be59..b88082d15 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -41,7 +41,7 @@ nextflow_workflow { input[7] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)]).collect() input[8] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[9] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[10] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[10] = Channel.from(System.getenv('PWD')).map { dir -> [[id:'genome'], file(dir)] } input[11] = channel.of([15, 2, 5, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) input[12] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 5c385b2da..ad635c4cb 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_workflow { input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() - input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = Channel.from(System.getenv('PWD')).map { dir -> [[id:'genome'], file(dir)] } input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = Channel.from("${projectDir}/subworkflows/local/variant_evaluation/tests").map { dir -> [[id:'mt'], file(dir)] } From 4c8edfda521420ae103aa7ee03924f0e5f3b7590 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 23 Jun 2026 11:46:09 +0200 Subject: [PATCH 836/872] update stub test and snaps --- .../local/call_sv_MT/tests/main.nf.test | 11 +- .../local/call_sv_MT/tests/main.nf.test.snap | 518 +++++------------- 2 files changed, 150 insertions(+), 379 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index 661eac137..55d393481 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -292,16 +292,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + workflow.out ).match() } ) } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 1eef5d460..ee2dcec40 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,7 +1,7 @@ { "CALL_SV_MT - 2 samples": { "content": [ - "106998c7742c3eb0abb532d32526015f", + "3d2eca57b18e5d0180b333d7370a2bfb", [ [ { @@ -54,7 +54,7 @@ ] ] ], - "timestamp": "2026-06-18T10:03:41.39258", + "timestamp": "2026-06-23T11:43:56.545028", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" @@ -62,406 +62,186 @@ }, "CALL_SV_MT - 2 samples - stub": { "content": [ - [ - [ - "0", + { + "0": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "1", + "1": [ [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], - [ - "2", + "2": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "3", + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "4", + "3": [ [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] - ] - ], - [ - "5", + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "mt_del_result", + "4": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "manta", + "tiddit", + "cnvnator", + "mitosalt" ] ], - [ - "publish", + "mt_del_result": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], [ - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] - ], - [ - "call_sv/", - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "saltshaker_html", + "saltshaker_html": [ [ - [ - { - "id": "justhusky" - }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" - ] + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" ] ], - [ - "saltshaker_plot", + "saltshaker_plot": [ [ - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - [ - { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "saltshaker_vcf", + "saltshaker_vcf": [ [ - [ - { - "id": "justhusky" - }, - "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "updated_priority", + "updated_priority": [ [ - [ - "manta", - "tiddit", - "cnvnator", - "mitosalt" - ] + "manta", + "tiddit", + "cnvnator", + "mitosalt" ] ] - ] + } ], - "timestamp": "2026-06-18T10:10:30.017086", + "timestamp": "2026-06-23T11:45:47.627815", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 3bd6abb7e123947ac16edf757910d39923b04474 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 23 Jun 2026 12:50:34 +0200 Subject: [PATCH 837/872] Update CHANGELOG.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce84b5a84..7ca877c62 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- Patch `deepvariant/rundeepvariant` to tee stdout/stderr to a log file and exit non-zero when `queue.Empty` or `BrokenPipeError` is detected, catching silent failures that previously caused the process to appear successful [#XXX](https://github.com/nf-core/raredisease/pull/XXX) +- Patch `deepvariant/rundeepvariant` to tee stdout/stderr to a log file and exit non-zero when `queue.Empty` or `BrokenPipeError` is detected, catching silent failures that previously caused the process to appear successful [#889](https://github.com/nf-core/raredisease/pull/889) ## 3.1.0 - Princess Peach [2026-06-16] From f9739689ebddc7719e912fe654474510e5a94b09 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 23 Jun 2026 13:11:18 +0200 Subject: [PATCH 838/872] update subworkflow tests --- .../local/call_sv_MT/tests/main.nf.test | 177 +++++++----- .../local/call_sv_MT/tests/main.nf.test.snap | 256 +++++++++++++++++- 2 files changed, 354 insertions(+), 79 deletions(-) diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test b/subworkflows/local/call_sv_MT/tests/main.nf.test index ab0ec2a4b..1f32a3123 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test @@ -66,18 +66,78 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[10] = channel.value(10000000) - input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[13] = false - input[14] = 16081 - input[15] = 407 - input[16] = 5730 - input[17] = 5763 - input[18] = 16569 - input[19] = 'chrM' - input[20] = 15 - input[21] = 0.01 + input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc']) + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + path(workflow.out.saltshaker_vcf.get(0).get(1)).vcf.variantsMD5, + workflow.out.saltshaker_html, + file(workflow.out.saltshaker_plot.get(0).get(1)).name, // pngs are unstable so we just check that the name matches + workflow.out.mt_del_result, + workflow.out.updated_priority + ).match() } + ) + } + } + + test("CALL_SV_MT - 1 sample - no sample map") { + + when { + params { + mt_del = "-s --insert-size 16000" + } + workflow { + """ + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) + input[1] = channel.of([id:'justhusky']) + input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() + input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() + input[5] = HISAT2_BUILD.out.index.collect() + input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[8] = LAST_LASTDB.out.index.collect() + input[9] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + [ + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) + ] + ]) + input[10] = channel.empty() + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 """ } } @@ -140,18 +200,19 @@ nextflow_workflow { ] ] ) - input[10] = channel.value(10000000) - input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[13] = false - input[14] = 16081 - input[15] = 407 - input[16] = 5730 - input[17] = 5763 - input[18] = 16569 - input[19] = 'chrM' - input[20] = 15 - input[21] = 0.01 + input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc'], [[id:'hugelymodelbat'], 'cust_hmb']) + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 """ } } @@ -216,7 +277,7 @@ nextflow_workflow { ] ] ) - input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc'], [[id:'hugelymodelbat'], 'cust_hmb']) + input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc']) input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) @@ -237,22 +298,13 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name + workflow.out ).match() } ) } } - test("CALL_SV_MT - no_sample_map - stub") { + test("CALL_SV_MT - 1 sample - no sample map - stub") { options "-stub" @@ -262,18 +314,11 @@ nextflow_workflow { } workflow { """ - input[0] = channel.of( - [ - [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) - ], - [ - [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_sorted_md.bam.bai', checkIfExists: true) - ] - ) + input[0] = channel.of([ + [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_sorted_md.bam.bai', checkIfExists: true) + ]) input[1] = channel.of([id:'justhusky']) input[2] = channel.of(file(params.pipelines_testdata_base_path + 'reference/reference_chr.sizes', checkIfExists: true)).collect() input[3] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)]).collect() @@ -285,13 +330,10 @@ nextflow_workflow { input[9] = channel.of([ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ - [id:'hugelymodelbat', sample:'hugelymodelbat', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:hugelymodelbat\\\\tPL:illumina\\\\tSM:hugelymodelbat'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], - [ - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_1.fastq.gz', checkIfExists: true), - file(params.pipelines_testdata_base_path + 'testdata/hugelymodelbat_mt_2.fastq.gz', checkIfExists: true) - ] + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_1.fastq.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] - ) + ]) input[10] = channel.empty() input[11] = channel.value(10000000) input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) @@ -349,7 +391,7 @@ nextflow_workflow { input[6] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() input[7] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() input[8] = LAST_LASTDB.out.index.collect() - input[9] = channel.of( + input[9] = channel.of( [ [id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", lane:1, sex:1, phenotype:1, paternal:0, maternal:0, case_id:'justhusky'], [ @@ -365,18 +407,19 @@ nextflow_workflow { ] ] ) - input[10] = channel.value(10000000) - input[11] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[12] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) - input[13] = false - input[14] = 16081 - input[15] = 407 - input[16] = 5730 - input[17] = 5763 - input[18] = 16569 - input[19] = 'chrM' - input[20] = 15 - input[21] = 0.01 + input[10] = channel.of([[id:'earlycasualcaiman'], 'cust_ecc'], [[id:'hugelymodelbat'], 'cust_hmb']) + input[11] = channel.value(10000000) + input[12] = channel.value(['manta', 'tiddit', 'cnvnator']) + input[13] = channel.of([15, 2, 2, 30000, 30, 0.00001, 5, 1000, 80, 10000, 5, 15]) + input[14] = false + input[15] = 16081 + input[16] = 407 + input[17] = 5730 + input[18] = 5763 + input[19] = 16569 + input[20] = 'chrM' + input[21] = 15 + input[22] = 0.01 """ } } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index ee2dcec40..552e1297f 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,13 +1,13 @@ { "CALL_SV_MT - 2 samples": { "content": [ - "3d2eca57b18e5d0180b333d7370a2bfb", + "77d88012f833253be9666bb792c60aee", [ [ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + "justhusky.saltshaker_classify.html:md5,d3e9be4deac01d3a53937edca7238709" ] ], "earlycasualcaiman.saltshaker.png", @@ -54,7 +54,7 @@ ] ] ], - "timestamp": "2026-06-23T11:43:56.545028", + "timestamp": "2026-06-23T12:41:13.382138", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" @@ -76,7 +76,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -190,7 +190,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "saltshaker_plot": [ @@ -241,7 +241,179 @@ ] } ], - "timestamp": "2026-06-23T11:45:47.627815", + "timestamp": "2026-06-23T12:43:15.024082", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "CALL_SV_MT - 1 sample - no sample map - stub": { + "content": [ + { + "0": [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ], + "mt_del_result": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_html": [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_plot": [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "saltshaker_vcf": [ + [ + { + "id": "justhusky" + }, + "justhusky_saltshaker.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "updated_priority": [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + } + ], + "timestamp": "2026-06-23T12:53:00.309943", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.3" + } + }, + "CALL_SV_MT - 1 sample - no sample map": { + "content": [ + "619fc9380aac6cccd9d3f4d1df17a0ed", + [ + [ + { + "id": "justhusky" + }, + "justhusky.saltshaker_classify.html:md5,3731f46a7d81fb5f43498eef28f46856" + ] + ], + "earlycasualcaiman.saltshaker.png", + [ + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_mitochondria_deletions.txt:md5,43ed4cf81974ace8ec3085340d56a294" + ] + ], + [ + [ + "manta", + "tiddit", + "cnvnator", + "mitosalt" + ] + ] + ], + "timestamp": "2026-06-23T12:39:18.333366", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" @@ -263,7 +435,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -280,6 +452,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "3": [ @@ -298,6 +484,22 @@ "case_id": "justhusky" }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ @@ -324,6 +526,22 @@ "case_id": "justhusky" }, "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "saltshaker_html": [ @@ -331,7 +549,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "saltshaker_plot": [ @@ -348,6 +566,20 @@ "case_id": "justhusky" }, "earlycasualcaiman.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "hugelymodelbat", + "sample": "hugelymodelbat", + "single_end": false, + "num_lanes": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "saltshaker_vcf": [ @@ -368,7 +600,7 @@ ] } ], - "timestamp": "2026-06-18T10:09:39.238569", + "timestamp": "2026-06-23T12:42:09.390542", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" @@ -376,13 +608,13 @@ }, "CALL_SV_MT - 1 sample": { "content": [ - "e591669a4985c6b4947b042d9461e8b5", + "619fc9380aac6cccd9d3f4d1df17a0ed", [ [ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,c3a6eea9dbaf8bcd7a3e90acffb1c24f" + "justhusky.saltshaker_classify.html:md5,1999c31d1c6880fc5f3021397f2111d3" ] ], "earlycasualcaiman.saltshaker.png", @@ -413,7 +645,7 @@ ] ] ], - "timestamp": "2026-06-18T09:55:02.460892", + "timestamp": "2026-06-23T12:37:46.672655", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From 109b461b4818537ad4b7655ba48064b9b094656e Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 23 Jun 2026 13:38:25 +0200 Subject: [PATCH 839/872] update pipeline test snap --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 038ea3751..cecfd9260 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1099,7 +1099,7 @@ "earlycasualcaiman_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", "hugelymodelbat_mitochondria_deletions.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522", + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e", "justhusky_sv.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", "justhusky_sv.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", "slowlycivilbuck.saltshaker.png:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1330,7 +1330,7 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-06-22T12:15:47.246320185", + "timestamp": "2026-06-23T13:26:12.616875047", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From f7a7edf69e2a501493782a83e44f6b6bc86f26b7 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 23 Jun 2026 13:51:59 +0200 Subject: [PATCH 840/872] update subworkflow snap --- .../local/call_structural_variants/tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 4cd3f615e..3d5232a8e 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -25,7 +25,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -83,7 +83,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,5ec112032a61697ad6e447fc71573522" + "justhusky.saltshaker_classify.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "saltshaker_plot": [ @@ -120,7 +120,7 @@ ] } ], - "timestamp": "2026-06-22T16:33:34.786105072", + "timestamp": "2026-06-23T13:51:42.00745", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" From e14690ae25316e1f63c37e27fd696e46fbaed8cb Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 23 Jun 2026 16:01:44 +0200 Subject: [PATCH 841/872] remove filter --- subworkflows/local/call_sv_MT/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/subworkflows/local/call_sv_MT/main.nf b/subworkflows/local/call_sv_MT/main.nf index 8c570a316..97512f9bc 100644 --- a/subworkflows/local/call_sv_MT/main.nf +++ b/subworkflows/local/call_sv_MT/main.nf @@ -121,8 +121,6 @@ workflow CALL_SV_MT { SALTSHAKER_CLASSIFY.out.txt .map { meta, txt -> [['id':meta.sample], meta.case_id, txt] } .join(ch_sample_id_map, remainder: true, failOnDuplicate: true) - // Only keep entries that have all 4 elements needed by map (for example stub tests without meta fail without this) - .filter { it.size() == 4 } .map { sample_meta, case_id, txt, cust_id -> cust_id ? [['id':case_id], txt, cust_id] : [['id':case_id], txt, sample_meta.id] } From fe1d12a434db697fc2df32088f992da18f5631f9 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 24 Jun 2026 08:59:04 +0200 Subject: [PATCH 842/872] bump-version --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 20 ++++++++++---------- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index c172a7673..6f80f3f89 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 3.1.0 + version: 3.1.1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 7ca877c62..6a5d03c3e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 3.1.1 - Princess Peach (patch) [2026-06-23] +## 3.1.1 - Princess Peach (patch) [2026-06-24] ### `Fixed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 455f20374..49b4e3560 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,7 +2,7 @@ custom_logo: "nf-core-raredisease_logo_light.png" custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/raredisease analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-raredisease-methods-description": diff --git a/nextflow.config b/nextflow.config index 2d81bb274..1b2991e64 100644 --- a/nextflow.config +++ b/nextflow.config @@ -485,7 +485,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.4' - version = '3.1.0' + version = '3.1.1' doi = '10.5281/zenodo.7995798' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index da7541994..91842fd2c 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2026-06-16T07:45:55+00:00", + "datePublished": "2026-06-24T06:58:25+00:00", "description": "

    \n \n \n \"nf-core/raredisease\"\n \n

    \n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/raredisease)\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\n> [!NOTE]\n> Right now, we only support paired-end data from Illumina. If you've got other types of data and the pipeline doesn't work for you, just open an issue. We'd be happy to chat about a solution.\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Preprocessing:**\n\n- [fastp](https://github.com/OpenGene/fastp)\n- [Spring](https://github.com/shubhamchandak94/Spring)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMultipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Sambamba](https://github.com/biod/sambamba)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n- [VerifyBamID2](https://github.com/Griffan/VerifyBamID)\n\n**4. Sex check:**\n\n- [NGSbits SampleGender](https://github.com/imgag/ngs-bits)\n- [Peddy](https://github.com/brentp/peddy)\n\n**5. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**6. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n - [SMNCopyNumberCaller](https://github.com/Illumina/SMNCopyNumberCaller)\n- Mitochondrial SV calling:\n - [MitoSAlt](https://mitosalt.sourceforge.io/)\n - [Saltshaker](https://gitlab.com/genomedx/annotation/saltshaker)\n\n**7. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**8. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**9. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- Annotation:\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**10. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**11. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**12. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**13. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma Västerviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Linköping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics Örebro); [Annick Renevey](https://github.com/rannick), [Peter Pruisscher](https://github.com/peterpru) and [Eva Caceres](https://github.com/fevac) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#b6b7b66d-5ce4-44de-ae44-7684e4d7e2cc" + "@id": "#5deee3fb-f65c-4d59-a5da-56bd88444462" } ], "name": "nf-core/raredisease" @@ -142,7 +142,7 @@ ], "contributor": [ { - "@id": "#dda7739c-42eb-464e-bf07-bbffb815b438" + "@id": "#154cf139-7669-444d-ba9d-feabac1a8900" }, { "@id": "https://orcid.org/0000-0002-5044-7754" @@ -173,7 +173,7 @@ } ], "dateCreated": "", - "dateModified": "2026-06-16T09:45:55Z", + "dateModified": "2026-06-24T08:58:25Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -209,10 +209,10 @@ }, "url": [ "https://github.com/nf-core/raredisease", - "https://nf-co.re/raredisease/3.1.0/" + "https://nf-co.re/raredisease/3.1.1/" ], "version": [ - "3.1.0" + "3.1.1" ] }, { @@ -228,11 +228,11 @@ "version": "!>=25.10.4" }, { - "@id": "#b6b7b66d-5ce4-44de-ae44-7684e4d7e2cc", + "@id": "#5deee3fb-f65c-4d59-a5da-56bd88444462", "@type": "TestSuite", "instance": [ { - "@id": "#bdffa306-a84f-4a05-95de-7f4a48125adc" + "@id": "#58bc7b3b-f820-4aa5-9b36-200db09761c5" } ], "mainEntity": { @@ -241,7 +241,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#bdffa306-a84f-4a05-95de-7f4a48125adc", + "@id": "#58bc7b3b-f820-4aa5-9b36-200db09761c5", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/nf-test.yml", @@ -396,7 +396,7 @@ "url": "https://github.com/jemten" }, { - "@id": "#dda7739c-42eb-464e-bf07-bbffb815b438", + "@id": "#154cf139-7669-444d-ba9d-feabac1a8900", "@type": "Person", "email": "25568561+projectoriented@users.noreply.github.com", "name": "Mei Wu", From 524be6906f50e94c2cf3b2253bb2f5553edf6935 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 24 Jun 2026 10:58:34 +0200 Subject: [PATCH 843/872] update snapshots --- tests/default.nf.test.snap | 4 ++-- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e429834ee..0851fb1a6 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -485,7 +485,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0" + "nf-core/raredisease": "v3.1.1" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -930,7 +930,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-16T10:21:33.741825577", + "timestamp": "2026-06-24T10:46:49.152086779", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index c2970c8f3..17fc0a8bb 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -443,7 +443,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0" + "nf-core/raredisease": "v3.1.1" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -846,7 +846,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-06-16T10:27:30.352705529", + "timestamp": "2026-06-24T10:52:57.0145818", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index a5793e9e3..0ca9a3041 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -465,7 +465,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0" + "nf-core/raredisease": "v3.1.1" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -654,7 +654,7 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-16T10:31:08.451259711", + "timestamp": "2026-06-24T10:56:37.634492341", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" From f9d5602acdcf62bac360ec97bfdbb64112caa7ed Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 24 Jun 2026 11:33:09 +0200 Subject: [PATCH 844/872] added non-stub tests for annotate_mt_snvs --- .../local/annotate_mt_snvs/tests/main.nf.test | 94 ++++++++++++++++++- .../annotate_mt_snvs/tests/main.nf.test.snap | 24 ++++- 2 files changed, 112 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 63910dd93..ec29be0ac 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -17,6 +17,84 @@ nextflow_workflow { config "./nextflow.config" + setup { + run("UNTAR") { + script "modules/nf-core/untar/main.nf" + process { + """ + input[0] = channel.of([ + [id:'vep_cache'], + file('https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz', checkIfExists: true) + ]) + """ + } + } + } + + test("ANNOTATE_MT_SNVS - GRCh37") { + when { + params { + homoplasmy_af_threshold = 0.95 + } + workflow { + """ + input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() + input[1] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[2] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[4] = channel.of([ + [id:'justhusky', case_id:'justhusky'], + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz.tbi', checkIfExists: true), + ]) + input[5] = channel.value([[]]) + input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[7] = [ + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz.tbi', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz.tbi', checkIfExists: true) + ] + input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[9] = UNTAR.out.untar.map { _meta, untar -> untar }.collect() + input[10] = [ + file(params.pipelines_testdata_base_path + 'reference/pLI_values.txt', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/LoFtool_scores.txt', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi', checkIfExists: true) + ] + input[11] = null + input[12] = 'GRCh37' + input[13] = 1.0 + input[14] = 107 + """ + } + } + + then { + // Get published vcf file for snapshot comparison (not tbi file) + def vcfPublish = file(workflow.out.publish[0][1][1]).name.endsWith('.gz') \ + ? workflow.out.publish[0][1][1] \ + : workflow.out.publish[1][1][1] + + assertAll( + { assert workflow.success }, + { assert workflow.out.vcf_ann }, + { assert workflow.out.tbi }, + { assert workflow.out.report }, + { assert workflow.out.publish }, + { assert snapshot( + "${file(workflow.out.vcf_ann[0][1]).name}:md5,${path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5}", + path(workflow.out.vcf_ann[0][1]).vcf.summary, + workflow.out.publish[0][0], // file destination path + "${file(vcfPublish).name}:md5,${path(vcfPublish).vcf.variantsMD5}" : + path(vcfPublish).vcf.summary, + workflow.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + } + test("ANNOTATE_MT_SNVS - GRCh37, stub") { options "-stub" @@ -38,10 +116,20 @@ nextflow_workflow { ]) input[5] = channel.value([[]]) input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() - input[7] = channel.value(file(params.pipelines_testdata_base_path + 'reference/grch38_gnomad_reformated_-r3.1.1-.vcf.gz', checkIfExists: true)) + input[7] = [ + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz.tbi', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz.tbi', checkIfExists: true) + ] input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() - input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz', checkIfExists: true)).collect() - input[10] = channel.value([]) + input[9] = UNTAR.out.untar.map { _meta, untar -> untar }.collect() + input[10] = [ + file(params.pipelines_testdata_base_path + 'reference/pLI_values.txt', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/LoFtool_scores.txt', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', checkIfExists: true), + file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi', checkIfExists: true) + ] input[11] = null input[12] = 'GRCh37' input[13] = 1.0 diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index 0dd128e2a..748400d24 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -1,4 +1,22 @@ { + "ANNOTATE_MT_SNVS - GRCh37": { + "content": [ + { + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,35b30b356d34416a56b262834cbeaf32": "VcfFile [chromosomes=[MT], sampleCount=0, variantCount=18164, phased=true, phasedAutodetect=true]" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,35b30b356d34416a56b262834cbeaf32", + "VcfFile [chromosomes=[MT], sampleCount=0, variantCount=18164, phased=true, phasedAutodetect=true]", + "annotate_snv/mitochondria/", + { + + } + ], + "timestamp": "2026-06-24T11:27:16.802351909", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.03.4" + } + }, "ANNOTATE_MT_SNVS - GRCh37, stub": { "content": [ [ @@ -140,10 +158,10 @@ ] ] ], - "timestamp": "2026-03-27T16:43:51.626374218", + "timestamp": "2026-06-24T11:04:00.579594708", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.03.4" } } } \ No newline at end of file From 692fced62047288c8c1108177c9a087a982eb581 Mon Sep 17 00:00:00 2001 From: sofiademmou Date: Wed, 24 Jun 2026 11:36:07 +0200 Subject: [PATCH 845/872] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3134453d4..f0e91c278 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- Added non-stub tests for `annotate_mt_snvs` [#890](https://github.com/nf-core/raredisease/pull/890) + ### `Changed` - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_snv, call_snv_deepvariant, and postprocess_MT_calls subworkflows [#863](https://github.com/nf-core/raredisease/pull/863) From 29f1b5f265686756750ea245e7f7a17cf0bab2d2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 25 Jun 2026 10:34:17 +0200 Subject: [PATCH 846/872] update snapshots --- tests/default.nf.test.snap | 11 ++++++++--- tests/test_bam.nf.test.snap | 4 ++-- tests/test_singleton.nf.test.snap | 11 ++++++++--- 3 files changed, 18 insertions(+), 8 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 58f15f374..bb48030c7 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -164,6 +164,11 @@ "FILTERVEP": { "filtervep": "1.0.0" }, + "FIND_CONCATENATE": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -488,7 +493,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0dev" + "nf-core/raredisease": "v3.2.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -1332,10 +1337,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-06-22T12:15:47.246320185", + "timestamp": "2026-06-25T10:06:29.744958455", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/tests/test_bam.nf.test.snap b/tests/test_bam.nf.test.snap index ba1e2bc27..99e8993b0 100644 --- a/tests/test_bam.nf.test.snap +++ b/tests/test_bam.nf.test.snap @@ -446,7 +446,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0dev" + "nf-core/raredisease": "v3.2.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -850,7 +850,7 @@ "vcf2cytosure/slowlycivilbuck.cgh" ] ], - "timestamp": "2026-05-27T15:22:23.152275002", + "timestamp": "2026-06-25T10:12:33.084372846", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index f3bff14c5..0a9592dd1 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -156,6 +156,11 @@ "FILTERVEP": { "filtervep": "1.0.0" }, + "FIND_CONCATENATE": { + "coreutils": 9.4, + "find": "4.6.0", + "pigz": 2.8 + }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -468,7 +473,7 @@ "vcfanno": "0.3.7" }, "Workflow": { - "nf-core/raredisease": "v3.1.0dev" + "nf-core/raredisease": "v3.2.0dev" }, "ZIP_TABIX_ROHCALL": { "bgzip": 1.21, @@ -657,10 +662,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-22T16:29:48.340109138", + "timestamp": "2026-06-25T10:16:14.231848002", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nextflow": "25.10.4" } } } \ No newline at end of file From 295ee9985c1c1aaa00f39833d53c55798701cd7b Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Thu, 25 Jun 2026 12:06:42 +0200 Subject: [PATCH 847/872] new metromaps with mitosalt and no eklipse --- docs/images/raredisease_metromap_dark.pdf | Bin 198329 -> 201027 bytes docs/images/raredisease_metromap_dark.png | Bin 445052 -> 450725 bytes docs/images/raredisease_metromap_dark.svg | 468 +++++++++++---------- docs/images/raredisease_metromap_light.pdf | Bin 129459 -> 132464 bytes docs/images/raredisease_metromap_light.png | Bin 433982 -> 438911 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b/docs/images/raredisease_metromap_light.svg index 77d7b608e..d3878cd07 100644 --- a/docs/images/raredisease_metromap_light.svg +++ b/docs/images/raredisease_metromap_light.svg @@ -8,7 +8,7 @@ version="1.1" id="svg1" xml:space="preserve" - inkscape:version="1.3.2 (091e20e, 2023-11-25)" + inkscape:version="1.4.3 (0d15f75, 2025-12-25)" sodipodi:docname="raredisease_metromap_light.svg" inkscape:export-filename="raredisease_metromap_light.pdf" inkscape:export-xdpi="96" @@ -28,13 +28,13 @@ inkscape:deskcolor="#d1d1d1" inkscape:document-units="mm" showgrid="true" - inkscape:zoom="0.31001843" - inkscape:cx="1533.7798" - inkscape:cy="864.46473" - inkscape:window-width="1712" - inkscape:window-height="1025" - inkscape:window-x="0" - inkscape:window-y="39" + inkscape:zoom="0.57178976" + inkscape:cx="2021.7221" + inkscape:cy="1102.678" + inkscape:window-width="1470" + inkscape:window-height="890" + inkscape:window-x="237" + inkscape:window-y="1238" inkscape:window-maximized="0" inkscape:current-layer="layer1" showguides="true" @@ -54,7 +54,24 @@ gridanglex="30" gridanglez="30" visible="true" />manta + id="tspan11">manta + + id="tspan12"> + tiddit + id="tspan13">tiddit + + id="tspan14"> + cnvnatorcnvnatorvepvepsvdb-querysvdb-querygermlinecnvcallergermlinecnvcallergenmodgenmod vcf vcfeklipsemantamanta + ry="2.6962883" />mitosaltsaltshaker From 59a9ab06d50592b6ee8d40fab570d7abaf10e3d7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 25 Jun 2026 12:47:20 +0200 Subject: [PATCH 848/872] fix test --- subworkflows/local/align/tests/main.nf.test | 45 ++++++++++----------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test b/subworkflows/local/align/tests/main.nf.test index 636570e5d..d08a1b802 100644 --- a/subworkflows/local/align/tests/main.nf.test +++ b/subworkflows/local/align/tests/main.nf.test @@ -385,11 +385,12 @@ nextflow_workflow { input[0] = channel.empty() input[1] = channel.empty() input[2] = channel.empty() - input[3] = GENOME_MEME.out.index.collect() - input[4] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() - input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() - input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() - input[7] = channel.fromList([ + input[3] = channel.empty() + input[4] = GENOME_MEME.out.index.collect() + input[5] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.dict', checkIfExists: true)).collect() + input[6] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta.fai', checkIfExists: true)).collect() + input[7] = channel.of([id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)).collect() + input[8] = channel.fromList([ [[ id:'earlycasualcaiman', sample:'earlycasualcaiman', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:earlycasualcaiman\\\\tPL:illumina\\\\tSM:earlycasualcaiman'", 'lane':1, 'sex':1, 'phenotype':1, 'paternal':0, 'maternal':0, 'case_id':'justhusky' ], // meta map [ file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_earlycasualcaiman_XXXXXX_1.fastq.gz', checkIfExists: true), @@ -406,28 +407,26 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + '/testdata/1_171015_HHT5NDSXX_slowlycivilbuck_XXXXXX_2.fastq.gz', checkIfExists: true) ]] ]) - input[8] = channel.empty() - input[9] = MT_MEM2.out.index.collect() - input[10] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[13] = channel.empty() - input[14] = SHIFTMT_MEM2.out.index.collect() - input[15] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() - input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() - input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() - input[18] = true - input[19] = "bwameme" - input[20] = "wgs" - input[21] = false + input[9] = channel.empty() + input[10] = MT_MEM2.out.index.collect() + input[11] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[12] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[13] = channel.of([id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[14] = channel.empty() + input[15] = SHIFTMT_MEM2.out.index.collect() + input[16] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.dict', checkIfExists: true)).collect() + input[17] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)).collect() + input[18] = channel.of([id:'shiftmt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)).collect() + input[19] = true + input[20] = "bwameme" + input[21] = "wes" input[22] = false - input[23] = 3072 + input[23] = false input[24] = "bwamem2" input[25] = "illumina" input[26] = false - input[27] = 4 - input[28] = true - input[29] = false + input[27] = true + input[28] = false """ } } From 749ba6edce2bd2d52939ab8d5722e3c11851b9d7 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 25 Jun 2026 13:36:08 +0200 Subject: [PATCH 849/872] update test --- .../local/align_bwa_bwamem2_bwameme/tests/main.nf.test | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 28471acd4..5ff30a08a 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -66,10 +66,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.markdup_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.stats, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getHeaderMD5() ] }, workflow.out.marked_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] } ).match() From f2de95d124175621ea5c77f29fb3b9e48f0375c2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 25 Jun 2026 14:57:14 +0200 Subject: [PATCH 850/872] update tests --- .../tests/main.nf.test | 32 +++++++++---------- .../annotate_genome_snvs/tests/main.nf.test | 4 +-- .../prepare_references/tests/main.nf.test | 27 ++++++++-------- 3 files changed, 31 insertions(+), 32 deletions(-) diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test index 5ff30a08a..a48f21698 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test @@ -216,22 +216,21 @@ nextflow_workflow { workflow { """ input[0] = [[:],[]] - input[1] = BWAMEM2_INDEX.out.index - input[2] = [[:],[]] - input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([ + input[1] = [[:],[]] + input[2] = BWAMEM2_INDEX.out.index + input[3] = [[:],[]] + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[6] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group: "'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[6] = "bwamem2" - input[7] = true - input[8] = 3072 + input[7] = "bwamem2" + input[8] = true input[9] = "illumina" - input[10] = 4 """ } } @@ -269,21 +268,20 @@ nextflow_workflow { """ input[0] = [[:],[]] input[1] = [[:],[]] - input[2] = BWAMEME_INDEX.out.index - input[3] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) - input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) - input[5] = channel.of([ + input[2] = [[:],[]] + input[3] = BWAMEME_INDEX.out.index + input[4] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]]) + input[5] = channel.of([[id:'sarscov2'], [file(params.sarscov_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]]) + input[6] = channel.of([ [ id:'test', sample:'test', single_end:false, num_lanes:1, read_group:"\'@RG\\\\tID:test\\\\tPL:illumina\\\\tSM:test\'" ], // meta map [ file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.sarscov_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[6] = "bwameme" - input[7] = true - input[8] = 3072 + input[7] = "bwameme" + input[8] = true input[9] = "illumina" - input[10] = 4 """ } } diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test index cdb8ca0e7..fe8164eff 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test @@ -37,7 +37,7 @@ nextflow_workflow { input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.value([[],[]]) input[7] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]]) input[9] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), @@ -94,7 +94,7 @@ nextflow_workflow { input[5] = channel.of([[id:'genome'], file(params.pipelines_testdata_base_path + 'reference/reference.fasta', checkIfExists: true)]).collect() input[6] = channel.value([[],[]]) input[7] = channel.of([id:'earlycasualcaiman', sample:'earlycasualcaiman', sex:1, phenotype:2, paternal:0, maternal:0, case_id:'justhusky']) - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)) + input[8] = channel.of([[id:'genome'], [file(params.pipelines_testdata_base_path + 'reference/target_wgs.interval_list', checkIfExists: true)]]) input[9] = channel.of([ [id:'justhusky', probands:['earlycasualcaiman'], upd_children:['earlycasualcaiman'], mother:'', father:''], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index f859da943..db9005f90 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -128,21 +128,22 @@ nextflow_workflow { input[3] = null input[4] = null input[5] = null - input[6] = params.pipelines_testdata_base_path + 'reference/reference.fasta' - input[7] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' - input[8] = null - input[9] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' - input[10] = null - input[11] = "bwa" - input[12] = null - input[13] = false + input[6] = null + input[7] = params.pipelines_testdata_base_path + 'reference/reference.fasta' + input[8] = params.pipelines_testdata_base_path + 'reference/gnomad_reformated.tab.gz' + input[9] = null + input[10] = params.pipelines_testdata_base_path + 'reference/dbsnp_-138-.vcf.gz' + input[11] = null + input[12] = "bwa" + input[13] = null input[14] = false - input[15] = null + input[15] = false input[16] = null - input[17] = params.pipelines_testdata_base_path + 'reference/target.bed' - input[18] = null - input[19] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' - input[20] = true + input[17] = null + input[18] = params.pipelines_testdata_base_path + 'reference/target.bed' + input[19] = null + input[20] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' + input[21] = true """ } } From 2223f10ceb72a65151b60e7c0d5f2c76915b38cf Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Thu, 25 Jun 2026 15:31:07 +0200 Subject: [PATCH 851/872] update snapshots --- .../local/align/tests/main.nf.test.snap | 273 +----------------- .../tests/main.nf.test.snap | 18 +- .../tests/main.nf.test.snap | 8 +- .../local/call_sv_MT/tests/main.nf.test.snap | 20 +- .../tests/main.nf.test.snap | 114 ++++---- 5 files changed, 95 insertions(+), 338 deletions(-) diff --git a/subworkflows/local/align/tests/main.nf.test.snap b/subworkflows/local/align/tests/main.nf.test.snap index 1975202c8..d42646af9 100644 --- a/subworkflows/local/align/tests/main.nf.test.snap +++ b/subworkflows/local/align/tests/main.nf.test.snap @@ -1051,159 +1051,6 @@ "nextflow": "25.10.4" } }, - "align bwamem2 - wes": { - "content": [ - [ - "earlycasualcaiman.fastp.html", - "earlycasualcaiman.fastp.json", - "earlycasualcaiman.fastp.log", - "earlycasualcaiman_R1.fastp.fastq.gz", - "earlycasualcaiman_R2.fastp.fastq.gz", - "earlycasualcaiman_sorted_md.cram", - "earlycasualcaiman_sorted_md.cram.crai", - "hugelymodelbat.fastp.html", - "hugelymodelbat.fastp.json", - "hugelymodelbat.fastp.log", - "hugelymodelbat_R1.fastp.fastq.gz", - "hugelymodelbat_R2.fastp.fastq.gz", - "hugelymodelbat_sorted_md.cram", - "hugelymodelbat_sorted_md.cram.crai", - "slowlycivilbuck.fastp.html", - "slowlycivilbuck.fastp.json", - "slowlycivilbuck.fastp.log", - "slowlycivilbuck_R1.fastp.fastq.gz", - "slowlycivilbuck_R2.fastp.fastq.gz", - "slowlycivilbuck_sorted_md.cram", - "slowlycivilbuck_sorted_md.cram.crai" - ], - [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat_sorted_md.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck_sorted_md.bam.bai" - ] - ], - [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck.bam.bai" - ] - ], - [ - - ] - ], - "timestamp": "2026-04-14T08:57:37.024004334", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, "align bwameme - wes, stub": { "content": [ [ @@ -1378,127 +1225,15 @@ ] ], [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck.bam.bai" - ] + ], [ - [ - { - "groupSize": 1, - "groupTarget": { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "earlycasualcaiman_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "hugelymodelbat", - "sample": "hugelymodelbat", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:hugelymodelbat\\tPL:illumina\\tSM:hugelymodelbat'", - "sex": 1, - "phenotype": 2, - "paternal": "earlycasualcaiman", - "maternal": "slowlycivilbuck", - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "hugelymodelbat_sorted_merged_md_sorted_shifted.bam.bai" - ], - [ - { - "groupSize": 1, - "groupTarget": { - "id": "slowlycivilbuck", - "sample": "slowlycivilbuck", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:slowlycivilbuck\\tPL:illumina\\tSM:slowlycivilbuck'", - "sex": 2, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - } - }, - "d41d8cd98f00b204e9800998ecf8427e", - "slowlycivilbuck_sorted_merged_md_sorted_shifted.bam.bai" - ] + ] ], - "timestamp": "2026-06-12T15:33:25.667453", + "timestamp": "2026-06-25T13:17:03.89564829", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap index f8d47f08a..9ea55417c 100644 --- a/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap +++ b/subworkflows/local/align_bwa_bwamem2_bwameme/tests/main.nf.test.snap @@ -2,10 +2,20 @@ "align bwafastalign": { "content": [ [ - "test_sorted_md.bam", - "test_sorted_md.bam.bai", "test_sorted_md.metrics.txt" ], + [ + [ + { + "id": "test", + "sample": "test", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:test\\tPL:illumina\\tSM:test'" + }, + "test.stats:md5,f0914a56ae73007ebd242cab27861700" + ] + ], [ [ { @@ -37,9 +47,9 @@ ] ] ], - "timestamp": "2026-06-12T15:46:43.756159921", + "timestamp": "2026-06-25T13:30:01.076823606", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } }, diff --git a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap index b849754fb..98d758912 100644 --- a/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_genome_snvs/tests/main.nf.test.snap @@ -292,9 +292,9 @@ ] ] ], - "timestamp": "2026-05-26T10:50:20.100647825", + "timestamp": "2026-06-25T15:16:55.298746259", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } }, @@ -715,9 +715,9 @@ ] ] ], - "timestamp": "2026-05-26T10:49:33.095592057", + "timestamp": "2026-06-25T15:14:21.312733081", "meta": { - "nf-test": "0.9.5", + "nf-test": "0.9.4", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index ee2dcec40..d09524e3b 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -1,13 +1,13 @@ { "CALL_SV_MT - 2 samples": { "content": [ - "3d2eca57b18e5d0180b333d7370a2bfb", + "77d88012f833253be9666bb792c60aee", [ [ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,ed534bf6ccd5c7a9bb7efd06e32ae064" + "justhusky.saltshaker_classify.html:md5,f8edbbe314bc4e5e7bfc10c0c92a59b3" ] ], "earlycasualcaiman.saltshaker.png", @@ -54,10 +54,10 @@ ] ] ], - "timestamp": "2026-06-23T11:43:56.545028", + "timestamp": "2026-06-25T14:07:56.059247461", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } }, "CALL_SV_MT - 2 samples - stub": { @@ -376,13 +376,13 @@ }, "CALL_SV_MT - 1 sample": { "content": [ - "e591669a4985c6b4947b042d9461e8b5", + "619fc9380aac6cccd9d3f4d1df17a0ed", [ [ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,c3a6eea9dbaf8bcd7a3e90acffb1c24f" + "justhusky.saltshaker_classify.html:md5,e3077e05ca959239f0b8ea25ff515bf3" ] ], "earlycasualcaiman.saltshaker.png", @@ -413,10 +413,10 @@ ] ] ], - "timestamp": "2026-06-18T09:55:02.460892", + "timestamp": "2026-06-25T14:05:52.399203922", "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.3" + "nf-test": "0.9.4", + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index 432dfbf24..f4518c257 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -28,12 +28,25 @@ { "id": "reference" }, - "reference.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + + ] ] ] ], [ "11", + [ + [ + { + "id": "reference" + }, + "reference.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + [ + "12", [ [ "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", @@ -42,7 +55,7 @@ ] ], [ - "12", + "13", [ [ { @@ -59,13 +72,13 @@ ] ], [ - "13", + "14", [ ] ], [ - "14", + "15", [ [ { @@ -76,7 +89,7 @@ ] ], [ - "15", + "16", [ [ { @@ -87,7 +100,7 @@ ] ], [ - "16", + "17", [ [ { @@ -98,7 +111,7 @@ ] ], [ - "17", + "18", [ [ "reference.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -106,7 +119,7 @@ ] ], [ - "18", + "19", [ [ { @@ -125,29 +138,29 @@ ] ], [ - "19", + "2", [ [ { - "id": "reference" + "id": "dbsnp_-138-" }, - "reference_shift.back_chain:md5,d41d8cd98f00b204e9800998ecf8427e" + "dbsnp_-138-.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], [ - "2", + "20", [ [ { - "id": "dbsnp_-138-" + "id": "reference" }, - "dbsnp_-138-.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "reference_shift.back_chain:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], [ - "20", + "21", [ [ { @@ -164,13 +177,13 @@ ] ], [ - "21", + "22", [ ] ], [ - "22", + "23", [ [ { @@ -181,7 +194,7 @@ ] ], [ - "23", + "24", [ [ { @@ -192,7 +205,7 @@ ] ], [ - "24", + "25", [ [ { @@ -203,7 +216,7 @@ ] ], [ - "25", + "26", [ [ "reference.shifted.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -211,13 +224,13 @@ ] ], [ - "26", + "27", [ ] ], [ - "27", + "28", [ [ { @@ -228,21 +241,11 @@ ] ] ], - [ - "28", - [ - [ - "target_target.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], [ "29", [ [ - [ - - ] + "target_target.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -275,6 +278,16 @@ ], [ "31", + [ + [ + [ + + ] + ] + ] + ], + [ + "32", [ [ "references/", @@ -555,6 +568,12 @@ ], [ "4", + [ + + ] + ], + [ + "5", [ [ { @@ -570,28 +589,17 @@ ] ] ], - [ - "5", - [ - - ] - ], [ "6", [ - [ - "reference.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ] ], [ "7", [ [ - { - "id": "reference" - }, - "reference.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" + "reference.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -602,7 +610,7 @@ { "id": "reference" }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" + "reference.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] ], @@ -613,9 +621,7 @@ { "id": "reference" }, - [ - - ] + "/nf-core/test-datasets/raredisease/reference/reference.fasta" ] ] ], @@ -666,6 +672,12 @@ ] ] ], + [ + "genome_bwafastalign_index", + [ + + ] + ], [ "genome_bwamem2_index", [ @@ -1238,7 +1250,7 @@ ] ] ], - "timestamp": "2026-04-23T09:48:42.84565", + "timestamp": "2026-06-25T15:27:39.363637388", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 8b3850719710b605a304fe67aebbdeeb6f6cf005 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Fri, 26 Jun 2026 15:36:00 +0200 Subject: [PATCH 852/872] update snaps --- .../call_structural_variants/tests/main.nf.test | 7 +++---- .../tests/main.nf.test.snap | 2 +- .../local/call_sv_MT/tests/main.nf.test.snap | 16 ++++++++-------- tests/default.nf.test.snap | 9 ++------- tests/test_singleton.nf.test.snap | 9 ++------- 5 files changed, 16 insertions(+), 27 deletions(-) diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test b/subworkflows/local/call_structural_variants/tests/main.nf.test index 0af50d226..ee60aa4fe 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test @@ -61,10 +61,9 @@ nextflow_workflow { file(params.pipelines_testdata_base_path + 'testdata/earlycasualcaiman_mt_2.fastq.gz', checkIfExists: true) ] ]) - input[19] = channel.empty() - input[20] = channel.value(10000000) - input[21] = channel.value(['manta', 'tiddit', 'cnvnator']) - input[22] = channel.of([[id:'target'], [], []]) + input[20] = channel.empty() + input[21] = channel.value(10000000) + input[22] = channel.value(['manta', 'tiddit', 'cnvnator']) input[23] = true input[24] = false input[25] = 'wgs' diff --git a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap index 3d5232a8e..0e2924421 100644 --- a/subworkflows/local/call_structural_variants/tests/main.nf.test.snap +++ b/subworkflows/local/call_structural_variants/tests/main.nf.test.snap @@ -120,7 +120,7 @@ ] } ], - "timestamp": "2026-06-23T13:51:42.00745", + "timestamp": "2026-06-26T14:04:04.593301052", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.3" diff --git a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap index 1df007610..3b742cad6 100644 --- a/subworkflows/local/call_sv_MT/tests/main.nf.test.snap +++ b/subworkflows/local/call_sv_MT/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,f8edbbe314bc4e5e7bfc10c0c92a59b3" + "justhusky.saltshaker_classify.html:md5,d3e9be4deac01d3a53937edca7238709" ] ], "earlycasualcaiman.saltshaker.png", @@ -54,10 +54,10 @@ ] ] ], - "timestamp": "2026-06-25T14:07:56.059247461", + "timestamp": "2026-06-26T14:11:01.187532567", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } }, "CALL_SV_MT - 2 samples - stub": { @@ -614,7 +614,7 @@ { "id": "justhusky" }, - "justhusky.saltshaker_classify.html:md5,e3077e05ca959239f0b8ea25ff515bf3" + "justhusky.saltshaker_classify.html:md5,1999c31d1c6880fc5f3021397f2111d3" ] ], "earlycasualcaiman.saltshaker.png", @@ -645,10 +645,10 @@ ] ] ], - "timestamp": "2026-06-25T14:05:52.399203922", + "timestamp": "2026-06-26T14:08:06.381190074", "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" + "nf-test": "0.9.5", + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 69bf204a9..998a99106 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -164,11 +164,6 @@ "FILTERVEP": { "filtervep": "1.0.0" }, - "FIND_CONCATENATE": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -1337,10 +1332,10 @@ "slowlycivilbuck.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "timestamp": "2026-06-25T10:06:29.744958455", + "timestamp": "2026-06-26T14:16:17.160260766", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file diff --git a/tests/test_singleton.nf.test.snap b/tests/test_singleton.nf.test.snap index 797a57764..8e5a6c186 100644 --- a/tests/test_singleton.nf.test.snap +++ b/tests/test_singleton.nf.test.snap @@ -156,11 +156,6 @@ "FILTERVEP": { "filtervep": "1.0.0" }, - "FIND_CONCATENATE": { - "coreutils": 9.4, - "find": "4.6.0", - "pigz": 2.8 - }, "GATK4_FILTERMUTECTCALLS_MT": { "gatk4": "4.6.2.0" }, @@ -662,10 +657,10 @@ "vcf2cytosure/hugelymodelbat.cgh" ] ], - "timestamp": "2026-06-25T10:16:14.231848002", + "timestamp": "2026-06-26T14:21:28.826151619", "meta": { "nf-test": "0.9.5", - "nextflow": "25.10.4" + "nextflow": "26.04.3" } } } \ No newline at end of file From efa0afdf3e709932f8e1518b1f4b6ae507e64794 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 15:40:28 +0200 Subject: [PATCH 853/872] update call repeat expansions --- CHANGELOG.md | 1 + main.nf | 15 +- .../local/call_repeat_expansions/main.nf | 11 +- .../call_repeat_expansions/tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 239 +++++++++--------- workflows/raredisease.nf | 22 +- 6 files changed, 161 insertions(+), 134 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index af6fd8c42..9ce42b55a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_snv, call_snv_deepvariant, and postprocess_MT_calls subworkflows [#863](https://github.com/nf-core/raredisease/pull/863) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) - Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858) diff --git a/main.nf b/main.nf index 862607601..d2ea73e6c 100644 --- a/main.nf +++ b/main.nf @@ -582,7 +582,12 @@ workflow NFCORE_RAREDISEASE { saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] - call_snv_bcftools_concat_csi = RAREDISEASE.out.call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] + call_repeat_expansions_expansionhunter_bai = RAREDISEASE.out.call_repeat_expansions_expansionhunter_bai // channel: [ val(meta), path(bai) ] + call_repeat_expansions_expansionhunter_bam = RAREDISEASE.out.call_repeat_expansions_expansionhunter_bam // channel: [ val(meta), path(bam) ] + call_repeat_expansions_expansionhunter_vcf = RAREDISEASE.out.call_repeat_expansions_expansionhunter_vcf // channel: [ val(meta), path(vcf) ] + call_repeat_expansions_stranger_tbi = RAREDISEASE.out.call_repeat_expansions_stranger_tbi // channel: [ val(meta), path(tbi) ] + call_repeat_expansions_stranger_vcf = RAREDISEASE.out.call_repeat_expansions_stranger_vcf // channel: [ val(meta), path(vcf) ] + call_snv_bcftools_concat_csi = RAREDISEASE.out.call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] call_snv_bcftools_concat_tbi = RAREDISEASE.out.call_snv_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] call_snv_bcftools_concat_vcf = RAREDISEASE.out.call_snv_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] call_snv_deepvariant_report = RAREDISEASE.out.call_snv_deepvariant_report // channel: [ val(meta), path(html) ] @@ -793,6 +798,11 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + call_repeat_expansions = NFCORE_RAREDISEASE.out.call_repeat_expansions_expansionhunter_bam + .mix(NFCORE_RAREDISEASE.out.call_repeat_expansions_expansionhunter_bai) + .mix(NFCORE_RAREDISEASE.out.call_repeat_expansions_expansionhunter_vcf) + .mix(NFCORE_RAREDISEASE.out.call_repeat_expansions_stranger_vcf) + .mix(NFCORE_RAREDISEASE.out.call_repeat_expansions_stranger_tbi) call_sv = NFCORE_RAREDISEASE.out.call_sv_vcf .mix(NFCORE_RAREDISEASE.out.call_sv_tbi) .mix(NFCORE_RAREDISEASE.out.saltshaker_html) @@ -831,6 +841,9 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + call_repeat_expansions { + path { _meta, _file -> "repeat_expansions/" } + } call_sv { path { _meta, _file -> "call_sv/" } } diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf index a3bac56e0..edc0afa45 100644 --- a/subworkflows/local/call_repeat_expansions/main.nf +++ b/subworkflows/local/call_repeat_expansions/main.nf @@ -57,12 +57,9 @@ workflow CALL_REPEAT_EXPANSIONS { SVDB_MERGE_REPEATS ( ch_svdb_merge_input, [], true ) - ch_publish = SAMTOOLS_SORT.out.bam - .mix(SAMTOOLS_SORT.out.bai) - .mix(BCFTOOLS_REHEADER_EXP.out.vcf) - .map { meta, value -> ['repeat_expansions/', [meta, value]] } - emit: - vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + expansionhunter_bai = SAMTOOLS_SORT.out.bai // channel: [ val(meta), path(bai) ] + expansionhunter_bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), path(bam) ] + expansionhunter_vcf = BCFTOOLS_REHEADER_EXP.out.vcf // channel: [ val(meta), path(vcf) ] + vcf = SVDB_MERGE_REPEATS.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test b/subworkflows/local/call_repeat_expansions/tests/main.nf.test index b708a4535..58d94e1e4 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test @@ -40,10 +40,9 @@ nextflow_workflow { then { assert workflow.success assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.expansionhunter_bam.collect { meta, bamfile -> [ meta, bam(bamfile).getReadsMD5() ] }, + workflow.out.expansionhunter_bai.collect { meta, f -> file(f).name }, + workflow.out.expansionhunter_vcf.collect { meta, f -> file(f).name }, path(workflow.out.vcf[0][1].toString()).vcf.variantsMD5, path(workflow.out.vcf[0][1].toString()).vcf.summary ).match() diff --git a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap index 7839b9b18..ed506b8b7 100644 --- a/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap +++ b/subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap @@ -5,127 +5,117 @@ "0": [ [ { - "id": "justhusky" + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" }, - "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "publish": [ + "expansionhunter_bai": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "expansionhunter_bam": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_exphunter_sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_exphunter_sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "expansionhunter_vcf": [ [ - "repeat_expansions/", - [ - { - "id": "earlycasualcaiman", - "sample": "earlycasualcaiman", - "single_end": false, - "num_lanes": 1, - "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", - "lane": 1, - "sex": 1, - "phenotype": 1, - "paternal": 0, - "maternal": 0, - "case_id": "justhusky" - }, - "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "earlycasualcaiman_repeat_expansion.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -138,25 +128,44 @@ ] } ], - "timestamp": "2026-04-20T14:48:04.074693", + "timestamp": "2026-06-26T00:25:14.58580944", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, "CALL_REPEAT_EXPANSIONS": { "content": [ [ - "earlycasualcaiman_exphunter_sorted.bam", - "earlycasualcaiman_exphunter_sorted.bam.bai", + [ + { + "id": "earlycasualcaiman", + "sample": "earlycasualcaiman", + "single_end": false, + "num_lanes": 1, + "read_group": "'@RG\\tID:earlycasualcaiman\\tPL:illumina\\tSM:earlycasualcaiman'", + "lane": 1, + "sex": 1, + "phenotype": 1, + "paternal": 0, + "maternal": 0, + "case_id": "justhusky" + }, + "79adf682f13384ba13be973a64e2db48" + ] + ], + [ + "earlycasualcaiman_exphunter_sorted.bam.bai" + ], + [ "earlycasualcaiman_repeat_expansion.vcf" ], "5f06dccb7fc4ad3758bc23e3232f9abb", "VcfFile [chromosomes=[21], sampleCount=1, variantCount=2, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-13T15:42:01.510910485", + "timestamp": "2026-06-26T00:35:51.559219111", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 97b52c49e..90ce85eb0 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -257,7 +257,11 @@ workflow RAREDISEASE { ch_call_snv_mt_tabix = channel.empty() ch_call_snv_mt_vcf = channel.empty() ch_call_sv_publish = channel.empty() - ch_call_repeat_expansions_publish = channel.empty() + ch_call_repeat_expansions_expansionhunter_bai = channel.empty() + ch_call_repeat_expansions_expansionhunter_bam = channel.empty() + ch_call_repeat_expansions_expansionhunter_vcf = channel.empty() + ch_call_repeat_expansions_stranger_tbi = channel.empty() + ch_call_repeat_expansions_stranger_vcf = channel.empty() ch_call_mobile_elements_publish = channel.empty() ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() ch_annotate_genome_snvs_bcftools_concat_vcf = channel.empty() @@ -421,17 +425,17 @@ workflow RAREDISEASE { ch_genome_fasta, ch_genome_fai ) - ch_call_repeat_expansions_publish = CALL_REPEAT_EXPANSIONS.out.publish + ch_call_repeat_expansions_expansionhunter_bai = CALL_REPEAT_EXPANSIONS.out.expansionhunter_bai + ch_call_repeat_expansions_expansionhunter_bam = CALL_REPEAT_EXPANSIONS.out.expansionhunter_bam + ch_call_repeat_expansions_expansionhunter_vcf = CALL_REPEAT_EXPANSIONS.out.expansionhunter_vcf if (!skip_repeat_annotation) { STRANGER ( CALL_REPEAT_EXPANSIONS.out.vcf, ch_variant_catalog ) - ch_call_repeat_expansions_publish = ch_call_repeat_expansions_publish - .mix(STRANGER.out.vcf - .mix(STRANGER.out.tbi) - .map { meta, value -> ['repeat_expansions/', [meta, value]] }) + ch_call_repeat_expansions_stranger_vcf = STRANGER.out.vcf + ch_call_repeat_expansions_stranger_tbi = STRANGER.out.tbi } } @@ -1097,6 +1101,11 @@ workflow RAREDISEASE { saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] + call_repeat_expansions_expansionhunter_bai = ch_call_repeat_expansions_expansionhunter_bai // channel: [ val(meta), path(bai) ] + call_repeat_expansions_expansionhunter_bam = ch_call_repeat_expansions_expansionhunter_bam // channel: [ val(meta), path(bam) ] + call_repeat_expansions_expansionhunter_vcf = ch_call_repeat_expansions_expansionhunter_vcf // channel: [ val(meta), path(vcf) ] + call_repeat_expansions_stranger_tbi = ch_call_repeat_expansions_stranger_tbi // channel: [ val(meta), path(tbi) ] + call_repeat_expansions_stranger_vcf = ch_call_repeat_expansions_stranger_vcf // channel: [ val(meta), path(vcf) ] call_snv_bcftools_concat_csi = ch_call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] call_snv_bcftools_concat_tbi = ch_call_snv_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] call_snv_bcftools_concat_vcf = ch_call_snv_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] @@ -1117,7 +1126,6 @@ workflow RAREDISEASE { subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions publish = ch_call_sv_publish - .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) From a85bbb716ad8f0b20ce216b0a6f6de010c5c8f9d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 16:09:49 +0200 Subject: [PATCH 854/872] update annotate_consequence_pli and call_mobile_elements --- CHANGELOG.md | 1 + main.nf | 14 +++++ .../local/annotate_consequence_pli/main.nf | 16 ++---- .../tests/main.nf.test | 9 +-- .../tests/main.nf.test.snap | 56 ++++++------------- .../local/call_mobile_elements/main.nf | 9 +-- .../tests/main.nf.test.snap | 44 +-------------- workflows/raredisease.nf | 29 +++++----- 8 files changed, 58 insertions(+), 120 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index af6fd8c42..48c0609ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_snv, call_snv_deepvariant, and postprocess_MT_calls subworkflows [#863](https://github.com/nf-core/raredisease/pull/863) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) - Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858) diff --git a/main.nf b/main.nf index 862607601..3220a8d07 100644 --- a/main.nf +++ b/main.nf @@ -582,6 +582,10 @@ workflow NFCORE_RAREDISEASE { saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] + call_mobile_elements_tbi = RAREDISEASE.out.call_mobile_elements_tbi // channel: [ val(meta), path(tbi) ] + call_mobile_elements_vcf = RAREDISEASE.out.call_mobile_elements_vcf // channel: [ val(meta), path(vcf) ] + ann_csq_pli_me_tbi = RAREDISEASE.out.ann_csq_pli_me_tbi // channel: [ val(meta), path(tbi) ] + ann_csq_pli_me_vcf_ann = RAREDISEASE.out.ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] call_snv_bcftools_concat_csi = RAREDISEASE.out.call_snv_bcftools_concat_csi // channel: [ val(meta), path(csi) ] call_snv_bcftools_concat_tbi = RAREDISEASE.out.call_snv_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] call_snv_bcftools_concat_vcf = RAREDISEASE.out.call_snv_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] @@ -793,6 +797,10 @@ workflow { .mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg) .mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y) + call_mobile_elements = NFCORE_RAREDISEASE.out.call_mobile_elements_vcf + .mix(NFCORE_RAREDISEASE.out.call_mobile_elements_tbi) + annotate_mobile_elements = NFCORE_RAREDISEASE.out.ann_csq_pli_me_vcf_ann + .mix(NFCORE_RAREDISEASE.out.ann_csq_pli_me_tbi) call_sv = NFCORE_RAREDISEASE.out.call_sv_vcf .mix(NFCORE_RAREDISEASE.out.call_sv_tbi) .mix(NFCORE_RAREDISEASE.out.saltshaker_html) @@ -831,6 +839,12 @@ output { qc_bam { path { _meta, _file -> "qc_bam/" } } + call_mobile_elements { + path { _meta, _file -> "call_mobile_elements/" } + } + annotate_mobile_elements { + path { _meta, _file -> "annotate_mobile_elements/" } + } call_sv { path { _meta, _file -> "call_sv/" } } diff --git a/subworkflows/local/annotate_consequence_pli/main.nf b/subworkflows/local/annotate_consequence_pli/main.nf index 50a2e6ee2..7629731ad 100644 --- a/subworkflows/local/annotate_consequence_pli/main.nf +++ b/subworkflows/local/annotate_consequence_pli/main.nf @@ -11,27 +11,19 @@ workflow ANNOTATE_CSQ_PLI { ch_variant_consequences // channel: [mandatory] [ path(consequences) ] ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] val_index // bool - val_publish_dir // val: destination string, or '' to skip publishing main: CUSTOM_ADDMOSTSEVERECONSEQUENCE (ch_vcf, ch_variant_consequences) CUSTOM_ADDMOSTSEVEREPLI (CUSTOM_ADDMOSTSEVERECONSEQUENCE.out.vcf) - ch_tbi_publish = channel.empty() + ch_tbi = channel.empty() if (val_index) { TABIX_TABIX(CUSTOM_ADDMOSTSEVEREPLI.out.vcf) - ch_tbi_publish = TABIX_TABIX.out.index - } - - ch_publish = channel.empty() - if (val_publish_dir) { - ch_publish = CUSTOM_ADDMOSTSEVEREPLI.out.vcf - .mix(ch_tbi_publish) - .map { meta, value -> [val_publish_dir, [meta, value]] } + ch_tbi = TABIX_TABIX.out.index } emit: - vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf_ann = CUSTOM_ADDMOSTSEVEREPLI.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test index f25124a68..35035998c 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test @@ -27,7 +27,6 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = false - input[3] = false """ } } @@ -57,7 +56,6 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = true - input[3] = "ann_csq" """ } } @@ -66,10 +64,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort(), + workflow.out.vcf_ann.collect { meta, f -> file(f).name }, + workflow.out.tbi.collect { meta, f -> file(f).name }, path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5, path(workflow.out.vcf_ann[0][1]).vcf.summary ).match() } @@ -92,7 +88,6 @@ nextflow_workflow { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/genmod_compound.vcf', checkIfExists: true) ]) input[2] = true - input[3] = "ann_csq" """ } } diff --git a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap index eb6659188..c50352284 100644 --- a/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_consequence_pli/tests/main.nf.test.snap @@ -2,15 +2,17 @@ "ANNOTATE_CSQ_PLI - with index": { "content": [ [ - "severepli.vcf.gz", + "severepli.vcf.gz" + ], + [ "severepli.vcf.gz.tbi" ], "58d9c7a329ee86094acc0826b671652c", "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]" ], - "timestamp": "2026-03-16T22:58:51.504628424", + "timestamp": "2026-06-26T16:05:57.762515171", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -33,47 +35,23 @@ { "id": "justhusky" }, - "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ [ - "ann_csq", - [ - { - "id": "justhusky" - }, - "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "ann_csq", - [ - { - "id": "justhusky" - }, - "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "publish": [ + "tbi": [ [ - "ann_csq", - [ - { - "id": "justhusky" - }, - "severepli.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "ann_csq", - [ - { - "id": "justhusky" - }, - "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky" + }, + "severepli.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf_ann": [ @@ -86,9 +64,9 @@ ] } ], - "timestamp": "2026-03-16T22:56:18.385999497", + "timestamp": "2026-06-26T15:58:14.350740472", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/call_mobile_elements/main.nf b/subworkflows/local/call_mobile_elements/main.nf index 2f8a46883..7756770a9 100644 --- a/subworkflows/local/call_mobile_elements/main.nf +++ b/subworkflows/local/call_mobile_elements/main.nf @@ -119,12 +119,7 @@ workflow CALL_MOBILE_ELEMENTS { SVDB_MERGE_ME ( ch_svdb_merge_me_input, [], true ) TABIX_ME ( SVDB_MERGE_ME.out.vcf ) - ch_publish = SVDB_MERGE_ME.out.vcf - .mix(TABIX_ME.out.index) - .map { meta, value -> ['call_mobile_elements/', [meta, value]] } - emit: - tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] - vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] - publish = ch_publish // channel: [ val(destination), val(value) ] + tbi = TABIX_ME.out.index // channel: [ val(meta), path(tbi) ] + vcf = SVDB_MERGE_ME.out.vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap index bf9b9c3a3..3fd01589b 100644 --- a/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap +++ b/subworkflows/local/call_mobile_elements/tests/main.nf.test.snap @@ -18,46 +18,6 @@ "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "2": [ - [ - "call_mobile_elements/", - [ - { - "id": "justhusky" - }, - "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_mobile_elements/", - [ - { - "id": "justhusky" - }, - "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "publish": [ - [ - "call_mobile_elements/", - [ - { - "id": "justhusky" - }, - "justhusky_mobile_elements.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "call_mobile_elements/", - [ - { - "id": "justhusky" - }, - "justhusky_mobile_elements.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], "tbi": [ [ { @@ -76,9 +36,9 @@ ] } ], - "timestamp": "2026-03-13T09:28:04.925769836", + "timestamp": "2026-06-26T16:04:01.036079356", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 97b52c49e..218b765bd 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -258,7 +258,10 @@ workflow RAREDISEASE { ch_call_snv_mt_vcf = channel.empty() ch_call_sv_publish = channel.empty() ch_call_repeat_expansions_publish = channel.empty() - ch_call_mobile_elements_publish = channel.empty() + ch_call_mobile_elements_tbi = channel.empty() + ch_call_mobile_elements_vcf = channel.empty() + ch_ann_csq_pli_me_tbi = channel.empty() + ch_ann_csq_pli_me_vcf_ann = channel.empty() ch_annotate_genome_snvs_bcftools_concat_tbi = channel.empty() ch_annotate_genome_snvs_bcftools_concat_vcf = channel.empty() ch_annotate_genome_snvs_chromograph_autozyg_plots = channel.empty() @@ -554,8 +557,7 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SNV ( ch_variant_consequences_snv, ch_ann_csq_snv_in, - false, - '' + false ) ANN_CSQ_PLI_SNV.out.vcf_ann @@ -626,8 +628,7 @@ workflow RAREDISEASE { ANN_CSQ_PLI_MT( ch_variant_consequences_snv, ch_ann_csq_mtsnv_in, - false, - '' + false ) ANN_CSQ_PLI_MT.out.vcf_ann @@ -756,8 +757,7 @@ workflow RAREDISEASE { ANN_CSQ_PLI_SV ( ch_variant_consequences_sv, ch_ann_csq_sv_in, - false, - '' + false ) ANN_CSQ_PLI_SV.out.vcf_ann @@ -794,7 +794,8 @@ workflow RAREDISEASE { ch_genome_fasta, ch_me_references ) - ch_call_mobile_elements_publish = CALL_MOBILE_ELEMENTS.out.publish + ch_call_mobile_elements_vcf = CALL_MOBILE_ELEMENTS.out.vcf + ch_call_mobile_elements_tbi = CALL_MOBILE_ELEMENTS.out.tbi if (!skip_me_annotation) { ANNOTATE_MOBILE_ELEMENTS( @@ -832,11 +833,10 @@ workflow RAREDISEASE { ANN_CSQ_PLI_ME( ch_variant_consequences_sv, ch_ann_csq_me_in, - true, - 'annotate_mobile_elements/' + true ) - ch_call_mobile_elements_publish = ch_call_mobile_elements_publish - .mix(ANN_CSQ_PLI_ME.out.publish) + ch_ann_csq_pli_me_vcf_ann = ANN_CSQ_PLI_ME.out.vcf_ann + ch_ann_csq_pli_me_tbi = ANN_CSQ_PLI_ME.out.tbi } } @@ -1113,12 +1113,15 @@ workflow RAREDISEASE { annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] annotate_genome_snvs_ucsc_wigtobigwig_bw = ch_annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + call_mobile_elements_tbi = ch_call_mobile_elements_tbi // channel: [ val(meta), path(tbi) ] + call_mobile_elements_vcf = ch_call_mobile_elements_vcf // channel: [ val(meta), path(vcf) ] + ann_csq_pli_me_tbi = ch_ann_csq_pli_me_tbi // channel: [ val(meta), path(tbi) ] + ann_csq_pli_me_vcf_ann = ch_ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions publish = ch_call_sv_publish .mix(ch_call_repeat_expansions_publish) - .mix(ch_call_mobile_elements_publish) .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) .mix(ch_generate_cytosure_files_publish) From e00431bb14d86903f2ec1825a3002cf0df01759b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 16:27:29 +0200 Subject: [PATCH 855/872] fix conflicts --- .../local/annotate_mt_snvs/tests/main.nf.test | 29 ++++++++++--------- 1 file changed, 15 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index dbb883788..78917c39d 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -39,34 +39,35 @@ nextflow_workflow { workflow { """ input[0] = channel.of([[id:'resources'], file('https://raw.githubusercontent.com/nf-core/raredisease/refs/heads/master/assets/cadd_to_vcf_header_-1.0-.txt', checkIfExists: true)]).collect() - input[1] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } - input[2] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() - input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() - input[4] = channel.of([ + input[1] = channel.value([[:], []]) + input[2] = Channel.from(env("PWD")).map { dir -> [ [ id: 'cadd_resources' ], dir ] } + input[3] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa', checkIfExists: true)]).collect() + input[4] = channel.of([[id:'mt'], file(params.pipelines_testdata_base_path + 'reference/reference_mt.fa.fai', checkIfExists: true)]).collect() + input[5] = channel.of([ [id:'justhusky', case_id:'justhusky'], file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/vcfanno_gnomad_mt.vcf.gz.tbi', checkIfExists: true), ]) - input[5] = channel.value([[]]) - input[6] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() - input[7] = [ + input[6] = channel.value([[]]) + input[7] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_functions.lua', checkIfExists: true)).collect() + input[8] = [ file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/grch37_gnomad_-r2.1.1-.vcf.gz.tbi', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/vcfanno_cadd.tsv.gz.tbi', checkIfExists: true) ] - input[8] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() - input[9] = UNTAR.out.untar.map { _meta, untar -> untar }.collect() - input[10] = [ + input[9] = channel.of(file(params.pipelines_testdata_base_path + 'reference/vcfanno_config.toml', checkIfExists: true)).collect() + input[10] = UNTAR.out.untar.map { _meta, untar -> untar }.collect() + input[11] = [ file(params.pipelines_testdata_base_path + 'reference/pLI_values.txt', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/LoFtool_scores.txt', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz', checkIfExists: true), file(params.pipelines_testdata_base_path + 'reference/spliceai_21_scores_raw_snv_-v1.3-.vcf.gz.tbi', checkIfExists: true) ] - input[11] = null - input[12] = 'GRCh37' - input[13] = 1.0 - input[14] = 107 + input[12] = null + input[13] = 'GRCh37' + input[14] = 1.0 + input[15] = 107 """ } } From 43fefa83fde249bd2d8932c223763aac73cb7b00 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 16:51:05 +0200 Subject: [PATCH 856/872] update the publish logic in annotate_mt_snvs --- main.nf | 5 + subworkflows/local/annotate_mt_snvs/main.nf | 13 +- .../local/annotate_mt_snvs/tests/main.nf.test | 27 +-- .../annotate_mt_snvs/tests/main.nf.test.snap | 213 +++++++----------- workflows/raredisease.nf | 9 +- 5 files changed, 107 insertions(+), 160 deletions(-) diff --git a/main.nf b/main.nf index 862607601..f5a0eaea9 100644 --- a/main.nf +++ b/main.nf @@ -814,6 +814,8 @@ workflow { .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig) annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw + annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf + .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -849,6 +851,9 @@ output { annotate_snv_genome_rhocallviz_bw { path { meta, _file -> "annotate_snv/genome/${meta.sample}_rhocallviz/" } } + annotate_snv_mt { + path { _meta, _file -> "annotate_snv/mitochondria/" } + } processed_references { path { _meta, _file -> "processed_references/" } enabled params.save_reference diff --git a/subworkflows/local/annotate_mt_snvs/main.nf b/subworkflows/local/annotate_mt_snvs/main.nf index c95545993..54da99c6c 100644 --- a/subworkflows/local/annotate_mt_snvs/main.nf +++ b/subworkflows/local/annotate_mt_snvs/main.nf @@ -92,13 +92,10 @@ workflow ANNOTATE_MT_SNVS { ch_tbi = BCFTOOLS_PLUGINSETGT.out.tbi } - ch_publish = ENSEMBLVEP_MT.out.vcf - .mix(ENSEMBLVEP_MT.out.tbi) - .map { meta, value -> ['annotate_snv/mitochondria/', [meta, value]] } - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] - report = ENSEMBLVEP_MT.out.report // channel: [ path(html) ] - tbi = ch_tbi // channel: [ val(meta), path(tbi) ] - vcf_ann = ch_vcf // channel: [ val(meta), path(vcf) ] + ensemblvep_mt_tbi = ENSEMBLVEP_MT.out.tbi // channel: [ val(meta), path(tbi) ] + ensemblvep_mt_vcf = ENSEMBLVEP_MT.out.vcf // channel: [ val(meta), path(vcf) ] + report = ENSEMBLVEP_MT.out.report // channel: [ val(meta), val(tool), val(toolver), path(html) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf_ann = ch_vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test index 78917c39d..8ce795e77 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test @@ -73,24 +73,16 @@ nextflow_workflow { } then { - // Get published vcf file for snapshot comparison (not tbi file) - def vcfPublish = file(workflow.out.publish[0][1][1]).name.endsWith('.gz') \ - ? workflow.out.publish[0][1][1] \ - : workflow.out.publish[1][1][1] - assertAll( { assert workflow.success }, { assert workflow.out.vcf_ann }, { assert workflow.out.tbi }, { assert workflow.out.report }, - { assert workflow.out.publish }, + { assert workflow.out.ensemblvep_mt_vcf }, + { assert workflow.out.ensemblvep_mt_tbi }, { assert snapshot( "${file(workflow.out.vcf_ann[0][1]).name}:md5,${path(workflow.out.vcf_ann[0][1]).vcf.variantsMD5}", - path(workflow.out.vcf_ann[0][1]).vcf.summary, - workflow.out.publish[0][0], // file destination path - "${file(vcfPublish).name}:md5,${path(vcfPublish).vcf.variantsMD5}" : - path(vcfPublish).vcf.summary, - workflow.out.findAll { key, val -> key.startsWith('versions') } + path(workflow.out.vcf_ann[0][1]).vcf.summary ).match() } ) } @@ -133,18 +125,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot( - workflow.out.collect { name, channel -> - def sorted_channel = channel.toList().sort { item -> - def sortKey = item - while (sortKey instanceof List) { - sortKey = sortKey[-1] - } - sortKey.toString().split(':md5,')[0].tokenize('/')[-1] - } - [name, sorted_channel] - }.sort { it[0] } // Sort by channel name - ).match() } + { assert snapshot(workflow.out).match() } ) } } diff --git a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap index 748400d24..77adf4738 100644 --- a/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap +++ b/subworkflows/local/annotate_mt_snvs/tests/main.nf.test.snap @@ -1,167 +1,128 @@ { "ANNOTATE_MT_SNVS - GRCh37": { "content": [ - { - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,35b30b356d34416a56b262834cbeaf32": "VcfFile [chromosomes=[MT], sampleCount=0, variantCount=18164, phased=true, phasedAutodetect=true]" - }, "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,35b30b356d34416a56b262834cbeaf32", - "VcfFile [chromosomes=[MT], sampleCount=0, variantCount=18164, phased=true, phasedAutodetect=true]", - "annotate_snv/mitochondria/", - { - - } + "VcfFile [chromosomes=[MT], sampleCount=0, variantCount=18164, phased=true, phasedAutodetect=true]" ], - "timestamp": "2026-06-24T11:27:16.802351909", + "timestamp": "2026-06-26T16:50:08.067805575", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "25.10.4" } }, "ANNOTATE_MT_SNVS - GRCh37, stub": { "content": [ - [ - [ - "0", + { + "0": [ [ - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "1", + "1": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", - "ensemblvep", - "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "2", + "2": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "3", + "3": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "publish", + "4": [ [ - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - [ - "annotate_snv/mitochondria/", - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "report", + "ensemblvep_mt_tbi": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", - "ensemblvep", - "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - [ - "tbi", + "ensemblvep_mt_vcf": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - [ - "vcf_ann", + "report": [ [ - [ - { - "id": "justhusky", - "case_id": "justhusky", - "prefix": "vcfanno_gnomad_mt_vcfanno_vep" - }, - "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "ANNOTATE_MT_SNVS:ENSEMBLVEP_MT", + "ensemblvep", + "vcfanno_gnomad_mt_vcfanno_vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf_ann": [ + [ + { + "id": "justhusky", + "case_id": "justhusky", + "prefix": "vcfanno_gnomad_mt_vcfanno_vep" + }, + "vcfanno_gnomad_mt_vcfanno_vep.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] - ] + } ], - "timestamp": "2026-06-24T11:04:00.579594708", + "timestamp": "2026-06-26T16:48:12.895866197", "meta": { "nf-test": "0.9.5", - "nextflow": "26.03.4" + "nextflow": "25.10.4" } } } \ No newline at end of file diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 97b52c49e..52731bef2 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -267,7 +267,8 @@ workflow RAREDISEASE { ch_annotate_genome_snvs_rhocall_viz_bed = channel.empty() ch_annotate_genome_snvs_rhocall_viz_wig = channel.empty() ch_annotate_genome_snvs_ucsc_wigtobigwig_bw = channel.empty() - ch_annotate_mt_snvs_publish = channel.empty() + ch_annotate_mt_snvs_ensemblvep_mt_tbi = channel.empty() + ch_annotate_mt_snvs_ensemblvep_mt_vcf = channel.empty() ch_annotate_sv_publish = channel.empty() ch_generate_cytosure_files_publish = channel.empty() ch_gens_publish = channel.empty() @@ -600,7 +601,8 @@ workflow RAREDISEASE { val_homoplasmy_af_threshold, val_vep_cache_version ).set { ch_mt_annotate } - ch_annotate_mt_snvs_publish = ch_mt_annotate.publish + ch_annotate_mt_snvs_ensemblvep_mt_tbi = ch_mt_annotate.ensemblvep_mt_tbi + ch_annotate_mt_snvs_ensemblvep_mt_vcf = ch_mt_annotate.ensemblvep_mt_vcf ch_mt_annotate.vcf_ann .multiMap { meta, vcf -> @@ -1113,13 +1115,14 @@ workflow RAREDISEASE { annotate_genome_snvs_rhocall_viz_bed = ch_annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] annotate_genome_snvs_rhocall_viz_wig = ch_annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] annotate_genome_snvs_ucsc_wigtobigwig_bw = ch_annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + annotate_mt_snvs_ensemblvep_mt_tbi = ch_annotate_mt_snvs_ensemblvep_mt_tbi // channel: [ val(meta), path(tbi) ] + annotate_mt_snvs_ensemblvep_mt_vcf = ch_annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions publish = ch_call_sv_publish .mix(ch_call_repeat_expansions_publish) .mix(ch_call_mobile_elements_publish) - .mix(ch_annotate_mt_snvs_publish) .mix(ch_annotate_sv_publish) .mix(ch_generate_cytosure_files_publish) .mix(ch_gens_publish) From 644ae6a483422e6ecbc20092771e96b067eed17e Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 16:53:00 +0200 Subject: [PATCH 857/872] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4a20b6a84..47f786245 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_snv, call_snv_deepvariant, and postprocess_MT_calls subworkflows [#863](https://github.com/nf-core/raredisease/pull/863) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858) - Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858) From af864d6d747044e8e01dc917b7989fbe598ce83b Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 26 Jun 2026 17:03:12 +0200 Subject: [PATCH 858/872] Fix error --- main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/main.nf b/main.nf index f5a0eaea9..086b6c89f 100644 --- a/main.nf +++ b/main.nf @@ -598,6 +598,8 @@ workflow NFCORE_RAREDISEASE { annotate_genome_snvs_rhocall_viz_bed = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ] annotate_genome_snvs_rhocall_viz_wig = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ] annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] + annotate_mt_snvs_ensemblvep_mt_tbi = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi // channel: [ val(meta), path(tbi) ] + annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish From d4a81a0a157e559d76718aad97d2c1766d98c9aa Mon Sep 17 00:00:00 2001 From: dorotejavujinovic Date: Mon, 29 Jun 2026 11:48:09 +0200 Subject: [PATCH 859/872] Address review: topic-channel versions, skip_tools gating, move params to main.nf, sync GATK modules, fix svdb/merge newline --- CHANGELOG.md | 3 +- conf/modules/contamination.config | 6 +- main.nf | 31 ++++- modules.json | 4 +- modules/local/parse_contamination/main.nf | 12 +- modules/local/parse_contamination/meta.yml | 77 +++++++---- .../gatk4/calculatecontamination/main.nf | 16 +-- .../gatk4/calculatecontamination/meta.yml | 26 +++- .../calculatecontamination/tests/main.nf.test | 33 ++--- .../tests/main.nf.test.snap | 120 ++++++++---------- .../nf-core/gatk4/getpileupsummaries/main.nf | 14 +- .../nf-core/gatk4/getpileupsummaries/meta.yml | 26 +++- .../getpileupsummaries/tests/main.nf.test | 24 ++-- .../tests/main.nf.test.snap | 60 ++++++--- modules/nf-core/svdb/merge/main.nf | 2 +- nextflow.config | 1 - nextflow_schema.json | 11 +- .../local/contamination_check/main.nf | 4 - .../contamination_check/tests/main.nf.test | 6 +- .../tests/main.nf.test.snap | 10 +- workflows/raredisease.nf | 25 +--- 21 files changed, 269 insertions(+), 242 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 62daa0342..fe938076b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` -- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2 [#758](https://github.com/nf-core/raredisease/pull/758) +- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2, enabled by providing `contamination_sites` and skippable via `--skip_tools contamination` [#758](https://github.com/nf-core/raredisease/pull/758) - GATK Contamination results displayed in MultiQC with color-coded thresholds [#758](https://github.com/nf-core/raredisease/pull/758) ### `Changed` @@ -28,7 +28,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Old parameter | New parameter | | ------------- | ----------------------- | -| | run_contamination | | | contamination_sites | | | contamination_sites_tbi | diff --git a/conf/modules/contamination.config b/conf/modules/contamination.config index f07ebeca2..3acea4ec3 100644 --- a/conf/modules/contamination.config +++ b/conf/modules/contamination.config @@ -14,8 +14,7 @@ process { ext.prefix = { "${meta.id}_pileups" } publishDir = [ path: { "${params.outdir}/qc/contamination/pileups" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } @@ -27,8 +26,7 @@ process { ext.prefix = { "${meta.id}_contamination" } publishDir = [ path: { "${params.outdir}/qc/contamination" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + mode: params.publish_dir_mode ] } diff --git a/main.nf b/main.nf index 6e5ad2214..187c84f4d 100644 --- a/main.nf +++ b/main.nf @@ -148,6 +148,8 @@ workflow NFCORE_RAREDISEASE { val_verifybamid_svd_mu val_verifybamid_svd_ud val_vep_cache + val_contamination_sites + val_contamination_sites_tbi main: @@ -323,6 +325,26 @@ workflow NFCORE_RAREDISEASE { skip_peddy = parseSkipList(val_skip_tools, 'peddy') skip_smncopynumbercaller = parseSkipList(val_skip_tools, 'smncopynumbercaller') skip_vcf2cytosure = parseSkipList(val_skip_tools, 'vcf2cytosure') + // GATK contamination check is also skipped when no contamination sites are supplied + skip_contamination = parseSkipList(val_skip_tools, 'contamination') || !val_contamination_sites + + // + // Build contamination check inputs (channel construction kept out of the named workflow) + // + ch_contamination_sites = channel.empty() + ch_intervals_contamination = channel.empty() + if (!skip_contamination) { + ch_contamination_sites = channel.of([ + file(val_contamination_sites, checkIfExists: true), + file(val_contamination_sites_tbi, checkIfExists: true) + ]).collect() + + // Use intervals for WES (target regions); WGS stays genome-wide. + // CRITICAL: keep channel.empty() for WGS, not channel.of([]), so downstream ifEmpty handling works. + if (val_analysis_type.equals("wes") && val_target_bed) { + ch_intervals_contamination = channel.fromPath(val_target_bed).collect() + } + } // Subworkflows skip_me_annotation = parseSkipList(val_skip_subworkflows, 'me_annotation') @@ -526,7 +548,10 @@ workflow NFCORE_RAREDISEASE { val_svdb_query_dbs, val_target_bed, val_variant_caller, - val_vep_cache_version + val_vep_cache_version, + skip_contamination, + ch_contamination_sites, + ch_intervals_contamination ) emit: align_fastp_out = RAREDISEASE.out.align_fastp_out // channel: [ val(meta), path(json|html|log|reads|reads_fail|reads_merged) ] @@ -728,7 +753,9 @@ workflow { params.verifybamid_svd_bed, params.verifybamid_svd_mu, params.verifybamid_svd_ud, - params.vep_cache + params.vep_cache, + params.contamination_sites, + params.contamination_sites_tbi ) // // SUBWORKFLOW: Run completion tasks diff --git a/modules.json b/modules.json index c050cb057..5af9f6f3a 100644 --- a/modules.json +++ b/modules.json @@ -258,12 +258,12 @@ }, "gatk4/calculatecontamination": { "branch": "master", - "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "gatk4/getpileupsummaries": { "branch": "master", - "git_sha": "ae8cd884f895585c6799ab4eb6a2c9f44df03336", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }, "gawk": { diff --git a/modules/local/parse_contamination/main.nf b/modules/local/parse_contamination/main.nf index d8be68d13..3faf8e1b1 100644 --- a/modules/local/parse_contamination/main.nf +++ b/modules/local/parse_contamination/main.nf @@ -12,7 +12,7 @@ process PARSE_CONTAMINATION { output: tuple val(meta), path("*_contamination_mqc.tsv"), emit: mqc_table - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //'"), topic: versions, emit: versions_python when: task.ext.when == null || task.ext.when @@ -24,21 +24,11 @@ process PARSE_CONTAMINATION { --input ${contamination_table} \\ --sample_id ${meta.id} \\ --prefix ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}_contamination_mqc.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //') - END_VERSIONS """ } diff --git a/modules/local/parse_contamination/meta.yml b/modules/local/parse_contamination/meta.yml index 6018fd2df..50803de8f 100644 --- a/modules/local/parse_contamination/meta.yml +++ b/modules/local/parse_contamination/meta.yml @@ -1,29 +1,62 @@ -name: parse_contamination -description: Parse GATK CalculateContamination output for MultiQC +name: "parse_contamination" +description: Parse GATK CalculateContamination output into a MultiQC custom-content table keywords: - contamination - - MultiQC + - multiqc - parsing tools: - - python: - description: Python programming language - homepage: https://www.python.org/ + - "python": + description: "Python programming language" + homepage: "https://www.python.org/" + documentation: "https://docs.python.org/" + licence: + - "PSF" + identifier: "" input: - - meta: - type: map - description: Groovy Map containing sample information - - contamination_table: - type: file - description: GATK CalculateContamination output table - pattern: "*.contamination.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - contamination_table: + type: file + description: GATK CalculateContamination output table + pattern: "*.contamination.table" + ontologies: [] output: - - mqc_table: - type: file - description: MultiQC custom content table - pattern: "*_contamination_mqc.tsv" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + mqc_table: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_contamination_mqc.tsv": + type: file + description: MultiQC custom-content table + pattern: "*_contamination_mqc.tsv" + ontologies: [] + versions_python: + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - python3 --version | sed 's/Python //': + type: eval + description: The expression to obtain the version of the tool +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - python: + type: string + description: The name of the tool + - python3 --version | sed 's/Python //': + type: eval + description: The expression to obtain the version of the tool authors: - - "56053vujinovic" + - "@dorotejavujinovic" +maintainers: + - "@dorotejavujinovic" diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf index 0b8706e76..2601a69d8 100644 --- a/modules/nf-core/gatk4/calculatecontamination/main.nf +++ b/modules/nf-core/gatk4/calculatecontamination/main.nf @@ -3,7 +3,7 @@ process GATK4_CALCULATECONTAMINATION { label 'process_low' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" @@ -12,8 +12,8 @@ process GATK4_CALCULATECONTAMINATION { output: tuple val(meta), path('*.contamination.table'), emit: contamination - tuple val(meta), path('*.segmentation.table'), emit: segmentation, optional: true - path "versions.yml", emit: versions + tuple val(meta), path('*.segmentation.table'), emit: segmentation, optional: true + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -38,11 +38,6 @@ process GATK4_CALCULATECONTAMINATION { ${matched_command} \\ --tmp-dir . \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: @@ -50,10 +45,5 @@ process GATK4_CALCULATECONTAMINATION { """ touch ${prefix}.contamination.table touch ${prefix}.segmentation.table - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml index 477e9d3b1..f07240b56 100644 --- a/modules/nf-core/gatk4/calculatecontamination/meta.yml +++ b/modules/nf-core/gatk4/calculatecontamination/meta.yml @@ -61,13 +61,27 @@ output: (optional) pattern: "*.segmentation.table" ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test index 81f048f67..6e4bb5ea9 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test @@ -22,13 +22,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match("versions") }, - { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() } + { assert snapshot( + file(process.out.contamination.get(0).get(1)).readLines()[0], + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("human - pileup-table - matched-pair") { @@ -45,13 +46,14 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match("versions_pair") }, - { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() } + { assert snapshot( + file(process.out.contamination.get(0).get(1)).readLines()[0], + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("human - pileup-table - segmentation") { @@ -70,14 +72,15 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, - { assert snapshot(process.out.versions).match("versions_segmentation") }, - { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match("contamination") }, - { assert snapshot(file(process.out.segmentation.get(0).get(1)).readLines()[0]).match("segmentation") } + { assert snapshot( + file(process.out.contamination.get(0).get(1)).readLines()[0], + file(process.out.segmentation.get(0).get(1)).readLines()[0], + process.out.findAll { key, val -> key.startsWith("versions") } + ).match() } ) } - } test("human - pileup-table - stub") { @@ -95,12 +98,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap index 4ef184bfc..33077c56c 100644 --- a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap @@ -1,59 +1,22 @@ { - "versions_pair": { - "content": [ - [ - "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T12:29:33.077296321" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T12:29:20.224234796" - }, - "versions_segmentation": { - "content": [ - [ - "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" - }, - "timestamp": "2025-09-15T12:29:45.806413439" - }, - "segmentation": { - "content": [ - "#SAMPLE=tumour" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-05-15T12:57:38.845287" - }, "human - pileup-table": { "content": [ - "sample\tcontamination\terror" + "sample\tcontamination\terror", + { + "versions_gatk4": [ + [ + "GATK4_CALCULATECONTAMINATION", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-15T11:09:16.292509" + "timestamp": "2026-01-21T15:50:57.391538082" }, "human - pileup-table - stub": { "content": [ @@ -75,7 +38,11 @@ ] ], "2": [ - "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + [ + "GATK4_CALCULATECONTAMINATION", + "gatk4", + "4.6.2.0" + ] ], "contamination": [ [ @@ -93,35 +60,58 @@ "test.segmentation.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,703ef3c3104ffcb977090771a8761da2" + "versions_gatk4": [ + [ + "GATK4_CALCULATECONTAMINATION", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2025-09-15T12:29:55.994434812" + "timestamp": "2026-01-21T15:51:38.901543934" }, "human - pileup-table - matched-pair": { "content": [ - "sample\tcontamination\terror" + "sample\tcontamination\terror", + { + "versions_gatk4": [ + [ + "GATK4_CALCULATECONTAMINATION", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-15T11:09:26.408848" + "timestamp": "2026-01-21T15:51:12.172307513" }, - "contamination": { + "human - pileup-table - segmentation": { "content": [ - "sample\tcontamination\terror" + "sample\tcontamination\terror", + "#SAMPLE=tumour", + { + "versions_gatk4": [ + [ + "GATK4_CALCULATECONTAMINATION", + "gatk4", + "4.6.2.0" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.3", + "nextflow": "25.10.2" }, - "timestamp": "2024-05-15T12:57:38.840651" + "timestamp": "2026-01-21T15:51:27.280277084" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf index d0cabdaf8..c7f6d3308 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/getpileupsummaries/main.nf @@ -3,7 +3,7 @@ process GATK4_GETPILEUPSUMMARIES { label 'process_low' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ce/ced519873646379e287bc28738bdf88e975edd39a92e7bc6a34bccd37153d9d0/data' : 'community.wave.seqera.io/library/gatk4_gcnvkernel:edb12e4f0bf02cd3'}" @@ -17,7 +17,7 @@ process GATK4_GETPILEUPSUMMARIES { output: tuple val(meta), path('*.pileups.table'), emit: table - path "versions.yml", emit: versions + tuple val("${task.process}"), val('gatk4'), eval("gatk --version | sed -n '/GATK.*v/s/.*v//p'"), topic: versions, emit: versions_gatk4 when: task.ext.when == null || task.ext.when @@ -45,21 +45,11 @@ process GATK4_GETPILEUPSUMMARIES { ${interval_command} \\ --tmp-dir . \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.pileups.table - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml index d7f66ad19..04113b110 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/meta.yml @@ -93,13 +93,27 @@ output: description: Table containing read counts for each site. pattern: "*.pileups.table" ontologies: [] + versions_gatk4: + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - gatk4: + type: string + description: The name of the tool + - gatk --version | sed -n '/GATK.*v/s/.*v//p': + type: eval + description: The expression to obtain the version of the tool authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test index 79cd6344c..27351bc49 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test @@ -29,12 +29,11 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("human - cram") { @@ -46,16 +45,16 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list', checkIfExists: true) - ] + ] input[1] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] input[2] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] input[3] = [ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + ] input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi', checkIfExists: true) """ @@ -63,12 +62,11 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } test("human - bam - stub") { @@ -93,12 +91,10 @@ nextflow_process { } then { + assert process.success assertAll( - { assert process.success }, { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap index fe713315a..8c5c61ec5 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/getpileupsummaries/tests/main.nf.test.snap @@ -11,7 +11,11 @@ ] ], "1": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ], "table": [ [ @@ -21,16 +25,20 @@ "test.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "versions": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + "versions_gatk4": [ + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-15T15:15:36.702715205" + "timestamp": "2026-02-05T12:53:49.568746566" }, "human - bam": { "content": [ @@ -44,7 +52,11 @@ ] ], "1": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ], "table": [ [ @@ -54,16 +66,20 @@ "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], - "versions": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + "versions_gatk4": [ + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-15T15:14:59.43518059" + "timestamp": "2026-02-05T12:53:07.424914004" }, "human - cram": { "content": [ @@ -77,7 +93,11 @@ ] ], "1": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ], "table": [ [ @@ -87,15 +107,19 @@ "test.pileups.table:md5,2d7ce4a54df6b9249e12d60737a67dac" ] ], - "versions": [ - "versions.yml:md5,e06a2d6fcf646da962971eab2035b3ee" + "versions_gatk4": [ + [ + "GATK4_GETPILEUPSUMMARIES", + "gatk4", + "4.6.2.0" + ] ] } ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.7" + "nf-test": "0.9.3", + "nextflow": "25.10.3" }, - "timestamp": "2025-09-15T15:15:25.628760353" + "timestamp": "2026-02-05T12:53:33.800648892" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index 96fe8a828..ab14c8d0f 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -94,4 +94,4 @@ process SVDB_MERGE { ${create_index} """ -} \ No newline at end of file +} diff --git a/nextflow.config b/nextflow.config index cf79abb78..f7117cb1e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,7 +35,6 @@ params { mt_subsample_approach = 'reads' mt_subsample_reads = 18000 restrict_to_contigs = null - run_contamination = false run_mt_for_wes = false run_rtgvcfeval = false run_vcfanno_db_sanity_check = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 5ea919533..14feab13d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -443,13 +443,6 @@ "description": "Path to UD matrix file from SVD result of genotype matrix. Used by verifybamid2.", "fa_icon": "fas fa-file-csv" }, - "run_contamination": { - "type": "boolean", - "default": false, - "description": "Run GATK contamination check in addition to VerifyBamID2.", - "help_text": "GATK contamination check works better for WES samples and provides validation for WGS.", - "fa_icon": "fas fa-toggle-on" - }, "contamination_sites": { "type": "string", "exists": true, @@ -643,8 +636,8 @@ "type": "string", "fa_icon": "fas fa-forward", "description": "Disable specified tools.", - "help_text": "Multiple tools can be specified, separated by commas.", - "pattern": "^((fastp|gens|germlinecnvcaller|peddy|smncopynumbercaller|vcf2cytosure|fastqc|ngsbits|mitosalt)?,?)*(? Date: Mon, 29 Jun 2026 15:47:43 +0200 Subject: [PATCH 860/872] update rank variants --- CHANGELOG.md | 1 + main.nf | 21 ++++++ subworkflows/local/rank_variants/main.nf | 18 ++--- .../local/rank_variants/tests/main.nf.test | 1 + .../rank_variants/tests/main.nf.test.snap | 66 ++++++++----------- .../local/rank_variants/tests/nextflow.config | 5 ++ workflows/raredisease.nf | 27 +++++--- 7 files changed, 78 insertions(+), 61 deletions(-) create mode 100644 subworkflows/local/rank_variants/tests/nextflow.config diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d06961cc..e64490ba3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `rank_variants` subworkflow [#896](https://github.com/nf-core/raredisease/pull/896) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) diff --git a/main.nf b/main.nf index 70c55a413..2e61fe95b 100644 --- a/main.nf +++ b/main.nf @@ -609,6 +609,12 @@ workflow NFCORE_RAREDISEASE { annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] annotate_mt_snvs_ensemblvep_mt_tbi = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi // channel: [ val(meta), path(tbi) ] annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] + rank_snv_tbi = RAREDISEASE.out.rank_snv_tbi // channel: [ val(meta), path(tbi) ] + rank_snv_vcf = RAREDISEASE.out.rank_snv_vcf // channel: [ val(meta), path(vcf) ] + rank_mt_tbi = RAREDISEASE.out.rank_mt_tbi // channel: [ val(meta), path(tbi) ] + rank_mt_vcf = RAREDISEASE.out.rank_mt_vcf // channel: [ val(meta), path(vcf) ] + rank_sv_tbi = RAREDISEASE.out.rank_sv_tbi // channel: [ val(meta), path(tbi) ] + rank_sv_vcf = RAREDISEASE.out.rank_sv_vcf // channel: [ val(meta), path(vcf) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish @@ -836,6 +842,12 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) + rank_snv = NFCORE_RAREDISEASE.out.rank_snv_vcf + .mix(NFCORE_RAREDISEASE.out.rank_snv_tbi) + rank_mt = NFCORE_RAREDISEASE.out.rank_mt_vcf + .mix(NFCORE_RAREDISEASE.out.rank_mt_tbi) + rank_sv = NFCORE_RAREDISEASE.out.rank_sv_vcf + .mix(NFCORE_RAREDISEASE.out.rank_sv_tbi) processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -883,6 +895,15 @@ output { annotate_snv_mt { path { _meta, _file -> "annotate_snv/mitochondria/" } } + rank_snv { + path { _meta, _file -> "rank_and_filter/" } + } + rank_mt { + path { _meta, _file -> "rank_and_filter/" } + } + rank_sv { + path { _meta, _file -> "rank_and_filter/" } + } processed_references { path { _meta, _file -> "processed_references/" } enabled params.save_reference diff --git a/subworkflows/local/rank_variants/main.nf b/subworkflows/local/rank_variants/main.nf index f2446196d..aaf7b3dbb 100644 --- a/subworkflows/local/rank_variants/main.nf +++ b/subworkflows/local/rank_variants/main.nf @@ -31,23 +31,17 @@ workflow RANK_VARIANTS { GENMOD_COMPOUND(GENMOD_SCORE.out.vcf) - ch_sort_publish = channel.empty() - ch_tabix_publish = channel.empty() + ch_tbi = channel.empty() if (process_with_sort) { ch_vcf = BCFTOOLS_SORT(GENMOD_COMPOUND.out.vcf).vcf // SV file needs to be sorted before indexing - ch_sort_publish = BCFTOOLS_SORT.out.vcf - .mix(BCFTOOLS_SORT.out.tbi) - .map { meta, value -> ['rank_and_filter/', [meta, value]] } + ch_tbi = BCFTOOLS_SORT.out.tbi } else { - ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_index.map {meta, vcf, _tbi -> return [meta, vcf]} //run only for SNVs - ch_tabix_publish = TABIX_BGZIPTABIX.out.gz_index - .map { meta, gz, tbi -> ['rank_and_filter/', [meta, gz, tbi]] } + ch_vcf = TABIX_BGZIPTABIX(GENMOD_COMPOUND.out.vcf).gz_index.map { meta, vcf, _tbi -> [meta, vcf] } //run only for SNVs + ch_tbi = TABIX_BGZIPTABIX.out.gz_index.map { meta, _gz, tbi -> [meta, tbi] } } - ch_publish = ch_sort_publish.mix(ch_tabix_publish) - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] - vcf = ch_vcf // channel: [ val(meta), path(vcf) ] + tbi = ch_tbi // channel: [ val(meta), path(tbi) ] + vcf = ch_vcf // channel: [ val(meta), path(vcf) ] } diff --git a/subworkflows/local/rank_variants/tests/main.nf.test b/subworkflows/local/rank_variants/tests/main.nf.test index 28c9e510f..1d76f92dc 100644 --- a/subworkflows/local/rank_variants/tests/main.nf.test +++ b/subworkflows/local/rank_variants/tests/main.nf.test @@ -45,6 +45,7 @@ nextflow_workflow { options "-stub" + config "./nextflow.config" when { workflow { """ diff --git a/subworkflows/local/rank_variants/tests/main.nf.test.snap b/subworkflows/local/rank_variants/tests/main.nf.test.snap index d1cc348be..91291db97 100644 --- a/subworkflows/local/rank_variants/tests/main.nf.test.snap +++ b/subworkflows/local/rank_variants/tests/main.nf.test.snap @@ -4,14 +4,11 @@ { "0": [ [ - "rank_and_filter/", - [ - { - "id": "justhusky", - "single_end": false - }, - "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -23,16 +20,13 @@ "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "publish": [ + "tbi": [ [ - "rank_and_filter/", - [ - { - "id": "justhusky", - "single_end": false - }, - "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -46,9 +40,9 @@ ] } ], - "timestamp": "2026-03-17T13:09:47.357626106", + "timestamp": "2026-06-29T15:43:51.267701775", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } }, @@ -57,15 +51,11 @@ { "0": [ [ - "rank_and_filter/", - [ - { - "id": "justhusky", - "single_end": false - }, - "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -77,17 +67,13 @@ "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "publish": [ + "tbi": [ [ - "rank_and_filter/", - [ - { - "id": "justhusky", - "single_end": false - }, - "justhusky.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + { + "id": "justhusky", + "single_end": false + }, + "justhusky.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "vcf": [ @@ -101,9 +87,9 @@ ] } ], - "timestamp": "2026-03-17T13:09:21.870979671", + "timestamp": "2026-06-29T15:39:16.158216602", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.5", "nextflow": "25.10.4" } } diff --git a/subworkflows/local/rank_variants/tests/nextflow.config b/subworkflows/local/rank_variants/tests/nextflow.config new file mode 100644 index 000000000..6770a0c79 --- /dev/null +++ b/subworkflows/local/rank_variants/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'RANK_VARIANTS:BCFTOOLS_SORT' { + ext.args = "--output-type z --write-index=tbi" + } +} diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2fcfae902..ba0eaa032 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -283,9 +283,12 @@ workflow RAREDISEASE { ch_smncopynumbercaller_publish = channel.empty() ch_peddy_publish = channel.empty() ch_multiqc_publish = channel.empty() - ch_rank_snv_publish = channel.empty() - ch_rank_mt_publish = channel.empty() - ch_rank_sv_publish = channel.empty() + ch_rank_snv_tbi = channel.empty() + ch_rank_snv_vcf = channel.empty() + ch_rank_mt_tbi = channel.empty() + ch_rank_mt_vcf = channel.empty() + ch_rank_sv_tbi = channel.empty() + ch_rank_sv_vcf = channel.empty() ch_variant_evaluation_publish = channel.empty() // @@ -581,7 +584,8 @@ workflow RAREDISEASE { ch_ranksnv_nuclear_in, false ) - ch_rank_snv_publish = RANK_VARIANTS_SNV.out.publish + ch_rank_snv_tbi = RANK_VARIANTS_SNV.out.tbi + ch_rank_snv_vcf = RANK_VARIANTS_SNV.out.vcf } // @@ -653,7 +657,8 @@ workflow RAREDISEASE { ch_ranksnv_mt_in, false ) - ch_rank_mt_publish = RANK_VARIANTS_MT.out.publish + ch_rank_mt_tbi = RANK_VARIANTS_MT.out.tbi + ch_rank_mt_vcf = RANK_VARIANTS_MT.out.vcf } } @@ -783,7 +788,8 @@ workflow RAREDISEASE { ch_ranksnv_sv_in, true ) - ch_rank_sv_publish = RANK_VARIANTS_SV.out.publish + ch_rank_sv_tbi = RANK_VARIANTS_SV.out.tbi + ch_rank_sv_vcf = RANK_VARIANTS_SV.out.vcf } } /* @@ -1131,6 +1137,12 @@ workflow RAREDISEASE { call_mobile_elements_vcf = ch_call_mobile_elements_vcf // channel: [ val(meta), path(vcf) ] ann_csq_pli_me_tbi = ch_ann_csq_pli_me_tbi // channel: [ val(meta), path(tbi) ] ann_csq_pli_me_vcf_ann = ch_ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] + rank_snv_tbi = ch_rank_snv_tbi // channel: [ val(meta), path(tbi) ] + rank_snv_vcf = ch_rank_snv_vcf // channel: [ val(meta), path(vcf) ] + rank_mt_tbi = ch_rank_mt_tbi // channel: [ val(meta), path(tbi) ] + rank_mt_vcf = ch_rank_mt_vcf // channel: [ val(meta), path(vcf) ] + rank_sv_tbi = ch_rank_sv_tbi // channel: [ val(meta), path(tbi) ] + rank_sv_vcf = ch_rank_sv_vcf // channel: [ val(meta), path(vcf) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions @@ -1142,9 +1154,6 @@ workflow RAREDISEASE { .mix(ch_smncopynumbercaller_publish) .mix(ch_peddy_publish) .mix(ch_multiqc_publish) - .mix(ch_rank_snv_publish) - .mix(ch_rank_mt_publish) - .mix(ch_rank_sv_publish) .mix(ch_variant_evaluation_publish) } From f1aff176de1781db4352d52472b0001f3ba02f21 Mon Sep 17 00:00:00 2001 From: Irene Duba Date: Tue, 30 Jun 2026 09:38:56 +0200 Subject: [PATCH 861/872] changelog entry --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d06961cc..d8ecae158 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850) - Update saltshaker modules to version 1.1.1 so they can run on empty mitosalt output [#856](https://github.com/nf-core/raredisease/pull/856) +- Update metromap to reflect the addition of mitosalt + saltshaker and removal of eklipse [#892](https://github.com/nf-core/raredisease/pull/892) ### `Fixed` From e1daea51105ff924f708292db62392da1ef237f5 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 09:48:03 +0200 Subject: [PATCH 862/872] merge channels --- main.nf | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/main.nf b/main.nf index 2e61fe95b..4ec4c426f 100644 --- a/main.nf +++ b/main.nf @@ -842,11 +842,11 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) - rank_snv = NFCORE_RAREDISEASE.out.rank_snv_vcf + rank_variants = NFCORE_RAREDISEASE.out.rank_snv_vcf .mix(NFCORE_RAREDISEASE.out.rank_snv_tbi) - rank_mt = NFCORE_RAREDISEASE.out.rank_mt_vcf + .mix(NFCORE_RAREDISEASE.out.rank_mt_vcf) .mix(NFCORE_RAREDISEASE.out.rank_mt_tbi) - rank_sv = NFCORE_RAREDISEASE.out.rank_sv_vcf + .mix(NFCORE_RAREDISEASE.out.rank_sv_vcf) .mix(NFCORE_RAREDISEASE.out.rank_sv_tbi) processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish @@ -895,13 +895,7 @@ output { annotate_snv_mt { path { _meta, _file -> "annotate_snv/mitochondria/" } } - rank_snv { - path { _meta, _file -> "rank_and_filter/" } - } - rank_mt { - path { _meta, _file -> "rank_and_filter/" } - } - rank_sv { + rank_variants { path { _meta, _file -> "rank_and_filter/" } } processed_references { From d73134523a509ef312cf14e6d76975fab55a1d08 Mon Sep 17 00:00:00 2001 From: dorotejavujinovic Date: Tue, 30 Jun 2026 10:00:24 +0200 Subject: [PATCH 863/872] Address review: drop stale QC_BAM.out.versions mix; publish contamination outputs via workflow outputs instead of publishDir --- conf/modules/contamination.config | 13 ------------- main.nf | 10 ++++++++++ workflows/raredisease.nf | 11 ++++++++--- 3 files changed, 18 insertions(+), 16 deletions(-) diff --git a/conf/modules/contamination.config b/conf/modules/contamination.config index 3acea4ec3..f761c2322 100644 --- a/conf/modules/contamination.config +++ b/conf/modules/contamination.config @@ -12,10 +12,6 @@ process { withName: '.*:CONTAMINATION_CHECK:GATK4_GETPILEUPSUMMARIES' { ext.args = '' ext.prefix = { "${meta.id}_pileups" } - publishDir = [ - path: { "${params.outdir}/qc/contamination/pileups" }, - mode: params.publish_dir_mode - ] } // @@ -24,10 +20,6 @@ process { withName: '.*:CONTAMINATION_CHECK:GATK4_CALCULATECONTAMINATION' { ext.args = '' ext.prefix = { "${meta.id}_contamination" } - publishDir = [ - path: { "${params.outdir}/qc/contamination" }, - mode: params.publish_dir_mode - ] } // @@ -35,10 +27,5 @@ process { // withName: '.*:RAREDISEASE:PARSE_CONTAMINATION' { ext.prefix = { "${meta.id}_contamination" } - publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - pattern: '*_mqc.tsv' - ] } } diff --git a/main.nf b/main.nf index 0e12aa77a..06bfbaf34 100644 --- a/main.nf +++ b/main.nf @@ -636,6 +636,8 @@ workflow NFCORE_RAREDISEASE { annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] + contamination_table = RAREDISEASE.out.contamination_table // channel: [ val(meta), path(table) ] + contamination_pileup = RAREDISEASE.out.contamination_pileup // channel: [ val(meta), path(table) ] publish = RAREDISEASE.out.publish .mix(ch_pedfile_publish) .mix(ch_references.publish) // channel: [ val(destination), val(value) ] @@ -863,6 +865,8 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) + contamination = NFCORE_RAREDISEASE.out.contamination_table + contamination_pileups = NFCORE_RAREDISEASE.out.contamination_pileup processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -910,6 +914,12 @@ output { annotate_snv_mt { path { _meta, _file -> "annotate_snv/mitochondria/" } } + contamination { + path { _meta, _file -> "qc/contamination/" } + } + contamination_pileups { + path { _meta, _file -> "qc/contamination/pileups/" } + } processed_references { path { _meta, _file -> "processed_references/" } enabled params.save_reference diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index ad36c5458..9902a24a3 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -411,12 +411,13 @@ workflow RAREDISEASE { val_target_bed, skip_ngsbits ) - ch_versions = ch_versions.mix(QC_BAM.out.versions) // // SUBWORKFLOW: Check for contamination using GATK // - ch_contamination_mqc = Channel.empty() + ch_contamination_mqc = Channel.empty() + ch_contamination_table = Channel.empty() + ch_contamination_pileup = Channel.empty() if (!skip_contamination) { @@ -438,7 +439,9 @@ workflow RAREDISEASE { CONTAMINATION_CHECK.out.contamination_table ) - ch_contamination_mqc = PARSE_CONTAMINATION.out.mqc_table + ch_contamination_mqc = PARSE_CONTAMINATION.out.mqc_table + ch_contamination_table = CONTAMINATION_CHECK.out.contamination_table + ch_contamination_pileup = CONTAMINATION_CHECK.out.pileup_table } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1171,6 +1174,8 @@ workflow RAREDISEASE { ann_csq_pli_me_vcf_ann = ch_ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] + contamination_table = ch_contamination_table // channel: [ val(meta), path(table) ] + contamination_pileup = ch_contamination_pileup // channel: [ val(meta), path(table) ] versions = ch_versions publish = ch_call_sv_publish .mix(ch_annotate_sv_publish) From f281a7c337da11c817706490d3fb9bdfa0a5c137 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 10:22:23 +0200 Subject: [PATCH 864/872] update variant evaluation --- CHANGELOG.md | 1 + main.nf | 29 +++++++++++++ subworkflows/local/variant_evaluation/main.nf | 29 ++++++------- workflows/raredisease.nf | 42 +++++++++++++++++-- 4 files changed, 82 insertions(+), 19 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d06961cc..f01247fff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `variant_evaluation` subworkflow [#897](https://github.com/nf-core/raredisease/pull/897) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) diff --git a/main.nf b/main.nf index 70c55a413..1afbba10a 100644 --- a/main.nf +++ b/main.nf @@ -609,6 +609,19 @@ workflow NFCORE_RAREDISEASE { annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] annotate_mt_snvs_ensemblvep_mt_tbi = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi // channel: [ val(meta), path(tbi) ] annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_baseline_tbi = RAREDISEASE.out.variant_evaluation_baseline_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_baseline_vcf = RAREDISEASE.out.variant_evaluation_baseline_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_fn_tbi = RAREDISEASE.out.variant_evaluation_fn_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_fn_vcf = RAREDISEASE.out.variant_evaluation_fn_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_fp_tbi = RAREDISEASE.out.variant_evaluation_fp_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_fp_vcf = RAREDISEASE.out.variant_evaluation_fp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_non_snp_roc = RAREDISEASE.out.variant_evaluation_non_snp_roc // channel: [ val(meta), path(tsv) ] + variant_evaluation_phasing = RAREDISEASE.out.variant_evaluation_phasing // channel: [ val(meta), path(txt) ] + variant_evaluation_snp_roc = RAREDISEASE.out.variant_evaluation_snp_roc // channel: [ val(meta), path(tsv) ] + variant_evaluation_summary = RAREDISEASE.out.variant_evaluation_summary // channel: [ val(meta), path(txt) ] + variant_evaluation_tp_tbi = RAREDISEASE.out.variant_evaluation_tp_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_tp_vcf = RAREDISEASE.out.variant_evaluation_tp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_weighted_roc = RAREDISEASE.out.variant_evaluation_weighted_roc // channel: [ val(meta), path(tsv) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish @@ -836,6 +849,19 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) + variant_evaluation = NFCORE_RAREDISEASE.out.variant_evaluation_tp_vcf + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_tp_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fn_vcf) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fn_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fp_vcf) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fp_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_baseline_vcf) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_baseline_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_snp_roc) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_non_snp_roc) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_weighted_roc) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_summary) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_phasing) processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -883,6 +909,9 @@ output { annotate_snv_mt { path { _meta, _file -> "annotate_snv/mitochondria/" } } + variant_evaluation { + path { _meta, _file -> "rtgvcfeval/" } + } processed_references { path { _meta, _file -> "processed_references/" } enabled params.save_reference diff --git a/subworkflows/local/variant_evaluation/main.nf b/subworkflows/local/variant_evaluation/main.nf index 68cad1d8d..458afce80 100644 --- a/subworkflows/local/variant_evaluation/main.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -40,21 +40,18 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) - ch_publish = RTGTOOLS_VCFEVAL.out.tp_vcf - .mix(RTGTOOLS_VCFEVAL.out.tp_tbi) - .mix(RTGTOOLS_VCFEVAL.out.fn_vcf) - .mix(RTGTOOLS_VCFEVAL.out.fn_tbi) - .mix(RTGTOOLS_VCFEVAL.out.fp_vcf) - .mix(RTGTOOLS_VCFEVAL.out.fp_tbi) - .mix(RTGTOOLS_VCFEVAL.out.baseline_vcf) - .mix(RTGTOOLS_VCFEVAL.out.baseline_tbi) - .mix(RTGTOOLS_VCFEVAL.out.snp_roc) - .mix(RTGTOOLS_VCFEVAL.out.non_snp_roc) - .mix(RTGTOOLS_VCFEVAL.out.weighted_roc) - .mix(RTGTOOLS_VCFEVAL.out.summary) - .mix(RTGTOOLS_VCFEVAL.out.phasing) - .map { meta, value -> ['rtgvcfeval/', [meta, value]] } - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] + baseline_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi // channel: [ val(meta), path(tbi) ] + baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf // channel: [ val(meta), path(vcf) ] + fn_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi // channel: [ val(meta), path(tbi) ] + fn_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf // channel: [ val(meta), path(vcf) ] + fp_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi // channel: [ val(meta), path(tbi) ] + fp_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf // channel: [ val(meta), path(vcf) ] + non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc // channel: [ val(meta), path(tsv) ] + phasing = RTGTOOLS_VCFEVAL.out.phasing // channel: [ val(meta), path(txt) ] + snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc // channel: [ val(meta), path(tsv) ] + summary = RTGTOOLS_VCFEVAL.out.summary // channel: [ val(meta), path(txt) ] + tp_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi // channel: [ val(meta), path(tbi) ] + tp_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf // channel: [ val(meta), path(vcf) ] + weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc // channel: [ val(meta), path(tsv) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2fcfae902..9217e42fe 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -286,7 +286,19 @@ workflow RAREDISEASE { ch_rank_snv_publish = channel.empty() ch_rank_mt_publish = channel.empty() ch_rank_sv_publish = channel.empty() - ch_variant_evaluation_publish = channel.empty() + ch_variant_evaluation_baseline_tbi = channel.empty() + ch_variant_evaluation_baseline_vcf = channel.empty() + ch_variant_evaluation_fn_tbi = channel.empty() + ch_variant_evaluation_fn_vcf = channel.empty() + ch_variant_evaluation_fp_tbi = channel.empty() + ch_variant_evaluation_fp_vcf = channel.empty() + ch_variant_evaluation_non_snp_roc = channel.empty() + ch_variant_evaluation_phasing = channel.empty() + ch_variant_evaluation_snp_roc = channel.empty() + ch_variant_evaluation_summary = channel.empty() + ch_variant_evaluation_tp_tbi = channel.empty() + ch_variant_evaluation_tp_vcf = channel.empty() + ch_variant_evaluation_weighted_roc = channel.empty() // // Input QC (ch_reads will be empty if fastq input isn't provided so FASTQC won't run if input is not fastq) @@ -953,7 +965,19 @@ workflow RAREDISEASE { ch_sdf, CALL_SNV.out.genome_vcf_tabix ) - ch_variant_evaluation_publish = VARIANT_EVALUATION.out.publish + ch_variant_evaluation_baseline_tbi = VARIANT_EVALUATION.out.baseline_tbi + ch_variant_evaluation_baseline_vcf = VARIANT_EVALUATION.out.baseline_vcf + ch_variant_evaluation_fn_tbi = VARIANT_EVALUATION.out.fn_tbi + ch_variant_evaluation_fn_vcf = VARIANT_EVALUATION.out.fn_vcf + ch_variant_evaluation_fp_tbi = VARIANT_EVALUATION.out.fp_tbi + ch_variant_evaluation_fp_vcf = VARIANT_EVALUATION.out.fp_vcf + ch_variant_evaluation_non_snp_roc = VARIANT_EVALUATION.out.non_snp_roc + ch_variant_evaluation_phasing = VARIANT_EVALUATION.out.phasing + ch_variant_evaluation_snp_roc = VARIANT_EVALUATION.out.snp_roc + ch_variant_evaluation_summary = VARIANT_EVALUATION.out.summary + ch_variant_evaluation_tp_tbi = VARIANT_EVALUATION.out.tp_tbi + ch_variant_evaluation_tp_vcf = VARIANT_EVALUATION.out.tp_vcf + ch_variant_evaluation_weighted_roc = VARIANT_EVALUATION.out.weighted_roc } /* @@ -1131,6 +1155,19 @@ workflow RAREDISEASE { call_mobile_elements_vcf = ch_call_mobile_elements_vcf // channel: [ val(meta), path(vcf) ] ann_csq_pli_me_tbi = ch_ann_csq_pli_me_tbi // channel: [ val(meta), path(tbi) ] ann_csq_pli_me_vcf_ann = ch_ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] + variant_evaluation_baseline_tbi = ch_variant_evaluation_baseline_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_baseline_vcf = ch_variant_evaluation_baseline_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_fn_tbi = ch_variant_evaluation_fn_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_fn_vcf = ch_variant_evaluation_fn_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_fp_tbi = ch_variant_evaluation_fp_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_fp_vcf = ch_variant_evaluation_fp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_non_snp_roc = ch_variant_evaluation_non_snp_roc // channel: [ val(meta), path(tsv) ] + variant_evaluation_phasing = ch_variant_evaluation_phasing // channel: [ val(meta), path(txt) ] + variant_evaluation_snp_roc = ch_variant_evaluation_snp_roc // channel: [ val(meta), path(tsv) ] + variant_evaluation_summary = ch_variant_evaluation_summary // channel: [ val(meta), path(txt) ] + variant_evaluation_tp_tbi = ch_variant_evaluation_tp_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_tp_vcf = ch_variant_evaluation_tp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_weighted_roc = ch_variant_evaluation_weighted_roc // channel: [ val(meta), path(tsv) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] versions = ch_versions @@ -1145,7 +1182,6 @@ workflow RAREDISEASE { .mix(ch_rank_snv_publish) .mix(ch_rank_mt_publish) .mix(ch_rank_sv_publish) - .mix(ch_variant_evaluation_publish) } From 392c002d51ea522ca44e8bbf8499bd91677b7752 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 11:35:49 +0200 Subject: [PATCH 865/872] update gens and generate_cytosure_files --- CHANGELOG.md | 1 + main.nf | 16 ++++++++ .../local/generate_cytosure_files/main.nf | 5 +-- .../tests/main.nf.test | 10 ++++- .../tests/main.nf.test.snap | 40 +++++++++++++++++++ subworkflows/local/gens/main.nf | 7 ---- subworkflows/local/gens/tests/main.nf.test | 12 +----- .../local/gens/tests/main.nf.test.snap | 12 ------ workflows/raredisease.nf | 21 +++++++--- 9 files changed, 83 insertions(+), 41 deletions(-) create mode 100644 subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d06961cc..780583069 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for gens and generate_cytosure_files subworkflows [#898](https://github.com/nf-core/raredisease/pull/898) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) diff --git a/main.nf b/main.nf index 70c55a413..9bdd09b5f 100644 --- a/main.nf +++ b/main.nf @@ -581,6 +581,7 @@ workflow NFCORE_RAREDISEASE { call_sv_tbi = RAREDISEASE.out.call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = RAREDISEASE.out.saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = RAREDISEASE.out.saltshaker_plot // channel: [ val(meta), path(png) ] + generate_cytosure_files_cgh = RAREDISEASE.out.generate_cytosure_files_cgh // channel: [ val(meta), path(cgh) ] mt_del_result = RAREDISEASE.out.mt_del_result // channel: [ val(meta), path(txt) ] call_repeat_expansions_expansionhunter_bai = RAREDISEASE.out.call_repeat_expansions_expansionhunter_bai // channel: [ val(meta), path(bai) ] call_repeat_expansions_expansionhunter_bam = RAREDISEASE.out.call_repeat_expansions_expansionhunter_bam // channel: [ val(meta), path(bam) ] @@ -599,6 +600,10 @@ workflow NFCORE_RAREDISEASE { call_snv_genome_vcf = RAREDISEASE.out.call_snv_genome_vcf // channel: [ val(meta), path(vcf) ] call_snv_mt_tabix = RAREDISEASE.out.call_snv_mt_tabix // channel: [ val(meta), path(tbi) ] call_snv_mt_vcf = RAREDISEASE.out.call_snv_mt_vcf // channel: [ val(meta), path(vcf) ] + gens_baf_bed_gz = RAREDISEASE.out.gens_baf_bed_gz // channel: [ val(meta), path(bed.gz) ] + gens_baf_bed_tbi = RAREDISEASE.out.gens_baf_bed_tbi // channel: [ val(meta), path(tbi) ] + gens_cov_bed_gz = RAREDISEASE.out.gens_cov_bed_gz // channel: [ val(meta), path(bed.gz) ] + gens_cov_bed_tbi = RAREDISEASE.out.gens_cov_bed_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] @@ -818,6 +823,7 @@ workflow { .mix(NFCORE_RAREDISEASE.out.saltshaker_html) .mix(NFCORE_RAREDISEASE.out.saltshaker_plot) .mix(NFCORE_RAREDISEASE.out.mt_del_result) + generate_cytosure_files = NFCORE_RAREDISEASE.out.generate_cytosure_files_cgh call_snv_genome = NFCORE_RAREDISEASE.out.call_snv_genome_vcf .mix(NFCORE_RAREDISEASE.out.call_snv_genome_tabix) .mix(NFCORE_RAREDISEASE.out.call_snv_deepvariant_report) @@ -826,6 +832,10 @@ workflow { call_snv_concatenated = NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_tbi) .mix(NFCORE_RAREDISEASE.out.call_snv_bcftools_concat_csi) + gens = NFCORE_RAREDISEASE.out.gens_baf_bed_gz + .mix(NFCORE_RAREDISEASE.out.gens_baf_bed_tbi) + .mix(NFCORE_RAREDISEASE.out.gens_cov_bed_gz) + .mix(NFCORE_RAREDISEASE.out.gens_cov_bed_tbi) annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi) .mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots) @@ -865,6 +875,9 @@ output { call_sv { path { _meta, _file -> "call_sv/" } } + generate_cytosure_files { + path { _meta, _file -> "vcf2cytosure/" } + } call_snv_genome { path { _meta, _file -> "call_snv/genome/" } } @@ -874,6 +887,9 @@ output { call_snv_concatenated { path { _meta, _file -> "call_snv/concatenated_calls/" } } + gens { + path { _meta, _file -> "gens/" } + } annotate_snv_genome { path { _meta, _file -> "annotate_snv/genome/" } } diff --git a/subworkflows/local/generate_cytosure_files/main.nf b/subworkflows/local/generate_cytosure_files/main.nf index 045722f16..c345bb6a3 100644 --- a/subworkflows/local/generate_cytosure_files/main.nf +++ b/subworkflows/local/generate_cytosure_files/main.nf @@ -87,9 +87,6 @@ workflow GENERATE_CYTOSURE_FILES { ch_blacklist ) - ch_publish = VCF2CYTOSURE.out.cgh - .map { meta, value -> ['vcf2cytosure/', [meta, value]] } - emit: - publish = ch_publish // channel: [ val(destination), val(value) ] + cgh = VCF2CYTOSURE.out.cgh // channel: [ val(meta), path(cgh) ] } diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test b/subworkflows/local/generate_cytosure_files/tests/main.nf.test index fa7d9442d..5cf59d25c 100644 --- a/subworkflows/local/generate_cytosure_files/tests/main.nf.test +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test @@ -42,7 +42,10 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.cgh).match() } + ) } } @@ -74,7 +77,10 @@ nextflow_workflow { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.cgh).match() } + ) } } } diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap b/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap new file mode 100644 index 000000000..a1942b1f9 --- /dev/null +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap @@ -0,0 +1,40 @@ +{ + "GENERATE_CYTOSURE_FILES - no sample_id_map, stub": { + "content": [ + [ + [ + { + "id": "earlycasualcaiman", + "custid": "earlycasualcaiman", + "sex": 1 + }, + "earlycasualcaiman.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "timestamp": "2026-06-30T10:43:45.932851408", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + }, + "GENERATE_CYTOSURE_FILES - with sample_id_map, stub": { + "content": [ + [ + [ + { + "id": "earlycasualcaiman", + "custid": "CUST_001", + "sex": 1 + }, + "CUST_001.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "timestamp": "2026-06-30T10:44:04.545576843", + "meta": { + "nf-test": "0.9.5", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file diff --git a/subworkflows/local/gens/main.nf b/subworkflows/local/gens/main.nf index 22343f8d1..9edb7a421 100644 --- a/subworkflows/local/gens/main.nf +++ b/subworkflows/local/gens/main.nf @@ -59,16 +59,9 @@ workflow GENS { ch_gnomad_pos ) - ch_publish = GENS_GENERATE.out.baf_gz - .mix(GENS_GENERATE.out.baf_tbi) - .mix(GENS_GENERATE.out.cov_gz) - .mix(GENS_GENERATE.out.cov_tbi) - .map { meta, value -> ['gens/', [meta, value]] } - emit: gens_baf_bed_gz = GENS_GENERATE.out.baf_gz // channel: [ val(meta), path(bed.gz) ] gens_baf_bed_tbi = GENS_GENERATE.out.baf_tbi // channel: [ val(meta), path(tbi) ] gens_cov_bed_gz = GENS_GENERATE.out.cov_gz // channel: [ val(meta), path(bed.gz) ] gens_cov_bed_tbi = GENS_GENERATE.out.cov_tbi // channel: [ val(meta), path(tbi) ] - publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/gens/tests/main.nf.test b/subworkflows/local/gens/tests/main.nf.test index de8af8f40..2fb340822 100644 --- a/subworkflows/local/gens/tests/main.nf.test +++ b/subworkflows/local/gens/tests/main.nf.test @@ -54,11 +54,7 @@ nextflow_workflow { workflow.out.gens_baf_bed_gz, workflow.out.gens_baf_bed_tbi, workflow.out.gens_cov_bed_gz, - workflow.out.gens_cov_bed_tbi, - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() + workflow.out.gens_cov_bed_tbi ).match() } ) } @@ -102,11 +98,7 @@ nextflow_workflow { workflow.out.gens_baf_bed_gz, workflow.out.gens_baf_bed_tbi, workflow.out.gens_cov_bed_gz, - workflow.out.gens_cov_bed_tbi, - workflow.out.publish.flatten() - .findAll { it instanceof String && (it.startsWith('/') || it.contains('.')) } - .collect { new File(it).name } - .sort() + workflow.out.gens_cov_bed_tbi ).match() } ) diff --git a/subworkflows/local/gens/tests/main.nf.test.snap b/subworkflows/local/gens/tests/main.nf.test.snap index 3cd91562a..d3822eed7 100644 --- a/subworkflows/local/gens/tests/main.nf.test.snap +++ b/subworkflows/local/gens/tests/main.nf.test.snap @@ -56,12 +56,6 @@ }, "slowlycivilbuck_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "slowlycivilbuck_gens.baf.bed.gz", - "slowlycivilbuck_gens.baf.bed.gz.tbi", - "slowlycivilbuck_gens.cov.bed.gz", - "slowlycivilbuck_gens.cov.bed.gz.tbi" ] ], "timestamp": "2026-03-17T11:26:00.382738988", @@ -127,12 +121,6 @@ }, "earlycasualcaiman_gens.cov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - [ - "earlycasualcaiman_gens.baf.bed.gz", - "earlycasualcaiman_gens.baf.bed.gz.tbi", - "earlycasualcaiman_gens.cov.bed.gz", - "earlycasualcaiman_gens.cov.bed.gz.tbi" ] ], "timestamp": "2026-03-17T11:25:27.677483077", diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 2fcfae902..3b666a153 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -277,8 +277,11 @@ workflow RAREDISEASE { ch_annotate_mt_snvs_ensemblvep_mt_tbi = channel.empty() ch_annotate_mt_snvs_ensemblvep_mt_vcf = channel.empty() ch_annotate_sv_publish = channel.empty() - ch_generate_cytosure_files_publish = channel.empty() - ch_gens_publish = channel.empty() + ch_generate_cytosure_files_cgh = channel.empty() + ch_gens_baf_bed_gz = channel.empty() + ch_gens_baf_bed_tbi = channel.empty() + ch_gens_cov_bed_gz = channel.empty() + ch_gens_cov_bed_tbi = channel.empty() ch_fastqc_publish = channel.empty() ch_smncopynumbercaller_publish = channel.empty() ch_peddy_publish = channel.empty() @@ -917,7 +920,7 @@ workflow RAREDISEASE { ch_sv_annotate.vcf_ann, val_sample_id_map ) - ch_generate_cytosure_files_publish = GENERATE_CYTOSURE_FILES.out.publish + ch_generate_cytosure_files_cgh = GENERATE_CYTOSURE_FILES.out.cgh } /* @@ -938,7 +941,10 @@ workflow RAREDISEASE { ch_gens_pon_female, ch_gens_pon_male ) - ch_gens_publish = GENS.out.publish + ch_gens_baf_bed_gz = GENS.out.gens_baf_bed_gz + ch_gens_baf_bed_tbi = GENS.out.gens_baf_bed_tbi + ch_gens_cov_bed_gz = GENS.out.gens_cov_bed_gz + ch_gens_cov_bed_tbi = GENS.out.gens_cov_bed_tbi } /* @@ -1103,6 +1109,7 @@ workflow RAREDISEASE { call_sv_tbi = ch_call_sv_tbi // channel: [ val(meta), path(tbi) ] saltshaker_html = ch_saltshaker_html // channel: [ val(meta), path(html) ] saltshaker_plot = ch_saltshaker_plot // channel: [ val(meta), path(png) ] + generate_cytosure_files_cgh = ch_generate_cytosure_files_cgh // channel: [ val(meta), path(cgh) ] mt_del_result = ch_mt_del_result // channel: [ val(meta), path(txt) ] call_repeat_expansions_expansionhunter_bai = ch_call_repeat_expansions_expansionhunter_bai // channel: [ val(meta), path(bai) ] call_repeat_expansions_expansionhunter_bam = ch_call_repeat_expansions_expansionhunter_bam // channel: [ val(meta), path(bam) ] @@ -1117,6 +1124,10 @@ workflow RAREDISEASE { call_snv_genome_vcf = ch_call_snv_genome_vcf // channel: [ val(meta), path(vcf) ] call_snv_mt_tabix = ch_call_snv_mt_tabix // channel: [ val(meta), path(tbi) ] call_snv_mt_vcf = ch_call_snv_mt_vcf // channel: [ val(meta), path(vcf) ] + gens_baf_bed_gz = ch_gens_baf_bed_gz // channel: [ val(meta), path(bed.gz) ] + gens_baf_bed_tbi = ch_gens_baf_bed_tbi // channel: [ val(meta), path(tbi) ] + gens_cov_bed_gz = ch_gens_cov_bed_gz // channel: [ val(meta), path(bed.gz) ] + gens_cov_bed_tbi = ch_gens_cov_bed_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_tbi = ch_annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ] annotate_genome_snvs_bcftools_concat_vcf = ch_annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ] annotate_genome_snvs_chromograph_autozyg_plots = ch_annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ] @@ -1136,8 +1147,6 @@ workflow RAREDISEASE { versions = ch_versions publish = ch_call_sv_publish .mix(ch_annotate_sv_publish) - .mix(ch_generate_cytosure_files_publish) - .mix(ch_gens_publish) .mix(ch_fastqc_publish) .mix(ch_smncopynumbercaller_publish) .mix(ch_peddy_publish) From 7e383a36f7f38eb2b3c26c811674b754625276c2 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 12:02:43 +0200 Subject: [PATCH 866/872] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 780583069..bf0ee16c9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` -- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for gens and generate_cytosure_files subworkflows [#898](https://github.com/nf-core/raredisease/pull/898) +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for gens and generate_cytosure_files subworkflows [#899](https://github.com/nf-core/raredisease/pull/899) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) From 9f1f595acdfd6e2bf59c264f2a08560524aa04c4 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 13:28:22 +0200 Subject: [PATCH 867/872] update prep refs --- CHANGELOG.md | 1 + main.nf | 74 +- subworkflows/local/prepare_references/main.nf | 45 - .../prepare_references/tests/main.nf.test | 2 - .../tests/main.nf.test.snap | 1588 +---------------- 5 files changed, 74 insertions(+), 1636 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d06961cc..8d5350361 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `prepare_references` subworkflow [#900](https://github.com/nf-core/raredisease/pull/900) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_repeat_expansions subworkflow [#893](https://github.com/nf-core/raredisease/pull/893) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for call_mobile_elements and annotate_consequence_pli subworkflows; remove `val_publish_dir` parameter from annotate_consequence_pli [#894](https://github.com/nf-core/raredisease/pull/894) - Replace `ch_publish`/`subworkflow_results` with named typed channel emits for `annotate_mt_snvs` subworkflow [#895](https://github.com/nf-core/raredisease/pull/895) diff --git a/main.nf b/main.nf index 70c55a413..93d10bf75 100644 --- a/main.nf +++ b/main.nf @@ -180,8 +180,7 @@ workflow NFCORE_RAREDISEASE { val_sequence_dictionary, val_target_bed, val_vcfanno_extra_resources, - val_vep_cache, - val_save_reference + val_vep_cache ) .set { ch_references } @@ -609,11 +608,42 @@ workflow NFCORE_RAREDISEASE { annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ] annotate_mt_snvs_ensemblvep_mt_tbi = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi // channel: [ val(meta), path(tbi) ] annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] + prepare_references_bait_intervals = ch_bait_intervals + prepare_references_dbsnp = ch_dbsnp + prepare_references_dbsnp_tbi = ch_dbsnp_tbi + prepare_references_genome_bwafastalignindex = ch_genome_bwafastalignindex + prepare_references_genome_bwaindex = ch_genome_bwaindex + prepare_references_genome_bwamem2index = ch_genome_bwamem2index + prepare_references_genome_bwamemeindex = ch_genome_bwamemeindex + prepare_references_genome_chrsizes = ch_genome_chrsizes + prepare_references_genome_dictionary = ch_genome_dictionary + prepare_references_genome_fai = ch_genome_fai + prepare_references_genome_fasta = ch_genome_fasta + prepare_references_genome_hisat2index = ch_genome_hisat2index + prepare_references_gnomad_af = ch_gnomad_af + prepare_references_mt_bwaindex = ch_mt_bwaindex + prepare_references_mt_bwamem2index = ch_mt_bwamem2index + prepare_references_mt_dictionary = ch_mt_dictionary + prepare_references_mt_fai = ch_mt_fai + prepare_references_mt_fasta = ch_mt_fasta + prepare_references_mt_intervals = ch_mt_intervals + prepare_references_mt_lastdb = ch_mt_lastdb + prepare_references_mtshift_backchain = ch_mtshift_backchain + prepare_references_mtshift_bwaindex = ch_mtshift_bwaindex + prepare_references_mtshift_bwamem2index = ch_mtshift_bwamem2index + prepare_references_mtshift_dictionary = ch_mtshift_dictionary + prepare_references_mtshift_fai = ch_mtshift_fai + prepare_references_mtshift_fasta = ch_mtshift_fasta + prepare_references_mtshift_intervals = ch_mtshift_intervals + prepare_references_sdf = ch_sdf + prepare_references_target_bed = ch_target_bed + prepare_references_target_intervals = ch_target_intervals + prepare_references_vcfanno_extra = ch_vcfanno_extra + prepare_references_vep_cache = ch_vep_cache subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] publish = RAREDISEASE.out.publish - .mix(ch_pedfile_publish) - .mix(ch_references.publish) // channel: [ val(destination), val(value) ] + .mix(ch_pedfile_publish) // channel: [ val(destination), val(value) ] } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -836,6 +866,38 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) + references = NFCORE_RAREDISEASE.out.prepare_references_dbsnp + .mix(NFCORE_RAREDISEASE.out.prepare_references_dbsnp_tbi) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_bwaindex) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_bwafastalignindex) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_bwamem2index) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_bwamemeindex) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_fai) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_fasta) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_hisat2index) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_dictionary) + .mix(NFCORE_RAREDISEASE.out.prepare_references_genome_chrsizes) + .mix(NFCORE_RAREDISEASE.out.prepare_references_bait_intervals) + .mix(NFCORE_RAREDISEASE.out.prepare_references_gnomad_af) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_bwaindex) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_bwamem2index) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_dictionary) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_fai) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_fasta) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_intervals) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mt_lastdb) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_backchain) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_bwaindex) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_bwamem2index) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_dictionary) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_fai) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_fasta) + .mix(NFCORE_RAREDISEASE.out.prepare_references_mtshift_intervals) + .mix(NFCORE_RAREDISEASE.out.prepare_references_sdf) + .mix(NFCORE_RAREDISEASE.out.prepare_references_target_bed) + .mix(NFCORE_RAREDISEASE.out.prepare_references_target_intervals) + .mix(NFCORE_RAREDISEASE.out.prepare_references_vcfanno_extra) + .mix(NFCORE_RAREDISEASE.out.prepare_references_vep_cache) processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals subworkflow_results = NFCORE_RAREDISEASE.out.publish } @@ -883,6 +945,10 @@ output { annotate_snv_mt { path { _meta, _file -> "annotate_snv/mitochondria/" } } + references { + path { _meta, _file -> "references/" } + enabled params.save_reference + } processed_references { path { _meta, _file -> "processed_references/" } enabled params.save_reference diff --git a/subworkflows/local/prepare_references/main.nf b/subworkflows/local/prepare_references/main.nf index fda4f87f8..9f9aa8bc8 100644 --- a/subworkflows/local/prepare_references/main.nf +++ b/subworkflows/local/prepare_references/main.nf @@ -58,7 +58,6 @@ workflow PREPARE_REFERENCES { val_target_bed // String: path to target bed file val_vcfanno_extra // String: path to additional annotation files used by vcfanno val_vep_cache // String: path to vep cache folder - val_save_reference // Boolean: whether to save generated reference files main: @@ -282,49 +281,6 @@ workflow PREPARE_REFERENCES { ch_sdf = RTGTOOLS_FORMAT(ch_rtgformat_in).out.sdf } - ch_publish = channel.empty() - if (val_save_reference) { - ch_publish = ch_dbsnp - .mix(ch_dbsnp_tbi) - .mix(ch_genome_bwa_index) - .mix(ch_genome_bwafastalign_index) - .mix(ch_genome_bwamem2_index) - .mix(ch_genome_bwameme_index) - .mix(ch_genome_fai) - .mix(ch_genome_fasta) - .mix(ch_genome_hisat2_index) - .mix(ch_genome_dict) - .mix(ch_mt_bwa_index) - .mix(ch_mt_bwamem2_index) - .mix(ch_mt_dict) - .mix(ch_mt_fai) - .mix(ch_mt_fasta) - .mix(ch_mt_last_index) - .mix(ch_mtshift_backchain) - .mix(ch_mtshift_bwa_index) - .mix(ch_mtshift_bwamem2_index) - .mix(ch_mtshift_dict) - .mix(ch_mtshift_fai) - .mix(ch_mtshift_fasta) - .mix(ch_sdf) - .map { meta, value -> ['references/', [meta, value]] } - .mix( - ch_target_bed_gz_tbi - .map { meta, gz, index -> ['references/', [meta, gz, index]] } - ) - .mix( - ch_bait_intervals - .mix(ch_chrom_sizes) - .mix(ch_shiftfasta_mtintervals) - .mix(ch_shiftfasta_mtshiftintervals) - .mix(ch_target_intervals) - .mix(ch_gnomad_af_idx) - .mix(ch_vcfanno_extra) - .mix(ch_vep_resources) - .map { value -> ['references/', [value]] } - ) - } - emit: bait_intervals = ch_bait_intervals // channel:[ path(intervals) ] dbsnp = ch_dbsnp // channel:[ val(meta), path(dbsnp) ] @@ -358,5 +314,4 @@ workflow PREPARE_REFERENCES { target_intervals = ch_target_intervals // channel:[ path(interval_list) ] vcfanno_extra = ch_vcfanno_extra // channel:[ [path(vcf), path(tbi)] ] vep_resources = ch_vep_resources // channel:[ path(cache) ] - publish = ch_publish // channel: [ val(destination), val(value) ] } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test b/subworkflows/local/prepare_references/tests/main.nf.test index db9005f90..893b7f46a 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test +++ b/subworkflows/local/prepare_references/tests/main.nf.test @@ -60,7 +60,6 @@ nextflow_workflow { input[18] = params.pipelines_testdata_base_path + 'reference/target.bed' input[19] = null input[20] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' - input[21] = true """ } } @@ -143,7 +142,6 @@ nextflow_workflow { input[18] = params.pipelines_testdata_base_path + 'reference/target.bed' input[19] = null input[20] = params.pipelines_testdata_base_path + 'reference/vep_cache_and_plugins.tar.gz' - input[21] = true """ } } diff --git a/subworkflows/local/prepare_references/tests/main.nf.test.snap b/subworkflows/local/prepare_references/tests/main.nf.test.snap index f4518c257..661ed64c5 100644 --- a/subworkflows/local/prepare_references/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_references/tests/main.nf.test.snap @@ -286,286 +286,6 @@ ] ] ], - [ - "32", - [ - [ - "references/", - [ - [ - [ - - ] - ] - ] - ], - [ - "references/", - [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" - ] - ], - [ - "references/", - [ - { - "id": "dbsnp_-138-" - }, - "dbsnp_-138-.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "gnomad_reformated.tab.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.sa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference.bck:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.des:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.prj:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.sds:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.ssp:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.suf:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.tis:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference.dict:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "/nf-core/test-datasets/raredisease/reference/reference.fasta" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference.fasta.0123:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.fasta.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.fasta.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.fasta.bwt.2bit.64:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.fasta.pac:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - [ - "reference.fasta.sizes:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - [ - "reference.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - [ - "reference.shifted.intervals:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference_mt.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_mt.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_mt.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_mt.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_mt.sa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_mt.dict:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_mt.fa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_mt.fa.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference_shift.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_shift.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_shift.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_shift.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference_shift.sa:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_shift.back_chain:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_shift.dict:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_shift.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - "reference_shift.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - [ - "target_bait.intervals_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "target" - }, - "target_pad100.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "target_pad100.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - [ - "target_target.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - [ - [ - - ] - ] - ] - ] - ] - ], [ "4", [ @@ -922,286 +642,6 @@ ] ] ], - [ - "publish", - [ - [ - "references/", - [ - [ - [ - - ] - ] - ] - ], - [ - "references/", - [ - { - "id": "dbsnp_-138-" - }, - "/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz" - ] - ], - [ - "references/", - [ - { - "id": "dbsnp_-138-" - }, - "dbsnp_-138-.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - [ - "references/", - [ - [ - "/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz", - "gnomad_reformated.tab.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - - ] - ] - ], - [ - "references/", - [ - { - "id": "reference" - }, - [ - "reference.amb:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.ann:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.bwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.pac:md5,d41d8cd98f00b204e9800998ecf8427e", - "reference.sa:md5,d41d8cd98f00b204e9800998ecf8427e" - 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Update saltshaker classification reporting by adding customer ID to samples' reports and displaying them as tabs in html [#856](https://github.com/nf-core/raredisease/pull/856) - Added non-stub tests for `annotate_mt_snvs` [#890](https://github.com/nf-core/raredisease/pull/890) -- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2, enabled by providing `contamination_sites` and skippable via `--skip_tools contamination` [#758](https://github.com/nf-core/raredisease/pull/758) +- Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2, enabled by providing `contamination_sites` and skippable via `--skip_tools gatkcontamination` [#758](https://github.com/nf-core/raredisease/pull/758) - GATK Contamination results displayed in MultiQC with color-coded thresholds [#758](https://github.com/nf-core/raredisease/pull/758) ### `Changed` diff --git a/modules/local/parse_contamination/bin/parse_contamination.py b/bin/parse_contamination.py similarity index 100% rename from modules/local/parse_contamination/bin/parse_contamination.py rename to bin/parse_contamination.py diff --git a/conf/modules/contamination.config b/conf/modules/contamination_check.config similarity index 100% rename from conf/modules/contamination.config rename to conf/modules/contamination_check.config diff --git a/main.nf b/main.nf index 06bfbaf34..f2f466f1f 100644 --- a/main.nf +++ b/main.nf @@ -336,7 +336,7 @@ workflow NFCORE_RAREDISEASE { skip_smncopynumbercaller = parseSkipList(val_skip_tools, 'smncopynumbercaller') skip_vcf2cytosure = parseSkipList(val_skip_tools, 'vcf2cytosure') // GATK contamination check is also skipped when no contamination sites are supplied - skip_contamination = parseSkipList(val_skip_tools, 'contamination') || !val_contamination_sites + skip_contamination = parseSkipList(val_skip_tools, 'gatkcontamination') || !val_contamination_sites // // Build contamination check inputs (channel construction kept out of the named workflow) diff --git a/modules/local/parse_contamination/main.nf b/modules/local/parse_contamination/main.nf index 3faf8e1b1..894556142 100644 --- a/modules/local/parse_contamination/main.nf +++ b/modules/local/parse_contamination/main.nf @@ -20,7 +20,7 @@ process PARSE_CONTAMINATION { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - python3 ${moduleDir}/bin/parse_contamination.py \\ + parse_contamination.py \\ --input ${contamination_table} \\ --sample_id ${meta.id} \\ --prefix ${prefix} diff --git a/nextflow.config b/nextflow.config index 6bb9ca89b..9991c8399 100644 --- a/nextflow.config +++ b/nextflow.config @@ -529,7 +529,7 @@ includeConfig 'conf/modules/variant_evaluation.config' includeConfig 'conf/modules/subsample_mt_frac.config' includeConfig 'conf/modules/subsample_mt_reads.config' includeConfig 'conf/modules/annotate_rhocallviz.config' -includeConfig 'conf/modules/contamination.config' +includeConfig 'conf/modules/contamination_check.config' // Nextflow plugins diff --git a/nextflow_schema.json b/nextflow_schema.json index e67894edf..9ea4f58e2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -669,8 +669,8 @@ "type": "string", "fa_icon": "fas fa-forward", "description": "Disable specified tools.", - "help_text": "Multiple tools can be specified, separated by commas. The GATK contamination check additionally requires `contamination_sites` to be set; it is skipped automatically when that file is not provided.", - "pattern": "^((fastp|gens|germlinecnvcaller|peddy|smncopynumbercaller|vcf2cytosure|fastqc|ngsbits|mitosalt|contamination)?,?)*(? Date: Tue, 30 Jun 2026 16:00:23 +0200 Subject: [PATCH 869/872] Update subworkflows/local/generate_cytosure_files/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- subworkflows/local/generate_cytosure_files/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test b/subworkflows/local/generate_cytosure_files/tests/main.nf.test index 5cf59d25c..833c2eb32 100644 --- a/subworkflows/local/generate_cytosure_files/tests/main.nf.test +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test @@ -79,7 +79,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out.cgh).match() } + { assert snapshot(workflow.out).match() } ) } } From b4ed7eec09227de72f7b3bf52456f01dac39ae23 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 16:00:37 +0200 Subject: [PATCH 870/872] Update subworkflows/local/generate_cytosure_files/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --- subworkflows/local/generate_cytosure_files/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test b/subworkflows/local/generate_cytosure_files/tests/main.nf.test index 833c2eb32..f124b6ef2 100644 --- a/subworkflows/local/generate_cytosure_files/tests/main.nf.test +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test @@ -44,7 +44,7 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out.cgh).match() } + { assert snapshot(workflow.out).match() } ) } } From 1c2d66a8031630fa1448e590c841663546172d5d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 20:05:29 +0200 Subject: [PATCH 871/872] review suggestion --- main.nf | 24 +++---- subworkflows/local/variant_evaluation/main.nf | 26 ++++---- workflows/raredisease.nf | 62 +++++++++---------- 3 files changed, 56 insertions(+), 56 deletions(-) diff --git a/main.nf b/main.nf index 1afbba10a..084908b09 100644 --- a/main.nf +++ b/main.nf @@ -611,16 +611,16 @@ workflow NFCORE_RAREDISEASE { annotate_mt_snvs_ensemblvep_mt_vcf = RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf // channel: [ val(meta), path(vcf) ] variant_evaluation_baseline_tbi = RAREDISEASE.out.variant_evaluation_baseline_tbi // channel: [ val(meta), path(tbi) ] variant_evaluation_baseline_vcf = RAREDISEASE.out.variant_evaluation_baseline_vcf // channel: [ val(meta), path(vcf) ] - variant_evaluation_fn_tbi = RAREDISEASE.out.variant_evaluation_fn_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_fn_vcf = RAREDISEASE.out.variant_evaluation_fn_vcf // channel: [ val(meta), path(vcf) ] - variant_evaluation_fp_tbi = RAREDISEASE.out.variant_evaluation_fp_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_fp_vcf = RAREDISEASE.out.variant_evaluation_fp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_false_negatives_tbi = RAREDISEASE.out.variant_evaluation_false_negatives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_false_negatives_vcf = RAREDISEASE.out.variant_evaluation_false_negatives_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_false_positives_tbi = RAREDISEASE.out.variant_evaluation_false_positives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_false_positives_vcf = RAREDISEASE.out.variant_evaluation_false_positives_vcf // channel: [ val(meta), path(vcf) ] variant_evaluation_non_snp_roc = RAREDISEASE.out.variant_evaluation_non_snp_roc // channel: [ val(meta), path(tsv) ] variant_evaluation_phasing = RAREDISEASE.out.variant_evaluation_phasing // channel: [ val(meta), path(txt) ] variant_evaluation_snp_roc = RAREDISEASE.out.variant_evaluation_snp_roc // channel: [ val(meta), path(tsv) ] variant_evaluation_summary = RAREDISEASE.out.variant_evaluation_summary // channel: [ val(meta), path(txt) ] - variant_evaluation_tp_tbi = RAREDISEASE.out.variant_evaluation_tp_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_tp_vcf = RAREDISEASE.out.variant_evaluation_tp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_true_positives_tbi = RAREDISEASE.out.variant_evaluation_true_positives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_true_positives_vcf = RAREDISEASE.out.variant_evaluation_true_positives_vcf // channel: [ val(meta), path(vcf) ] variant_evaluation_weighted_roc = RAREDISEASE.out.variant_evaluation_weighted_roc // channel: [ val(meta), path(tsv) ] subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ] @@ -849,12 +849,12 @@ workflow { annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw annotate_snv_mt = NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_vcf .mix(NFCORE_RAREDISEASE.out.annotate_mt_snvs_ensemblvep_mt_tbi) - variant_evaluation = NFCORE_RAREDISEASE.out.variant_evaluation_tp_vcf - .mix(NFCORE_RAREDISEASE.out.variant_evaluation_tp_tbi) - .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fn_vcf) - .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fn_tbi) - .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fp_vcf) - .mix(NFCORE_RAREDISEASE.out.variant_evaluation_fp_tbi) + variant_evaluation = NFCORE_RAREDISEASE.out.variant_evaluation_true_positives_vcf + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_true_positives_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_false_negatives_vcf) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_false_negatives_tbi) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_false_positives_vcf) + .mix(NFCORE_RAREDISEASE.out.variant_evaluation_false_positives_tbi) .mix(NFCORE_RAREDISEASE.out.variant_evaluation_baseline_vcf) .mix(NFCORE_RAREDISEASE.out.variant_evaluation_baseline_tbi) .mix(NFCORE_RAREDISEASE.out.variant_evaluation_snp_roc) diff --git a/subworkflows/local/variant_evaluation/main.nf b/subworkflows/local/variant_evaluation/main.nf index 458afce80..052c98b05 100644 --- a/subworkflows/local/variant_evaluation/main.nf +++ b/subworkflows/local/variant_evaluation/main.nf @@ -41,17 +41,17 @@ workflow VARIANT_EVALUATION { RTGTOOLS_VCFEVAL ( ch_vcfeval_in, ch_sdf ) emit: - baseline_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi // channel: [ val(meta), path(tbi) ] - baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf // channel: [ val(meta), path(vcf) ] - fn_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi // channel: [ val(meta), path(tbi) ] - fn_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf // channel: [ val(meta), path(vcf) ] - fp_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi // channel: [ val(meta), path(tbi) ] - fp_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf // channel: [ val(meta), path(vcf) ] - non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc // channel: [ val(meta), path(tsv) ] - phasing = RTGTOOLS_VCFEVAL.out.phasing // channel: [ val(meta), path(txt) ] - snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc // channel: [ val(meta), path(tsv) ] - summary = RTGTOOLS_VCFEVAL.out.summary // channel: [ val(meta), path(txt) ] - tp_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi // channel: [ val(meta), path(tbi) ] - tp_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf // channel: [ val(meta), path(vcf) ] - weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc // channel: [ val(meta), path(tsv) ] + baseline_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi // channel: [ val(meta), path(tbi) ] + baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf // channel: [ val(meta), path(vcf) ] + false_negatives_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi // channel: [ val(meta), path(tbi) ] + false_negatives_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf // channel: [ val(meta), path(vcf) ] + false_positives_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi // channel: [ val(meta), path(tbi) ] + false_positives_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf // channel: [ val(meta), path(vcf) ] + non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc // channel: [ val(meta), path(tsv) ] + phasing = RTGTOOLS_VCFEVAL.out.phasing // channel: [ val(meta), path(txt) ] + snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc // channel: [ val(meta), path(tsv) ] + summary = RTGTOOLS_VCFEVAL.out.summary // channel: [ val(meta), path(txt) ] + true_positives_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi // channel: [ val(meta), path(tbi) ] + true_positives_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf // channel: [ val(meta), path(vcf) ] + weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc // channel: [ val(meta), path(tsv) ] } diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf index 9217e42fe..2cade3f0b 100644 --- a/workflows/raredisease.nf +++ b/workflows/raredisease.nf @@ -286,18 +286,18 @@ workflow RAREDISEASE { ch_rank_snv_publish = channel.empty() ch_rank_mt_publish = channel.empty() ch_rank_sv_publish = channel.empty() - ch_variant_evaluation_baseline_tbi = channel.empty() - ch_variant_evaluation_baseline_vcf = channel.empty() - ch_variant_evaluation_fn_tbi = channel.empty() - ch_variant_evaluation_fn_vcf = channel.empty() - ch_variant_evaluation_fp_tbi = channel.empty() - ch_variant_evaluation_fp_vcf = channel.empty() - ch_variant_evaluation_non_snp_roc = channel.empty() - ch_variant_evaluation_phasing = channel.empty() - ch_variant_evaluation_snp_roc = channel.empty() - ch_variant_evaluation_summary = channel.empty() - ch_variant_evaluation_tp_tbi = channel.empty() - ch_variant_evaluation_tp_vcf = channel.empty() + ch_variant_evaluation_baseline_tbi = channel.empty() + ch_variant_evaluation_baseline_vcf = channel.empty() + ch_variant_evaluation_false_negatives_tbi = channel.empty() + ch_variant_evaluation_false_negatives_vcf = channel.empty() + ch_variant_evaluation_false_positives_tbi = channel.empty() + ch_variant_evaluation_false_positives_vcf = channel.empty() + ch_variant_evaluation_non_snp_roc = channel.empty() + ch_variant_evaluation_phasing = channel.empty() + ch_variant_evaluation_snp_roc = channel.empty() + ch_variant_evaluation_summary = channel.empty() + ch_variant_evaluation_true_positives_tbi = channel.empty() + ch_variant_evaluation_true_positives_vcf = channel.empty() ch_variant_evaluation_weighted_roc = channel.empty() // @@ -965,19 +965,19 @@ workflow RAREDISEASE { ch_sdf, CALL_SNV.out.genome_vcf_tabix ) - ch_variant_evaluation_baseline_tbi = VARIANT_EVALUATION.out.baseline_tbi - ch_variant_evaluation_baseline_vcf = VARIANT_EVALUATION.out.baseline_vcf - ch_variant_evaluation_fn_tbi = VARIANT_EVALUATION.out.fn_tbi - ch_variant_evaluation_fn_vcf = VARIANT_EVALUATION.out.fn_vcf - ch_variant_evaluation_fp_tbi = VARIANT_EVALUATION.out.fp_tbi - ch_variant_evaluation_fp_vcf = VARIANT_EVALUATION.out.fp_vcf - ch_variant_evaluation_non_snp_roc = VARIANT_EVALUATION.out.non_snp_roc - ch_variant_evaluation_phasing = VARIANT_EVALUATION.out.phasing - ch_variant_evaluation_snp_roc = VARIANT_EVALUATION.out.snp_roc - ch_variant_evaluation_summary = VARIANT_EVALUATION.out.summary - ch_variant_evaluation_tp_tbi = VARIANT_EVALUATION.out.tp_tbi - ch_variant_evaluation_tp_vcf = VARIANT_EVALUATION.out.tp_vcf - ch_variant_evaluation_weighted_roc = VARIANT_EVALUATION.out.weighted_roc + ch_variant_evaluation_baseline_tbi = VARIANT_EVALUATION.out.baseline_tbi + ch_variant_evaluation_baseline_vcf = VARIANT_EVALUATION.out.baseline_vcf + ch_variant_evaluation_false_negatives_tbi = VARIANT_EVALUATION.out.false_negatives_tbi + ch_variant_evaluation_false_negatives_vcf = VARIANT_EVALUATION.out.false_negatives_vcf + ch_variant_evaluation_false_positives_tbi = VARIANT_EVALUATION.out.false_positives_tbi + ch_variant_evaluation_false_positives_vcf = VARIANT_EVALUATION.out.false_positives_vcf + ch_variant_evaluation_non_snp_roc = VARIANT_EVALUATION.out.non_snp_roc + ch_variant_evaluation_phasing = VARIANT_EVALUATION.out.phasing + ch_variant_evaluation_snp_roc = VARIANT_EVALUATION.out.snp_roc + ch_variant_evaluation_summary = VARIANT_EVALUATION.out.summary + ch_variant_evaluation_true_positives_tbi = VARIANT_EVALUATION.out.true_positives_tbi + ch_variant_evaluation_true_positives_vcf = VARIANT_EVALUATION.out.true_positives_vcf + ch_variant_evaluation_weighted_roc = VARIANT_EVALUATION.out.weighted_roc } /* @@ -1157,16 +1157,16 @@ workflow RAREDISEASE { ann_csq_pli_me_vcf_ann = ch_ann_csq_pli_me_vcf_ann // channel: [ val(meta), path(vcf) ] variant_evaluation_baseline_tbi = ch_variant_evaluation_baseline_tbi // channel: [ val(meta), path(tbi) ] variant_evaluation_baseline_vcf = ch_variant_evaluation_baseline_vcf // channel: [ val(meta), path(vcf) ] - variant_evaluation_fn_tbi = ch_variant_evaluation_fn_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_fn_vcf = ch_variant_evaluation_fn_vcf // channel: [ val(meta), path(vcf) ] - variant_evaluation_fp_tbi = ch_variant_evaluation_fp_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_fp_vcf = ch_variant_evaluation_fp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_false_negatives_tbi = ch_variant_evaluation_false_negatives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_false_negatives_vcf = ch_variant_evaluation_false_negatives_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_false_positives_tbi = ch_variant_evaluation_false_positives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_false_positives_vcf = ch_variant_evaluation_false_positives_vcf // channel: [ val(meta), path(vcf) ] variant_evaluation_non_snp_roc = ch_variant_evaluation_non_snp_roc // channel: [ val(meta), path(tsv) ] variant_evaluation_phasing = ch_variant_evaluation_phasing // channel: [ val(meta), path(txt) ] variant_evaluation_snp_roc = ch_variant_evaluation_snp_roc // channel: [ val(meta), path(tsv) ] variant_evaluation_summary = ch_variant_evaluation_summary // channel: [ val(meta), path(txt) ] - variant_evaluation_tp_tbi = ch_variant_evaluation_tp_tbi // channel: [ val(meta), path(tbi) ] - variant_evaluation_tp_vcf = ch_variant_evaluation_tp_vcf // channel: [ val(meta), path(vcf) ] + variant_evaluation_true_positives_tbi = ch_variant_evaluation_true_positives_tbi // channel: [ val(meta), path(tbi) ] + variant_evaluation_true_positives_vcf = ch_variant_evaluation_true_positives_vcf // channel: [ val(meta), path(vcf) ] variant_evaluation_weighted_roc = ch_variant_evaluation_weighted_roc // channel: [ val(meta), path(tsv) ] subsample_mt_bai = ch_subsample_mt_bai // channel: [ val(meta), path(bai) ] subsample_mt_bam = ch_subsample_mt_bam // channel: [ val(meta), path(bam) ] From 34526c066c812b19c3093c22a4d1f0998e846d85 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Tue, 30 Jun 2026 21:00:07 +0200 Subject: [PATCH 872/872] update snap --- .../tests/main.nf.test.snap | 64 +++++++++++++------ 1 file changed, 44 insertions(+), 20 deletions(-) diff --git a/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap b/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap index a1942b1f9..5cf68acf0 100644 --- a/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap +++ b/subworkflows/local/generate_cytosure_files/tests/main.nf.test.snap @@ -1,18 +1,30 @@ { "GENERATE_CYTOSURE_FILES - no sample_id_map, stub": { "content": [ - [ - [ - { - "id": "earlycasualcaiman", - "custid": "earlycasualcaiman", - "sex": 1 - }, - "earlycasualcaiman.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "custid": "earlycasualcaiman", + "sex": 1 + }, + "earlycasualcaiman.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cgh": [ + [ + { + "id": "earlycasualcaiman", + "custid": "earlycasualcaiman", + "sex": 1 + }, + "earlycasualcaiman.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ] + } ], - "timestamp": "2026-06-30T10:43:45.932851408", + "timestamp": "2026-06-30T20:58:21.226904272", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4" @@ -20,18 +32,30 @@ }, "GENERATE_CYTOSURE_FILES - with sample_id_map, stub": { "content": [ - [ - [ - { - "id": "earlycasualcaiman", - "custid": "CUST_001", - "sex": 1 - }, - "CUST_001.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "earlycasualcaiman", + "custid": "CUST_001", + "sex": 1 + }, + "CUST_001.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cgh": [ + [ + { + "id": "earlycasualcaiman", + "custid": "CUST_001", + "sex": 1 + }, + "CUST_001.cgh:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] - ] + } ], - "timestamp": "2026-06-30T10:44:04.545576843", + "timestamp": "2026-06-30T20:58:44.411334018", "meta": { "nf-test": "0.9.5", "nextflow": "25.10.4"